Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 38 of 136
Found at i:12416523 original size:27 final size:27
Alignment explanation
Indices: 12416493--12416553 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
12416483 GGCATCCTTT
*
12416493 GATAGTCTGA-TGGGAAAATAATCACAG
1 GATAGTCT-ATTGGGAAAATAAACACAG
* * *
12416520 GATAGTCTATTGGGACACTAAACATAG
1 GATAGTCTATTGGGAAAATAAACACAG
12416547 GATAGTC
1 GATAGTC
12416554 CACCGGGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (27 bp):
GATAGTCTATTGGGAAAATAAACACAG
Found at i:12420575 original size:13 final size:14
Alignment explanation
Indices: 12420557--12420598 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
12420547 GCTAGGGAGG
12420557 TTTTGACAATAA-A
1 TTTTGACAATAATA
*
12420570 TTTTGAAAATAATA
1 TTTTGACAATAATA
*
12420584 TTTTCACAATTAATA
1 TTTTGACAA-TAATA
12420599 AGATAAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 8 0.33
15 5 0.21
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (14 bp):
TTTTGACAATAATA
Found at i:12427419 original size:22 final size:22
Alignment explanation
Indices: 12427359--12427416 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
12427349 AATCTTCAAG
12427359 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12427378 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
12427400 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12427417 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:12427696 original size:3 final size:3
Alignment explanation
Indices: 12427690--12427784 Score: 61
Period size: 3 Copynumber: 31.0 Consensus size: 3
12427680 ATTTTTTTAT
* * * *
12427690 TTA TTA TTTA TTA TTTA TTA TTTA TTT TTA TTA -AA TT- TGA TT- TTC
1 TTA TTA -TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
12427735 TTG TTA TTAA GTTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12427782 TTA
1 TTA
12427785 CTATATATAC
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
2 4 0.06
3 55 0.76
4 11 0.15
5 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12427698 original size:7 final size:7
Alignment explanation
Indices: 12427686--12427722 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
12427676 TTTAATTTTT
12427686 TTATTTA
1 TTATTTA
12427693 TTATTTA
1 TTATTTA
12427700 TTATTTA
1 TTATTTA
12427707 TTATTTA
1 TTATTTA
12427714 TT-TTTA
1 TTATTTA
12427720 TTA
1 TTA
12427723 AATTTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:12427942 original size:17 final size:17
Alignment explanation
Indices: 12427920--12427952 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12427910 ATAGACATAT
*
12427920 TATACATTTACATTTTA
1 TATACATATACATTTTA
12427937 TATACATATACATTTT
1 TATACATATACATTTT
12427953 TTATTTCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATACATATACATTTTA
Found at i:12432749 original size:44 final size:44
Alignment explanation
Indices: 12432636--12433160 Score: 395
Period size: 44 Copynumber: 11.9 Consensus size: 44
12432626 GCAGGTCCTA
* * * * *
12432636 TCTTCCTATATTGGTACGAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
** *** * *
12432679 TCTTCCCATATTGGTGGCGGAGTAGATCGTAGAAAGCAGATCTTG
1 TCTTCATATATTGG-CATGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
12432724 CCTTCATATATTGGCATGAAGTAGATCGAAGATAGCAGATCCTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * *
12432768 TCTTCCTATATTGGTAGCGAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCATATATTGGCA-TGAAGTAGATCGAAGAAAGCAGATCTTG
**
12432812 TCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTT--CATA-TATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * ** *
12432857 TCTTCATGTATTGGTATGAAGTAGATCGAAGATAGCAGGCCCTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * ** *
12432901 TCTTCCTATATTGGTAGGAAGGGGATCGAAG-ATGCAGATCTTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
*
12432944 TCTTTCCATACTAGTGGC--GAAGTAGATCGAAGAAAGCAGATCTTG
1 TC-TT-CATA-TATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * * * *
12432989 TCTTCATGTATTGGCATAAAGTAGATCAAAGATAGTAGGTCCTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * ** *
12433033 TCTTCCTATATTGGTAGGAAGGGGATCGAAG-ATGCAGATCTTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
*
12433076 TCTTTCCATACTAGTGGC--GAAGTAGATCGAAGAAAGCAGATCTTG
1 TC-TT-CATA-TATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * *
12433121 TCTTCATGTATTGGCGTGAAGTAGAACAAAGATAGCAGAT
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGAT
12433161 ATTGCCTTTC
Statistics
Matches: 374, Mismatches: 87, Indels: 41
0.75 0.17 0.08
Matches are distributed among these distances:
42 16 0.04
43 40 0.11
44 219 0.59
45 82 0.22
46 13 0.03
47 4 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
Found at i:12432751 original size:88 final size:87
Alignment explanation
Indices: 12432636--12433160 Score: 445
Period size: 88 Copynumber: 6.0 Consensus size: 87
12432626 GCAGGTCCTA
* * * * * *
12432636 TCTTCCTATATTGGTACGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGGAG
1 TCTTCATATATTGGCA-GAAGTAGATCGAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAG
*
12432701 TAGATCGTAGAAAGCAGATCTTG
65 TAGATCGAAGAAAGCAGATCTTG
* *
12432724 CCTTCATATATTGGCATGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAA
1 TCTTCATATATTGGCA-GAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAA
* *
12432789 GTGGATCGAAG-ATGCAGATCTTG
64 GTAGATCGAAGAAAGCAGATCTTG
** * * * *
12432812 TCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTA-TG
1 TCTT--CATA-TATTGGCAGAAGTAGATCGAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCG
* ** *
12432875 AAGTAGATCGAAGATAGCAGGCCCTG
62 AAGTAGATCGAAGAAAGCAGATCTTG
* * ** * * *
12432901 TCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTTCC-ATACTAGTGGCGAA
1 TCTTCATATATTGGCA-GAAGTAGATCGAAGATGCAGATCTTGTC-TTCCTATATTGGTAGCGAA
12432965 GTAGATCGAAGAAAGCAGATCTTG
64 GTAGATCGAAGAAAGCAGATCTTG
* * * * * *
12432989 TCTTCATGTATTGGCATAAAGTAGATCAAAGATAGTAGGTCCTGTCTTCCTATATTGGTAG-GAA
1 TCTTCATATATTGGCA-GAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAA
** *
12433053 GGGGATCGAAG-ATGCAGATCTTG
64 GTAGATCGAAGAAAGCAGATCTTG
* * * * * *
12433076 TCTTTCCATACTAGTGGC-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTG
1 TC-TT-CATA-TATTGGCAGAAGTAGATCGAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCG
* * *
12433139 AAGTAGAACAAAGATAGCAGAT
62 AAGTAGATCGAAGAAAGCAGAT
12433161 ATTGCCTTTC
Statistics
Matches: 342, Mismatches: 77, Indels: 35
0.75 0.17 0.08
Matches are distributed among these distances:
86 4 0.01
87 35 0.10
88 177 0.52
89 110 0.32
90 11 0.03
91 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (87 bp):
TCTTCATATATTGGCAGAAGTAGATCGAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGT
AGATCGAAGAAAGCAGATCTTG
Found at i:12432989 original size:132 final size:132
Alignment explanation
Indices: 12432619--12433158 Score: 873
Period size: 132 Copynumber: 4.1 Consensus size: 132
12432609 GCAGATCAGT
* * *
12432619 GAAGATAGCAGGTCCTATCTTCCTATATTGGTACGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTC
* * * * * *
12432684 CCATATTGGTGGCGGAGTAGATCGTAGAAAGCAGATCTTGCCTTCATATATTGGCATGAAGTAGA
66 CCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
12432749 TC
131 TC
* *
12432751 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGGGGATCGAAGATGCAGATCTTGTCTT
* *
12432816 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTATGAAGTAG
65 CCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
12432881 ATC
130 ATC
* *
12432884 GAAGATAGCAGGCCCTGTCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTT
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTC
*
12432949 CCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATAAAGTAGA
66 CCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
12433014 TC
131 TC
* * *
12433016 AAAGATAGTAGGTCCTGTCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTT
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTC
*
12433081 CCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
*
12433146 AC
131 TC
*
12433148 AAAGATAGCAG
1 GAAGATAGCAG
12433159 ATATTGCCTT
Statistics
Matches: 384, Mismatches: 23, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
132 260 0.68
133 124 0.32
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (132 bp):
GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGATCTTGTCTTC
CCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
TC
Found at i:12433232 original size:43 final size:43
Alignment explanation
Indices: 12433179--12433320 Score: 124
Period size: 43 Copynumber: 3.3 Consensus size: 43
12433169 TCTACACCGA
*
12433179 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 CAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTG
* * * * * * * ****
12433222 CAGCGGAGCAG-GCTAAAAATAGCAGATCTTGCCTTCCTGCACCG
1 CAGCGAAGCAGATC-GAAGATACCAG-CCTTGCCTCCCTGGGTTG
*
12433266 ACAGCGAAGCAGATCGAAGATACTAGCCTTGCCTCCCTGGGTTG
1 -CAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTG
*
12433310 CAGCGGAGCAG
1 CAGCGAAGCAG
12433321 GCTAAAAAAT
Statistics
Matches: 70, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
42 1 0.01
43 27 0.39
44 24 0.34
45 17 0.24
46 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (43 bp):
CAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTG
Found at i:12433253 original size:44 final size:43
Alignment explanation
Indices: 12433202--12433328 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 43
12433192 CGAAGACACC
12433202 AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGC-
1 AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATA-CT
* * **** * * * *
12433245 AGATCTTGCCTTCCTGCACCGACAGCGAAGCA-GATCGAAGATACT
1 AG-CCTTGCCTCCCTGGGTTG-CAGCGGAGCAGGCT-AAAAATACT
12433290 AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAA
1 AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAA
12433329 ATCTCCCTGG
Statistics
Matches: 59, Mismatches: 20, Indels: 10
0.66 0.22 0.11
Matches are distributed among these distances:
43 14 0.24
44 29 0.49
45 16 0.27
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (43 bp):
AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATACT
Found at i:12433265 original size:88 final size:88
Alignment explanation
Indices: 12433152--12433328 Score: 309
Period size: 88 Copynumber: 2.0 Consensus size: 88
12433142 TAGAACAAAG
*
12433152 ATAGCAGATATTGCCTTTCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATATTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
12433217 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* * * *
12433240 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGATACTAGCCTTGCCTCCCTG
1 ATAGCAGATATTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
12433305 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
12433328 A
1 A
12433329 ATCTCCCTGG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (88 bp):
ATAGCAGATATTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGCTAAAA
Found at i:12433533 original size:44 final size:44
Alignment explanation
Indices: 12433329--12433535 Score: 283
Period size: 44 Copynumber: 4.7 Consensus size: 44
12433319 AGGCTAAAAA
*
12433329 ATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCT
1 ATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCT
* * *
12433373 ATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCT
1 ATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCT
** ** * *
12433417 ATCTCCCTGGGAAGCAGTGGAATATATTGAAAATTGT-AGGTCCT
1 ATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGA-ATCCT
12433461 ATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCT
1 ATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCT
*
12433505 ATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
1 ATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
12433536 AATAGCAAAT
Statistics
Matches: 140, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.01
44 137 0.98
45 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (44 bp):
ATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCT
Found at i:12434375 original size:22 final size:22
Alignment explanation
Indices: 12434315--12434372 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
12434305 AATCTTCAAG
12434315 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12434334 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
12434356 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12434373 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:12447544 original size:1 final size:1
Alignment explanation
Indices: 12447538--12447578 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
12447528 ACATATCACC
**
12447538 TTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12447579 CATAAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:12447905 original size:20 final size:20
Alignment explanation
Indices: 12447880--12447917 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12447870 TCACCTATCA
* *
12447880 AAATTAAATTATAATTTTTT
1 AAATTAAAATAAAATTTTTT
12447900 AAATTAAAATAAAATTTT
1 AAATTAAAATAAAATTTT
12447918 ATTATTGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTAAAATAAAATTTTTT
Found at i:12452354 original size:21 final size:24
Alignment explanation
Indices: 12452329--12452388 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 24
12452319 AACTTACATG
12452329 GTTATTAATAATAAA-AT-AATTT
1 GTTATTAATAATAAATATCAATTT
12452351 -TTATTAATAATAAATATCAATTT
1 GTTATTAATAATAAATATCAATTT
12452374 GTTAAATTAATAATA
1 GTT--ATTAATAATA
12452389 TTTTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 14 0.42
22 2 0.06
23 5 0.15
24 2 0.06
26 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (24 bp):
GTTATTAATAATAAATATCAATTT
Found at i:12453640 original size:13 final size:13
Alignment explanation
Indices: 12453592--12453642 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
12453582 ACATTCTTTC
12453592 AAAAT-AATAAAG
1 AAAATGAATAAAG
12453604 AAAATGTAAATAAA-
1 AAAATG--AATAAAG
* *
12453618 TAATTGAATAAAG
1 AAAATGAATAAAG
12453631 AAAATGAATAAA
1 AAAATGAATAAA
12453643 ATTATAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 11 0.35
13 10 0.32
14 4 0.13
15 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (13 bp):
AAAATGAATAAAG
Found at i:12453725 original size:43 final size:43
Alignment explanation
Indices: 12453678--12453769 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 43
12453668 AAGTATGTAC
* * *
12453678 ATATATGTA-TATTAAGATTAT-AAAGTATAAAATATATATATAT
1 ATATATGTATTAATAAGATTATGAAA-TA-AAAATACATATATAG
* *
12453721 ATATATGTATTAATATGTTTATGAAATAAAAATACATATATAG
1 ATATATGTATTAATAAGATTATGAAATAAAAATACATATATAG
12453764 ATATAT
1 ATATAT
12453770 ATAGATATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 28 0.67
44 11 0.26
45 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (43 bp):
ATATATGTATTAATAAGATTATGAAATAAAAATACATATATAG
Found at i:12462390 original size:21 final size:24
Alignment explanation
Indices: 12462365--12462424 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 24
12462355 AACTTACATG
12462365 GTTATTAATAATAAA-AT-AATTT
1 GTTATTAATAATAAATATCAATTT
12462387 -TTATTAATAATAAATATCAATTT
1 GTTATTAATAATAAATATCAATTT
12462410 GTTAAATTAATAATA
1 GTT--ATTAATAATA
12462425 TTTTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 14 0.42
22 2 0.06
23 5 0.15
24 2 0.06
26 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (24 bp):
GTTATTAATAATAAATATCAATTT
Found at i:12463936 original size:3 final size:3
Alignment explanation
Indices: 12463921--12464089 Score: 62
Period size: 3 Copynumber: 57.0 Consensus size: 3
12463911 GATAGCAGTG
* * * * *
12463921 ATA ATA TTA ATA ATA A-A GTA ATA CATA CTA ATA ATA ATA TTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * * *
12463966 ATA ACA AAA ATA ATA GTA ATA A-A AGTA ATA A-A GATA ATA ATA CT-
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA
* * * ** * * * * *
12464010 ATA GTA ATG ATG ACG TTA ATA ATA ATA ATA TTA AAA ATA AAA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
12464058 A-A ACTA CTA ATA ATA AAA ATA ATG ATA A-A ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12464090 GCAAAGATAT
Statistics
Matches: 119, Mismatches: 37, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
2 9 0.08
3 103 0.87
4 7 0.06
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:12463986 original size:33 final size:33
Alignment explanation
Indices: 12463921--12463987 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
12463911 GATAGCAGTG
**
12463921 ATAATATTAATAATAAAGTAATACATACTAATA
1 ATAATATTAATAATAAAAAAATACATACTAATA
* *
12463954 ATAATATTAGTAATAACAAAAATA-ATAGTAATA
1 ATAATATTAATAATAA-AAAAATACATACTAATA
12463987 A
1 A
12463988 AAGTAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (33 bp):
ATAATATTAATAATAAAAAAATACATACTAATA
Found at i:12465639 original size:100 final size:100
Alignment explanation
Indices: 12465470--12465740 Score: 355
Period size: 100 Copynumber: 2.7 Consensus size: 100
12465460 AATCTGCTTG
* * * * * *
12465470 ACTGTGATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTATTCCACTGCACCGCCTGGA
1 ACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGG
* *
12465535 AAGTAAGATTCACCATTGTGGCTTTATTCTTTATA
66 AAGTAAGATTCACCATTGTAGCTTTAATCTTTATA
* * * * *
12465570 ACTGTAATGTCAGGGATGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCACTACACTGCTTGGG
1 ACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGG
* * *
12465635 AAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTA
66 AAGTAAGATTCACCATTGTAGCTTTAATCTTTATA
* * *
12465670 ACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA-TCGCCTGG
1 ACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACT-GCCTGG
12465734 GAAGTAA
65 GAAGTAA
12465741 AACTGGTATT
Statistics
Matches: 146, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
99 1 0.01
100 145 0.99
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
ACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGG
AAGTAAGATTCACCATTGTAGCTTTAATCTTTATA
Found at i:12465643 original size:50 final size:49
Alignment explanation
Indices: 12465482--12465740 Score: 182
Period size: 50 Copynumber: 5.2 Consensus size: 49
12465472 TGTGATGTCG
* * * * * *
12465482 GGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTATTCCACTGCACCGCCT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA-TGCTT
* * * * ** * *
12465532 GGAAAGTAAGATTCACCATTGTGGCTTTATTCT-TTATAACTGTAATG-TCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTT-CCACTG-CATGCT-T
* * * *
12465582 GGGATGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCACTACACTGCTT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA-TGCTT
* * ** *
12465632 GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATG-TCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGC-ATGCT-T
* * * *
12465682 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAT-GCTT
12465732 GGGAAGTAA
1 GGGAAGTAA
12465741 AACTGGTATT
Statistics
Matches: 155, Mismatches: 44, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
49 6 0.04
50 144 0.93
51 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCATGCTT
Found at i:12472952 original size:3 final size:3
Alignment explanation
Indices: 12472937--12473099 Score: 57
Period size: 3 Copynumber: 55.0 Consensus size: 3
12472927 GATAGCAGTG
* * * * *
12472937 ATA ATA TTA ATA ATA A-A AGTA ATA CTA ACA ATA ATA TTA GTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
12472982 AGA AAA ATA ATA GTA ATA ATA GTA ATA A-A GATA ATA ATA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * ** * * * * *
12473026 GTA ATG ATG ACG TTA ATA ATA ATA TTA AAA ATA AAA ATA ACA A-A ACTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * *
12473074 CTA ATA ATA AAA ATA ATG ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
12473100 GCAAAGATAT
Statistics
Matches: 113, Mismatches: 39, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
2 8 0.07
3 101 0.89
4 4 0.04
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:12474589 original size:100 final size:100
Alignment explanation
Indices: 12474449--12474739 Score: 393
Period size: 100 Copynumber: 2.9 Consensus size: 100
12474439 GATTCGTAAC
* ** * * * *
12474449 TTGTAACTTTAATCTACTTGACTGTGATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCT
1 TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
*
12474514 GTTCCACTGTACCACCTGGGAAGTAAGATTCACCA
66 GTTCCACTGCACCACCTGGGAAGTAAGATTCACCA
* * *
12474549 TTGTGGCTTTATTCTTTTTAACTGTAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
1 TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
* * * * *
12474614 GTTACACTGCACTACTTGGGAAGTAAGATTCGCCG
66 GTTCCACTGCACCACCTGGGAAGTAAGATTCACCA
* * *
12474649 TTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCT
1 TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
* *
12474714 GTTCCACTGCATCGCCTGGGAAGTAA
66 GTTCCACTGCACCACCTGGGAAGTAA
12474740 AACTAGTATT
Statistics
Matches: 164, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 164 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (100 bp):
TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
GTTCCACTGCACCACCTGGGAAGTAAGATTCACCA
Found at i:12474723 original size:50 final size:50
Alignment explanation
Indices: 12474475--12474724 Score: 232
Period size: 50 Copynumber: 5.0 Consensus size: 50
12474465 CTTGACTGTG
* * *
12474475 ATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTGTTCCACTGTA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
**** * * * * * * ** *
12474525 CCACCTGGGAAGTAAGATTCACCATTGTGGCTTTATTCTTTTTAACTGTA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
* *
12474575 ATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTACACTGCA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
* * * * * * **
12474625 CT-ACTTGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCA
1 ATGTC-GGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
* *
12474675 ATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
12474725 TCGCCTGGGA
Statistics
Matches: 153, Mismatches: 45, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
49 1 0.01
50 151 0.99
51 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
Found at i:12475290 original size:14 final size:14
Alignment explanation
Indices: 12475271--12475306 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
12475261 ACCTCTTCCT
12475271 ATTGCTTGGTGATC
1 ATTGCTTGGTGATC
12475285 ATTGCTTGGTGATC
1 ATTGCTTGGTGATC
12475299 ATTGCTTG
1 ATTGCTTG
12475307 CTTGTTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44
Consensus pattern (14 bp):
ATTGCTTGGTGATC
Found at i:12478537 original size:19 final size:19
Alignment explanation
Indices: 12478513--12478554 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
12478503 TTTTAAATTT
*
12478513 AAAAAATTA-AAAATTATTA
1 AAAAAAGTATAAAATTA-TA
12478532 AAAAAAGTATAAAATTATA
1 AAAAAAGTATAAAATTATA
12478551 AAAA
1 AAAA
12478555 TATTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAAAGTATAAAATTATA
Found at i:12491488 original size:20 final size:19
Alignment explanation
Indices: 12491463--12491511 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
12491453 TTCAAGGGTC
12491463 ATTTTGAAACAAAATAGAAA
1 ATTTTGAAA-AAAATAGAAA
* *
12491483 ATTTTGGAAAAAATTGAAA
1 ATTTTGAAAAAAATAGAAA
12491502 ATTTTGAAAA
1 ATTTTGAAAA
12491512 CAAGGGTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (19 bp):
ATTTTGAAAAAAATAGAAA
Found at i:12493314 original size:12 final size:10
Alignment explanation
Indices: 12493284--12493326 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
12493274 AATATGAACA
*
12493284 TAATGAATTT
1 TAATTAATTT
12493294 TAATTAATTT
1 TAATTAATTT
12493304 TATAGTTAATTT
1 TA-A-TTAATTT
*
12493316 TGATTAATTT
1 TAATTAATTT
12493326 T
1 T
12493327 GACTATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (10 bp):
TAATTAATTT
Found at i:12504561 original size:48 final size:47
Alignment explanation
Indices: 12504486--12504641 Score: 179
Period size: 47 Copynumber: 3.3 Consensus size: 47
12504476 ATCCACAATT
* * * * *
12504486 ATTTGGACAACATTGATTTG-TACAAAAATGAACAGCATTTAAGCACC
1 ATTTGGACAACATTAATATGCTA-AAAAATGGACAGCATTTAAACAAC
* * * *
12504533 AATTTGGACAGCATTAATATGCTAAAAAACGGACAGCATTCAACCAAC
1 -ATTTGGACAACATTAATATGCTAAAAAATGGACAGCATTTAAACAAC
* * *
12504581 ATTCGAACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAAC
1 ATTTGGACAACATTAATATGCTAAAAAATGGACAGCATTTAAACAAC
12504628 ATTTGGACAACATT
1 ATTTGGACAACATT
12504642 TAATCAACAT
Statistics
Matches: 90, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
47 52 0.58
48 36 0.40
49 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (47 bp):
ATTTGGACAACATTAATATGCTAAAAAATGGACAGCATTTAAACAAC
Found at i:12504651 original size:69 final size:69
Alignment explanation
Indices: 12504562--12504843 Score: 429
Period size: 69 Copynumber: 4.1 Consensus size: 69
12504552 TGCTAAAAAA
* * * *
12504562 CGGACAGCATTCAACCAACATTCGAACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
12504627 CATT
66 CATT
* * * *
12504631 TGGACAACATTTAATCAACATTTGGACATCATTAGTATGCTAAAAAATGGACAGTATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
12504696 CATT
66 CATT
* *
12504700 CAGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAACATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
**
12504765 CAGC
66 CATT
* *
12504769 CGGACAACATTTAGCCAACATTTGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
12504834 CATT
66 CATT
*
12504838 TGGACA
1 CGGACA
12504844 GCATCTTGTC
Statistics
Matches: 190, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 190 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (69 bp):
CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
CATT
Found at i:12504708 original size:11 final size:11
Alignment explanation
Indices: 12504686--12504732 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
12504676 AATGGACAGT
*
12504686 ATTTAAACAAC
1 ATTTAGACAAC
*
12504697 ATTCAGACAAC
1 ATTTAGACAAC
12504708 ATTTA-ACCAAC
1 ATTTAGA-CAAC
*
12504719 ATTTGGACAAC
1 ATTTAGACAAC
12504730 ATT
1 ATT
12504733 AGTATGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 1 0.03
11 28 0.93
12 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (11 bp):
ATTTAGACAAC
Found at i:12504847 original size:22 final size:22
Alignment explanation
Indices: 12504609--12504843 Score: 119
Period size: 22 Copynumber: 10.3 Consensus size: 22
12504599 TGCTAAAAAA
*
12504609 TGGACAGCATTTAAACAACATT
1 TGGACAACATTTAAACAACATT
*
12504631 TGGACAACATTTAATCAACATT
1 TGGACAACATTTAAACAACATT
* ** * **
12504653 TGGACATCATTAGTATGCTAAAAAA
1 TGGACAACATT--TAAAC-AACATT
**
12504678 TGGACAGTATTTAAACAACATT
1 TGGACAACATTTAAACAACATT
** *
12504700 CAGACAACATTTAACCAACATT
1 TGGACAACATTTAAACAACATT
** * **
12504722 TGGACAACATTAGTATGCTAAAAAA
1 TGGACAACATT--TAAAC-AACATT
**
12504747 TGGACAACATTTAAACAACAGC
1 TGGACAACATTTAAACAACATT
* **
12504769 CGGACAACATTTAGCCAACATT
1 TGGACAACATTTAAACAACATT
* ** * **
12504791 TGGACAGCATTAGTATGCTAAAAAA
1 TGGACAACATT--TAAAC-AACATT
*
12504816 TGGACAGCATTTAAACAACATT
1 TGGACAACATTTAAACAACATT
12504838 TGGACA
1 TGGACA
12504844 GCATCTTGTC
Statistics
Matches: 155, Mismatches: 49, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
22 97 0.63
23 9 0.06
24 9 0.06
25 40 0.26
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (22 bp):
TGGACAACATTTAAACAACATT
Found at i:12507920 original size:28 final size:27
Alignment explanation
Indices: 12507856--12507921 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
12507846 GAAAATGGAG
* *
12507856 GCCTTTGTGGCAATCTCTATATAGGAA
1 GCCTTTGTGGCAATCTCTATAAAAGAA
* *
12507883 GCCTTTGTGGCTATCTCTGTAAAAGAA
1 GCCTTTGTGGCAATCTCTATAAAAGAA
*
12507910 TGCCTTCGTGGC
1 -GCCTTTGTGGC
12507922 GTAATCTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (27 bp):
GCCTTTGTGGCAATCTCTATAAAAGAA
Found at i:12512776 original size:27 final size:27
Alignment explanation
Indices: 12512734--12512793 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
12512724 AAACCGCTAG
* *
12512734 AAATATATATACGTGG-CTAAGCCACC
1 AAATAGATATACGTGGTCTAAACCACC
*
12512760 ATAATAGATATATGTGGTTCTAAACCACC
1 A-AATAGATATACGTGG-TCTAAACCACC
12512789 AAATA
1 AAATA
12512794 AGGCAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 13 0.46
28 4 0.14
29 10 0.36
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (27 bp):
AAATAGATATACGTGGTCTAAACCACC
Found at i:12513819 original size:5 final size:5
Alignment explanation
Indices: 12513809--12513833 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12513799 TCTTTTTCTA
12513809 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
12513834 TATAAGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:12516574 original size:24 final size:25
Alignment explanation
Indices: 12516522--12516580 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
12516512 TGGCTCTCAC
* * *
12516522 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGA
*
12516547 GAGCTTCCCGTTA-ATAGCTCTTTA
1 GAGCTTCCCGTTATATAGCTCTTGA
*
12516571 GAGCATCCCG
1 GAGCTTCCCG
12516581 ATTGGTTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGA
Found at i:12528179 original size:29 final size:29
Alignment explanation
Indices: 12528125--12528183 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
12528115 AGCCCATATA
*
12528125 TTTCACAATTTCTCACATTTGACCCACAAT
1 TTTCACAATTTCTCACATTTAACCCA-AAT
12528155 TTTCAC-ATTTCTCA-ATTTAACCCCAAAT
1 TTTCACAATTTCTCACATTTAA-CCCAAAT
12528183 T
1 T
12528184 GACATTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 9 0.33
29 12 0.44
30 6 0.22
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTCACAATTTCTCACATTTAACCCAAAT
Found at i:12542577 original size:14 final size:13
Alignment explanation
Indices: 12542553--12542607 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 13
12542543 TTGTTACCGC
*
12542553 TATTATGTTATAT
1 TATTATTTTATAT
*
12542566 CATTAGTTTTATAT
1 TATTA-TTTTATAT
12542580 TATTATTGTTATAT
1 TATTATT-TTATAT
*
12542594 TTTTATTTTATAT
1 TATTATTTTATAT
12542607 T
1 T
12542608 TACTTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 13 0.36
14 23 0.64
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (13 bp):
TATTATTTTATAT
Found at i:12542583 original size:27 final size:27
Alignment explanation
Indices: 12542553--12542607 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
12542543 TTGTTACCGC
12542553 TATTA-TGTTATATCATTAGTTTTATAT
1 TATTATTGTTATATCATTA-TTTTATAT
**
12542580 TATTATTGTTATATTTTTATTTTATAT
1 TATTATTGTTATATCATTATTTTATAT
12542607 T
1 T
12542608 TACTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTATTGTTATATCATTATTTTATAT
Found at i:12548898 original size:47 final size:48
Alignment explanation
Indices: 12548829--12548923 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 48
12548819 TTGCCCGTTT
12548829 GAAGTCGAGTTTCTATCCCTTCAAGATGTTGGATTTTAT-CTGATGGA
1 GAAGTCGAGTTTCTATCCCTTCAAGATGTTGGATTTTATCCTGATGGA
12548876 GAAGTCGAGTTTCTATCCCTTCAAGATGTTGGATTTTATCCTGATGGA
1 GAAGTCGAGTTTCTATCCCTTCAAGATGTTGGATTTTATCCTGATGGA
12548924 AGAGGAAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 39 0.83
48 8 0.17
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (48 bp):
GAAGTCGAGTTTCTATCCCTTCAAGATGTTGGATTTTATCCTGATGGA
Found at i:12548915 original size:23 final size:23
Alignment explanation
Indices: 12548842--12548916 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
12548832 GTCGAGTTTC
12548842 TATCCCTTCAAGATGTTGGATTT
1 TATCCCTTCAAGATGTTGGATTT
*** ** * *
12548865 TATCTGATGGAGAAG-TCGAGTTT
1 TATCCCTTCAAGATGTTGGA-TTT
12548888 CTATCCCTTCAAGATGTTGGATTT
1 -TATCCCTTCAAGATGTTGGATTT
12548912 TATCC
1 TATCC
12548917 TGATGGAAGA
Statistics
Matches: 35, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 3 0.09
23 17 0.49
24 12 0.34
25 3 0.09
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (23 bp):
TATCCCTTCAAGATGTTGGATTT
Found at i:12549097 original size:23 final size:24
Alignment explanation
Indices: 12549088--12549153 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
12549078 GAAAAAAATC
12549088 AAAATCAAAATCAAAATAAAGAAA
1 AAAATCAAAATCAAAATAAAGAAA
** *
12549112 AAAA-CAAAAAGAAAA-AGAGAAA
1 AAAATCAAAATCAAAATAAAGAAA
** *
12549134 TCAATCAAAGTCAAAATAAA
1 AAAATCAAAATCAAAATAAA
12549154 AATATGAAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
22 8 0.26
23 17 0.55
24 6 0.19
ACGTcount: A:0.73, C:0.09, G:0.08, T:0.11
Consensus pattern (24 bp):
AAAATCAAAATCAAAATAAAGAAA
Found at i:12549113 original size:52 final size:50
Alignment explanation
Indices: 12549057--12549178 Score: 145
Period size: 52 Copynumber: 2.3 Consensus size: 50
12549047 TCGATTCGAA
*
12549057 AAAAAAAGGAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATCAAAATAAAG
1 AAAAAAA-GAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT-AAG
* ** * *
12549109 AAAAAAACAAAAAGAAAAAGAGAAATCAATCAAAGTCAAAATAAAAATATG
1 AAAAAAA-GAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAATAAG
12549160 AAAAGCAAAGAAAAGAAAA
1 AAAA--AAAGAAAAGAAAA
12549179 GAAGAGGCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 6 0.10
52 51 0.85
53 3 0.05
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (50 bp):
AAAAAAAGAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAATAAG
Found at i:12549576 original size:7 final size:6
Alignment explanation
Indices: 12549540--12549567 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12549530 AAAAGGATGA
12549540 AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
12549568 AAATGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:12549582 original size:15 final size:15
Alignment explanation
Indices: 12549539--12549576 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 15
12549529 AAAAAGGATG
12549539 AAAAATGAAAATG--
1 AAAAATGAAAATGAA
12549552 -AAAATGAAAATGAA
1 AAAAATGAAAATGAA
12549566 AAAAATGAAAA
1 AAAAATGAAAA
12549577 GTAAAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.55
15 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAATGAA
Found at i:12551022 original size:86 final size:86
Alignment explanation
Indices: 12550808--12551927 Score: 1520
Period size: 86 Copynumber: 13.0 Consensus size: 86
12550798 CAGATTAGTG
* * * *
12550808 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGTGAAGCAGATTGAAAACAAAACCTTGCCTCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
12550873 TCGGTGGCAATGGAGCTGGTT-
65 TCGGTTGCAGTGGAGCTGGTTA
*
12550894 -A-AA--AGATCTTGCCTTCCTGCGTTAAGAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
12550955 CGGTTGCAGTGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* *
12550976 AAGAAGCAGATATTGTCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
12551041 CGGTTGCAGTGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* * *
12551062 AAGAAGCAGATCTTACCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCTAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
*
12551127 CGGTTACAGTGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
** *
12551148 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAATCTTGTCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
* *
12551213 CGGTGGCAATGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
*
12551234 AAGAAGCAGCTCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
* * * *
12551299 CGATTACAGTGGAACTGGATA
66 CGGTTGCAGTGGAGCTGGTTA
* * * *
12551320 AAAAAGTAGATCTTACCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
*
12551385 CGGTTGCAATGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
12551406 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
12551471 CGGTTGCAGTGGAGCTGGTTA
66 CGGTTGCAGTGGAGCTGGTTA
* * * *
12551492 AAAAAGCAGATCTTGCCTTCCTGCCTTAACAGCGAAGCAGATCGAAAACAAAACCTTACCTCTC-
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC-CA
* * *
12551556 TCGGTTGTAGTGGAGCGGGTTG
65 TCGGTTGCAGTGGAGCTGGTTA
* * * * **
12551578 AAGACAACAGATCTTGTCTTCCTGCCTTGACAGCGAAGCAGATCGAAGATACAAA-CCTTTTCTC
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC
* **
12551642 TC-TCGGTTGTAGCAGAGCTGGTTA
63 -CATCGGTTGCAGTGGAGCTGGTTA
* * * * * *
12551666 AAGATAGCAGATTTTACCTTCCTGCATTAACAGCGAAGCAGA-CAAAAAAAAAGCATTGCCTCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
12551730 TCGGTTGCAGGGGAGCTGGTTT
65 TCGGTTGCAGTGGAGCTGGTTA
* *
12551752 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
12551817 TCGGTTGCAATGGAGCTGGTTG
65 TCGGTTGCAGTGGAGCTGGTTA
* * * * *
12551839 AAGATAGCAGCTCTTGCCTTCCTGCATTAACAGCGATGCAGATCAAAAACAAAGTCTTGCCTCCA
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* * *
12551904 TCGATTACAGTGGAGCGGGTTA
65 TCGGTTGCAGTGGAGCTGGTTA
12551926 AA
1 AA
12551928 ATAAAAGATC
Statistics
Matches: 920, Mismatches: 102, Indels: 23
0.88 0.10 0.02
Matches are distributed among these distances:
81 71 0.08
83 2 0.00
84 3 0.00
85 6 0.01
86 611 0.66
87 159 0.17
88 63 0.07
89 5 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (86 bp):
AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
CGGTTGCAGTGGAGCTGGTTA
Found at i:12551164 original size:43 final size:43
Alignment explanation
Indices: 12551030--12551165 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 43
12551020 AAAACAAAGC
* *
12551030 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTCTATCGGTTACAGTGGAGCTGGTTAAAGAAGCAGAT
* * * * * ** * *
12551073 CTTACCT-T-CCTGCGTTAACAGTGAAGCAGATCGAA-AA-CAAAGC
1 CTTGCCTCTATC-G-GTT-ACAGTGGAGCTGGTTAAAGAAGCAGA-T
12551116 CTTGCCTCTATCGGTTACAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTCTATCGGTTACAGTGGAGCTGGTTAAAGAAGCAGAT
12551159 CTTGCCT
1 CTTGCCT
12551166 TCCTGCGTTA
Statistics
Matches: 65, Mismatches: 20, Indels: 16
0.64 0.20 0.16
Matches are distributed among these distances:
41 1 0.02
42 17 0.26
43 29 0.45
44 17 0.26
45 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (43 bp):
CTTGCCTCTATCGGTTACAGTGGAGCTGGTTAAAGAAGCAGAT
Found at i:12552165 original size:129 final size:129
Alignment explanation
Indices: 12551973--12552214 Score: 396
Period size: 129 Copynumber: 1.9 Consensus size: 129
12551963 TAGATCACAT
12551973 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
* * * *
12552038 ATTTTTCTAAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAG
66 ATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCTGAGATTACAGCGGAG
* **
12552102 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAT-AAGTGATCT
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-GATCT
*
12552166 TATCTCTCTAAAGTTACACTAGAGTATATCGTATCAGGTCTTACCTCCC
65 TATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCC
12552215 AGGCGGTCCA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 3 0.03
129 101 0.97
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (129 bp):
CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
ATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCTGAGATTACAGCGGAG
Found at i:12552170 original size:44 final size:43
Alignment explanation
Indices: 12551993--12552171 Score: 132
Period size: 44 Copynumber: 4.1 Consensus size: 43
12551983 CCAAAAATCC
*
12551993 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGGATCT
* ** * * * *** *
12552037 TATTTTTCT-AAAGTTACAGTAGAGTAGA-TCGTATCAGG-TCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAGGATCT
* ** * *
12552078 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAG-GATCT
*
12552122 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAGTGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAG-GATCT
12552166 TATCTC
1 TATCTC
12552172 TCTAAAGTTA
Statistics
Matches: 98, Mismatches: 30, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
41 21 0.21
42 8 0.08
43 9 0.09
44 60 0.61
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (43 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAGGATCT
Found at i:12552236 original size:129 final size:129
Alignment explanation
Indices: 12551973--12552243 Score: 375
Period size: 129 Copynumber: 2.1 Consensus size: 129
12551963 TAGATCACAT
*
12551973 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCTAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
* * * * * * *
12552038 ATTTTTCTAAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAG
66 ATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCAGAGAGTACAGCGGAA
**
12552102 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAT-AAGTGATCT
1 CAGATTGAAGCTAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-GATCT
* * * *
12552166 TATCTCTCTAAAGTTACACTAGAGTATATCGTATCAGGTCTTACCTCCCAG-GCGGTCCAGTGGA
65 TATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCAGAG-AGTACAGCGGA
12552230 A
129 A
*
12552231 TAGATTGAAGCTA
1 CAGATTGAAGCTA
12552244 CGACGACGAA
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 4 0.03
129 121 0.97
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (129 bp):
CAGATTGAAGCTAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
ATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCAGAGAGTACAGCGGAA
Found at i:12552441 original size:44 final size:44
Alignment explanation
Indices: 12552336--12552458 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 44
12552326 GATTAAAACC
*
12552336 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
1 ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
* * * * *
12552380 ACAAACCTTACCCCCCTGAAGTTGCATTGGGGTAGGTTGAAG-A
1 ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
*** * * *
12552423 TACAGGTCTTATCTCCCTGACGTAGCAGTGGAGTAG
1 -ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAG
12552459 ACTAAAACCA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
43 1 0.02
44 62 0.98
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
Found at i:12553954 original size:16 final size:16
Alignment explanation
Indices: 12553933--12553966 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12553923 ATACATGTAC
12553933 ATACATACTTTTATAT
1 ATACATACTTTTATAT
**
12553949 ATACATGTTTTTATAT
1 ATACATACTTTTATAT
12553965 AT
1 AT
12553967 TTCCTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (16 bp):
ATACATACTTTTATAT
Found at i:12555398 original size:9 final size:9
Alignment explanation
Indices: 12555384--12555414 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12555374 GTTAAACGAA
12555384 TCGAGTTAT
1 TCGAGTTAT
*
12555393 TCGAGTTAA
1 TCGAGTTAT
12555402 TCGAGTTAT
1 TCGAGTTAT
12555411 TCGA
1 TCGA
12555415 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12556269 original size:5 final size:5
Alignment explanation
Indices: 12556259--12556289 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
12556249 CTCGAAAATT
12556259 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
12556290 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12564168 original size:30 final size:31
Alignment explanation
Indices: 12564112--12564169 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
12564102 ATTATTGAAC
*
12564112 TATTCAAAAGTTTTCATTTAAGTCATTAAAT
1 TATTCAAAAGTTTTCATTTAAATCATTAAAT
*
12564143 TATTCAAAA-TTTTTATTTAAATCATTA
1 TATTCAAAAGTTTTCATTTAAATCATTA
12564170 GGCTGCTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAATCATTAAAT
Found at i:12564827 original size:13 final size:14
Alignment explanation
Indices: 12564795--12564827 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12564785 ATAAATTAAA
*
12564795 AAAATTAAATGTTG
1 AAAATTAAATATTG
12564809 AAAATTAAATATT-
1 AAAATTAAATATTG
12564822 AAAATT
1 AAAATT
12564828 TTCAGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
AAAATTAAATATTG
Found at i:12565169 original size:30 final size:31
Alignment explanation
Indices: 12565100--12565173 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
12565090 TGATTGAATA
*
12565100 ACAATCAAAGTTTCATGTATATATTTGAACC
1 ACAATCAAAGTTTCATGTATATAATTGAACC
* * *
12565131 ACAATCAAAGTTTTATGTGTATAATTGTACC
1 ACAATCAAAGTTTCATGTATATAATTGAACC
12565162 A-AATCAAAGTTT
1 ACAATCAAAGTTT
12565174 ATATATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (31 bp):
ACAATCAAAGTTTCATGTATATAATTGAACC
Found at i:12570847 original size:15 final size:15
Alignment explanation
Indices: 12570827--12570858 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12570817 CATTTCACTA
*
12570827 TTATGTCTTTTATAT
1 TTATGTATTTTATAT
12570842 TTATGTATTTTATAT
1 TTATGTATTTTATAT
12570857 TT
1 TT
12570859 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATTTTATAT
Found at i:12572544 original size:26 final size:26
Alignment explanation
Indices: 12572474--12572546 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
12572464 TTTTAGTAGT
12572474 TTAATATTAAATTTAATTTAATACTTATC
1 TTAATATTAAATTTAA---AATACTTATC
*
12572503 TTAATAGT-AATATTAAAATGA-TTATC
1 TTAATATTAAAT-TTAAAAT-ACTTATC
12572529 TTAATATTAAATTTAAAA
1 TTAATATTAAATTTAAAA
12572547 CATTCTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 21 0.54
27 4 0.10
28 3 0.08
29 11 0.28
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (26 bp):
TTAATATTAAATTTAAAATACTTATC
Found at i:12572584 original size:12 final size:12
Alignment explanation
Indices: 12572567--12572614 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
12572557 TTTTAATAAG
12572567 ATTTAATATTAA
1 ATTTAATATTAA
12572579 ATTTAATCA-TAA
1 ATTTAAT-ATTAA
12572591 ATATT-ATATT-A
1 AT-TTAATATTAA
12572602 ATTTAATATTAA
1 ATTTAATATTAA
12572614 A
1 A
12572615 GGATTAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.06
11 9 0.29
12 17 0.55
13 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:12574780 original size:26 final size:26
Alignment explanation
Indices: 12574744--12574816 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
12574734 TATTTTCTTG
*
12574744 AAATTTTACCAGGGGTAAAATCG-TTA
1 AAATTTTACCAGGGGTAAAAT-GATCA
*
12574770 AAATTTTACCAAGGGTAAAATGATCA
1 AAATTTTACCAGGGGTAAAATGATCA
***
12574796 AAATTTTGTTAGGGGTAAAAT
1 AAATTTTACCAGGGGTAAAAT
12574817 AGGGATGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAGGGGTAAAATGATCA
Found at i:12593505 original size:3 final size:3
Alignment explanation
Indices: 12593497--12593533 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12593487 ATTTAAAAAC
12593497 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12593534 GTTGTTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12603487 original size:17 final size:17
Alignment explanation
Indices: 12603465--12603499 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12603455 AAATGGATCA
12603465 TGGTTTATCTTTAGTTC
1 TGGTTTATCTTTAGTTC
12603482 TGGTTTATCTTTAGTTC
1 TGGTTTATCTTTAGTTC
12603499 T
1 T
12603500 CAATTTGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (17 bp):
TGGTTTATCTTTAGTTC
Found at i:12604274 original size:43 final size:43
Alignment explanation
Indices: 12604206--12604304 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
12604196 TAGCTCTCTC
*
12604206 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAGCGTGG
1 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
* * *
12604249 TTATGATTACCATTAGTGTTG-CTTAATTGGACATTTAACGTTG
1 TTATAACTACCATTAGTG-TGCCTTAATTGGACATTTAACGTGG
12604292 TTATAACTACCAT
1 TTATAACTACCAT
12604305 CAAACTTTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 47 0.96
44 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (43 bp):
TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
Found at i:12604609 original size:16 final size:16
Alignment explanation
Indices: 12604573--12604621 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
12604563 GCAATCAAGC
12604573 CTCTATTCCATTAC-G
1 CTCTATTCCATTACAG
*
12604588 CATCTATTCCATTACAT
1 C-TCTATTCCATTACAG
*
12604605 CTCTATTCTATTACAG
1 CTCTATTCCATTACAG
12604621 C
1 C
12604622 GAACCAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.04, T:0.41
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:12605035 original size:47 final size:47
Alignment explanation
Indices: 12604976--12605123 Score: 164
Period size: 47 Copynumber: 3.2 Consensus size: 47
12604966 TCATATAAGA
*
12604976 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTAATATTAAGAATTTTATGAAATTATATATCATTATTAAATT
** *
12605023 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTAATATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* * *
12605067 AAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTAATATTAAGAATTTTATGAAATTATATATCATTATTAAATT
12605114 ATATTTAATA
1 ATATTTAATA
12605124 NNNNNNNNNN
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
43 3 0.04
44 24 0.30
45 8 0.10
46 8 0.10
47 34 0.43
48 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (47 bp):
ATATTTAATATTAAGAATTTTATGAAATTATATATCATTATTAAATT
Found at i:12605087 original size:44 final size:44
Alignment explanation
Indices: 12604961--12605088 Score: 127
Period size: 44 Copynumber: 2.8 Consensus size: 44
12604951 ATGGTTTTAG
12604961 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATA
1 TAAATTCATATAAGAATATTTATTATTAAGAA-TTT-T-AAATTATA
* * **
12605008 TATCATT-AT-TAA-ATTATATTTAATATTAATTATTTTAAATTATA
1 TA-AATTCATATAAGA--ATATTTATTATTAAGAATTTTAAATTATA
* *
12605052 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTA
1 TAAATTCATATAAGAATATTTATTATTAAGAATTTTA
12605089 TGAAATTATA
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
45 5 0.08
46 7 0.11
47 18 0.28
48 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (44 bp):
TAAATTCATATAAGAATATTTATTATTAAGAATTTTAAATTATA
Found at i:12605550 original size:9 final size:9
Alignment explanation
Indices: 12605538--12606127 Score: 1119
Period size: 9 Copynumber: 65.4 Consensus size: 9
12605528 AAAATAAAAA
12605538 AATTCGGGT
1 AATTCGGGT
12605547 AATTCGGGT
1 AATTCGGGT
*
12605556 ATTTTTC-GGT
1 A--ATTCGGGT
*
12605566 AATTCGGTT
1 AATTCGGGT
*
12605575 AATTCGGTT
1 AATTCGGGT
12605584 AATTCGGGT
1 AATTCGGGT
*
12605593 AATTCGGTT
1 AATTCGGGT
12605602 AATTCGGGT
1 AATTCGGGT
12605611 AATTCGGGT
1 AATTCGGGT
12605620 AATTCGGGT
1 AATTCGGGT
12605629 AATTCGGGT
1 AATTCGGGT
12605638 AATTCGGGT
1 AATTCGGGT
12605647 AATTCGGGT
1 AATTCGGGT
12605656 AATTCGGGT
1 AATTCGGGT
12605665 AATTCGGGT
1 AATTCGGGT
12605674 AATTCGGGT
1 AATTCGGGT
12605683 AATTCGGGT
1 AATTCGGGT
12605692 AATTCGGGT
1 AATTCGGGT
12605701 AATTCGGGT
1 AATTCGGGT
12605710 AATTCGGGT
1 AATTCGGGT
12605719 AATTCGGGT
1 AATTCGGGT
12605728 AATTCGGGT
1 AATTCGGGT
12605737 AATTCGGGT
1 AATTCGGGT
12605746 AATTCGGGT
1 AATTCGGGT
12605755 AATTCGGGT
1 AATTCGGGT
12605764 AATTCGGGT
1 AATTCGGGT
12605773 AATTCGGGT
1 AATTCGGGT
12605782 AATTCGGGT
1 AATTCGGGT
12605791 AATTCGGGT
1 AATTCGGGT
12605800 AATTCGGGT
1 AATTCGGGT
12605809 AATTCGGGT
1 AATTCGGGT
12605818 AATTCGGGT
1 AATTCGGGT
12605827 AATTCGGGT
1 AATTCGGGT
12605836 AATTCGGGT
1 AATTCGGGT
12605845 AATTCGGGT
1 AATTCGGGT
12605854 AATTCGGGT
1 AATTCGGGT
12605863 AATTCGGGT
1 AATTCGGGT
12605872 AATTCGGGT
1 AATTCGGGT
12605881 AATTCGGGT
1 AATTCGGGT
12605890 AATTCGGGT
1 AATTCGGGT
12605899 AATTCGGGT
1 AATTCGGGT
12605908 AATTCGGGT
1 AATTCGGGT
12605917 AATTCGGGT
1 AATTCGGGT
12605926 AATTCGGGT
1 AATTCGGGT
12605935 AATTCGGGT
1 AATTCGGGT
12605944 AATTCGGGT
1 AATTCGGGT
12605953 AATTCGGGT
1 AATTCGGGT
12605962 AATTCGGGT
1 AATTCGGGT
12605971 AATTCGGGT
1 AATTCGGGT
12605980 AATTCGGGT
1 AATTCGGGT
12605989 AATTCGGGT
1 AATTCGGGT
12605998 AATTCGGGT
1 AATTCGGGT
12606007 AATTCGGGT
1 AATTCGGGT
12606016 AATTCGGGT
1 AATTCGGGT
12606025 AATTCGGGT
1 AATTCGGGT
12606034 AATTCGGGT
1 AATTCGGGT
12606043 AATTCGGGT
1 AATTCGGGT
12606052 AATTCGGGT
1 AATTCGGGT
12606061 AATTCGGGT
1 AATTCGGGT
12606070 AATTCGGGT
1 AATTCGGGT
12606079 AATTCGGGT
1 AATTCGGGT
12606088 AATTCGGGT
1 AATTCGGGT
12606097 AATTCGGGT
1 AATTCGGGT
12606106 AATTCGGGT
1 AATTCGGGT
12606115 AATTCGGGT
1 AATTCGGGT
12606124 AATT
1 AATT
12606128 TTTAACCAAA
Statistics
Matches: 572, Mismatches: 6, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
8 3 0.01
9 562 0.98
10 4 0.01
11 3 0.01
ACGTcount: A:0.22, C:0.11, G:0.32, T:0.34
Consensus pattern (9 bp):
AATTCGGGT
Found at i:12609272 original size:18 final size:16
Alignment explanation
Indices: 12609262--12609306 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
12609252 TTTGAGTTGA
12609262 GAAAATTATTTAATTG
1 GAAAATTATTTAATTG
*
12609278 GAAAATTAATTAATT-
1 GAAAATTATTTAATTG
12609293 -AAAATTAATTTAAT
1 GAAAATT-ATTTAAT
12609307 AAATAATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (16 bp):
GAAAATTATTTAATTG
Found at i:12618496 original size:22 final size:22
Alignment explanation
Indices: 12618471--12618538 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
12618461 ATAAATTGCT
12618471 AGAAATATGTGGATAAACCACC
1 AGAAATATGTGGATAAACCACC
** ** *
12618493 AG-AAT-TGCAGATAAACTGCT
1 AGAAATATGTGGATAAACCACC
*
12618513 AGAAATATGTGGATAAACCATC
1 AGAAATATGTGGATAAACCACC
12618535 AGAA
1 AGAA
12618539 TTGCAGATAA
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 15 0.45
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (22 bp):
AGAAATATGTGGATAAACCACC
Found at i:12618506 original size:42 final size:42
Alignment explanation
Indices: 12618459--12618553 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
12618449 AAGTATTTGT
*
12618459 AGATAAATTGCTAGAAATATGTGGATAAACCACCAGAATTGC
1 AGATAAACTGCTAGAAATATGTGGATAAACCACCAGAATTGC
*
12618501 AGATAAACTGCTAGAAATATGTGGATAAACCATCAGAATTGC
1 AGATAAACTGCTAGAAATATGTGGATAAACCACCAGAATTGC
12618543 AGATAAACTGC
1 AGATAAACTGC
12618554 CATAACTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (42 bp):
AGATAAACTGCTAGAAATATGTGGATAAACCACCAGAATTGC
Found at i:12618507 original size:20 final size:20
Alignment explanation
Indices: 12618482--12618550 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
12618472 GAAATATGTG
12618482 GATAAACCACCAGAATTGCA
1 GATAAACCACCAGAATTGCA
** * **
12618502 GATAAACTGCTAGAAATATGTG
1 GATAAACCACCAG-AAT-TGCA
*
12618524 GATAAACCATCAGAATTGCA
1 GATAAACCACCAGAATTGCA
12618544 GATAAAC
1 GATAAAC
12618551 TGCCATAACT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 19 0.53
21 6 0.17
22 11 0.31
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.20
Consensus pattern (20 bp):
GATAAACCACCAGAATTGCA
Found at i:12627269 original size:25 final size:25
Alignment explanation
Indices: 12627241--12627388 Score: 121
Period size: 25 Copynumber: 6.0 Consensus size: 25
12627231 GGATCGGTAT
*
12627241 GCTTTCACGAGCTGTAG-ATTAGTAA
1 GCTTTCACGAGCTG-AGAATCAGTAA
*
12627266 GCTTAT-ACGAGCTGAGAATCGGTAA
1 GCTT-TCACGAGCTGAGAATCAGTAA
* *
12627291 GCTCTCACGAGCT-ACAATCAGTAA
1 GCTTTCACGAGCTGAGAATCAGTAA
*
12627315 GCTCAT-ACGAGCTGAGAATC-GATAA
1 GCT-TTCACGAGCTGAGAATCAG-TAA
* *
12627340 GCTCTCACGAGCT-ACAATCAGTAA
1 GCTTTCACGAGCTGAGAATCAGTAA
* *
12627364 GCTCAT-ACGAGCTGAGAATCGGTAA
1 GCT-TTCACGAGCTGAGAATCAGTAA
12627389 TCCCTAATGA
Statistics
Matches: 101, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
24 42 0.42
25 58 0.57
26 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (25 bp):
GCTTTCACGAGCTGAGAATCAGTAA
Found at i:12627314 original size:24 final size:25
Alignment explanation
Indices: 12627261--12627388 Score: 140
Period size: 25 Copynumber: 5.2 Consensus size: 25
12627251 GCTGTAGATT
* *
12627261 AGTAAGCTTATACGAGCTGAGAATC
1 AGTAAGCTCATACGAGCTGACAATC
*
12627286 GGTAAGCTC-TCACGAGCT-ACAATC
1 AGTAAGCTCAT-ACGAGCTGACAATC
*
12627310 AGTAAGCTCATACGAGCTGAGAATC
1 AGTAAGCTCATACGAGCTGACAATC
12627335 -GATAAGCTC-TCACGAGCT-ACAATC
1 AG-TAAGCTCAT-ACGAGCTGACAATC
*
12627359 AGTAAGCTCATACGAGCTGAGAATC
1 AGTAAGCTCATACGAGCTGACAATC
*
12627384 GGTAA
1 AGTAA
12627389 TCCCTAATGA
Statistics
Matches: 87, Mismatches: 8, Indels: 16
0.78 0.07 0.14
Matches are distributed among these distances:
24 42 0.48
25 45 0.52
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (25 bp):
AGTAAGCTCATACGAGCTGACAATC
Found at i:12627328 original size:49 final size:49
Alignment explanation
Indices: 12627216--12627388 Score: 249
Period size: 49 Copynumber: 3.5 Consensus size: 49
12627206 GTACATGTAT
* * * ** *
12627216 GCTCATACGAGCT-ATGGATCGGTATGCTTTCACGAGCTGTAGATTAGTAA
1 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCTACA-ATCAGTAA
*
12627266 GCTTATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTACAATCAGTAA
1 GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTACAATCAGTAA
*
12627315 GCTCATACGAGCTGAGAATCGATAAGCTCTCACGAGCTACAATCAGTAA
1 GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTACAATCAGTAA
12627364 GCTCATACGAGCTGAGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
12627389 TCCCTAATGA
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 78 0.70
50 33 0.29
51 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (49 bp):
GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTACAATCAGTAA
Found at i:12628663 original size:19 final size:19
Alignment explanation
Indices: 12628639--12628679 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12628629 AATCAACCAG
12628639 TAAACACAAGCCATAAATC
1 TAAACACAAGCCATAAATC
*
12628658 TAAACACAAGCCATAATTC
1 TAAACACAAGCCATAAATC
12628677 TAA
1 TAA
12628680 GCGTTTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (19 bp):
TAAACACAAGCCATAAATC
Found at i:12633351 original size:20 final size:19
Alignment explanation
Indices: 12633326--12633399 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
12633316 TACCTCTGAA
*
12633326 TTGCACATTGGTGCCCTTG
1 TTGCACATTTGTGCCCTTG
* *
12633345 TTTGCAC-TTCAGTGCCCCTG
1 -TTGCACATT-TGTGCCCTTG
**
12633365 AAGCACATTTGTGCCCTTG
1 TTGCACATTTGTGCCCTTG
12633384 ATTGCACATTTGTGCC
1 -TTGCACATTTGTGCC
12633400 TCTATAAGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 14 0.33
20 29 0.67
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (19 bp):
TTGCACATTTGTGCCCTTG
Found at i:12633378 original size:19 final size:20
Alignment explanation
Indices: 12633356--12633425 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
12633346 TTGCACTTCA
12633356 GTGCCCCTGA-AGCACATTT
1 GTGCCCCTGATAGCACATTT
* *
12633375 GTGCCCTTGATTGCACATTT
1 GTGCCCCTGATAGCACATTT
* *
12633395 GTGCCTCT-ATAAGCAC-TTCG
1 GTGCCCCTGAT-AGCACATT-T
12633415 GTGCCCCTGAT
1 GTGCCCCTGAT
12633426 TATACACTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 13 0.32
20 25 0.62
21 2 0.05
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.31
Consensus pattern (20 bp):
GTGCCCCTGATAGCACATTT
Found at i:12634337 original size:17 final size:18
Alignment explanation
Indices: 12634315--12634348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12634305 GTGTGACCCC
*
12634315 TATTTT-CCAAATTTTCA
1 TATTTTGCCAAAATTTCA
12634332 TATTTTGCCAAAATTTC
1 TATTTTGCCAAAATTTC
12634349 TTAATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTTGCCAAAATTTCA
Found at i:12640196 original size:23 final size:23
Alignment explanation
Indices: 12640170--12640223 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
12640160 ATATGCACAA
* *
12640170 AAGTGCTAGAATA-AGTTGCATTG
1 AAGTGCCAGAATATA-TTGCACTG
12640193 AAGTGCCAGAATATATTGCACTG
1 AAGTGCCAGAATATATTGCACTG
12640216 AAGTGCCA
1 AAGTGCCA
12640224 AAATGCTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (23 bp):
AAGTGCCAGAATATATTGCACTG
Found at i:12643019 original size:22 final size:21
Alignment explanation
Indices: 12642977--12643019 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
12642967 TACATTTTTT
*
12642977 TAATTTAAAATGTTAAAATAA
1 TAATTTAAAATGTAAAAATAA
12642998 TAATATTAAAA-GTAAAACATAA
1 TAAT-TTAAAATGTAAAA-ATAA
12643020 GTTAAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
TAATTTAAAATGTAAAAATAA
Found at i:12644222 original size:44 final size:44
Alignment explanation
Indices: 12644155--12644256 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
12644145 TATTCTCTGA
* **
12644155 AGCTTGAGTGAGCAGCATCGTGTATTTGTTAATGTCCTTTTGTT
1 AGCTTGTGTGAGCAGCATCGTGTATCCGTTAATGTCCTTTTGTT
* *
12644199 AGCTTTTGTGAGCAGCATTGTGTATCCGTTAATGTCCTTTTGTT
1 AGCTTGTGTGAGCAGCATCGTGTATCCGTTAATGTCCTTTTGTT
*
12644243 ATCTTGTGTGAGCA
1 AGCTTGTGTGAGCA
12644257 TTACCCTCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (44 bp):
AGCTTGTGTGAGCAGCATCGTGTATCCGTTAATGTCCTTTTGTT
Found at i:12646494 original size:20 final size:20
Alignment explanation
Indices: 12646469--12646510 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12646459 GAATCCGGTG
12646469 TCATTTTTTTAATCTATTAA
1 TCATTTTTTTAATCTATTAA
12646489 TCATTTTTTTAATCTATTAA
1 TCATTTTTTTAATCTATTAA
12646509 TC
1 TC
12646511 TTCTATCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
TCATTTTTTTAATCTATTAA
Found at i:12647569 original size:11 final size:11
Alignment explanation
Indices: 12647553--12647595 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
12647543 ATTTTGCATA
12647553 AAAATGATTTT
1 AAAATGATTTT
12647564 AAAATGATTTT
1 AAAATGATTTT
* *
12647575 AAACTTATTTT
1 AAAATGATTTT
*
12647586 AACATGATTT
1 AAAATGATTT
12647596 AGAGGTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
AAAATGATTTT
Found at i:12654847 original size:60 final size:60
Alignment explanation
Indices: 12654779--12654897 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
12654769 GAACAAGGAA
** * * * *
12654779 TGCCAAGGCCTCCATTTGGTGTGGGTAGCTCCTCAAATGTTGTTGCTAATGGCTTGGGGT
1 TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTAATGGATTGGGGT
*
12654839 TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTTATGGATTGGGG
1 TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTAATGGATTGGGG
12654898 CTACCAAGCC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (60 bp):
TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTAATGGATTGGGGT
Found at i:12655142 original size:120 final size:120
Alignment explanation
Indices: 12654928--12655145 Score: 276
Period size: 120 Copynumber: 1.8 Consensus size: 120
12654918 TGAGGGTAGC
* * * *
12654928 GTTGTTGATCACTTAGGGCTACCAATGCCTTCATTTGGTGAGGGTAGCTCCTTAAATGTTGCTTC
1 GTTGTTGATCACTTAGGGCTACCAAGGCCTCCATTTGGGGAGGGTAGCTCCTCAAATGTTGCTTC
* * * **
12654993 TGATCACTTAGGATTACCAAGGCTTCCATTTGGTGAAGGTCGCTCCTCAAATATT
66 TGATCACTTAGGACTACAAAGACCACCATTTGGTGAAGGTCGCTCCTCAAATATT
* * * *
12655048 GTTGTTGATCATTTGGGGCTACCAGGGCCTCCGTTTGGGGAGGGTAGCTCCTCAAATGTTG-TTG
1 GTTGTTGATCACTTAGGGCTACCAAGGCCTCCATTTGGGGAGGGTAGCTCCTCAAATGTTGCTT-
* * *
12655112 TTGATCACTTGGGGCTACAAAGACCACCATTTGG
65 CTGATCACTTAGGACTACAAAGACCACCATTTGG
12655146 CGGTAGTTCA
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
119 2 0.02
120 79 0.98
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (120 bp):
GTTGTTGATCACTTAGGGCTACCAAGGCCTCCATTTGGGGAGGGTAGCTCCTCAAATGTTGCTTC
TGATCACTTAGGACTACAAAGACCACCATTTGGTGAAGGTCGCTCCTCAAATATT
Found at i:12655145 original size:60 final size:60
Alignment explanation
Indices: 12654928--12655145 Score: 231
Period size: 60 Copynumber: 3.6 Consensus size: 60
12654918 TGAGGGTAGC
* * * *
12654928 GTTGTTGATCACTTAGGGCTACCAATGCCTTCATTTGGTGAGGGTAGCTCCTTAAATGTT
1 GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT
* ** * * * * *
12654988 GCTT-CTGATCACTTAGGATTACCAAGGCTTCCATTTGGTGAAGGTCGCTCCTCAAATATT
1 G-TTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT
* * * * * *
12655048 GTTGTTGATCATTTGGGGCTACCAGGGCCTCCGTTTGGGGAGGGTAGCTCCTCAAATGTT
1 GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT
* * *
12655108 GTTGTTGATCACTTGGGGCTACAAAGACCACCATTTGG
1 GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGG
12655146 CGGTAGTTCA
Statistics
Matches: 128, Mismatches: 28, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 2 0.02
60 124 0.97
61 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (60 bp):
GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT
Found at i:12661064 original size:20 final size:21
Alignment explanation
Indices: 12661026--12661066 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12661016 AAAATATATT
*
12661026 TCAAAAAAATAATATTAAAAA
1 TCAAAAAAATAATAATAAAAA
12661047 TCAAAAAAATAA-AATAAAAA
1 TCAAAAAAATAATAATAAAAA
12661067 GATAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
TCAAAAAAATAATAATAAAAA
Found at i:12664156 original size:14 final size:14
Alignment explanation
Indices: 12664139--12664171 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12664129 AAAAAATATT
*
12664139 TAAAATCAAATAAA
1 TAAAATAAAATAAA
12664153 TAAAATAAAATAAA
1 TAAAATAAAATAAA
12664167 TAAAA
1 TAAAA
12664172 AGATAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:12672379 original size:37 final size:38
Alignment explanation
Indices: 12672337--12672418 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
12672327 CATGGTGTGT
* *
12672337 AGGGTGGATGGACCTAACAT-GGTCCTATGTGGTGTAC
1 AGGGTGGATGGACCTAACATAGCTCATATGTGGTGTAC
* * *
12672374 AGGGTGGATGGACTTGATATAGCTCATATGTGGTGTAC
1 AGGGTGGATGGACCTAACATAGCTCATATGTGGTGTAC
*
12672412 AAGGTGG
1 AGGGTGG
12672419 TCGAAGTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
37 17 0.45
38 21 0.55
ACGTcount: A:0.23, C:0.12, G:0.37, T:0.28
Consensus pattern (38 bp):
AGGGTGGATGGACCTAACATAGCTCATATGTGGTGTAC
Found at i:12677563 original size:63 final size:63
Alignment explanation
Indices: 12677394--12677585 Score: 206
Period size: 63 Copynumber: 3.1 Consensus size: 63
12677384 TGCAGGGTTC
* * * * *
12677394 ACACGGGCGTGTGTCTAGGCCACGTGACTCACTGTTGTGA-TTAGAGATCACAAGGGACAAGG
1 ACACGGGCGTGTGTCCAGGCCATGTGACTCACTGTTGTGATTTAGAGAACACAAGGGCCAAAG
* * * * * * *
12677456 ACATGGGCGTGTGTCCAGGCCATGCGAATCACTATCGTGTTTTAGAGAACACACGGGCCAAAG
1 ACACGGGCGTGTGTCCAGGCCATGTGACTCACTGTTGTGATTTAGAGAACACAAGGGCCAAAG
* * * * * * *
12677519 ACACGGGCATGTGTCCGGGCCATGTGACTCACTGTTATGATTTAGAGACCACATGGGCTAGAG
1 ACACGGGCGTGTGTCCAGGCCATGTGACTCACTGTTGTGATTTAGAGAACACAAGGGCCAAAG
12677582 ACAC
1 ACAC
12677586 AAGCATGTTT
Statistics
Matches: 104, Mismatches: 25, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
62 32 0.31
63 72 0.69
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (63 bp):
ACACGGGCGTGTGTCCAGGCCATGTGACTCACTGTTGTGATTTAGAGAACACAAGGGCCAAAG
Found at i:12683206 original size:63 final size:62
Alignment explanation
Indices: 12683035--12683226 Score: 224
Period size: 63 Copynumber: 3.0 Consensus size: 62
12683025 ACCATTGTCG
* * * *
12683035 TGTGTCCAGGCCGTGTGACTCACTGTTGTGATTCAGAGACCACACAAGCTAGAGACACGGGCG
1 TGTGTCCAGGCCGTGTGACTCACTGTTGTGATTTAGAGACCACAC-GGCCAGAGACACGGGCA
* * * * *
12683098 TGTGTACAAGCCGTGTGACTCATTGTTGTGATTTAGAGGCCACACGGGCCAGAGACACTGGCA
1 TGTGTCCAGGCCGTGTGACTCACTGTTGTGATTTAGAGACCACAC-GGCCAGAGACACGGGCA
* * * *
12683161 TGTGTCCGGGCTGTGTGACTCACTGTTTGTGATTTAG-GACCACACGGCCAGACAACACGGGTA
1 TGTGTCCAGGCCGTGTGACTCACTG-TTGTGATTTAGAGACCACACGGCCAGA-GACACGGGCA
12683224 TGT
1 TGT
12683227 AGGTCAGGGT
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
62 7 0.06
63 90 0.83
64 11 0.10
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.24
Consensus pattern (62 bp):
TGTGTCCAGGCCGTGTGACTCACTGTTGTGATTTAGAGACCACACGGCCAGAGACACGGGCA
Found at i:12687421 original size:3 final size:3
Alignment explanation
Indices: 12687413--12687437 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12687403 TTGATGCAAA
12687413 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
12687438 TGGTAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12692692 original size:40 final size:40
Alignment explanation
Indices: 12692604--12692693 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 40
12692594 CGAGATTTGA
* *
12692604 ACTTCGGTGCCTCTGTATACACTTTAGTGTCCTTGTTCGC
1 ACTTCGGTGCCTCTGTATACACTTTAGTGCCCTTGTTCAC
** * *
12692644 ACCACGGTGCCTCTGTTTGCACATTT-GTGCCCTTG-TCTAC
1 ACTTCGGTGCCTCTGTATACAC-TTTAGTGCCCTTGTTC-AC
12692684 ACTTCGGTGC
1 ACTTCGGTGC
12692694 TCTTCTTATG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
39 2 0.05
40 35 0.88
41 3 0.08
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.37
Consensus pattern (40 bp):
ACTTCGGTGCCTCTGTATACACTTTAGTGCCCTTGTTCAC
Found at i:12699090 original size:43 final size:42
Alignment explanation
Indices: 12698977--12699096 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 42
12698967 GCCCTACAGT
*
12698977 ATGTTATGCAATCCATGTTATAATTTCA-GCAAGCTTTGCAAA
1 ATGTTATGCAAT-CATGTTATAATTTCATGCAAGCGTTGCAAA
* * * * **
12699019 ATGTTATGTGAACCATGTTATAAATTCATGCTAGCGTTGCAGC
1 ATGTTATG-CAATCATGTTATAATTTCATGCAAGCGTTGCAAA
* *
12699062 ATGTTATGCAAATCATGTTATATTTTCATTCAAGC
1 ATGTTATGC-AATCATGTTATAATTTCATGCAAGC
12699097 TTTGTGGTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
42 22 0.35
43 40 0.65
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (42 bp):
ATGTTATGCAATCATGTTATAATTTCATGCAAGCGTTGCAAA
Found at i:12699309 original size:25 final size:25
Alignment explanation
Indices: 12699265--12699387 Score: 120
Period size: 25 Copynumber: 4.9 Consensus size: 25
12699255 GCGAATATGT
* * *
12699265 TATGTTGATTGATATGTGAACATGT
1 TATGTTGAATGATATATGAACATGC
* * *
12699290 TATGTTGAATAATGTATGAACATGA
1 TATGTTGAATGATATATGAACATGC
* *
12699315 TAGGTTGAATGATATGTGAACATGC
1 TATGTTGAATGATATATGAACATGC
* ***
12699340 TAGGTTGAATGATATGCAAACATGC
1 TATGTTGAATGATATATGAACATGC
* *
12699365 TATGTTGAATGATGTACGAACAT
1 TATGTTGAATGATATATGAACAT
12699388 ATATTAAATG
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 82 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (25 bp):
TATGTTGAATGATATATGAACATGC
Found at i:12699362 original size:75 final size:72
Alignment explanation
Indices: 12699251--12699407 Score: 188
Period size: 75 Copynumber: 2.1 Consensus size: 72
12699241 TACCTTGTTT
* * * * ** * *
12699251 ATATGCGAATATGTTATGTTGATTGATATGTGAACATGTTATGTTGAATAATGTATGAACATGAT
1 ATATGCGAACATGCTAGGTTGAATGATATGCAAACATGCTATGTTGAATAATGTACGAACAT-AT
*
12699316 AGGTTGAATG
65 A--TTAAATG
* *
12699326 ATATGTGAACATGCTAGGTTGAATGATATGCAAACATGCTATGTTGAATGATGTACGAACATATA
1 ATATGCGAACATGCTAGGTTGAATGATATGCAAACATGCTATGTTGAATAATGTACGAACATATA
12699391 TTAAATG
66 TTAAATG
12699398 ATATGCGAAC
1 ATATGCGAAC
12699408 CCTCACATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
72 15 0.21
74 3 0.04
75 52 0.74
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (72 bp):
ATATGCGAACATGCTAGGTTGAATGATATGCAAACATGCTATGTTGAATAATGTACGAACATATA
TTAAATG
Found at i:12699596 original size:16 final size:16
Alignment explanation
Indices: 12699575--12699606 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12699565 GTGAACCTAC
12699575 CCATAGTGCGAACCCT
1 CCATAGTGCGAACCCT
*
12699591 CCATAGTGTGAACCCT
1 CCATAGTGCGAACCCT
12699607 TTGTGCGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (16 bp):
CCATAGTGCGAACCCT
Found at i:12699891 original size:22 final size:22
Alignment explanation
Indices: 12699857--12699996 Score: 84
Period size: 22 Copynumber: 6.2 Consensus size: 22
12699847 TTACATTAAA
* *
12699857 GTGACATGTGAACCTATGCTAT
1 GTGATATGCGAACCTATGCTAT
* *
12699879 GTGATATGCGAACCTATGTTTAA
1 GTGATATGCGAACCTATG-CTAT
* * * *
12699902 GTGAAATGCGAATCTAAGTTAT
1 GTGATATGCGAACCTATGCTAT
* * * * *
12699924 ATGGTATGCAAACTTATGCTAAA
1 GTGATATGCGAACCTATGCT-AT
* * *
12699947 GTGATATGTGAACCTAAGTTAT
1 GTGATATGCGAACCTATGCTAT
*
12699969 GTGGTATGCGAA-CTATGACTTAT
1 GTGATATGCGAACCTATG-C-TAT
12699992 GTGAT
1 GTGAT
12699997 CTATGGCATG
Statistics
Matches: 84, Mismatches: 30, Indels: 7
0.69 0.25 0.06
Matches are distributed among these distances:
21 4 0.05
22 42 0.50
23 38 0.45
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (22 bp):
GTGATATGCGAACCTATGCTAT
Found at i:12699904 original size:45 final size:45
Alignment explanation
Indices: 12699832--12699985 Score: 157
Period size: 45 Copynumber: 3.4 Consensus size: 45
12699822 TTTGACTTCC
* ** * * *
12699832 ATGTGATATGCGAACTTACATTAAAGTGACATGTGAACCTATGCT
1 ATGTGATATGCGAACCTATGTTAAAGTGAAATGTGAACCTAAGTT
* * *
12699877 ATGTGATATGCGAACCTATGTTTAAGTGAAATGCGAATCTAAGTT
1 ATGTGATATGCGAACCTATGTTAAAGTGAAATGTGAACCTAAGTT
* * * * * *
12699922 ATATGGTATGCAAACTTATGCTAAAGTGATATGTGAACCTAAGTT
1 ATGTGATATGCGAACCTATGTTAAAGTGAAATGTGAACCTAAGTT
*
12699967 ATGTGGTATGCGAA-CTATG
1 ATGTGATATGCGAACCTATG
12699986 ACTTATGTGA
Statistics
Matches: 88, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 4 0.05
45 84 0.95
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (45 bp):
ATGTGATATGCGAACCTATGTTAAAGTGAAATGTGAACCTAAGTT
Found at i:12700572 original size:17 final size:17
Alignment explanation
Indices: 12700552--12700594 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
12700542 TTATGGTGTA
* *
12700552 GTATGAATTGTTATTTT
1 GTATGAATTGCTATTTG
12700569 GTATGAATTGCTATTTG
1 GTATGAATTGCTATTTG
*
12700586 GTATAAATT
1 GTATGAATT
12700595 ATTGTCTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (17 bp):
GTATGAATTGCTATTTG
Found at i:12702760 original size:53 final size:52
Alignment explanation
Indices: 12702697--12702836 Score: 196
Period size: 50 Copynumber: 2.7 Consensus size: 52
12702687 TACTGGTTCA
** *
12702697 CATAGTAGCCTGCACACGGTACTACACATGTGACCATTTTCA-TCCGATACACG
1 CATAGTAGCCTGCACATAGTACTACACATGTGACC--TATCATTCCGATACACG
*
12702750 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACACG
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCTATCATTCCGATACACG
*
12702802 --TAGTAGCCTGCACATAGTACTACACACGTGACCTA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCTA
12702837 GCAACTTCAC
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
50 33 0.41
51 4 0.05
52 11 0.14
53 32 0.40
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (52 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCTATCATTCCGATACACG
Found at i:12706014 original size:49 final size:48
Alignment explanation
Indices: 12705958--12706103 Score: 211
Period size: 49 Copynumber: 3.0 Consensus size: 48
12705948 TTTATTTTCT
*
12705958 CGATGCCATAGTCCAACTATTGTCTTACACGTAATCACATATCACATAC
1 CGATGCCATAG-CCAACTATGGTCTTACACGTAATCACATATCACATAC
* * *
12706007 CGATGCCATAGCTCAGCTATGGTCTTACACGTAATCACACATCATATAC
1 CGATGCCATAGC-CAACTATGGTCTTACACGTAATCACATATCACATAC
*
12706056 CGATGCCATAGCCCAACTATGGTCTTACACGGAATCACATTATCACAT
1 CGATGCCATAG-CCAACTATGGTCTTACACGTAATCACA-TATCACAT
12706104 TTTCACATGT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
48 1 0.01
49 78 0.91
50 7 0.08
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (48 bp):
CGATGCCATAGCCAACTATGGTCTTACACGTAATCACATATCACATAC
Found at i:12708742 original size:12 final size:13
Alignment explanation
Indices: 12708712--12708744 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
12708702 AGCTCTCCGG
12708712 TACACATAGTAGCC
1 TACACATAGTA-CC
12708726 TACACATAGTA-C
1 TACACATAGTACC
12708738 TACACAT
1 TACACAT
12708745 GCGACCTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:12708782 original size:50 final size:50
Alignment explanation
Indices: 12708616--12708802 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
12708606 CTAGTTCACA
* * * * * **
12708616 TAGTAGCCTGCACATGGTACTACACATGTGACCATTTTAATCCGATACGTG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTACACG
* ** * *
12708667 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TCTCCGGTACACA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCTATCAT-TCCGGTACACG
* *
12708718 TAGTAGCCTACACATAGTACTACACATGCGACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCTATCATTCCGGTACACG
*
12708768 TAGTAGCCTGCACATAGTACTACACAAGTGACCTA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCTA
12708803 GAAACTTCAC
Statistics
Matches: 111, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 45 0.41
51 65 0.59
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCTATCATTCCGGTACACG
Found at i:12708820 original size:102 final size:102
Alignment explanation
Indices: 12708609--12708833 Score: 267
Period size: 102 Copynumber: 2.2 Consensus size: 102
12708599 AATGATACTA
* * * * * **
12708609 GTTCACATAGTAGCCTGCACATGGTACTACACATGTGACCATTTTAATCCGATACGTGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATATCAATCCGATACACGTAGTAGC
* * *
12708674 CTGCACATAGTACTACACACGTGATCGAAGCTCTCCG
66 CTGCACATAGTACTACACAAGTGATAGAAACTCTCCG
* * *
12708711 GTACACATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATATCAATCCGATACACGTAGTAGC
12708775 CTGCACATAGTACTACACAAGTGACCTAGAAACT-TCAC-
66 CTGCACATAGTACTACACAAGTGA--TAGAAACTCTC-CG
* *
12708813 TTTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTACACA
12708834 CAGTCCATGC
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
101 41 0.39
102 56 0.54
103 7 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (102 bp):
GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATATCAATCCGATACACGTAGTAGC
CTGCACATAGTACTACACAAGTGATAGAAACTCTCCG
Found at i:12711086 original size:13 final size:13
Alignment explanation
Indices: 12711068--12711092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12711058 TAATCATTGC
12711068 ATAATTTAATCAT
1 ATAATTTAATCAT
12711081 ATAATTTAATCA
1 ATAATTTAATCA
12711093 AAATTAAACC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTAATCAT
Found at i:12714070 original size:22 final size:22
Alignment explanation
Indices: 12714045--12714088 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12714035 ACAAAAATCA
* *
12714045 ATCAATCATGTATACTTACCAT
1 ATCAATCATGCATACATACCAT
12714067 ATCAATCATGCATACATACCAT
1 ATCAATCATGCATACATACCAT
12714089 TTAAACCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (22 bp):
ATCAATCATGCATACATACCAT
Found at i:12717449 original size:42 final size:41
Alignment explanation
Indices: 12717391--12717506 Score: 128
Period size: 40 Copynumber: 2.8 Consensus size: 41
12717381 TAGATGTTAC
* *
12717391 TTAGTATTATTGTTAGTAAAAAACTAGTATTATTATT-ATGG
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATTATTGATAG
** *
12717432 TTAGTTATTATTTTTAGTAAAACCCTA-ATTATTATTGTTAG
1 TTAG-TATTATTTTTAGTAAAAAACTATATTATTATTGATAG
* *
12717473 TTAGTATTATTTTGAGTATAAAACTATTATTATT
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATT
12717507 GTGTTAGTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 27 0.44
41 10 0.16
42 25 0.40
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.50
Consensus pattern (41 bp):
TTAGTATTATTTTTAGTAAAAAACTATATTATTATTGATAG
Found at i:12717463 original size:37 final size:36
Alignment explanation
Indices: 12717421--12717519 Score: 101
Period size: 40 Copynumber: 2.6 Consensus size: 36
12717411 AAACTAGTAT
* *
12717421 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATGGTTAGTTATTATTTTGAGTATAAA-AC
*
12717457 TAATTATTATTGTTAGTTAGTATTATTTTGAGTATAAAAC
1 T-ATTATTATGGTTAG-T--TATTATTTTGAGTATAAAAC
12717497 TATTATTATTGTGTTAGTTATTA
1 TATTATTA-TG-GTTAGTTATTA
12717520 GGGTTAGTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
36 1 0.02
37 13 0.25
38 6 0.12
39 7 0.13
40 17 0.33
41 8 0.15
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (36 bp):
TATTATTATGGTTAGTTATTATTTTGAGTATAAAAC
Found at i:12719236 original size:18 final size:18
Alignment explanation
Indices: 12719213--12719248 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12719203 TGGAGTCTTG
12719213 GGAATTCTTCCTCACTAA
1 GGAATTCTTCCTCACTAA
12719231 GGAATTCTTCCTCACTAA
1 GGAATTCTTCCTCACTAA
12719249 CCTGTAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (18 bp):
GGAATTCTTCCTCACTAA
Found at i:12722306 original size:43 final size:43
Alignment explanation
Indices: 12722251--12722486 Score: 357
Period size: 43 Copynumber: 5.5 Consensus size: 43
12722241 CCGCTAAAAG
*
12722251 TCATGACCTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGA
* * *
12722294 TCATGAATTTTAGCGACGC-TCTTCCCACAAACGCCACTATAGA
1 TCATGACTTTTAGCGGCGCTTC-TCCCACAAACGCCGCTATAGA
* * *
12722337 TCATGACTTTTAGTGGCGCTTCTCCCACAAACGGCGCTATACA
1 TCATGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGA
* *
12722380 TCATGACTTTTAGCGGCGCTTCTCCCATAAACGCCACTATAGA
1 TCATGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGA
* *
12722423 TCATGACTTTTAGCGGCACTTCTCCCATAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGA
12722466 TCATGACTTTTAGCGGCGCTT
1 TCATGACTTTTAGCGGCGCTT
12722487 TTTTATAGAC
Statistics
Matches: 173, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 2 0.01
43 169 0.98
44 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.28
Consensus pattern (43 bp):
TCATGACTTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGA
Found at i:12722541 original size:42 final size:42
Alignment explanation
Indices: 12722451--12722535 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 42
12722441 CTTCTCCCAT
* * * *
12722451 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTTAT
1 AAACGCCGCTAAAGAACACGACTTTTAGCGGCGCTTTTTTAA
* *
12722493 AGACGCCGCTAAAGAACACGAC-TTTAGTGGCG-TTTTTTAA
1 AAACGCCGCTAAAGAACACGACTTTTAGCGGCGCTTTTTTAA
12722533 AAA
1 AAA
12722536 AACGCCACTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 9 0.25
41 9 0.25
42 18 0.50
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACACGACTTTTAGCGGCGCTTTTTTAA
Found at i:12722983 original size:86 final size:87
Alignment explanation
Indices: 12722836--12723033 Score: 272
Period size: 86 Copynumber: 2.3 Consensus size: 87
12722826 CCTCTGCTCT
* * *
12722836 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCGCTGCTGCATCAACTTTAAGTTGTAGCTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTGCTTCTCTCGCTGCTGCATCAACTTTAAGTTGTAGCTGGAGTTC
12722901 TTCATATTTTCTTTAAACCTCA
66 TTCATATTTTCTTTAAACCTCA
* * * ** *
12722923 TCTTCTCTCGATGTTGCCTCTGCTTC-CTCGTTGCTGCATCTGCTTTAAGTTGTAGTTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTGCTTCTCTCGCTGCTGCATCAACTTTAAGTTGTAGCTGGAGTTC
**
12722987 TTCATATTTTCTTTGGACCTCA
66 TTCATATTTTCTTTAAACCTCA
* *
12723009 GCTTCTCTTGATGCTGCCTCCGCTT
1 GCTTCTCTCGATGCTGCCTCTGCTT
12723034 TAAGTTGAGT
Statistics
Matches: 96, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
86 75 0.78
87 21 0.22
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (87 bp):
GCTTCTCTCGATGCTGCCTCTGCTTCTCTCGCTGCTGCATCAACTTTAAGTTGTAGCTGGAGTTC
TTCATATTTTCTTTAAACCTCA
Found at i:12725352 original size:9 final size:9
Alignment explanation
Indices: 12725295--12725521 Score: 114
Period size: 9 Copynumber: 25.2 Consensus size: 9
12725285 TAAGTATAAT
12725295 TAAGTTATG
1 TAAGTTATG
*
12725304 TAACTTATG
1 TAAGTTATG
* *
12725313 ATAAGAATATA
1 -TAAG-TTATG
12725324 TAA-TTATG
1 TAAGTTATG
12725332 T-A-TTATG
1 TAAGTTATG
*
12725339 CAAGTTATG
1 TAAGTTATG
12725348 TAAGTTATG
1 TAAGTTATG
* *
12725357 ATATGATATATA
1 -TAAG-T-TATG
*
12725369 TAAGTTGT-
1 TAAGTTATG
12725377 TAAGTTATG
1 TAAGTTATG
*
12725386 TAAGTTGTG
1 TAAGTTATG
*
12725395 TGAGTTATG
1 TAAGTTATG
12725404 T-AGATTATG
1 TAAG-TTATG
* * *
12725413 ATATGATACATA
1 -TAAG-T-TATG
12725425 TAAGTTAT-
1 TAAGTTATG
*
12725433 TAAGTTAGG
1 TAAGTTATG
12725442 TAAGTTATG
1 TAAGTTATG
*
12725451 CAAGTTATG
1 TAAGTTATG
*
12725460 CAAGTTATG
1 TAAGTTATG
12725469 TAAGTTATG
1 TAAGTTATG
*
12725478 --A-TATATA
1 TAAGT-TATG
*
12725485 TAAGTTGT-
1 TAAGTTATG
*
12725493 TAACTTATG
1 TAAGTTATG
*
12725502 TAAGTTATA
1 TAAGTTATG
*
12725511 TGAGTTATG
1 TAAGTTATG
12725520 TA
1 TA
12725522 GATTATGATA
Statistics
Matches: 166, Mismatches: 34, Indels: 36
0.70 0.14 0.15
Matches are distributed among these distances:
6 1 0.01
7 10 0.06
8 27 0.16
9 97 0.58
10 13 0.08
11 13 0.08
12 5 0.03
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (9 bp):
TAAGTTATG
Found at i:12725391 original size:47 final size:47
Alignment explanation
Indices: 12725295--12725459 Score: 140
Period size: 56 Copynumber: 3.4 Consensus size: 47
12725285 TAAGTATAAT
* *
12725295 TAAGTTATGTAACTTATGATAAGA-ATATATAA-TTATGT-A-TTATG
1 TAAGTTATGTAAGTTATGATATGATATATATAAGTTAT-TAAGTTATG
* *
12725339 CAAGTTATGTAAGTTATGATATGATATATATAAGTTGTTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATG
* * *
12725386 TAAGTTGTGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGG
1 TAAG-T-TAT--G-TA---AG-TTATGATATGATATATATAAGTTATTAAGTTATG
*
12725442 TAAGTTATGCAAGTTATG
1 TAAGTTATGTAAGTTATG
12725460 CAAGTTATGT
Statistics
Matches: 97, Mismatches: 11, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
44 21 0.22
45 9 0.09
46 4 0.04
47 13 0.13
48 3 0.03
49 2 0.02
51 2 0.02
52 3 0.03
54 2 0.02
55 3 0.03
56 35 0.36
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.42
Consensus pattern (47 bp):
TAAGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATG
Found at i:12725405 original size:56 final size:56
Alignment explanation
Indices: 12725341--12725613 Score: 263
Period size: 56 Copynumber: 4.8 Consensus size: 56
12725331 GTATTATGCA
* * *
12725341 AGTTATGTAAGTTATGATATGATATATATAAGTTGTTAAGTTATGTAAGTTGTGTG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATATG
* * ***
12725397 AGTTATGT-AGATTATGATATGATACATATAAGTTATTAAGTTAGGTAAGTTATGCA
1 AGTTATGTAAG-TTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATATG
* * *
12725453 AGTTATGCAAGTTATGTAAGTTATGATATATATAAGTTGTTAACTTATGTAAGTTATATG
1 AGTTATGTAAGTTATG--A--TATGATATATATAAGTTATTAAGTTATGTAAGTTATATG
* *
12725513 AGTTATGT-AGATTATGATATGATGTATATAAGTTATT-A-TTCA-CTAA-TT-TATG
1 AGTTATGTAAG-TTATGATATGATATATATAAGTTATTAAGTT-ATGTAAGTTATATG
* * * *
12725565 AGATACATTTAAGTTACGGTATGATATATATAAGTTATTAAGTTATGTA
1 AG-T-TATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTA
12725614 GACTATGATA
Statistics
Matches: 179, Mismatches: 24, Indels: 28
0.77 0.10 0.12
Matches are distributed among these distances:
52 6 0.03
53 3 0.02
54 31 0.17
55 8 0.04
56 81 0.45
57 2 0.01
58 2 0.01
59 2 0.01
60 44 0.25
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.43
Consensus pattern (56 bp):
AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATATG
Done.