Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold93
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1685797
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 216 characters in sequence are not A, C, G, or T
File 10 of 14
Found at i:1172587 original size:13 final size:13
Alignment explanation
Indices: 1172569--1172684 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
1172559 AGCTTCGTAG
1172569 CGATACATTGTAT
1 CGATACATTGTAT
1172582 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1172601 CGATACATTGTAT
1 CGATACATTGTAT
1172614 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1172633 CGATACATTGTAT
1 CGATACATTGTAT
1172646 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1172665 CGATACATTGTAT
1 CGATACATTGTAT
1172678 CGATACA
1 CGATACA
1172685 ACACTTATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 36
0.70 0.00 0.30
Matches are distributed among these distances:
13 35 0.41
14 2 0.02
15 2 0.02
16 14 0.16
17 2 0.02
18 2 0.02
19 28 0.33
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1172601 original size:19 final size:18
Alignment explanation
Indices: 1172577--1172705 Score: 108
Period size: 19 Copynumber: 7.8 Consensus size: 18
1172567 AGCGATACAT
1172577 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1172596 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1172609 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1172628 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1172641 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1172660 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1172673 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
1172692 TGTATCAATACAAA
1 TGTATCGATACAAA
1172706 TCGTTGAAAT
Statistics
Matches: 91, Mismatches: 1, Indels: 37
0.71 0.01 0.29
Matches are distributed among these distances:
13 33 0.36
14 3 0.03
16 6 0.07
18 4 0.04
19 45 0.49
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1172610 original size:32 final size:32
Alignment explanation
Indices: 1172569--1172703 Score: 252
Period size: 32 Copynumber: 4.2 Consensus size: 32
1172559 AGCTTCGTAG
*
1172569 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1172601 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1172633 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1172665 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
1172697 CAATACA
1 CGATACA
1172704 AATCGTTGAA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 101 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1173539 original size:49 final size:48
Alignment explanation
Indices: 1173476--1173755 Score: 302
Period size: 49 Copynumber: 5.8 Consensus size: 48
1173466 CGAAGAATGA
* * *
1173476 CAATGTGCTGATTCATGGCCAGCGATATTGATCTTAAAGTTGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGA-CTTAAAGATGACGGTGC
* *** * *
1173525 CAATATGCTGATTCAAAGCCAGCGATGCCGGACTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGAT-ATTGACTTAAAGATGACGGTGC
* * * * *
1173574 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATT-GACTTAAAGATGACGGTGC
*
1173623 CAATATACTGATTCAAGGCCAGCGATATTGGACTT--A-A--A-GGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATT-GACTTAAAGATGACGGTGC
* *
1173666 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATT-GACTTAAAGATGACGGTGC
1173715 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 CAATATGCTGATTCAAGGCCAGCGATATT-GACTTA-AAGA
1173756 AGATGCGACC
Statistics
Matches: 192, Mismatches: 30, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
43 37 0.19
44 1 0.01
45 1 0.01
46 2 0.01
47 1 0.01
48 1 0.01
49 143 0.74
50 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGACTTAAAGATGACGGTGC
Found at i:1173711 original size:92 final size:96
Alignment explanation
Indices: 1173476--1173750 Score: 389
Period size: 92 Copynumber: 2.9 Consensus size: 96
1173466 CGAAGAATGA
* * *
1173476 CAATGTGCTGATTCATGGCCAGCGATATT-GATCTTAAAGTTGACGGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGA-CTTAAAGATGACGGTGCCAATATGCTGATTCA
* ***
1173540 AAGCCAGCGATGCCGGACTTAAAGATGAAGATGC
65 AGGCCAGCGATATTGGACTT-AAGATG-AGATGC
* * * *
1173574 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACGACGGTGCCAATATACTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
1173639 GGCCAGCGATATTGGACTTAA-A-G-G-TGC
66 GGCCAGCGATATTGGACTTAAGATGAGATGC
1173666 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
1173731 GGCCAGCGATATTGGACTTA
66 GGCCAGCGATATTGGACTTA
1173751 GAAGAAGATG
Statistics
Matches: 161, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
92 84 0.52
93 1 0.01
95 1 0.01
96 1 0.01
97 2 0.01
98 71 0.44
99 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (96 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAGATGAGATGC
Found at i:1173839 original size:28 final size:28
Alignment explanation
Indices: 1173772--1174182 Score: 455
Period size: 28 Copynumber: 14.4 Consensus size: 28
1173762 GACCAACTTG
**
1173772 TGTGGGCTTTTGATAGGGTTG-CACCAACT
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACT
*
1173801 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * *
1173829 TGTGGGTTTTTGAAAAGATACCACTAACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* *
1173858 TGTAGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
1173886 TATGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
1173916 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
1173944 TGTAGGCTTTAGAAGGTTGGCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
1173972 TATGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
*
1174002 TGTGGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
1174030 TATGGGCTTTGGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
1174060 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
1174088 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
1174116 TGTAGGCTTTGGAAGGTTGCCACTGACC
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
1174144 TGTGGGCTTTGGAAAGGATGCCACGGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1174173 TGTGGGCTTT
1 TGTGGGCTTT
1174183 GAAAAAGGTG
Statistics
Matches: 325, Mismatches: 48, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
27 5 0.02
28 190 0.58
29 57 0.18
30 73 0.22
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:1173933 original size:58 final size:57
Alignment explanation
Indices: 1173772--1174183 Score: 429
Period size: 58 Copynumber: 7.2 Consensus size: 57
1173762 GACCAACTTG
* * ** *
1173772 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGGA-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * * * * *
1173829 TGTGGGTTTTTGAAAAGATACCACTAACTTGTAGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* *
1173886 TATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGG-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * * *
1173944 TGTAGGCTTTAG-AAGGTTGGCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGGAAAGGTTGCCACTGACTTGTGGGCTTTTG--AAGGTTGCCACTGACT
* * * * * *
1174002 TGTGGGCTTTTG-AAGGTTGCCACTAACTTATGGGCTTTGGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGGAAAGGTTGCCACTGACTTGTGGGCTTTTG--AAGGTTGCCACTGACT
*
1174060 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * *
1174116 TGTAGGCTTTGG-AAGGTTGCCACTGACCTGTGGGCTTTGGAAAGGATGCCACGGACT
1 TGTGGGCTTTGGAAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1174173 TGTGGGCTTTG
1 TGTGGGCTTTG
1174184 AAAAAGGTGA
Statistics
Matches: 307, Mismatches: 43, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
56 77 0.25
57 77 0.25
58 153 0.50
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (57 bp):
TGTGGGCTTTGGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:1173950 original size:86 final size:85
Alignment explanation
Indices: 1173788--1174182 Score: 490
Period size: 86 Copynumber: 4.6 Consensus size: 85
1173778 CTTTTGATAG
* * * * * * * * *
1173788 GGTTG-CACCAACTTGTGTGCTTTTG-AAGGTTGCCACTGACTTGTGGGTTTTTGAAAAGATACC
1 GGTTGCCACTAACTTATGGGCTTTGGAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCC
*
1173851 ACTAACTTGTAGGCTTTTGAA
65 ACTAACTTGTAGGCTTTGGAA
1173872 GGTTGCCACTAACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCC
1 GGTTGCCACTAACTTATGGGCTTTGG-AAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCC
* *
1173937 ACTGACTTGTAGGCTTTAGAA
65 ACTAACTTGTAGGCTTTGGAA
* *
1173958 GGTTGGCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCC
1 GGTTGCCACTAACTTATGGGCTTTGG-AAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCC
* *
1174023 ACTAACTTATGGGCTTTGGAAAA
65 ACTAACTTGTAGGCTTTGG--AA
* * * *
1174046 GGGTGCCACTAACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCA
1 GGTTGCCACTAACTTATGGGCTTTGGAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCA
*
1174110 CTGACTTGTAGGCTTTGGAA
66 CTAACTTGTAGGCTTTGGAA
* * * * *
1174130 GGTTGCCACTGACCTGTGGGCTTTGGAAAGGATGCCACGGACTTGTGGGCTTT
1 GGTTGCCACTAACTTATGGGCTTTGGAAAGGGTGCCACTGACTTGTGGGCTTT
1174183 GAAAAAGGTG
Statistics
Matches: 273, Mismatches: 32, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
84 29 0.11
85 40 0.15
86 155 0.57
87 26 0.10
88 23 0.08
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (85 bp):
GGTTGCCACTAACTTATGGGCTTTGGAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCA
CTAACTTGTAGGCTTTGGAA
Found at i:1174032 original size:144 final size:143
Alignment explanation
Indices: 1173772--1174190 Score: 567
Period size: 144 Copynumber: 2.9 Consensus size: 143
1173762 GACCAACTTG
** *
1173772 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGT
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACTTGTG-GCTTTTGAAGGTTGCCACTGACTTGTGGGC
* * * *
1173836 TTTTGAAAA-GATACCACTAACTTGTAGGCTTTTGAAGGTTGCCACTAACTTATGGGCTTTGGAA
63 TTTGGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTATGGGCTTTGGAA
*
1173900 AAGGGTGCCACTGACT
128 AAGGGTGCCACTAACT
* * *
1173916 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTAGGCTTTAGAAGGTTGGCACTGACTTATGGGCTT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGT-GGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
*
1173981 TGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTATGGGCTTTGGAAAA
65 TGGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTATGGGCTTTGGAAAA
1174046 GGGTGCCACTAACT
130 GGGTGCCACTAACT
*
1174060 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTAGGCTT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGT-GGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
* * * * ** * *
1174125 TGG--AAGGTTGCCACTGACCTGTGGGCTTTGGAAAGGATGCCACGGACTTGTGGGCTTTGAAAA
65 TGGAAAAGGATGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTAACTTATGGGCTTTGGAAA
1174188 AGG
129 AGG
1174191 TGAGGAATAT
Statistics
Matches: 246, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
142 30 0.12
143 73 0.30
144 143 0.58
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (143 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
GGAAAAGGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTATGGGCTTTGGAAAAG
GGTGCCACTAACT
Found at i:1175666 original size:22 final size:21
Alignment explanation
Indices: 1175638--1175697 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1175628 TTTGTTGTTG
*
1175638 TTGTTTTTATTTTTTTT-TCCT
1 TTGTTTTT-TTTTTTTTGTTCT
*
1175659 TTGTTTTTTTGTTTTTTGTTTT
1 TTGTTTTTTT-TTTTTTGTTCT
1175681 TTGTTTTTTGTTTTTTT
1 TTGTTTTTT-TTTTTTT
1175698 CATCTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 2 0.06
21 14 0.41
22 17 0.50
23 1 0.03
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (21 bp):
TTGTTTTTTTTTTTTTGTTCT
Found at i:1175667 original size:15 final size:13
Alignment explanation
Indices: 1175626--1175728 Score: 64
Period size: 14 Copynumber: 7.2 Consensus size: 13
1175616 ATCTAGACCC
*
1175626 TTTTTGTTGTTGTTG
1 TTTTTGTT-TT-TTT
*
1175641 TTTTTATTTTTTT
1 TTTTTGTTTTTTT
1175654 TTCCTTTGTTTTTTTGT
1 TT--TTTG-TTTTTT-T
1175671 TTTTTGTTTTTTGT
1 TTTTTGTTTTTT-T
1175685 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
1175698 CATCTTTT-TTTTGTTT
1 --T-TTTTGTTTT-TTT
* *
1175714 ATTTGGTTTTTTT
1 TTTTTGTTTTTTT
1175727 TT
1 TT
1175729 GTGGAGGACG
Statistics
Matches: 73, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
13 12 0.16
14 26 0.36
15 19 0.26
16 13 0.18
17 3 0.04
ACGTcount: A:0.03, C:0.04, G:0.12, T:0.82
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:1175675 original size:7 final size:7
Alignment explanation
Indices: 1175626--1175696 Score: 74
Period size: 7 Copynumber: 9.7 Consensus size: 7
1175616 ATCTAGACCC
1175626 TTTTTGT
1 TTTTTGT
1175633 TGTTGTTGT
1 T-TT-TTGT
1175642 TTTTAT-T
1 TTTT-TGT
1175649 TTTTT-T
1 TTTTTGT
*
1175655 TCCTTTGTT
1 T-TTTTG-T
1175664 TTTTTGT
1 TTTTTGT
1175671 TTTTTGT
1 TTTTTGT
1175678 TTTTTGT
1 TTTTTGT
1175685 TTTTTGT
1 TTTTTGT
1175692 TTTTT
1 TTTTT
1175697 TCATCTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
6 3 0.05
7 37 0.66
8 9 0.16
9 7 0.12
ACGTcount: A:0.01, C:0.03, G:0.13, T:0.83
Consensus pattern (7 bp):
TTTTTGT
Found at i:1183042 original size:21 final size:20
Alignment explanation
Indices: 1182997--1183072 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 20
1182987 AAAAATTCCA
1182997 AATGTATCGATACATTGTA-G
1 AATGTATCGATACATT-TATG
1183017 AATGTATCGATACATTTATGG
1 AATGTATCGATACATTTAT-G
**
1183038 AATGTATCGATACATTATACA
1 AATGTATCGATACATT-TATG
1183059 AATGTATCGATACA
1 AATGTATCGATACA
1183073 AGGTCCCAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.04
20 16 0.31
21 31 0.61
22 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTTATG
Found at i:1183133 original size:19 final size:19
Alignment explanation
Indices: 1183109--1183172 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1183099 TTTCAACGAT
1183109 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
1183128 TTGTATCGAT--AT-A--A
1 TTGTATCGATACATAAGTA
*
1183142 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
1183160 TTGTATCGATACA
1 TTGTATCGATACA
1183173 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 2 0.05
16 2 0.05
17 2 0.05
19 22 0.58
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:1183146 original size:32 final size:32
Alignment explanation
Indices: 1183110--1183180 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1183100 TTCAACGATT
*
1183110 TGTATCGATACATAAGTATTGTATCGATATAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
1183142 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1183174 TGTATCG
1 TGTATCG
1183181 CTAGGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1183242 original size:13 final size:13
Alignment explanation
Indices: 1183224--1183249 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1183214 CATTTTTCTG
1183224 TGTATCGATACAT
1 TGTATCGATACAT
1183237 TGTATCGATACAT
1 TGTATCGATACAT
1183250 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1183246 original size:33 final size:33
Alignment explanation
Indices: 1183204--1183270 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1183194 GCCAAGGAAA
***
1183204 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1183237 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1183270 T
1 T
1183271 TGGGAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1185652 original size:80 final size:79
Alignment explanation
Indices: 1185509--1185730 Score: 278
Period size: 80 Copynumber: 2.8 Consensus size: 79
1185499 TTCTATAATC
* * * *
1185509 GGGGATACTCCAACTCCGA-TTTTATTTCTAAAACATCAATTTT-TC--ATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCCAGTTTTATTTCTAAAATAT-TATTTTCTCAAATCGGGGATACTCCAA
*
1185570 CCCCATTATTTTCGA
65 CCCCATTATCTTCGA
*
1185585 GGGGATACTCCAACCCCCAGCTTTATTTCTAAAATATTATTTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCCAGTTTTATTTCTAAAATATTATTTTCTCA-AATCGGGGATACTCCAA
*
1185650 CCCCGTTATCTTCGA
65 CCCCATTATCTTCGA
*
1185665 GGGGATACTCCAA-CCCCGGTTTTATTTCT-AAATCATTGATTTTC-CACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCCAGTTTTATTTCTAAAAT-ATT-ATTTTCTCA-AATCGGGGATACTCC
1185727 AACC
63 AACC
1185731 TCGGCTTTAT
Statistics
Matches: 129, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
76 22 0.17
77 17 0.13
78 4 0.03
79 38 0.29
80 48 0.37
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCCAGTTTTATTTCTAAAATATTATTTTCTCAAATCGGGGATACTCCAAC
CCCATTATCTTCGA
Found at i:1185758 original size:51 final size:52
Alignment explanation
Indices: 1185665--1185837 Score: 156
Period size: 52 Copynumber: 3.3 Consensus size: 52
1185655 TTATCTTCGA
* * * ***
1185665 GGGGATACTCCAACCCCGGTTTTA-TTTCTAAATCATTGATTTTCCACAATC
1 GGGGATACTCCAACCTCGGTTTTATTTTCAAAAACACCAATTTTCCACAATC
* **
1185716 GGGGATACTCCAACCTCGGCTTTATTTTC-AAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCTCGGTTTTATTTTCAAAAACACCAATTTTCC-ACAATC
* * * * *
1185768 GGGGATAC-CGTAA-CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTC-CAACCT-CGGTTTTATTTTCAAAAACACCAATTTTCCACAATC
*
1185820 GAGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
1185838 TTATTTCATC
Statistics
Matches: 97, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
51 37 0.38
52 42 0.43
53 18 0.19
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCTCGGTTTTATTTTCAAAAACACCAATTTTCCACAATC
Found at i:1185854 original size:28 final size:28
Alignment explanation
Indices: 1185822--1185893 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
1185812 TCACAATTGA
* ** *
1185822 GGATACTCCAACCTCGTTATTTCAT-CGG
1 GGATACTCCAACCCCGTTACCTC-TGAGG
1185850 GGATACTCCAACCCCGTTACCTCTGAGG
1 GGATACTCCAACCCCGTTACCTCTGAGG
1185878 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1185894 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCTGAGG
Found at i:1198334 original size:11 final size:11
Alignment explanation
Indices: 1198318--1198373 Score: 78
Period size: 11 Copynumber: 5.1 Consensus size: 11
1198308 CCTTCTCTTT
1198318 AAAAAAACAAA
1 AAAAAAACAAA
*
1198329 AAAAAAAGAAA
1 AAAAAAACAAA
*
1198340 AAAAAAGC-AA
1 AAAAAAACAAA
1198350 AAAAAAACAAA
1 AAAAAAACAAA
1198361 ACAAAAAACAAA
1 A-AAAAAACAAA
1198373 A
1 A
1198374 CAAAGAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
10 9 0.23
11 19 0.49
12 11 0.28
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:1198335 original size:12 final size:12
Alignment explanation
Indices: 1198318--1198383 Score: 64
Period size: 12 Copynumber: 5.3 Consensus size: 12
1198308 CCTTCTCTTT
1198318 AAAAAAACAAAA
1 AAAAAAACAAAA
1198330 AAAAAAGA-AAAA
1 AAAAAA-ACAAAA
1198342 AAAAGCAAA-AAAA
1 AAAA--AAACAAAA
*
1198355 AACAAAACAAAA
1 AAAAAAACAAAA
*
1198367 AACAAAACAAAGA
1 AAAAAAACAAA-A
1198380 AAAA
1 AAAA
1198384 GAGAGAAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
11 3 0.06
12 29 0.62
13 13 0.28
14 2 0.04
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:1198351 original size:17 final size:16
Alignment explanation
Indices: 1198318--1198383 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
1198308 CCTTCTCTTT
*
1198318 AAAAAAACAAAAAA--
1 AAAAAAAAAAAAAAGC
*
1198332 AAAAGAAAAAAAAAGC
1 AAAAAAAAAAAAAAGC
*
1198348 AAAAAAAAACAAAA-C
1 AAAAAAAAAAAAAAGC
*
1198363 AAAAAACAAAACAAAG-
1 AAAAAA-AAAAAAAAGC
1198379 AAAAA
1 AAAAA
1198384 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.29
15 7 0.17
16 23 0.55
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGC
Found at i:1198383 original size:22 final size:20
Alignment explanation
Indices: 1198318--1198383 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1198308 CCTTCTCTTT
*
1198318 AAAAAAACAAAAAAAAAAGAA
1 AAAAAAACAAAAAAAACA-AA
1198339 AAAAAAAGCAAAAAAAAACAAA
1 AAAAAAA-C-AAAAAAAACAAA
* *
1198361 ACAAAAAACAAAACAAAGAAA
1 A-AAAAAACAAAAAAAACAAA
1198382 AA
1 AA
1198384 GAGAGAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 18 0.46
22 5 0.13
23 15 0.38
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAACAAA
Found at i:1198398 original size:1 final size:1
Alignment explanation
Indices: 1198318--1198383 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
1198308 CCTTCTCTTT
* * ** * * * * *
1198318 AAAAAAACAAAAAAAAAAGAAAAAAAAAGCAAAAAAAAACAAAACAAAAAACAAAACAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1198383 A
1 A
1198384 GAGAGAAAAG
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1199609 original size:120 final size:118
Alignment explanation
Indices: 1199369--1200087 Score: 762
Period size: 120 Copynumber: 6.2 Consensus size: 118
1199359 TCCGCTTTTT
* * *
1199369 AGTCCTCAAAAAGCAGGATGCCTGTTCCTTTTAAAGGCCACACAAGTTGGTGGCACCTTCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCT-TTCC-TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCC
* * * *
1199434 TCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
64 TCAAAGAGCAGGACGC-CTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
1199490 AGTCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACGCC-TTTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
*
1199555 CAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCC
65 CAAAGAGCAGGACGCCTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * ** *
1199610 AGTCCTCAAAGAGAAGGATGCCTTT-C---AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCT
* * * * **
1199671 CAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-C
65 CAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* **
1199724 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTT-AAAGCCCACACAAGTTGGTGGCACCTT-CAGTC
* * * * * * *
1199789 CCCAAAGAGGAGGACGCCTTTTCTTTTAAAGCCCACACAGGTTAGTGGCACCTTT--
63 CTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
**
1199844 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTT-AAAGCCCACACAAGTTGGTGGCACCTT-CAGTC
* *
1199909 CTCAAAGAGCAGGA-----TGCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCC
63 CTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
1199960 AGTCCTCAAAGAGCAGGACACCTTT-C---AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCA
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCT
* * *
1200021 CAAGGAGCAGGACG-----CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
65 CAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*
1200070 AGTCCTCAAAGAGTAGGA
1 AGTCCTCAAAGAGCAGGA
1200088 TACACTTTAT
Statistics
Matches: 528, Mismatches: 53, Indels: 45
0.84 0.08 0.07
Matches are distributed among these distances:
110 83 0.16
111 6 0.01
114 26 0.05
115 80 0.15
116 46 0.09
119 5 0.01
120 255 0.48
121 26 0.05
122 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
AAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1199671 original size:175 final size:174
Alignment explanation
Indices: 1199369--1200087 Score: 847
Period size: 175 Copynumber: 4.1 Consensus size: 174
1199359 TCCGCTTTTT
* * * * **
1199369 AGTCCTCAAAAAGCAGGATGCCTGTTCCTTTTAAAGGCCACACAAGTTGGTGGCACCTT-CAGTC
1 AGTCCTCAAAGAGCAGGACGCCT-TTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
*
1199433 CTCAAAGAGCAA-GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCC
65 CTCAAAGAG-AAGGACGC-----CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT--AGTCCC
1199496 CAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
122 CAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
*
1199549 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* *
1199614 CTCAAAGAGAAGGATGCC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCCCAAAGAG
65 CTCAAAGAGAAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTT-TAGTCCCCAAAGAG
*
1199678 CAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
129 CAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
*
1199724 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * * * * *
1199789 CCCAAAGAGGAGGACGCCTTTTCTTTTAAAGCCCACACAGGTTAGTGGCACCTTTAGTCCTCAAA
65 CTCAAAGAGAAGGACGCCTTTTC----AAAGCCCACACAAGTTGGTGGCACTTTTAGTCCCCAAA
* * * **
1199854 GAGCAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
126 GAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-C
* *
1199905 AGTCCTCAAAGAGCAGGA-----TGCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* * * *
1199965 TCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCACAAGGAGC
66 TCAAAGAGAAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCCCAAAGAGC
* * * *
1200029 AGGACGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTT
130 AGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCAC-CTTC
*
1200070 AGTCCTCAAAGAGTAGGA
1 AGTCCTCAAAGAGCAGGA
1200088 TACACTTTAT
Statistics
Matches: 485, Mismatches: 40, Indels: 43
0.85 0.07 0.08
Matches are distributed among these distances:
165 39 0.08
166 3 0.01
169 2 0.00
170 22 0.05
171 24 0.05
174 4 0.01
175 216 0.45
176 9 0.02
177 1 0.00
179 24 0.05
180 104 0.21
181 37 0.08
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (174 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
TCAAAGAGAAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCCCAAAGAGCA
GGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
Found at i:1199926 original size:295 final size:293
Alignment explanation
Indices: 1199364--1200087 Score: 1092
Period size: 295 Copynumber: 2.5 Consensus size: 293
1199354 CTCCTTCCGC
* * *
1199364 TTTT-TAGTCCTCAAAAAGCAGGATGCCTGTTCCTTTTAAAGGCCACACAAGTTGGTGGCACCTT
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCT-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
1199428 CAGTCCTCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
65 CAGTCCTCAAAGAGCAAGACGC--TTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1199493 CCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAA
128 CCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAA
1199558 AGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
193 AGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
1199623 AAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
258 AAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1199659 TTTTCTAGTCCCCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1199724 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
66 AGTCCTCAAAGAGCAAGACG-CTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * *
1199789 CCCAAAGAGGAGGACGCCTTTTCTTTTAAAGCCCACACAGGTTAGTGGCACCTTTAGTCCTCAAA
129 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAA
* *
1199854 GAGCAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
194 GAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGA
*
1199919 AGGATGCCTTTCGAAGCCCACACAAGTTGGTGGCA
259 AGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* **
1199954 TTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTT
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TT
* * * * * *
1200014 TAGTCCACAAGGAGCAGGACG----CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTC
65 CAGTCCTCAAAGAGCAAGACGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTC
* *
1200074 CTCAAAGAGTAGGA
129 CCCAAAGAGCAGGA
1200088 TACACTTTAT
Statistics
Matches: 398, Mismatches: 26, Indels: 20
0.90 0.06 0.05
Matches are distributed among these distances:
285 44 0.11
286 4 0.01
290 24 0.06
291 19 0.05
294 6 0.02
295 278 0.70
296 23 0.06
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (293 bp):
TTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
AGTCCTCAAAGAGCAAGACGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCC
CAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGA
GCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGAAG
GATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1200880 original size:21 final size:20
Alignment explanation
Indices: 1200835--1200951 Score: 144
Period size: 21 Copynumber: 5.7 Consensus size: 20
1200825 AAAATTTCCA
* *
1200835 AATGTATCAATATATTGTAG
1 AATGTATCGATACATTGTAG
*
1200855 AATGTATCGATACATTCGTGG
1 AATGTATCGATACATT-GTAG
1200876 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGTAG
*
1200896 AATGTATCGATACATTTGTGG
1 AATGTATCGATACA-TTGTAG
* * *
1200917 AGTGTATCGATACATTATACA
1 AATGTATCGATACATTGTA-G
1200938 AATGTATCGATACA
1 AATGTATCGATACA
1200952 AGGTCCCAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
20 34 0.40
21 50 0.60
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGTAG
Found at i:1200893 original size:41 final size:41
Alignment explanation
Indices: 1200835--1200951 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 41
1200825 AAAATTTCCA
* *
1200835 AATGTATCAATATATTGTAGAATGTATCGATACATTCGTGG
1 AATGTATCGATACATTGTAGAATGTATCGATACATTCGTGG
*
1200876 AATGTATCGATACATTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTGTAGAATGTATCGATACATTCGTGG
* * *
1200917 AGTGTATCGATACATTATACAAATGTATCGATACA
1 AATGTATCGATACATTGTA-GAATGTATCGATACA
1200952 AGGTCCCAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 55 0.80
42 14 0.20
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (41 bp):
AATGTATCGATACATTGTAGAATGTATCGATACATTCGTGG
Found at i:1201012 original size:19 final size:19
Alignment explanation
Indices: 1200988--1201051 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1200978 TTTCAGCGAT
1200988 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
1201007 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
1201021 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
1201039 TTGTATCGATACA
1 TTGTATCGATACA
1201052 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
19 24 0.63
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:1201025 original size:32 final size:32
Alignment explanation
Indices: 1200989--1201059 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1200979 TTCAGCGATT
1200989 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
1201021 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1201053 TGTATCG
1 TGTATCG
1201060 CTAGGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1201026 original size:13 final size:13
Alignment explanation
Indices: 1201008--1201032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1200998 ACATAAGTAT
1201008 TGTATCGATACAA
1 TGTATCGATACAA
1201021 TGTATCGATACA
1 TGTATCGATACA
1201033 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1203636 original size:28 final size:27
Alignment explanation
Indices: 1203564--1203636 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1203554 CATCAATTTT
* *
1203564 TCATTGGGGATACTCCAACCCCGTTAA
1 TCATAGGGGATACTCCAACCCCATTAA
* *
1203591 TCATCGGGGATACTCCAACCCCATTATTT
1 TCATAGGGGATACTCCAACCCCATTA--A
1203620 TCA-AGGGGATACTCCAA
1 TCATAGGGGATACTCCAA
1203637 GATTTATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 24 0.60
28 13 0.32
29 3 0.08
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (27 bp):
TCATAGGGGATACTCCAACCCCATTAA
Found at i:1203758 original size:51 final size:52
Alignment explanation
Indices: 1203698--1203867 Score: 175
Period size: 51 Copynumber: 3.3 Consensus size: 52
1203688 TTATCTCTAA
* * *
1203698 GGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
* * * **
1203749 GGGGATACTCCAACCCTGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
* * * *
1203801 GGGGATAC-CCTAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATT
1 GGGGATACTCC-AACCCCGGTTTTATTTCC-AAAACACCAATTTTCCTACAATC
**
1203853 AAGGATACTCCAACC
1 GGGGATACTCCAACC
1203868 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
51 41 0.43
52 37 0.39
53 17 0.18
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
Found at i:1203760 original size:79 final size:74
Alignment explanation
Indices: 1203593--1203764 Score: 197
Period size: 74 Copynumber: 2.3 Consensus size: 74
1203583 CCCGTTAATC
* *
1203593 ATCGGGGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAAGATTTATTTCTAAAATATTAT
1 ATCGGGGATACTCCAACCCCATTATTCTCAAGGGGATACTCCAAGATTTATTTCTAAAATATGAT
*
1203658 TTTCTCATA
66 TTTCTCACA
* * *
1203667 ATCGGGGATACTCCAACCCCGTTA-TCTCTAAGGGGATACTCCAACCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCATTATTCTC-AAGGGGATACTCCAA-----GATTTATTTCTAAAA
1203730 TCATCGATTTTC-CACA
60 T-AT-GATTTTCTCACA
1203746 ATCGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
1203765 TGGCTTTATT
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
73 3 0.04
74 38 0.45
78 4 0.05
79 33 0.39
80 6 0.07
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (74 bp):
ATCGGGGATACTCCAACCCCATTATTCTCAAGGGGATACTCCAAGATTTATTTCTAAAATATGAT
TTTCTCACA
Found at i:1209360 original size:13 final size:13
Alignment explanation
Indices: 1209342--1209398 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1209332 CATAAAGTGT
1209342 TGTATCGATACAA
1 TGTATCGATACAA
1209355 TGTATCGATACATAA
1 TGTATCGATAC--AA
1209370 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
1209387 TATATCGATACA
1 TGTATCGATACA
1209399 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1209377 original size:32 final size:32
Alignment explanation
Indices: 1209322--1209422 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
1209312 TTCAACGATT
*
1209322 TGTATCAATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1209355 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1209387 TATATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1209419 TGTA
1 TGTA
1209423 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 52 0.81
33 12 0.19
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1209379 original size:19 final size:18
Alignment explanation
Indices: 1209320--1209417 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
1209310 ATTTCAACGA
*
1209320 TTTGTATCAATACATAAAG
1 TTTGTATCGATACAT-AAG
1209339 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1209355 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1209371 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
1209387 --TATATCGATACATAAG
1 TTTGTATCGATACATAAG
1209403 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1209418 ATGTAAGCTA
Statistics
Matches: 63, Mismatches: 3, Indels: 26
0.68 0.03 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 23 0.37
20 11 0.17
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1209522 original size:52 final size:52
Alignment explanation
Indices: 1209480--1209608 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1209470 CACTGATCTT
*
1209480 TGTATCGATACATGCAGGCAAATTTGTCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1209532 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1209584 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1209609 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1214191 original size:52 final size:52
Alignment explanation
Indices: 1214113--1214265 Score: 270
Period size: 52 Copynumber: 2.9 Consensus size: 52
1214103 CACGAAATAT
1214113 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1214165 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* * *
1214217 GCAAATTTGCCTGCATGTATCGATACATTTGAGTAATGTATCGATACAT
1 GAAAATTTGCCTGCATGTATCGATACATTTCA-TAGTGTATCGATACAT
1214266 TTTCTTGGCA
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 82 0.85
53 15 0.15
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:1214320 original size:19 final size:19
Alignment explanation
Indices: 1214296--1214347 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1214286 AGCGATACAT
1214296 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1214315 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1214334 TGTATCGATACAAA
1 TGTATCGATACAAA
1214348 TCATTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1215175 original size:17 final size:17
Alignment explanation
Indices: 1215151--1215189 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1215141 CCTTAATAAA
1215151 ACAT-TTTCCTTTAATC
1 ACATGTTTCCTTTAATC
* *
1215167 ATATGTTTCTTTTAATC
1 ACATGTTTCCTTTAATC
1215184 ACATGT
1 ACATGT
1215190 ATCTTTCTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (17 bp):
ACATGTTTCCTTTAATC
Found at i:1215194 original size:17 final size:17
Alignment explanation
Indices: 1215160--1215195 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1215150 AACATTTTCC
* *
1215160 TTTAATCATATGTTTCT
1 TTTAATCACATGTATCT
1215177 TTTAATCACATGTATCT
1 TTTAATCACATGTATCT
1215194 TT
1 TT
1215196 CTCCCCCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAATCACATGTATCT
Found at i:1217049 original size:13 final size:13
Alignment explanation
Indices: 1217031--1217055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1217021 ATAAACCCTT
1217031 TGTATCGATACAC
1 TGTATCGATACAC
1217044 TGTATCGATACA
1 TGTATCGATACA
1217056 TCTAAGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1217251 original size:8 final size:8
Alignment explanation
Indices: 1217233--1217263 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1217223 ATTTCAACAT
1217233 CAAACATCA
1 CAAA-ATCA
1217242 CAAAATCA
1 CAAAATCA
1217250 CAAAATCA
1 CAAAATCA
1217258 CAAAAT
1 CAAAAT
1217264 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:1220719 original size:13 final size:13
Alignment explanation
Indices: 1220701--1220726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1220691 TACAGCAAGT
1220701 ATGTATCGATACA
1 ATGTATCGATACA
1220714 ATGTATCGATACA
1 ATGTATCGATACA
1220727 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1228057 original size:10 final size:10
Alignment explanation
Indices: 1228042--1228098 Score: 60
Period size: 10 Copynumber: 5.2 Consensus size: 10
1228032 CATTCTCTTT
1228042 AAAAAAACAA
1 AAAAAAACAA
*
1228052 AAAAAAAGAA
1 AAAAAAACAA
1228062 AAAAAAAGCAAA
1 AAAAAAA-C-AA
1228074 AAAAAAACAAA
1 AAAAAAAC-AA
1228085 GCAAAAAAACAA
1 --AAAAAAACAA
1228097 AA
1 AA
1228099 CAAAGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 18 0.44
11 4 0.10
12 11 0.27
13 8 0.20
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1228074 original size:16 final size:17
Alignment explanation
Indices: 1228043--1228110 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 17
1228033 ATTCTCTTTA
**
1228043 AAAAAACAAAAAAAAAG
1 AAAAAACAAAGCAAAAG
1228060 AAAAAA-AAAGCAAAA-
1 AAAAAACAAAGCAAAAG
*
1228075 AAAAAACAAAGCAAAAA
1 AAAAAACAAAGCAAAAG
*
1228092 AACAAAACAAAGAAAAAG
1 AA-AAAACAAAGCAAAAG
1228110 A
1 A
1228111 GAGAAAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
15 6 0.14
16 16 0.36
17 8 0.18
18 14 0.32
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAGCAAAAG
Found at i:1229330 original size:120 final size:118
Alignment explanation
Indices: 1229093--1229811 Score: 724
Period size: 120 Copynumber: 6.2 Consensus size: 118
1229083 TCCGCTTTTT
* * *
1229093 AGTCCTCAAAAAGCAGGATGCCTGTTTCTTTTAAAGGCCACACAAGTTGGTGGCACCTTCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCT-TTTC-TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCC
* * *
1229158 TCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
64 TCAAAGAGCAGGATGC-CTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
1229214 AATCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCTACACAAGTTAGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTC-TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
* *
1229279 CAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCC
65 CAAAGAGCAGGATGCCTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * ** *
1229334 AATCCTCAAAGAGAAGGATGCC-TTTC---AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCT
* * * **
1229395 CAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-C
65 CAAAGAGCAGGATGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * **
1229448 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TTCTTT-AAAGCCCACACAAGTTGGTGGCACCTT-CAGTC
* * * * * * * **
1229513 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACATAGGTTAGTGGCACCTT-C
63 CTCAAAGAGCAGGATGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * **
1229568 AGTCCTCAAAGAGAAGGATGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TTCTTT-AAAGCCCACACAAGTTGGTGGCACCTTC-AGTC
* *
1229633 CTCAAAGAGCAAGATG-----CCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCC
63 CTCAAAGAGCAGGATGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
1229684 AGTCCTCAAAGAGCAGGACACC-TTTC---AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCA
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCT
* * *
1229745 CAAGGAGCAGGATG-----CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
65 CAAAGAGCAGGATGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1229794 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1229812 TACACTTTAT
Statistics
Matches: 523, Mismatches: 62, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
110 85 0.16
111 6 0.01
114 21 0.04
115 79 0.15
116 44 0.08
119 7 0.01
120 261 0.50
121 20 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (118 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
AAAGAGCAGGATGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1229397 original size:175 final size:175
Alignment explanation
Indices: 1229093--1229811 Score: 795
Period size: 175 Copynumber: 4.1 Consensus size: 175
1229083 TCCGCTTTTT
* * * * * **
1229093 AGTCCTCAAAAAGCAGGATGCCTGTTTCTTTTAAAGGCCACACAAGTTGGTGGCACCTT-CAGTC
1 AGTCCTCAAAGAGCAGGACGCCT-TTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * * *
1229157 CTCAAAGAGCAA-GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCCC
65 CTCAAAGAG-AAGGACGC-----CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCCC
* *
1229221 AAAGAGCAGGACGCCTTTTCTTTTAAAGCCTACACAAGTTAGTGGCACCTTC
124 AAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
* *
1229273 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* *
1229338 CTCAAAGAGAAGGATGCC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCCCAAAGAG
65 CTCAAAGAGAAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCCCAAAGAG
1229402 CAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
130 CAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
*
1229448 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * * * * * *
1229513 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACATAGGTTAGTGGCACCTTC-AGTCCTCAA
65 CTCAAAGAGAAGGACGCCTTTTC----AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCCCAA
* * * * **
1229577 AGAGAAGGATGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
126 AGAGCAGGATGCCTT-TTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
* * *
1229628 TAGTCCTCAAAGAGCA--A-G--ATGCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 -AGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * * *
1229688 CTCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCACAAGGA
65 CTCAAAGAGAAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCCCAAAGA
* * * *
1229751 GCAGGATGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTT
129 GCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCAC-CTTC
1229794 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1229812 TACACTTTAT
Statistics
Matches: 477, Mismatches: 47, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
165 37 0.08
166 3 0.01
167 1 0.00
169 2 0.00
170 21 0.04
171 22 0.05
174 4 0.01
175 219 0.46
176 6 0.01
178 1 0.00
179 24 0.05
180 104 0.22
181 33 0.07
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (175 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
TCAAAGAGAAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCCCAAAGAGC
AGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
Found at i:1229651 original size:295 final size:292
Alignment explanation
Indices: 1229088--1229811 Score: 1047
Period size: 295 Copynumber: 2.5 Consensus size: 292
1229078 CTCCTTCCGC
* *
1229088 TTTT-TAGTCCTCAAAAAGCAGGATGCCTGTTTCTTTTAAAGGCCACACAAGTTGGTGGCACCTT
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCT-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
1229152 CAGTCCTCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
65 CAGTCCTCAAAGAGCAAGA-GC--TTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
*
1229217 CCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCTACACAAGTTAGTGGCACCTTCAGTCCTCAA
127 CCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAA
*
1229282 AGAGCAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAG
192 AGAGAAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAG
1229347 AAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
257 AAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1229383 TTTTCTAGTCCCCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1229448 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
66 AGTCCTCAAAGAGCAAGA-G-CTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* *
1229513 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACATAGGTTAGTGGCACCTTCAGTCCTCAAA
128 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAA
* * * *
1229578 GAGAAGGATGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGC
193 GAGAAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAG-
*
1229643 AA-GATGCCTTTCGAAGCCCACACAAGTTGGTGGCA
257 AAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* **
1229678 TTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTT
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TT
* * * * * * *
1229738 TAGTCCACAAGGAGC-AG-G-ATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCC
65 CAGTCCTCAAAGAGCAAGAGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
*
1229799 TCAAAGAGCAGGA
129 CCAAAGAGCAGGA
1229812 TACACTTTAT
Statistics
Matches: 394, Mismatches: 29, Indels: 22
0.89 0.07 0.05
Matches are distributed among these distances:
285 45 0.11
286 5 0.01
288 1 0.00
290 26 0.07
291 14 0.04
294 6 0.02
295 272 0.69
296 25 0.06
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (292 bp):
TTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
AGTCCTCAAAGAGCAAGAGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCC
AAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAG
AAGGACGCCTTCTCCTTTCAAAGCCAACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGAAGG
ATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1229791 original size:28 final size:28
Alignment explanation
Indices: 1229705--1229791 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
1229695 AGCAGGACAC
*
1229705 CTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAAAGCCCACACGAGTTGGTGGCA
* * * **
1229733 CCTTT--TAGTCCACAAGGAGCAGGAT-GC-
1 -CTTTCAAAGCCCAC-ACGAGTTGG-TGGCA
1229760 CTTTCAAAGCCCACACGAGTTGGTGGCA
1 CTTTCAAAGCCCACACGAGTTGGTGGCA
1229788 CTTT
1 CTTT
1229792 TTAGTCCTCA
Statistics
Matches: 41, Mismatches: 11, Indels: 13
0.63 0.17 0.20
Matches are distributed among these distances:
26 5 0.12
27 14 0.34
28 17 0.41
29 5 0.12
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (28 bp):
CTTTCAAAGCCCACACGAGTTGGTGGCA
Found at i:1230602 original size:21 final size:21
Alignment explanation
Indices: 1230559--1230675 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
1230549 AAAATTTCCA
* *
1230559 AATGTATCAATATA-TTGTAG
1 AATGTATCGATACATTTGTAG
* *
1230579 AATGTATCTATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1230600 AATGTATCGATACA-TTGTAG
1 AATGTATCGATACATTTGTAG
*
1230620 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
1230641 AGTGTATCGATACA-TTATACA
1 AATGTATCGATACATTTGTA-G
1230662 AATGTATCGATACA
1 AATGTATCGATACA
1230676 AGGTCCCAAC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
20 34 0.41
21 49 0.59
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1230617 original size:41 final size:41
Alignment explanation
Indices: 1230559--1230675 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 41
1230549 AAAATTTCCA
* * *
1230559 AATGTATCAATATATTGTAGAATGTATCTATACATTTGTGG
1 AATGTATCGATACATTGTAGAATGTATCGATACATTTGTGG
1230600 AATGTATCGATACATTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTGTAGAATGTATCGATACATTTGTGG
* * *
1230641 AGTGTATCGATACATTATACAAATGTATCGATACA
1 AATGTATCGATACATTGTA-GAATGTATCGATACA
1230676 AGGTCCCAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 55 0.80
42 14 0.20
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (41 bp):
AATGTATCGATACATTGTAGAATGTATCGATACATTTGTGG
Found at i:1231879 original size:79 final size:79
Alignment explanation
Indices: 1231714--1231915 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 79
1231704 GATAATAACA
* * ** * *
1231714 GGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGAT
1 GGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGAT
**
1231778 TAGAAAAAAAAATTG
65 TAGAAAAAAAAACCG
*
1231793 GGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATT
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA-T
* ** * *
1231857 TTGGGAATAAAGCCG
65 TAGAAAAAAAAACCG
* * *
1231872 GGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1231916 GATGAAATAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
78 7 0.07
79 96 0.93
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGATT
AGAAAAAAAAACCG
Found at i:1231926 original size:28 final size:28
Alignment explanation
Indices: 1231870--1231946 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1231860 GGAATAAAGC
*** *
1231870 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1231898 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * *
1231926 CGAGGTTGGAGCATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1231947 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1232028 original size:52 final size:52
Alignment explanation
Indices: 1231966--1232102 Score: 154
Period size: 52 Copynumber: 2.6 Consensus size: 52
1231956 ATTGGTGTTT
* * *
1231966 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-AAAATTGGCG
1 TTTTGAAAATAAAACCGGAGTTGGAGTATCCCCGATT-AAGGAAAAATTAGCG
** *
1232018 TTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTTTGAAAATAAAACC-GGAGTTGGAGTATCCCCGATTAAGGAAAAATTAGCG
**
1232070 TTTT-AGCGATAAAACCGGAGTTGGAGTATCCCC
1 TTTTGA-AAATAAAACCGGAGTTGGAGTATCCCC
1232103 TCGAAAATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
51 6 0.08
52 64 0.88
53 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (52 bp):
TTTTGAAAATAAAACCGGAGTTGGAGTATCCCCGATTAAGGAAAAATTAGCG
Found at i:1232073 original size:107 final size:105
Alignment explanation
Indices: 1231931--1232275 Score: 285
Period size: 107 Copynumber: 3.2 Consensus size: 105
1231921 AATAACGAGG
* *
1231931 TTGGAGCATCCTCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 TTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATC
*
1231996 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
66 CCCGATTAAAGGAAAATTGGAGTTTTGAAAATAAAA-C-GGA
* * *
1232038 TTGGAGTATCCCCGATTGTGGAA-AAATTAGTG--TTTTAGCG--ATAAAACCGGAGTTGGAGTA
1 TTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTTG-GAAATAAAATCGGAGTTGGAGTA
* * ** ** ** * *
1232098 TCCCCTCGAAAATAACGG--GGTTGGAGTATCCCCGATGAT-TAACGGGG
64 T-CCC-CG--ATTAAAGGAAAATTGGAGT-T--TTGAAAATAAAAC-GGA
**
1232145 TTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTACAGTATC
1 TTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATC
* * *
1232210 CCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGA
66 CCCGATTAAAGGAAAATTGGAGTTTTGAAAATAAAA-CGGA
* * *
1232250 GTTGGAATATCCTCGATTGTGGAGAA
1 -TTGGAGTATCCCCGATTGTGAAGAA
1232276 TTGATAAACT
Statistics
Matches: 181, Mismatches: 38, Indels: 39
0.70 0.15 0.15
Matches are distributed among these distances:
104 24 0.13
105 13 0.07
106 39 0.22
107 61 0.34
108 14 0.08
109 12 0.07
110 18 0.10
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (105 bp):
TTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATC
CCCGATTAAAGGAAAATTGGAGTTTTGAAAATAAAACGGA
Found at i:1232121 original size:28 final size:28
Alignment explanation
Indices: 1232076--1232157 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
1232066 AGTGTTTTAG
* *
1232076 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1232103 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
1232130 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1232158 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:1232193 original size:214 final size:214
Alignment explanation
Indices: 1231863--1232272 Score: 644
Period size: 214 Copynumber: 1.9 Consensus size: 214
1231853 TATTTTGGGA
* * * *
1231863 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* **
1231928 AGGTTGGAGCATCCTCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGT
66 AGGTTGGAGCATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTACAGT
* *
1231993 ATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGT
131 ATCCCCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGT
1232057 GGAAAAATTAGTGTTTTAGCG
194 GGAAAAATTAGTGTTTTAGCG
*
1232078 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
1232142 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTACAGT
66 AGGTTGGAGCATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTACAGT
* * * *
1232207 ATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
131 ATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
1232272 A
196 A
1232273 GAATTGATAA
Statistics
Matches: 178, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
212 3 0.02
213 44 0.25
214 78 0.44
215 53 0.30
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (214 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGCATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTACAGT
ATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
AAAAATTAGTGTTTTAGCG
Found at i:1234643 original size:13 final size:13
Alignment explanation
Indices: 1234625--1234650 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1234615 ACAAAGATCC
1234625 ATGTATCGATACA
1 ATGTATCGATACA
1234638 ATGTATCGATACA
1 ATGTATCGATACA
1234651 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1234646 original size:33 final size:33
Alignment explanation
Indices: 1234604--1234670 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1234594 AAAATTTCCA
***
1234604 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1234637 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1234670 A
1 A
1234671 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1234714 original size:19 final size:18
Alignment explanation
Indices: 1234690--1234755 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
1234680 CAGTAGCTAA
1234690 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1234709 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1234724 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1234741 TTATGTATCGATACA
1 TTATGTATCGATACA
1234756 TTCTACAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
16 2 0.05
18 2 0.05
19 25 0.61
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1234730 original size:13 final size:13
Alignment explanation
Indices: 1234712--1234736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1234702 ACAATACTTA
1234712 TGTATCGATACAT
1 TGTATCGATACAT
1234725 TGTATCGATACA
1 TGTATCGATACA
1234737 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1234734 original size:32 final size:32
Alignment explanation
Indices: 1234693--1234757 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1234683 TAGCTAATTA
*
1234693 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1234725 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1234757 T
1 T
1234758 CTACAAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1237551 original size:27 final size:27
Alignment explanation
Indices: 1237513--1237565 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1237503 CATCAATTTT
*
1237513 TCATTGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
1237540 TCATCGGGGATACTCCAACCCCGTTA
1 TCATCGGGGATACTCCAACCCCGTTA
1237566 TTTTCAAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:1237585 original size:28 final size:27
Alignment explanation
Indices: 1237513--1237585 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1237503 CATCAATTTT
*
1237513 TCATTGGGGATACTCCAACCCCGTTAA
1 TCATAGGGGATACTCCAACCCCGTTAA
* *
1237540 TCATCGGGGATACTCCAACCCCGTTATTT
1 TCATAGGGGATACTCCAACCCCGTTA--A
1237569 TCA-AGGGGATACTCCAA
1 TCATAGGGGATACTCCAA
1237586 GATTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 25 0.61
28 13 0.32
29 3 0.07
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (27 bp):
TCATAGGGGATACTCCAACCCCGTTAA
Found at i:1237707 original size:51 final size:52
Alignment explanation
Indices: 1237647--1237816 Score: 184
Period size: 51 Copynumber: 3.3 Consensus size: 52
1237637 TTATCTCTGA
* * *
1237647 GGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
* * **
1237698 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
* * * *
1237750 GGGGATAC-CCTAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATT
1 GGGGATACTCC-AACCCCGGTTTTATTTCC-AAAACACCAATTTTCCTACAATC
**
1237802 AAGGATACTCCAACC
1 GGGGATACTCCAACC
1237817 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
51 42 0.43
52 38 0.39
53 17 0.18
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
Found at i:1237714 original size:79 final size:74
Alignment explanation
Indices: 1237542--1237715 Score: 201
Period size: 74 Copynumber: 2.3 Consensus size: 74
1237532 CCCGTTAATC
* *
1237542 ATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAAGATTTATTTCTAAAATATTAT
1 ATCGGGGATACTCCAACCCCGTTATTCTCAAGGGGATACTCCAAGATTTATTTCTAAAATATGAT
*
1237607 TTTCTCATA
66 TTTCTCACA
* * *
1237616 ATCGGGGATACTCCAACCCCGTTA-TCTCTGAGGGGATACTCCAACCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATTCTC-AAGGGGATACTCCAA-----GATTTATTTCTAAAA
1237679 TCATCGATTTTC-CACA
60 T-AT-GATTTTCTCACA
1237695 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1237716 GCTTTATTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
73 3 0.03
74 38 0.44
78 4 0.05
79 35 0.41
80 6 0.07
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (74 bp):
ATCGGGGATACTCCAACCCCGTTATTCTCAAGGGGATACTCCAAGATTTATTTCTAAAATATGAT
TTTCTCACA
Found at i:1243306 original size:13 final size:13
Alignment explanation
Indices: 1243288--1243344 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1243278 CATAAAGTGT
1243288 TGTATCGATACAA
1 TGTATCGATACAA
1243301 TGTATCGATACATAA
1 TGTATCGATAC--AA
1243316 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1243333 TGTATCGATACA
1 TGTATCGATACA
1243345 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1243323 original size:32 final size:32
Alignment explanation
Indices: 1243268--1243368 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1243258 TTCAACGATT
*
1243268 TGTATCAATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1243301 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1243333 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1243365 TGTA
1 TGTA
1243369 AGCTACTGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 54 0.82
33 12 0.18
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1243325 original size:19 final size:18
Alignment explanation
Indices: 1243266--1243363 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1243256 ATTTCAACGA
*
1243266 TTTGTATCAATACATAAAG
1 TTTGTATCGATACAT-AAG
1243285 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1243301 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1243317 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1243333 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1243349 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1243364 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 24 0.37
20 11 0.17
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1243468 original size:52 final size:52
Alignment explanation
Indices: 1243426--1243554 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1243416 CACTGATCTT
*
1243426 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGACCAGATGTATCGATACACTATAAAA
1243478 TGTATCGATACATGCAGGCAAATTTGACCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGACCAGATGTATCGATACACTATAAAA
*
1243530 TGTATCGATACGTGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1243555 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGACCAGATGTATCGATACACTATAAAA
Found at i:1248197 original size:52 final size:52
Alignment explanation
Indices: 1248119--1248249 Score: 253
Period size: 52 Copynumber: 2.5 Consensus size: 52
1248109 CACGAAATAT
1248119 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1248171 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
1248223 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
1248250 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:1248255 original size:13 final size:13
Alignment explanation
Indices: 1248237--1248262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1248227 ATTTGCCTGC
1248237 ATGTATCGATACA
1 ATGTATCGATACA
1248250 ATGTATCGATACA
1 ATGTATCGATACA
1248263 TTTGAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1248339 original size:19 final size:19
Alignment explanation
Indices: 1248315--1248366 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1248305 AGCGATACAT
1248315 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1248334 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1248353 TGTATCGATACAAA
1 TGTATCGATACAAA
1248367 TCGTTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1249194 original size:17 final size:17
Alignment explanation
Indices: 1249170--1249208 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1249160 CCTTAATAAA
1249170 ACAT-TTTCCTTTAATC
1 ACATGTTTCCTTTAATC
* *
1249186 ATATGTTTCTTTTAATC
1 ACATGTTTCCTTTAATC
1249203 ACATGT
1 ACATGT
1249209 ATCTTTCTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (17 bp):
ACATGTTTCCTTTAATC
Found at i:1249213 original size:17 final size:17
Alignment explanation
Indices: 1249179--1249214 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1249169 AACATTTTCC
* *
1249179 TTTAATCATATGTTTCT
1 TTTAATCACATGTATCT
1249196 TTTAATCACATGTATCT
1 TTTAATCACATGTATCT
1249213 TT
1 TT
1249215 CTCCCCCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAATCACATGTATCT
Found at i:1250597 original size:20 final size:21
Alignment explanation
Indices: 1250574--1250615 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1250564 TGGGGGCTGC
*
1250574 CCGATTGCGACC-GGGGAGTG
1 CCGATCGCGACCTGGGGAGTG
*
1250594 CCGATCGCGACCTGGTGAGTG
1 CCGATCGCGACCTGGGGAGTG
1250615 C
1 C
1250616 TGCCTAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (21 bp):
CCGATCGCGACCTGGGGAGTG
Found at i:1251068 original size:13 final size:13
Alignment explanation
Indices: 1251050--1251074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1251040 ATAAACCCTT
1251050 TGTATCGATACAC
1 TGTATCGATACAC
1251063 TGTATCGATACA
1 TGTATCGATACA
1251075 TCTAAGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1251270 original size:8 final size:8
Alignment explanation
Indices: 1251252--1251282 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1251242 ATTTCAACAT
1251252 CAAACATCA
1 CAAA-ATCA
1251261 CAAAATCA
1 CAAAATCA
1251269 CAAAATCA
1 CAAAATCA
1251277 CAAAAT
1 CAAAAT
1251283 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:1258165 original size:63 final size:62
Alignment explanation
Indices: 1258093--1258275 Score: 192
Period size: 63 Copynumber: 2.9 Consensus size: 62
1258083 GGATTACAAC
* ** * *
1258093 CTAGGTCTTTTCTCTTAAGTTGAATTTATTTTCCTAGAAATAGTTCGAGCTTAGGATCGCAGT
1 CTAGGTCTTTTCTTTTAAGTCAAATTTATTTTCCTAGAAATAGTT-GAGCCTAGGATCACAGT
* * * * * *
1258156 CTAGGTCTTTTCTTTTTAGTCAAATCTATTTTCCTTA-AAATAAG-TGAAGCCCAGTATTATAGT
1 CTAGGTCTTTTCTTTTAAGTCAAATTTATTTTCC-TAGAAAT-AGTTG-AGCCTAGGATCACAGT
1258219 CTAGGGT-TTTTCTTTTAAGTCAAATTTATTTTCCTAGAAATAGTTTGAGCCTAGGAT
1 CTA-GGTCTTTTCTTTTAAGTCAAATTTATTTTCCTAGAAATAG-TTGAGCCTAGGAT
1258276 TGCAATTTAG
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
62 5 0.05
63 84 0.86
64 9 0.09
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (62 bp):
CTAGGTCTTTTCTTTTAAGTCAAATTTATTTTCCTAGAAATAGTTGAGCCTAGGATCACAGT
Found at i:1258764 original size:49 final size:49
Alignment explanation
Indices: 1258711--1259072 Score: 205
Period size: 50 Copynumber: 7.3 Consensus size: 49
1258701 GATAAGGTGC
* * * *
1258711 TTAAGCCTTATAAAGTGAATGTCCA-ACTAACTGGCACTTGGTAAAAAGG
1 TTAAGCCTTATAAAGTTAAAGTCCACACTAGCTGGCACTT-ATAAAAAGG
* * *
1258760 TTAAGCC-TATAGAGTTAAAG-CCTATACTAGCTGGCACCTTATAAGAAGG
1 TTAAGCCTTATAAAGTTAAAGTCC-ACACTAGCTGGCA-CTTATAAAAAGG
* * * * * *
1258809 TTAAGCCCTAGAAAATTAAAGTCCACATTAGCTGGCACCTACTAGAAAGG
1 TTAAGCCTTATAAAGTTAAAGTCCACACTAGCTGGCACTTA-TAAAAAGG
* * * * ** **
1258859 TTAAGCCTTATAAAGTCAAAG-CCTATATTAGCTAGCACCTGCTAGGAAGG
1 TTAAGCCTTATAAAGTTAAAGTCC-ACACTAGCTGGCA-CTTATAAAAAGG
* * * * ** *
1258909 TTAAGCCTTATAAAGTCAAAG-CCTATATTAGTTGGCACGAAATAGGAAA-G
1 TTAAGCCTTATAAAGTTAAAGTCC-ACACTAGCTGGCAC-TTATA-AAAAGG
* ** * * *
1258959 TTAAGCCCTATGGAGTTAAAGTCCATACTAGCTGGCACCTTATAAGAATG
1 TTAAGCCTTATAAAGTTAAAGTCCACACTAGCTGGCA-CTTATAAAAAGG
* * * * ** *
1259009 TTAAGCCTTATAGAGATAAAGCCCACACTAGTTGGCACTTGATAGGAATG
1 TTAAGCCTTATAAAGTTAAAGTCCACACTAGCTGGCACTT-ATAAAAAGG
*
1259059 TTAAGCCCTATAAA
1 TTAAGCCTTATAAA
1259073 ATCAAAATCC
Statistics
Matches: 250, Mismatches: 49, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
47 2 0.01
48 11 0.04
49 42 0.17
50 186 0.74
51 9 0.04
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (49 bp):
TTAAGCCTTATAAAGTTAAAGTCCACACTAGCTGGCACTTATAAAAAGG
Found at i:1258845 original size:50 final size:50
Alignment explanation
Indices: 1258756--1259085 Score: 217
Period size: 50 Copynumber: 6.6 Consensus size: 50
1258746 ACTTGGTAAA
* * * *
1258756 AAGGTTAAG-CCTATAGAGTTAAAG-CCTATACTAGCTGGCACCTTATAAG
1 AAGGTTAAGCCCTATAAAATCAAAGTCC-ATATTAGCTGGCACCTTATAAG
* * *
1258805 AAGGTTAAGCCCTAGAAAATTAAAGTCCACATTAGCTGGCACC-TACT-AG
1 AAGGTTAAGCCCTATAAAATCAAAGTCCATATTAGCTGGCACCTTA-TAAG
* * * ** *
1258854 AAAGGTTAAGCCTTATAAAGTCAAAG-CCTATATTAGCTAGCACCTGCTAGG
1 -AAGGTTAAGCCCTATAAAATCAAAGTCC-ATATTAGCTGGCACCTTATAAG
* * * *** *
1258905 AAGGTTAAGCCTTATAAAGTCAAAG-CCTATATTAGTTGGCACGAAATAGG
1 AAGGTTAAGCCCTATAAAATCAAAGTCC-ATATTAGCTGGCACCTTATAAG
* ** * * *
1258955 AAAGTTAAGCCCTATGGAGTTAAAGTCCATACTAGCTGGCACCTTATAAG
1 AAGGTTAAGCCCTATAAAATCAAAGTCCATATTAGCTGGCACCTTATAAG
* * * * * * * *
1259005 AATGTTAAGCCTTATAGAGAT-AAAGCCCACACTAGTTGGCA-CTTGATAGG
1 AAGGTTAAGCCCTATA-AAATCAAAGTCCATATTAGCTGGCACCTT-ATAAG
* *
1259055 AATGTTAAGCCCTATAAAATCAAAATCCATA
1 AAGGTTAAGCCCTATAAAATCAAAGTCCATA
1259086 CTAACCGGCA
Statistics
Matches: 224, Mismatches: 46, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
49 21 0.09
50 197 0.88
51 6 0.03
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (50 bp):
AAGGTTAAGCCCTATAAAATCAAAGTCCATATTAGCTGGCACCTTATAAG
Found at i:1258966 original size:150 final size:149
Alignment explanation
Indices: 1258756--1259078 Score: 348
Period size: 150 Copynumber: 2.2 Consensus size: 149
1258746 ACTTGGTAAA
* * ** *
1258756 AAGGTTAAGCCTATAGAGTTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCCTA-G
1 AAGGTTAAGCCTATAAAGTCAAAGCCTATACTAGCTGGCACCAAATAAGAAAGTTAAGCCCTATG
*
1258820 AAAATTAAAGTCCACATTAGCTGGCACC-TACT-AGAAAGGTTAAGCCTTATAAAG-TCAAAGCC
66 -AAATTAAAGTCCACACTAGCTGGCACCTTA-TAAG-AAGGTTAAGCCTTATAAAGAT-AAAGCC
* * * *
1258882 TATATTAGCTAGCACCTGCTAGG
127 CACACTAGCTAGCACCTGATAGG
* * * *
1258905 AAGGTTAAGCCTTATAAAGTCAAAGCCTATATTAGTTGGCACGAAATAGGAAAGTTAAGCCCTAT
1 AAGGTTAAGCC-TATAAAGTCAAAGCCTATACTAGCTGGCACCAAATAAGAAAGTTAAGCCCTAT
* * * * *
1258970 GGAGTTAAAGTCCATACTAGCTGGCACCTTATAAGAATGTTAAGCCTTATAGAGATAAAGCCCAC
65 GAAATTAAAGTCCACACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTATAAAGATAAAGCCCAC
* * *
1259035 ACTAGTTGGCACTTGATAGG
130 ACTAGCTAGCACCTGATAGG
* *
1259055 AATGTTAAGCCCTATAAAATCAAA
1 AAGGTTAAG-CCTATAAAGTCAAA
1259079 ATCCATACTA
Statistics
Matches: 144, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
149 11 0.08
150 125 0.87
151 8 0.06
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (149 bp):
AAGGTTAAGCCTATAAAGTCAAAGCCTATACTAGCTGGCACCAAATAAGAAAGTTAAGCCCTATG
AAATTAAAGTCCACACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTATAAAGATAAAGCCCACA
CTAGCTAGCACCTGATAGG
Found at i:1259016 original size:100 final size:98
Alignment explanation
Indices: 1258658--1259070 Score: 341
Period size: 100 Copynumber: 4.2 Consensus size: 98
1258648 ATCTGGTAAG
* * * * * ** *
1258658 AAGTTAAGCCCTATAGAGTCAAAGCCTACACGAGTTGGCACCTGATAAGGTGCTTAAGCCTTATA
1 AAGTTAAGCCCTATAGAGTTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTATA
* * ** * ** *
1258723 AAGTGAATGTCCA-ACTAACTGGCACTTGGTA-AA
66 AAGT-AAAG-CCACATTAGTTGGCACCTAATAGGA
*
1258756 AAGGTTAAG-CCTATAGAGTTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCCTAG
1 AA-GTTAAGCCCTATAGAGTTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTA-
* * * *
1258820 AAAATTAAAGTCCACATTAGCTGGCACCTACTA-GA
64 TAAAGTAAAG-CCACATTAGTTGGCACCTAATAGGA
* * * * * ** *
1258855 AAGGTTAAGCCTTATAAAGTCAAAGCCTATATTAGCTAGCACCTGCTAGGAAGGTTAAGCCTTAT
1 AA-GTTAAGCCCTATAGAGTTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTAT
* **
1258920 AAAGTCAAAGCCTATATTAGTTGGCACGAAATAGGA
65 AAAGT-AAAGCC-ACATTAGTTGGCACCTAATAGGA
* *
1258956 AAGTTAAGCCCTATGGAGTTAAAGTCC-ATACTAGCTGGCACCTTATAAGAATGTTAAGCCTTAT
1 AAGTTAAGCCCTATAGAGTTAAAG-CCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTAT
* * * *
1259020 AGAGATAAAGCCCACACTAGTTGGCACTTGATAGGA
65 AAAG-TAAAG-CCACATTAGTTGGCACCTAATAGGA
*
1259056 ATGTTAAGCCCTATA
1 AAGTTAAGCCCTATA
1259071 AAATCAAAAT
Statistics
Matches: 253, Mismatches: 52, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
98 54 0.21
99 39 0.15
100 151 0.60
101 9 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (98 bp):
AAGTTAAGCCCTATAGAGTTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCTTATA
AAGTAAAGCCACATTAGTTGGCACCTAATAGGA
Found at i:1259096 original size:150 final size:150
Alignment explanation
Indices: 1258711--1259096 Score: 318
Period size: 150 Copynumber: 2.6 Consensus size: 150
1258701 GATAAGGTGC
* * * * * * * ** * *
1258711 TTAAGCCTTATAAAGTGAATGTCCA-ACTAACTGGCACTTGGTAAAAAGGTTAAG-CCTATAGAG
1 TTAAGCCTTATAAAGTCAAAGCCCACACTAGCTAGCACCTGATAGGAAGGTTAAGCCCTATAAAA
* * * *** * * * * *
1258774 TTAAAGCCTATACTAGCTGGCACCTTATAAGAAGGTTAAGCCCTA-GAAAATTAAAGTCCACATT
66 TCAAAGCCTATACTAACCGGCACGAAATAGGAAAGTTAAGCCCTATG-GAGTTAAAGTCCACACT
1258838 AGCTGGCACCTACTAGAAAGG
130 AGCTGGCACCTACTAGAAAGG
* * * * * *
1258859 TTAAGCCTTATAAAGTCAAAGCCTATATTAGCTAGCACCTGCTAGGAAGGTTAAGCCTTATAAAG
1 TTAAGCCTTATAAAGTCAAAGCCCACACTAGCTAGCACCTGATAGGAAGGTTAAGCCCTATAAAA
* *** *
1258924 TCAAAGCCTATATTAGTTGGCACGAAATAGGAAAGTTAAGCCCTATGGAGTTAAAGTCCATACTA
66 TCAAAGCCTATACTAACCGGCACGAAATAGGAAAGTTAAGCCCTATGGAGTTAAAGTCCACACTA
*
1258989 GCTGGCACCTTA-TA-AGAATG
131 GCTGGCACC-TACTAGA-AAGG
* * * * *
1259009 TTAAGCCTTATAGAGAT-AAAGCCCACACTAGTTGGCACTTGATAGGAATGTTAAGCCCTATAAA
1 TTAAGCCTTATAAAG-TCAAAGCCCACACTAGCTAGCACCTGATAGGAAGGTTAAGCCCTATAAA
*
1259073 ATCAAAATCC-ATACTAACCGGCAC
65 ATC-AAAGCCTATACTAACCGGCAC
1259097 TTGATAGGGT
Statistics
Matches: 189, Mismatches: 42, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
148 21 0.11
149 23 0.12
150 136 0.72
151 9 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (150 bp):
TTAAGCCTTATAAAGTCAAAGCCCACACTAGCTAGCACCTGATAGGAAGGTTAAGCCCTATAAAA
TCAAAGCCTATACTAACCGGCACGAAATAGGAAAGTTAAGCCCTATGGAGTTAAAGTCCACACTA
GCTGGCACCTACTAGAAAGG
Found at i:1262115 original size:20 final size:20
Alignment explanation
Indices: 1262092--1262165 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1262082 ACAATTCAAA
1262092 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1262112 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1262133 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1262153 GTATCGATACATG
1 GTATCGATACATG
1262166 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1262136 original size:21 final size:21
Alignment explanation
Indices: 1262110--1262185 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1262100 ACATGTTGCA
1262110 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1262131 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1262151 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1262172 ATGTATCGATACAT
1 ATGTATCGATACAT
1262186 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1262143 original size:41 final size:41
Alignment explanation
Indices: 1262092--1262185 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1262082 ACAATTCAAA
1262092 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1262133 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1262174 GTATCGATACAT
1 GTATCGATACAT
1262186 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1264496 original size:21 final size:21
Alignment explanation
Indices: 1264463--1264507 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1264453 TTGCAAGTTG
*
1264463 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1264485 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1264505 AAA
1 AAA
1264508 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1268434 original size:20 final size:20
Alignment explanation
Indices: 1268355--1268434 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1268345 AATGTCCAAA
*
1268355 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1268375 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1268400 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1268420 TTGTATCGATACATT
1 ATGTATCGATACATT
1268435 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1268438 original size:13 final size:13
Alignment explanation
Indices: 1268420--1268458 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1268410 ACATTTTTCT
1268420 TTGTATCGATACA
1 TTGTATCGATACA
1268433 TTGTATCGATACA
1 TTGTATCGATACA
*
1268446 CTGTATCGATACA
1 TTGTATCGATACA
1268459 GGGAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1271018 original size:13 final size:13
Alignment explanation
Indices: 1271000--1271025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1270990 TACAGCAAGT
1271000 ATGTATCGATACA
1 ATGTATCGATACA
1271013 ATGTATCGATACA
1 ATGTATCGATACA
1271026 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1273346 original size:20 final size:21
Alignment explanation
Indices: 1273323--1273375 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1273313 CATTAAGGGA
1273323 TGTATCGATACATTATGT-AT-
1 TGTATCGATACATT-TGTCATG
*
1273343 TGTATCGATACATTTTTCATG
1 TGTATCGATACATTTGTCATG
1273364 TGTATCGATACA
1 TGTATCGATACA
1273376 AATAAGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 12 0.40
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (21 bp):
TGTATCGATACATTTGTCATG
Found at i:1273448 original size:21 final size:21
Alignment explanation
Indices: 1273424--1273472 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1273414 GATGGTATTG
1273424 ATACATTCACATAATGTATCA
1 ATACATTCACATAATGTATCA
**
1273445 ATACATTCACATAATGTATTG
1 ATACATTCACATAATGTATCA
1273466 ATACATT
1 ATACATT
1273473 TTCATTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (21 bp):
ATACATTCACATAATGTATCA
Found at i:1275240 original size:20 final size:20
Alignment explanation
Indices: 1275215--1275267 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1275205 TCCAAATCTA
1275215 TCGATACATTATT-CATTGTC
1 TCGATACATT-TTGCATTGTC
*
1275235 TCGATACATTTTGCATTGTA
1 TCGATACATTTTGCATTGTC
* *
1275255 TTGATAAATTTTG
1 TCGATACATTTTG
1275268 AAAAAAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (20 bp):
TCGATACATTTTGCATTGTC
Found at i:1280151 original size:22 final size:23
Alignment explanation
Indices: 1280112--1280156 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1280102 GAATTGATGG
1280112 AGGAAGAAGATTTGAAGGAATTTA
1 AGGAAGAAGATTTGAAGG-ATTTA
1280136 AGGAAGAA-A-TTGAAGGATTTA
1 AGGAAGAAGATTTGAAGGATTTA
1280157 GTGGCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 1 0.05
24 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (23 bp):
AGGAAGAAGATTTGAAGGATTTA
Found at i:1289561 original size:22 final size:20
Alignment explanation
Indices: 1289534--1289588 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1289524 CATAACTAAA
*
1289534 TGTATCAATACATGCTTTCAAT
1 TGTATCGATACAT-CTTTC-AT
* *
1289556 TGTATCGATATATTTTTCAT
1 TGTATCGATACATCTTTCAT
1289576 TGTATCGATACAT
1 TGTATCGATACAT
1289589 TCTGGGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.48
21 4 0.14
22 11 0.38
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATCTTTCAT
Found at i:1290643 original size:20 final size:20
Alignment explanation
Indices: 1290618--1290661 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1290608 AACTTGATAA
1290618 GTGTTTGCTGCTTTATGCTT
1 GTGTTTGCTGCTTTATGCTT
1290638 GTGTTTGCTGCTTTATGCTT
1 GTGTTTGCTGCTTTATGCTT
1290658 GTGT
1 GTGT
1290662 AAAGTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.14, G:0.27, T:0.55
Consensus pattern (20 bp):
GTGTTTGCTGCTTTATGCTT
Found at i:1290929 original size:79 final size:78
Alignment explanation
Indices: 1290803--1291045 Score: 251
Period size: 79 Copynumber: 3.1 Consensus size: 78
1290793 AAAAATATTG
* * * *
1290803 ATTTTTCATTTCAGGGATATTCCAACCTTATTAA-TTCTGAAGGGATACTCCAACCCTGTTTTTA
1 ATTTTTCATCTCGGGGATACTCCAACCCTATTAATTTC-G-AGGGATACTCCAACCCT-TTTTTA
1290867 TTTCAAAAATATTAAA
63 TTTCAAAAATATTAAA
* * * *
1290883 ATTTTT-ATCTCGGGGATACTCCAACCCTATCAATTTCGAGGAGATACTCTAACTCTATTTTTAC
1 ATTTTTCATCTCGGGGATACTCCAACCCTATTAATTTCGAGG-GATACTCCAACCCT-TTTTTAT
* **
1290947 TTCCAAAATA-T-CG
64 TTCAAAAATATTAAA
* * * *
1290960 ATTTTTCATCTCGGGAATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCCCATTTTTTA
1 ATTTTTCATCTCGGGGATACTCCAACCCTATTAATTTCGA-GGGATACTCCAA-CCC-TTTTTTA
1291025 TTTCAAAAATATTAAA
63 TTTCAAAAATATTAAA
1291041 ATTTT
1 ATTTT
1291046 CAATCTTGAG
Statistics
Matches: 132, Mismatches: 23, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
77 6 0.05
78 41 0.31
79 69 0.52
80 11 0.08
81 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (78 bp):
ATTTTTCATCTCGGGGATACTCCAACCCTATTAATTTCGAGGGATACTCCAACCCTTTTTTATTT
CAAAAATATTAAA
Found at i:1291080 original size:78 final size:77
Alignment explanation
Indices: 1290844--1291093 Score: 231
Period size: 78 Copynumber: 3.2 Consensus size: 77
1290834 TAATTCTGAA
*
1290844 GGGATACTCCAA-CCC-TGTTTTTATTTCAAAAATATTAAAATTTTTATCTCGGGGATACTCCAA
1 GGGATACTCCAACCCCAT-TTTTTATTTCAAAAATATTAAAATTTTCATCTC-GGGATACTCCAA
*
1290907 CCCTATCAATTTCGAG
64 CCCTGT--ATTTCGAG
* * * * * * ** *
1290923 GAGATACTCTAACTCTA-TTTTTACTTCCAAAATA-TCGATTTTTCATCTCGGGAATACTCCAAC
1 GGGATACTCCAACCCCATTTTTTATTTCAAAAATATTAAAATTTTCATCTCGGG-ATACTCCAAC
*
1290986 CCTGTTATTTTTGAG
65 CCTG-TA-TTTCGAG
* * *
1291001 GGGATACTCCAACCCCATTTTTTATTTCAAAAATATTAAAATTTTCAATCTTGAGGAGACTCAAA
1 GGGATACTCCAACCCCATTTTTTATTTCAAAAATATTAAAATTTTC-ATCTCG-GGATACTCCAA
1291066 CCCTGTA-TTCGAG
64 CCCTGTATTTCGAG
* *
1291079 GGGACACTCTAACCC
1 GGGATACTCCAACCC
1291094 TGCTTCTTAT
Statistics
Matches: 135, Mismatches: 27, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
77 4 0.03
78 61 0.45
79 41 0.30
80 10 0.07
81 17 0.13
82 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (77 bp):
GGGATACTCCAACCCCATTTTTTATTTCAAAAATATTAAAATTTTCATCTCGGGATACTCCAACC
CTGTATTTCGAG
Found at i:1297226 original size:31 final size:33
Alignment explanation
Indices: 1297154--1297280 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 33
1297144 TAAAGCAACC
*
1297154 TTTTCAAAG-CC-CATGACTCAGTGGCATCTCT
1 TTTTCAAAGTCCACATGACTCAGTGGCATCCCT
1297185 TTCTTCAAAGTCCACA-G-CTCAGTGGCATCCCT
1 TT-TTCAAAGTCCACATGACTCAGTGGCATCCCT
* *
1297217 TTTTCAAAGTCCAC--GACTTAGTAGCA--CCT
1 TTTTCAAAGTCCACATGACTCAGTGGCATCCCT
* *
1297246 CTTTTCAAAGT-C-TATGACTCCGTGGCA-CCCT
1 -TTTTCAAAGTCCACATGACTCAGTGGCATCCCT
1297277 TTTT
1 TTTT
1297281 ACACTTTAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.05
30 24 0.30
31 25 0.31
32 23 0.28
33 3 0.04
34 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (33 bp):
TTTTCAAAGTCCACATGACTCAGTGGCATCCCT
Found at i:1297274 original size:30 final size:29
Alignment explanation
Indices: 1297152--1297279 Score: 114
Period size: 30 Copynumber: 4.2 Consensus size: 29
1297142 AGTAAAGCAA
*
1297152 CCTTTTCAAAGCCCATGACTCAGTGGCATC
1 CCTTTTCAAAGTCCATGACTCAGTGGCA-C
* *
1297182 TCTTTCTTCAAAGTCCA-CAGCTCAGTGGCATC
1 -CCTT-TTCAAAGTCCATGA-CTCAGTGGCA-C
* * *
1297214 CCTTTTTCAAAGTCCACGACTTAGTAGCAC
1 CC-TTTTCAAAGTCCATGACTCAGTGGCAC
* *
1297244 CTCTTTTCAAAGTCTATGACTCCGTGGCAC
1 C-CTTTTCAAAGTCCATGACTCAGTGGCAC
1297274 CCTTTT
1 CCTTTT
1297280 TACACTTTAG
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
29 5 0.06
30 25 0.31
31 25 0.31
32 25 0.31
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (29 bp):
CCTTTTCAAAGTCCATGACTCAGTGGCAC
Found at i:1297362 original size:63 final size:62
Alignment explanation
Indices: 1297285--1301699 Score: 3345
Period size: 62 Copynumber: 70.2 Consensus size: 62
1297275 CTTTTTACAC
* * * * *
1297285 TTTAGTCTTCAAAGAGCAAGATGTCTTTTCTCTTTTTAAAGCCCACATGAGTTGGGGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTT-TCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1297348 TTTAGTCATCAAAGAGCAGGACGCCTTTTTTCTTCTTAAAACCCGCACAAGTTGATGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCC-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* *** * * * * *
1297411 TTTAGTCCTCAAAGAGCAAGACATCTTTTTCTTTTTAGAGTCCACACGAATTGATGGCACAT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* **
1297473 TTTAGTCCTCAGAGAATAGGATGCCTTTTT-TATTTATAAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCT-TTT-TAAAGCCCACACGAGTTGGTGGCACCT
* * * *
1297536 TTTAGTCCTCAAAAAGCAGGATGCCTTTTTCCTTTTCAAGCCCACACGAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
1297598 TTTAGTCCTTAAAAAGTAGGATGCCTTTTT-TTTTTTAAGCCCATACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* ** * *
1297659 TTTAGTCCTCAAAGAGTAGGATGTTTTTTTTCTTTATAAAGCCCACATGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATG-CCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
1297722 TTTAGTCATCAAAGAGCAGGATGCTTTTTTCCTTTTTAAAGCCCGCACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* *
1297785 TTTAG-CCTTCAAAGAGGAGGAGGCCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCC-TCAAAGAGCAGGATGCC-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * ** * * * *
1297848 TTTAGTCCTAAAAAACCAGGACGTTTTTTTCTTTTCAAAACCTACACGAGTTGTTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
1297910 TTTAGTCCTCAAAGAGCAGGA--CCGGTTCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCA
1 TTTAGTCCTCAAAGAGCAGGATGCC--TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
1297972 TTTAGTCCTCAAAGAGCAGGATGCC-TTTTCTTTTTCAGAGCCCACATGAGTTGGTGGAACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTT-AAAGCCCACACGAGTTGGTGGCACCT
* * * * *
1298034 TTTAGTTCTCAAAAAGCATGATGCCTTTTT-TTCTTATAAAACCCATACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTT-TT-TAAAGCCCACACGAGTTGGTGGCACCT
* * ** * * * *
1298097 TTTAGTCCTTAAA-AGGTAGGACACC-TTTT-TTTTTAAAGCACAGACGAGTTGGTGGCGCAT
1 TTTAGTCCTCAAAGA-GCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
1298157 TTTATTCCTTAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGCTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
1298219 TTCAGTCCAT-AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCCACATGAGCTAGTGGCACCT
1 TTTAGTCC-TCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
1298281 TTTAGTCCTCAAAGAGCCA-TACGCCTGTTCCTTTTTAAAGCCCACATGAGTTCGTGGCACCT
1 TTTAGTCCTCAAAGAG-CAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
1298343 TTTAGTCCTCAAA-ACGCAAGATGCCTTTTTTCTTTTCAAAGCCTAAATGATTTGGTGGCACCT
1 TTTAGTCCTCAAAGA-GCAGGATGCC-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
** *
1298406 TTTAGTCCTCAAAGAGCAGGATGTTTTTTTCTTTTTGAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* *
1298468 TTTAGTCCTCGAAA-AGTAGG-T-CACTTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACCT
1 TTTAGTCCTC-AAAGAGCAGGATGC-C-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1298530 TTTAGTCCTCGAAGAGTAAGACACTTTCCTTTTTCTTTCTCGAAA-ACCACACAAGTTGGTGGCA
1 TTTAGTCCTCAAAGAG-CAG-GA--TGCCTTTTTCTTT-T-TAAAGCCCACACGAGTTGGTGGCA
1298594 CCT
60 CCT
* * * ** ** * * * *
1298597 TTTAGTTCTCAAAGGGAAGGGCGTTTTTTTTCTTTTTAAAGCCCACACAAGTGGGTGGTAGCT
1 TTTAGTCCTCAAAGAGCAGGATG-CCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
1298660 TTTAGTCCTCAAAAAGCAGGATGCCTTTTTCTTTTCAAAGCCAACACAAGTTGTTTGCACCTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACC-T
* * * **
1298723 TTTA-TCCTCAAAGAGCATGATGCCTTTTTTCCTTTTAAAGCCCACACGAGTTAGCAGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCC-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *** * * *
1298785 TTTAGTTCTCAAAGAGCATGATGCCTTTTTCTTTTCAAATTGCACACAAGTTGGCGGCTCCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
1298847 TTTAGTCCTCAAAGAGCAAGATGTCTTTTTCTTTTTAAAGCCCATATGAGTTGGAGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
** * * *
1298909 TTTAGTCCTCAAAGAGCAGGACCCCTTCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCA
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* *
1298971 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * * * *
1299033 TTTAGTCCTCAAAAAACATGACG-CTTTTTTTTCTTATAAATCTCATACGAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTT-TT-TAAAGCCCACACGAGTTGGTGGCACCT
* ** * * * *
1299096 TTTAGTCCTTAAA-AGGCAGGACACC-TTTT-TTTTAAAAGCACAGACGAGTTGGTGGCATCT
1 TTTAGTCCTCAAAGA-GCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1299156 TTTATTCCTCAAAAAGCAAGATGCCTTTTTCTTTTCAAAGCCCACAGGAGCTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1299218 TTCAATCCACAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCCACATGAGTTAGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
1299280 TTTAGTCCTCAAAGAGCCA-TACGCCTTTTCCTTTTTAAAGCCCACACAAGTTTGTGGCACCT
1 TTTAGTCCTCAAAGAG-CAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** * * * * * * *
1299342 TTTAGTCCTCACCTTTTAGTCGTCAAAAAGCAAGATGCCTTTTTTCTTTTCAAAGCCTACATGAT
1 TTTAGTCCTCA-----AAG-AG-CAGGATGC---CT--TTTT---CTTTTTAAAGCCCACACGAG
*
1299407 TTGGTGGCAACT
51 TTGGTGGCACCT
* * *
1299419 TTTAGTCCTCAAAGAGCAGGATGCTTTTTTTCTTTATAAAGCCCACATGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
1299482 TTTAGTCCTCAAAGAGGAGGATGTCTTTTTCCCTTTTAAAGCCCGCACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* *
1299545 TTTAG-CCTTCAAAGAGGAGGAGGCCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCC-TCAAAGAGCAGGATGCC-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * ** * * *
1299608 TTTACTCCTAAAAAACCAAGACGTTTTTTTCTTTTCAAAACCTACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
1299670 TTTAGTCCTCAAAGAGCAGGA--CCTGCTTTTCTTTTTAAAGCCAACACAAGTTGGTGGCACCA
1 TTTAGTCCTCAAAGAGCAGGATGCCT--TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
1299732 TTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAGAGCCTACAAGAGTTGGTGACACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
1299794 TTTAGTCCTCTAAA-AGCATGACGCCTTTTT-TTCTTATAAAACCCATACGAGTTGGTGGCACCT
1 TTTAGTCCTC-AAAGAGCAGGATGCCTTTTTCTT-TT-TAAAGCCCACACGAGTTGGTGGCACCT
* * ** * * *
1299857 TTTAGTCCTTAAA-AGGTAGGACACCTTTTT-TTTCTAAAAGCACAGACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGA-GCAGGATGCCTTTTTCTTT-TTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
1299919 TTTATTCCTCAAAAAGCAGGATGCCTTTTTCTTTTCAAAGCTCACACAAGCTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* ** * * * * *
1299981 TTCAGTCCAAAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACATGAGTTAGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
1300043 TTTAGTCCTCAAAGAGC--CATACGCTTGTTTCTTTTTAAAGCCCACACGAGTTCGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGC-CTT-TTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* ** ** * * * * * * *
1300105 TTTAGTCCTCACCTTTTAGTCCTCAAAAAGCAAGATGCCTTTTTTCTTTTCAAAGCCTACATGAT
1 TTTAGTCCTCA-----AAG--AGCAGGATGC---CT--TTTT---CTTTTTAAAGCCCACACGAG
1300170 TTGGTGGCACCT
51 TTGGTGGCACCT
** *
1300182 TTTAGTCCTCAAAGAGCAGGATGTTTTTTTCTTTTTGAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
*
1300244 TTTAGTCCTCGAAA-AGTAGG-T-CACTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCCTC-AAAGAGCAGGATGC-C-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * ** * * *
1300306 TTTAGTCCTTAAAGAGTAAGACACTTTCCTTTTTCTTTCCCGAAA-ACCATACAAGTTGGTGGCA
1 TTTAGTCCTCAAAGAG-CAG-GA--TGCCTTTTTCTTT--TTAAAGCCCACACGAGTTGGTGGCA
1300370 CCT
60 CCT
* * ** * * * * *
1300373 TTTAGTTCTCAAAGAGAAGGGCAT-TTTTTTTCTTTTTAAAGCCCATACAAGTGGGTGGTAGCT
1 TTTAGTCCTCAAAGAGCA-GG-ATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
1300436 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCAACACAAGTTGTTTGCACCTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACC-T
* * * * **
1300499 TTTA-TCCTCAAAGAGCATGATCCCTTTTTTCCTTTTAAAGCCCACACGAGTTAGCAGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCC-TTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1300561 TTTAGTCCTCAAAGAGCATGATCCCTTTTTCTTTTCAAAGTCCACACAAGTTGGCGGCTCCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
** * * * *
1300623 TTTAGTCCTCAAAGAGTGGGATGTCTTTTTCTTTTTAAAGCCCATATGAGTTGGAGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
1300685 TTTAGTCCTCAAAGAGCAGGATGCC--TTT-TTTTAAAATCCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *** ** *
1300744 TTTAGTTCTCAAAGAGCAGGACG-TTTTTTCATTTCGGAGCCCACACGACATGGTGGCACAT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * ** * * * * *
1300805 TTTAGTCTTCAAAAAGTAGGACACATTTTCCTTTTAAAAGCCCACTCAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1300867 TTTAG-CCTAGAAAAAACATGG-TG-TTTTTTCCTTTTCAAAGCCCAC-CCACGTTGGTGGCACT
1 TTTAGTCCT-CAAAGAGCA-GGATGCCTTTTT-CTTTTTAAAGCCCACACGA-GTTGGTGGCACC
1300928 T
62 T
* * * * **** * *
1300929 TTTAGTCCCCACCTTTTACTCTTCAAAG-AGCAAGAAGCCTTT-TTTTTCAAAGCCTACACAAGT
1 TTTAGTCCTCA------A------AGAGCAGGATG-CCTTTTTCTTTTT-AAAGCCCACACGAGT
*
1300992 TGGTGCCACCT
52 TGGTGGCACCT
* * * * * * *
1301003 TTTAGTCTTCAAAAAGGAAGATG-TTTTTTCTTTTTAAAGCGCACACGAGTTGGTCGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * ** **
1301064 TTTACTCCTCAAAGAGTAGGTTGTTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGTAACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * ** * * *
1301126 TCTAGTCTTCGAAGAGTAAAATGCTTTCCGTTTTCTTTCTCAAAGCCCACACGAGTTGGTGG-AA
1 TTTAGTCCTCAAAGAGCAGGATG----CCTTTTTCTTT-TTAAAGCCCACACGAGTTGGTGGCAC
1301190 CT
61 CT
* * ** * * * * *
1301192 ATTTTGTCTTCAAAGAGTAACACGCTTTCTTTTTTCTTTTAAAAGCCAACACGAGTTGGCGGCAC
1 -TTTAGTCCTCAAAGAG---CA-GGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCAC
1301257 CT
61 CT
* * * * * *
1301259 TTTAGTCCTTAAAGAGCAAGACGCC-TTTTC-TTTCATAGCCCACACGAGTTGGTGACACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1301319 TTTCA-TCCTCAAAAAGCATGATGCCTTTTTTTCTTTTATAGCCC-CTATGAGTTGGTGGTACTT
1 TTT-AGTCCTCAAAGAGCAGGATGCCTTTTTCT-TTTTAAAGCCCAC-ACGAGTTGGTGGCACCT
* * * * * * **
1301382 TTTGGTCTTCAAAGAG-AAGATGCCTTTTTCTTTTCAAAGCACACACAAGTTGGTGGCATTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** * *** * * **
1301443 TTTA-TCCTCAAAGGGCATGACACCTTTTT-TTTCTAAAGTTTACATGAGTTGCTGGCATGT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** * * ** * *
1301503 TTTAGTCCTTAAAGAGTAGGACACC-TTTTC--TTAAAAGCTCACATAAGATGGTGGCATCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
1301562 TTTAGTCCTCAAAGAGTAGGATGCATTTTCCTTTTCAAAGCCCACAAGAGTTAGTGGCACAT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
1301624 TTTAGTCCTCAAAGAGCATGATGCATTTTT-TTCTTAAACAGTCCATACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTT-TTTAA-AGCCCACACGAGTTGGTGGCACCT
1301687 TTTAGTCCTCAAA
1 TTTAGTCCTCAAA
1301700 AGGGAGGACA
Statistics
Matches: 3469, Mismatches: 707, Indels: 352
0.77 0.16 0.08
Matches are distributed among these distances:
59 88 0.03
60 178 0.05
61 249 0.07
62 1698 0.49
63 854 0.25
64 44 0.01
65 4 0.00
66 70 0.02
67 123 0.04
68 14 0.00
69 4 0.00
70 10 0.00
71 4 0.00
72 6 0.00
73 8 0.00
74 36 0.01
75 5 0.00
77 74 0.02
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (62 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
Found at i:1299423 original size:77 final size:76
Alignment explanation
Indices: 1299275--1299429 Score: 186
Period size: 77 Copynumber: 2.0 Consensus size: 76
1299265 GAGTTAGTGG
* * * * *
1299275 CACCTTTTAGTCCTCAAAGAGCCATACGCCTTTTCCTTTTTAAAGCCCACACAAGTTTGTGGCAC
1 CACCTTTTAGTCCTCAAAAAGCAAGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTTGTGGCAA
1299340 CTTTTAGTCCT
66 CTTTTAGTCCT
* * * * **
1299351 CACCTTTTAGTCGTCAAAAAGCAAGATGCCTTTTTTCTTTTCAAAGCCTACATGA-TTTGGTGGC
1 CACCTTTTAGTCCTCAAAAAGCAAGACGCC-TTTTCCTTTTCAAAGCCCACACAAGTTT-GTGGC
1299415 AACTTTTAGTCCT
64 AACTTTTAGTCCT
1299428 CA
1 CA
1299430 AAGAGCAGGA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
76 28 0.42
77 38 0.58
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (76 bp):
CACCTTTTAGTCCTCAAAAAGCAAGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTTGTGGCAA
CTTTTAGTCCT
Found at i:1300119 original size:14 final size:14
Alignment explanation
Indices: 1300100--1300129 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1300090 GAGTTCGTGG
1300100 CACCTTTTAGTCCT
1 CACCTTTTAGTCCT
1300114 CACCTTTTAGTCCT
1 CACCTTTTAGTCCT
1300128 CA
1 CA
1300130 AAAAGCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.37, G:0.07, T:0.40
Consensus pattern (14 bp):
CACCTTTTAGTCCT
Found at i:1300177 original size:77 final size:76
Alignment explanation
Indices: 1300038--1300192 Score: 211
Period size: 77 Copynumber: 2.0 Consensus size: 76
1300028 GAGTTAGTGG
* * * *
1300038 CACCTTTTAGTCCTCAAAGAGCCATACGCTTGTTTCTTTTTAAAGCCCACACGAGTTCGTGGCAC
1 CACCTTTTAGTCCTCAAAAAGCAAGACGCTTGTTTCTTTTCAAAGCCCACACGAGTTCGTGGCAC
1300103 CTTTTAGTCCT
66 CTTTTAGTCCT
* * * * * *
1300114 CACCTTTTAGTCCTCAAAAAGCAAGATGCCTTTTTTCTTTTCAAAGCCTACATGATTTGGTGGCA
1 CACCTTTTAGTCCTCAAAAAGCAAGACG-CTTGTTTCTTTTCAAAGCCCACACGAGTTCGTGGCA
1300179 CCTTTTAGTCCT
65 CCTTTTAGTCCT
1300191 CA
1 CA
1300193 AAGAGCAGGA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
76 24 0.35
77 44 0.65
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (76 bp):
CACCTTTTAGTCCTCAAAAAGCAAGACGCTTGTTTCTTTTCAAAGCCCACACGAGTTCGTGGCAC
CTTTTAGTCCT
Found at i:1300277 original size:201 final size:199
Alignment explanation
Indices: 1299914--1300314 Score: 538
Period size: 201 Copynumber: 2.0 Consensus size: 199
1299904 GAGTTGGTGG
* *
1299914 CACCTTTTATTCCTCAAAAAGCAGGATGCCTTTTTCTTTTCAAAGCTCACACAAGCTGGTGGCAC
1 CACCTTTTAGTCCTCAAAAAGCAAGATGCCTTTTTCTTTTCAAAGCTCACACAAGCTGGTGGCAC
* *
1299979 CTTTCAGTCCAAAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACATGAGTTAGTGGCACCTT
66 CTTTCAGTCCAAAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCACCTT
*
1300044 TTAGTCCTCAAAGAGCCATACGCTTGTTTCTTTTTAAAGCCCACACGAGTTCGTGGCACCTTTTA
131 TTAGTCCTCAAAGAG-CATACACTTGTTTCTTTTTAAAGCCCACACGAGTTCGTGGCACCTTTTA
1300109 GTCCT
195 GTCCT
** **
1300114 CACCTTTTAGTCCTCAAAAAGCAAGATGCCTTTTTTCTTTTCAAAGC-CTACATGATTTGGTGGC
1 CACCTTTTAGTCCTCAAAAAGCAAGATGCC-TTTTTCTTTTCAAAGCTC-ACACAAGCTGGTGGC
* ** *** ** *
1300178 ACCTTTTAGTCCTCAAAGAGCAGGATGTTTTTTTCTTTTTGAAGCCCACACGAGTTGGTGGCACC
64 ACCTTTCAGTCCAAAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCACC
* * *
1300243 TTTTAGTCCTCGAAAAGTAG-GT-CACTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
129 TTTTAGTCCTC--AAAG-AGCATACACTTGTTTCTTTTTAAAGCCCACACGAGTTCGTGGCACCT
1300306 TTTAGTCCT
191 TTTAGTCCT
1300315 TAAAGAGTAA
Statistics
Matches: 175, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
200 29 0.17
201 139 0.79
202 1 0.01
203 4 0.02
204 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (199 bp):
CACCTTTTAGTCCTCAAAAAGCAAGATGCCTTTTTCTTTTCAAAGCTCACACAAGCTGGTGGCAC
CTTTCAGTCCAAAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCACCTT
TTAGTCCTCAAAGAGCATACACTTGTTTCTTTTTAAAGCCCACACGAGTTCGTGGCACCTTTTAG
TCCT
Found at i:1301064 original size:61 final size:60
Alignment explanation
Indices: 1300937--1301436 Score: 233
Period size: 61 Copynumber: 8.0 Consensus size: 60
1300927 TTTTTAGTCC
* ** * *
1300937 CCACCTTTTACTCTTCAAAGAGCAAGAAGCCTTTT-TTTTCAAAGCCTACACAAGTTGGTG
1 CCACCTTTTACTCTTCAAAGAGCAAGATGTTTTTTCTTTTTAAAGCC-ACACGAGTTGGTG
* * *
1300997 CCACCTTTTAGTCTTCAAAAAGGAAGATGTTTTTTCTTTTTAAAGCGCACACGAGTTGGT-
1 CCACCTTTTACTCTTCAAAGAGCAAGATGTTTTTTCTTTTTAAAGC-CACACGAGTTGGTG
* * * *
1301057 CGCACCTTTTACTCCTCAAAGAGTAGGTTGTTTTTTTCTTTTTAAAGCCCACACGAGTTGGTG
1 C-CACCTTTTACTCTTCAAAGAGCAAGATG-TTTTTTCTTTTTAAAG-CCACACGAGTTGGTG
** * * * * * *
1301120 TAACCTTCTAGTCTTCGAAGAGTAAAATGCTTTCCGTTTTCTTTCTCAAAGCCCACACGAGTTGG
1 CCACCTTTTACTCTTCAAAGAGCAAGATG--TT---TTTTCTTT-TTAAAG-CCACACGAGTTGG
1301185 TG
59 TG
* * ** * * * *
1301187 -GAACTATTTTGTCTTCAAAGAGTAACACGCTTTCTTTTTTCTTTTAAAAGCCAACACGAGTTGG
1 CCACCT-TTTACTCTTCAAAGAG---CAAG--ATGTTTTTTCTTTTTAAAGCC-ACACGAGTTGG
*
1301251 CG
59 TG
* * * ** * *
1301253 GCACCTTTTAGTCCTT-AAAGAGCAAGACGCCTTTTC-TTTCATAGCCCACACGAGTTGGTG
1 CCACCTTTTACT-CTTCAAAGAGCAAGATGTTTTTTCTTTTTAAAG-CCACACGAGTTGGTG
* * * * * * *
1301313 ACACCTTTT-CATCCTCAAAAAGCATGATGCCTTTTTT-TCTTTTATAGCCCCTATGAGTTGGTG
1 CCACCTTTTAC-TCTTCAAAGAGCAAGATG--TTTTTTCT-TTTTAAAGCCAC-ACGAGTTGGTG
** * ** * * *
1301376 GTACTTTTTGGTCTTCAAAGAG-AAGATGCCTTTTTCTTTTCAAAGCACACACAAGTTGGTG
1 CCACCTTTTACTCTTCAAAGAGCAAGATG-TTTTTTCTTTTTAAAGC-CACACGAGTTGGTG
1301437 GCATTTTTTA
Statistics
Matches: 337, Mismatches: 72, Indels: 61
0.72 0.15 0.13
Matches are distributed among these distances:
59 2 0.01
60 67 0.20
61 71 0.21
62 65 0.19
63 39 0.12
65 2 0.01
66 39 0.12
67 48 0.14
70 3 0.01
72 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (60 bp):
CCACCTTTTACTCTTCAAAGAGCAAGATGTTTTTTCTTTTTAAAGCCACACGAGTTGGTG
Found at i:1301201 original size:67 final size:66
Alignment explanation
Indices: 1301090--1301274 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 66
1301080 TAGGTTGTTT
* * * *
1301090 TTTTCTTTTTAAAGCCCACACGAGTTGGTGTAACCTTCTAGTCTTCGAAGAGTAAAATGCTTTCC
1 TTTTCTTTTAAAAGCCCACACGAGTTGGTGGAACCTTCTAGTCTTCAAAGAGTAAAACGCTTTCC
1301155 G
66 G
* * * *
1301156 TTTTCTTTCTCAAAGCCCACACGAGTTGGTGGAA-CTATTTTGTCTTCAAAGAGTAACACGCTTT
1 TTTTCTTT-TAAAAGCCCACACGAGTTGGTGGAACCT-TCTAGTCTTCAAAGAGTAAAACGCTTT
**
1301220 CTT
64 CCG
* * * *
1301223 TTTTCTTTTAAAAGCCAACACGAGTTGGCGGCACCTTTTAGTCCTT-AAAGAG
1 TTTTCTTTTAAAAGCCCACACGAGTTGGTGGAACCTTCTAGT-CTTCAAAGAG
1301275 CAAGACGCCT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
66 42 0.42
67 59 0.58
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (66 bp):
TTTTCTTTTAAAAGCCCACACGAGTTGGTGGAACCTTCTAGTCTTCAAAGAGTAAAACGCTTTCC
G
Found at i:1301445 original size:61 final size:61
Alignment explanation
Indices: 1300938--1301699 Score: 408
Period size: 60 Copynumber: 12.3 Consensus size: 61
1300928 TTTTAGTCCC
* * * *
1300938 CACCTTTTACTCTTCAAAGAGCAAGAAGCC-TTTT-TTTTCAAAGCCTACACAAGTTGGTGC
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCC-ACACGAGTTGGTGG
* * * * *
1300998 CACCTTTTAGTCTTCAAAAAGGAAGATG-TTTTTTCTTTTTAAAGCGCACACGAGTTGGTCG
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGC-CACACGAGTTGGTGG
* * * * * ** * *
1301059 CACCTTTTACTCCTCAAAGAGTAGGTTGTTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGT
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAG-CCACACGAGTTGGTGG
* * * * * *
1301121 AACCTTCTAGTCTTCGAAGAGTAAAATGCTTTCCGTTTTCTTTCTCAAAGCCCACACGAGTTGGT
1 CACCTTTTAGTCTTCAAAGAGCAAGATG----CCTTTTTCTTT-TCAAAG-CCACACGAGTTGGT
1301186 GG
60 GG
* * * * * * *
1301188 -AACTATTTTGTCTTCAAAGAGTAACACGCTTTCTTTTTTCTTTTAAAAGCCAACACGAGTTGGC
1 CACCT-TTTAGTCTTCAAAGAGCAAGATGC---C-TTTTTCTTTTCAAAGCC-ACACGAGTTGGT
1301252 GG
60 GG
* * *
1301254 CACCTTTTAGTCCTT-AAAGAGCAAGACGCC-TTTTC-TTTCATAGCCCACACGAGTTGGTGA
1 CACCTTTTAGT-CTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAG-CCACACGAGTTGGTGG
* * * * * *
1301314 CACCTTTTCA-TCCTCAAAAAGCATGATGCCTTTTTTTCTTTT-ATAGCCCCTATGAGTTGGTGG
1 CACCTTTT-AGTCTTCAAAGAGCAAGATGCC--TTTTTCTTTTCAAAGCCAC-ACGAGTTGGTGG
* * * *
1301377 TACTTTTTGGTCTTCAAAGAG-AAGATGCCTTTTTCTTTTCAAAGCACACACAAGTTGGTGG
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGC-CACACGAGTTGGTGG
** * * * ** ** * *
1301438 CATTTTTTA-TCCTCAAAGGGCATGACACC-TTTT-TTTTCTAAAGTTTACATGAGTTGCTGG
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTC-AAAG-CCACACGAGTTGGTGG
** * * ** * ** *
1301498 CATGTTTTAGTCCTT-AAAGAGTAGGACACC-TTTTC--TTAAAAGCTCACATAAGATGGTGG
1 CACCTTTTAGT-CTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGC-CACACGAGTTGGTGG
* * * * * * * *
1301557 CATCTTTTAGTCCTCAAAGAGTAGGATGCATTTTCCTTTTCAAAGCCCACAAGAGTTAGTGG
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAG-CCACACGAGTTGGTGG
* * * * * *
1301619 CACATTTTAGTCCTCAAAGAGCATGATGCATTTTT-TTCTTAAACAGTCCATACGAGTTGGTGG
1 CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTT-TTCAA-AG-CCACACGAGTTGGTGG
*
1301682 CACCTTTTAGTCCTCAAA
1 CACCTTTTAGTCTTCAAA
1301700 AGGGAGGACA
Statistics
Matches: 549, Mismatches: 110, Indels: 83
0.74 0.15 0.11
Matches are distributed among these distances:
58 2 0.00
59 44 0.08
60 119 0.22
61 94 0.17
62 115 0.21
63 70 0.13
64 3 0.01
65 2 0.00
66 47 0.09
67 53 0.10
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (61 bp):
CACCTTTTAGTCTTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCACACGAGTTGGTGG
Found at i:1301890 original size:162 final size:161
Alignment explanation
Indices: 1301616--1301913 Score: 372
Period size: 162 Copynumber: 1.8 Consensus size: 161
1301606 CAAGAGTTAG
* *
1301616 TGGCACATTTTAGTCCTCAAAGAGCATGATGCATTTTTTTCTTAAACAGTCCATACGAGTTGGTG
1 TGGCACATTTTAGTCCTCAAAGAGCAGGA-GCATTTTTTTCTTAAACAGCCCATACGAGTTGGTG
* *
1301681 GCACCTTTTAGTCCTCAAAAGGGAGGACACATTTTTTATTTTAAAGCC-AGCACAAGTTGATGGC
65 GCACCTTTTAATCCTCAAAAGGGAGGACACATTTTTCATTTTAAAGCCTA-CACAAGTTGATGGC
1301745 ACATTTTTTCTTTTTGAAGTCCATACGAGTTGA
129 ACATTTTTTCTTTTTGAAGTCCATACGAGTTGA
* *
1301778 TGGCACCTTTTAGTCCTCAAAGAGTC-GGA-CATTTTTTTTCTTTGTAA-AGCCCATACGAGTTG
1 TGGCACATTTTAGTCCTCAAAGAG-CAGGAGCA-TTTTTTTC-TT-AAACAGCCCATACGAGTTG
* ** * * * *
1301840 GTGGCACCTTTTAATCCTC-AAAGAGTAGGATGCCTTTTTCCTTTTAAAGCCTACACGAGTTGGT
62 GTGGCACCTTTTAATCCTCAAAAG-GGAGGACACATTTTTCATTTTAAAGCCTACACAAGTTGAT
*
1301904 GGTACATTTT
126 GGCACATTTT
1301914 AGTCCTCGAA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
160 2 0.02
161 12 0.10
162 98 0.84
163 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (161 bp):
TGGCACATTTTAGTCCTCAAAGAGCAGGAGCATTTTTTTCTTAAACAGCCCATACGAGTTGGTGG
CACCTTTTAATCCTCAAAAGGGAGGACACATTTTTCATTTTAAAGCCTACACAAGTTGATGGCAC
ATTTTTTCTTTTTGAAGTCCATACGAGTTGA
Found at i:1301914 original size:62 final size:62
Alignment explanation
Indices: 1301749--1302160 Score: 346
Period size: 62 Copynumber: 6.6 Consensus size: 62
1301739 GATGGCACAT
* * * * * * ****
1301749 TTTTTCTTTTTGAAGTCCATACGAGTTGATGGCACCTTTTAGTCCTCAAAGAGTCGGACATT
1 TTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCC
* * *
1301811 TTTTTTCTTTGTAAAGCCCATACGAGTTGGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCC
1 TTTTTCCTTT-TAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCC
* * * * * **
1301874 TTTTTCCTTTTAAAGCCTACACGAGTTGGTGGTACATTTTAGTCCTCGAAGAGTACGACACC
1 TTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCC
* * * * * * * *
1301936 ATTTTCTTTTTAAAGCCCACACGAGTTCGTGGCA-CTGATTAGTCTTCAAAAAATAGGAGGCC
1 TTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCT-TTTAGTCCTCAAAGAGTAGGATGCC
* * ** * *
1301998 TTTTTTCTTTTTAAAGCTCACACGAGTTGGCAGCACCTTTTAGACCTCAAAGA-TGAGGATG-T
1 -TTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-AGGATGCC
* * * * * **
1302060 TTTTTTCTTTTCAAAGCCTACATGAGTTGGTAGCACCTTTTAGTTCTCAAAGAGTAAAAATGCC
1 TTTTTCCTTTT-AAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-AGGATGCC
* *
1302124 -TTCTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTTTCC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
1302161 CCTTTTCCTT
Statistics
Matches: 277, Mismatches: 64, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
61 10 0.04
62 133 0.48
63 128 0.46
64 6 0.02
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (62 bp):
TTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCC
Found at i:1302078 original size:187 final size:187
Alignment explanation
Indices: 1301811--1302158 Score: 445
Period size: 187 Copynumber: 1.9 Consensus size: 187
1301801 GTCGGACATT
* **
1301811 TTTTTTCTTTGTAAAGCCCATACGAGTTGGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCCTT
1 TTTTTTCTTTGTAAAGCCCACACGAGTTGGCAGCACCTTTTAATCCTCAAAGAGTAGGATGCCTT
* * * * *
1301876 TTTCCTTTTAAAGCCTACACGAGTTGGTGGTACATTTTAGTCCTCGAAGAGTACGACA-CCATT-
66 TTTCCTTTTAAAGCCTACACGAGTTGGTAGCACATTTTAGTCCTCAAAGAGTA-AAAAGCC-TTC
* *
1301939 TTCTTTTTAAAGCCCACACGAGTTCGTGGCACTGATTAGTCTTCAAAAAATAGGAGGCC
129 TCCTTTTTAAAGCCCACACAAGTTCGTGGCACTGATTAGTCTTCAAAAAATAGGAGGCC
* * *
1301998 TTTTTTCTTTTTAAAGCTCACACGAGTTGGCAGCACCTTTTAGA-CCTCAAAGA-TGAGGATG-T
1 TTTTTTCTTTGTAAAGCCCACACGAGTTGGCAGCACCTTTTA-ATCCTCAAAGAGT-AGGATGCC
* * * *
1302060 TTTTTTCTTTTCAAAGCCTACATGAGTTGGTAGCACCTTTTAGTTCTCAAAGAGTAAAAATGCCT
64 TTTTTCCTTTT-AAAGCCTACACGAGTTGGTAGCACATTTTAGTCCTCAAAGAGTAAAAA-GCCT
*
1302125 TCTCCTTTTTAAAGCCCACACAAGTTGGTGGCAC
127 TCTCCTTTTTAAAGCCCACACAAGTTCGTGGCAC
1302159 CTCCTTTTCC
Statistics
Matches: 137, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
186 13 0.09
187 92 0.67
188 32 0.23
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (187 bp):
TTTTTTCTTTGTAAAGCCCACACGAGTTGGCAGCACCTTTTAATCCTCAAAGAGTAGGATGCCTT
TTTCCTTTTAAAGCCTACACGAGTTGGTAGCACATTTTAGTCCTCAAAGAGTAAAAAGCCTTCTC
CTTTTTAAAGCCCACACAAGTTCGTGGCACTGATTAGTCTTCAAAAAATAGGAGGCC
Found at i:1302103 original size:125 final size:123
Alignment explanation
Indices: 1301748--1302160 Score: 327
Period size: 125 Copynumber: 3.3 Consensus size: 123
1301738 TGATGGCACA
* * * *
1301748 TTTTTTCTTTTTGAAG-TCCATACGAGTTGATGGCACCTTTTAGTCCTCAAAGAGTCG-GACATT
1 TTTTTTCTTTTTAAAGCT-CACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGA-T-GAG-GATT
* * * * *
1301811 TTTTTTCTTTGTAAAGCCCATACGAGTTGGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCC
62 TTTTTTCTTT-TAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAATAGGAGGCC
* * * * * ***
1301874 -TTTTTCCTTTTAAAGC-CTACACGAGTTGGTGGTACATTTTAGTCCTCGAAGA-GTACGACACC
1 TTTTTTCTTTTTAAAGCTC-ACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGATG-AGGA-TTT
* * * *
1301936 ATTTTCTTTTTAAAGCCCACACGAGTTCGTGGCA-CTGATTAGTCTTCAAAAAATAGGAGGCC
63 TTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT-TTTAGTCCTCAAAAAATAGGAGGCC
** *
1301998 TTTTTTCTTTTTAAAGCTCACACGAGTTGGCAGCACCTTTTAGACCTCAAAGATGAGGATGTTTT
1 TTTTTTCTTTTTAAAGCTCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGATGAGGAT-TTTT
* * * * * * ** *
1302063 TTTCTTTTCAAAGCCTACATGAGTTGGTAGCACCTTTTAGTTCTCAAAGAGTAAAAATGCC
65 TTTCTTTT-AAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAAT-AGGAGGCC
* * * *
1302124 -TTCTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTTTTCTTTTTAAAGCTCACACGAGTTGGTGGCACCT
1302161 CCTTTTCCTT
Statistics
Matches: 222, Mismatches: 51, Indels: 29
0.74 0.17 0.10
Matches are distributed among these distances:
122 1 0.00
123 3 0.01
124 51 0.23
125 158 0.71
126 9 0.04
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (123 bp):
TTTTTTCTTTTTAAAGCTCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGATGAGGATTTTTT
TTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAATAGGAGGCC
Found at i:1302181 original size:39 final size:39
Alignment explanation
Indices: 1302122--1302199 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
1302112 AGTAAAAATG
*
1302122 CCTTCTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 CCTTCTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* *
1302161 CCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
1 CCTTCTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
1302200 TTTAGTTCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (39 bp):
CCTTCTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
Found at i:1302212 original size:36 final size:37
Alignment explanation
Indices: 1302135--1302213 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
1302125 TCTCCTTTTT
* *
1302135 AAAGCCCACACAAGTTGGTGGCACCTCCTTTTCCTTTTC
1 AAAGCCCACACAAGTTGGTGGCA-C-CCTTTTACTTCTC
* *
1302174 AAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTTCTC
1 AAAGCCCACACAAGTTGGTGGCACCCTTTTACTTCTC
1302210 AAAG
1 AAAG
1302214 AGCATGATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 14 0.39
39 22 0.61
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (37 bp):
AAAGCCCACACAAGTTGGTGGCACCCTTTTACTTCTC
Found at i:1302311 original size:164 final size:164
Alignment explanation
Indices: 1301999--1302324 Score: 363
Period size: 164 Copynumber: 2.0 Consensus size: 164
1301989 TAGGAGGCCT
* * *
1301999 TTTTTCTTTTTAAAGCTCACACGAGTTGGCAGCACCTTTTAGACCTCAAAGATGAGGATGTTTTT
1 TTTTCCTTTTCAAAGCCCACACGAGTTGGCAGCACCTTTTAGACCTCAAAGATGAGGATGTTTTT
* * * * * *
1302064 TTCTTTTCAAAGCCTACATGAGTTGGTAGCACCTTTTAGTTCTCAAAGAGTAAAAATGCCTTCTC
66 TTCTTATCAAAGCCTACACGAGTTGGTAGCACCTATTAGTCCTCAAAGAGGAAAAACGCCTTCTC
* * * *
1302129 CTTTTTAAAGCCCACACAAGTTGGTGGCACCTCC
131 CTTTTAAAAGCACACACAAGTCGGTGGAACCTCC
** ** *
1302163 TTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTTCTCAAAGA-GCATGATGCCTT
1 TTTTCCTTTTCAAAGCCCACACGAGTTGGCAGCACCTTTTAGACCTCAAAGATG-AGGATG--TT
* * * * * *
1302227 TTTTTCTTAT-AAAGCCTATACGAGTTGGTGGCACCTATTAGTCCTTAAA-AGGCAAGACGCGTT
63 TTTTTCTTATCAAAGCCTACACGAGTTGGTAGCACCTATTAGTCCTCAAAGAGGAAAAACGCCTT
*
1302290 -TTCTTTTGAAAAGCACACACAAGTCGGTGGAACCT
128 CTCCTTTT-AAAAGCACACACAAGTCGGTGGAACCT
1302325 TTTAGTCCTC
Statistics
Matches: 133, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
163 7 0.05
164 82 0.62
165 33 0.25
166 11 0.08
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (164 bp):
TTTTCCTTTTCAAAGCCCACACGAGTTGGCAGCACCTTTTAGACCTCAAAGATGAGGATGTTTTT
TTCTTATCAAAGCCTACACGAGTTGGTAGCACCTATTAGTCCTCAAAGAGGAAAAACGCCTTCTC
CTTTTAAAAGCACACACAAGTCGGTGGAACCTCC
Done.