Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 24 of 52
Found at i:3952131 original size:35 final size:35
Alignment explanation
Indices: 3952085--3952153 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
3952075 ATACATGTAA
*
3952085 GATAACAAAAGGAAAGAATGTCTAAATAAAACTAT
1 GATAACAAAAGGAAAGAATGTCCAAATAAAACTAT
3952120 GATAACAAAAGGAAAGAATGTCCAAATAAAACTA
1 GATAACAAAAGGAAAGAATGTCCAAATAAAACTA
3952154 CGTTGTCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.17
Consensus pattern (35 bp):
GATAACAAAAGGAAAGAATGTCCAAATAAAACTAT
Found at i:3953240 original size:3 final size:3
Alignment explanation
Indices: 3953232--3953277 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3953222 TTCAAATCCT
3953232 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3953278 CTATAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3955596 original size:9 final size:9
Alignment explanation
Indices: 3955582--3955611 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3955572 AGGTTCAACT
3955582 AAAAAAAGA
1 AAAAAAAGA
3955591 AAAAAAAGA
1 AAAAAAAGA
3955600 AAAAATAAGA
1 AAAAA-AAGA
3955610 AA
1 AA
3955612 GTGTAGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:3956020 original size:20 final size:20
Alignment explanation
Indices: 3955995--3956047 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 20
3955985 CTGCCAAGGA
*
3955995 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATAC
3956015 AATGTATCGAT--A-TATAC
1 AATGTATCGATACATTATAC
*
3956032 ATTGTATCGATACATT
1 AATGTATCGATACATT
3956048 GATCTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 14 0.50
18 1 0.04
19 1 0.04
20 12 0.43
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTATAC
Found at i:3957736 original size:9 final size:10
Alignment explanation
Indices: 3957712--3957737 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3957702 CTAGCAGACG
3957712 ATTTTTTCAA
1 ATTTTTTCAA
3957722 ATTTTTTCAA
1 ATTTTTTCAA
3957732 ATTTTT
1 ATTTTT
3957738 AATAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTCAA
Found at i:3960944 original size:27 final size:27
Alignment explanation
Indices: 3960914--3960969 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3960904 CGGGAATACT
* *
3960914 CCCTATTCCTCCGAGGGGATACTCTAA
1 CCCTATTCCTCCGAGGAGATACTCCAA
*
3960941 CCCTATTCCTCTGAGGAGATACTCCAA
1 CCCTATTCCTCCGAGGAGATACTCCAA
3960968 CC
1 CC
3960970 TCACTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (27 bp):
CCCTATTCCTCCGAGGAGATACTCCAA
Found at i:3969312 original size:18 final size:18
Alignment explanation
Indices: 3969285--3969324 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3969275 TCTGTGCCAC
*
3969285 TTGATTTCTTACGATTAG
1 TTGATCTCTTACGATTAG
3969303 TTGATCTCTTACGATTAG
1 TTGATCTCTTACGATTAG
3969321 TTGA
1 TTGA
3969325 ACAAGAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (18 bp):
TTGATCTCTTACGATTAG
Found at i:3972701 original size:19 final size:18
Alignment explanation
Indices: 3972675--3972762 Score: 86
Period size: 19 Copynumber: 4.4 Consensus size: 18
3972665 TATTTGTACA
*
3972675 AAAAAAAACAAAAAAACT
1 AAAAAAAACAAAAAAACC
3972693 AAGAAAAAACAAAAAAACC
1 AA-AAAAAACAAAAAAACC
3972712 AAAAAAAAAAAACAAAAGAAACC
1 ----AAAAAAAACAAAA-AAACC
*
3972735 AAAAACACAAAAAAAAAACC
1 AAAAA-A-AACAAAAAAACC
3972755 AAAAAAAA
1 AAAAAAAA
3972763 AACAAACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
18 4 0.07
19 21 0.35
20 11 0.18
21 6 0.10
22 11 0.18
23 7 0.12
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (18 bp):
AAAAAAAACAAAAAAACC
Found at i:3972709 original size:31 final size:29
Alignment explanation
Indices: 3972674--3972777 Score: 86
Period size: 32 Copynumber: 3.5 Consensus size: 29
3972664 TTATTTGTAC
3972674 AAAAAAAAACAAAAAAACTAAGAAAAAACAA
1 AAAAAAAAACAAAAAAAC-AA-AAAAAACAA
* *
3972705 AAAAACCAAAAAAAAAAAACAAAAGAAACCAA
1 AAAAA--AAAACAAAAAAACAAAA-AAAACAA
* * *
3972737 AAACACAAA-AAAAAAACCAAAAAAA-AA
1 AAAAAAAAACAAAAAAACAAAAAAAACAA
* *
3972764 ACAAACAAACAAAA
1 AAAAAAAAACAAAA
3972778 CAGAAGTGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 9 0.15
28 7 0.11
29 11 0.18
30 3 0.05
31 7 0.11
32 12 0.20
33 12 0.20
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (29 bp):
AAAAAAAAACAAAAAAACAAAAAAAACAA
Found at i:3972719 original size:13 final size:13
Alignment explanation
Indices: 3972674--3972779 Score: 90
Period size: 13 Copynumber: 7.8 Consensus size: 13
3972664 TTATTTGTAC
3972674 AAAAAAAAACAAA
1 AAAAAAAAACAAA
3972687 AAAACTAAGAAA-AAA
1 AAAA--AA-AAACAAA
* *
3972702 CAAAAAAACCAAA
1 AAAAAAAAACAAA
3972715 AAAAAAAAACAAA
1 AAAAAAAAACAAA
*
3972728 AGAAACCAAAAACACA
1 A-AAA--AAAAACAAA
*
3972744 AAAAAAAAAC-CA
1 AAAAAAAAACAAA
3972756 AAAAAAAAACAAA
1 AAAAAAAAACAAA
* *
3972769 CAAACAAAACA
1 AAAAAAAAACA
3972780 GAAGTGTCTA
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
12 14 0.18
13 37 0.48
14 3 0.04
15 11 0.14
16 12 0.16
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.01
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:3972728 original size:41 final size:43
Alignment explanation
Indices: 3972674--3972778 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 43
3972664 TTATTTGTAC
* *
3972674 AAAAAAAAACAAAAAAACTAAGAAA-A-AACAAAAAAACC-AAA
1 AAAAAAAAACAAAAAAACCAA-AAACACAAAAAAAAAACCAAAA
3972715 AAAAAAAAACAAAAGAAACCAAAAACACAAAAAAAAAACCAAAA
1 AAAAAAAAACAAAA-AAACCAAAAACACAAAAAAAAAACCAAAA
3972759 AAAAAACAAACAAACAAAAC
1 AAAAAA-AAACAAA-AAAAC
3972779 AGAAGTGTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
41 17 0.30
42 7 0.12
43 11 0.20
44 9 0.16
45 11 0.20
46 1 0.02
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.01
Consensus pattern (43 bp):
AAAAAAAAACAAAAAAACCAAAAACACAAAAAAAAAACCAAAA
Found at i:3972738 original size:32 final size:32
Alignment explanation
Indices: 3972674--3972777 Score: 99
Period size: 33 Copynumber: 3.3 Consensus size: 32
3972664 TTATTTGTAC
*
3972674 AAAAA-AAAACAAAAAAACTAAGAAAAAACAA
1 AAAAACAAAAAAAAAAAACTAAGAAAAAACAA
* *
3972705 AAAAACCAAAAAAAAAAAAC-AA-AAGAAAC-C
1 AAAAA-CAAAAAAAAAAAACTAAGAAAAAACAA
* * *
3972735 AAAAACACAAAAAAAAAACCAAAAAAAAAACAA
1 AAAAACA-AAAAAAAAAAACTAAGAAAAAACAA
*
3972768 ACAAACAAAA
1 AAAAACAAAA
3972778 CAGAAGTGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.03
30 16 0.27
31 13 0.22
32 11 0.18
33 18 0.30
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (32 bp):
AAAAACAAAAAAAAAAAACTAAGAAAAAACAA
Found at i:3974104 original size:29 final size:28
Alignment explanation
Indices: 3974071--3974715 Score: 776
Period size: 28 Copynumber: 22.7 Consensus size: 28
3974061 CAATACGACC
*
3974071 CTTTTTAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974099 CTTTTTTAAAGCCCATAAGTCAGTGGCAT
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
*
3974128 CCTTTTAAAAG-CCACAAGTCAGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974156 ATTTTCAAAGCCCACAAGTCAGTAGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974184 CCTTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
3974212 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974240 CCTTTCAAAGCCCACAAGTCAGCGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974268 CCTTTCAAAAGCCCACAAGTTAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
3974297 CCTTTCAAAGCCCACCAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
3974325 CTTTTTTAAAGCCCACAAGTCAGTGGCAT
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
* **
3974354 CTTTTAAAAGCCCATGAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
3974382 CCTTTCAAAAGCCCACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
*
3974411 CTTTTCAAAGCCCACAAGTCGGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974439 CTTTTTAAAGCTCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974467 CCTTTTTAAAGCCCACAAGTTAGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
3974496 CTTTTCAATAGCCCACGAGTCAGTGGCAT
1 CTTTTCAA-AGCCCACAAGTCAGTGGCAT
* *
3974525 CCTTTCAAAAGCCCATAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
3974554 CCTTTCAAAGCCCACAAGTTAGTGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
3974581 CCTTTCAAAGCCCACAAGTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
3974608 CTTTTCAAAAGCCAACAAGTCAGTGGCA-
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
* * ** * *
3974636 CCTTTCAAAAGCCAACAAGTCAACGACAC
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
*
3974665 CTTTTCAAAGCCCACAAGTCAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-T
3974695 CTTTTCAAAGCTCACACAAGT
1 CTTTTCAAAGC-C-CACAAGT
3974716 TGGTGGCACC
Statistics
Matches: 547, Mismatches: 55, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
27 38 0.07
28 297 0.54
29 189 0.35
30 15 0.03
31 1 0.00
32 7 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:3974306 original size:57 final size:56
Alignment explanation
Indices: 3974077--3974715 Score: 784
Period size: 57 Copynumber: 11.2 Consensus size: 56
3974067 GACCCTTTTT
* * * *
3974077 AAAGCCCACAAGTCAGTGGCATCTTTTTTAAAGCCCATAAGTCAGTGGCATCCTTTTA
1 AAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTC
** *
3974135 AAAG-CCACAAGTCAGTGGCATATTTTCAAAGCCCACAAGTCAGTAGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
*
3974190 AAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* *
3974246 AAAGCCCACAAGTCAGCGGCATCCTTTCAAAAGCCCACAAGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * *
3974303 AAAGCCCACCAGTCAGTGGCATCTTTTTTAAAGCCCACAAGTCAGTGGCATCTTTTA
1 AAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
** *
3974360 AAAGCCCATGAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * *
3974417 AAAGCCCACAAGTCGGTGGCATCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTC
* * *
3974474 AAAGCCCACAAGTTAGTGGCATCTTTTCAATAGCCCACGAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAA-AGCCCACAAGTCAGTGGCATCCTTTC
* *
3974531 AAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTC
1 -AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
3974587 AAAGCCCACAAGTCAATGGCA-CTTTTCAAAAGCCAACAAGTCAGTGGCA-CCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTC
* ** * *
3974642 AAAAGCCAACAAGTCAACGACA-CCTTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGC-ATCC-TTTC
3974701 AAAGCTCACACAAGT
1 AAAGC-C-CACAAGT
3974716 TGGTGGCACC
Statistics
Matches: 512, Mismatches: 54, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
54 5 0.01
55 51 0.10
56 168 0.33
57 216 0.42
58 61 0.12
59 5 0.01
60 6 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:3974734 original size:31 final size:30
Alignment explanation
Indices: 3974669--3974756 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
3974659 CGACACCTTT
** **
3974669 TCAAAGCC-CACAAGTCAGTGGCAACCCTTT
1 TCAAAGCCACACAAGTTGGTGGC-ACCCTAG
3974699 TCAAAGCTCACACAAGTTGGTGGCACCCTAG
1 TCAAAGC-CACACAAGTTGGTGGCACCCTAG
*
3974730 TCAAAGACCACACAAATTGGTGGCACC
1 TCAAAG-CCACACAAGTTGGTGGCACC
3974757 TATGTCCGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.14
31 30 0.60
32 13 0.26
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (30 bp):
TCAAAGCCACACAAGTTGGTGGCACCCTAG
Found at i:3976493 original size:12 final size:12
Alignment explanation
Indices: 3976476--3976508 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3976466 TTACACCATG
3976476 ATTATTTTTATT
1 ATTATTTTTATT
*
3976488 ATTATTGTTATT
1 ATTATTTTTATT
3976500 ATTATTTTT
1 ATTATTTTT
3976509 TTCTCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:3977774 original size:79 final size:79
Alignment explanation
Indices: 3977675--3977860 Score: 194
Period size: 79 Copynumber: 2.4 Consensus size: 79
3977665 TGTCCCCTTG
* * * * * * **
3977675 AAAATGACGGGGCTGAAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGGAAAAAAAATTGGGAT
1 AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGGAAAAAAAACCGGGAT
3977739 TGGAGTATCCCCTCA
65 TGGAGTATCCCCTCA
* * * * * *
3977754 AAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTT
1 AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAACCGGGATT
3977819 GGAGTATCCCCTCA
66 GGAGTATCCCCTCA
* ** *
3977833 GAGGTAACTGGGTTGGAGTATCCCCGAT
1 AAAATAACGGGGTTGGAGTATCCCCGAT
3977861 GAAATAACGA
Statistics
Matches: 87, Mismatches: 19, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
78 1 0.01
79 86 0.99
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (79 bp):
AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAACCGGGATT
GGAGTATCCCCTCA
Found at i:3977868 original size:28 final size:27
Alignment explanation
Indices: 3977814--3977888 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
3977804 AATAAAGCCG
* **
3977814 GGGTTGGAGTATCCCCTCA-GAGGTAAC
1 GGGTTGGAGTATCCCC-GATGAAATAAC
3977841 TGGGTTGGAGTATCCCCGATGAAATAAC
1 -GGGTTGGAGTATCCCCGATGAAATAAC
*
3977869 GAGGTTGGAGTATCCTCGAT
1 G-GGTTGGAGTATCCCCGAT
3977889 TGTGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGATGAAATAAC
Found at i:3977942 original size:53 final size:53
Alignment explanation
Indices: 3977874--3978046 Score: 147
Period size: 52 Copynumber: 3.3 Consensus size: 53
3977864 ATAACGAGGT
* *** *
3977874 TGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATTGGAGC
1 TGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTCAAAAATAAAATCGGAGC
* * * *
3977927 TGGAGTGTCCCCGA-T-TAAAGGAAAATTGGTG-TTTCAAAAATAAAATCGGGGT
1 TGGAGTATCCCCGATTGTGAA--AAAATTGGTGTTTTCAAAAATAAAATCGGAGC
* * ** * *
3977979 TGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAATCGGGGT
1 TGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTCAAAAATAAAATCGGAGC
* *
3978031 TTGAGTATCTCCGATT
1 TGGAGTATCCCCGATT
3978047 ATGAGAAATC
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
51 3 0.03
52 67 0.68
53 26 0.27
54 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (53 bp):
TGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTCAAAAATAAAATCGGAGC
Found at i:3977990 original size:52 final size:53
Alignment explanation
Indices: 3977912--3978047 Score: 150
Period size: 52 Copynumber: 2.6 Consensus size: 53
3977902 GTGTTTTTGG
* * * * *
3977912 AAATAAAATTGGAGCTGGAGTGTCCCCGATTAAAGG-AAAATTGGTGTTTCAA
1 AAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTCAA
** * *
3977964 AAATAAAATCGGGGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTGTTTTAG
1 AAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTCAA
* * *
3978016 CAATAAAATCGGGGTTTGAGTATCTCCGATTA
1 AAATAAAATCGGGGTTGGAGTATCCCCGATTA
3978048 TGAGAAATCA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 2 0.03
52 68 0.97
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (53 bp):
AAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTGTTTCAA
Found at i:3978195 original size:55 final size:51
Alignment explanation
Indices: 3978107--3978230 Score: 133
Period size: 51 Copynumber: 2.4 Consensus size: 51
3978097 GATTAACGGG
* * *
3978107 GTTGGAGTATCCCCAATTGTGAAAAATTTGTGTTTTTTTTAAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG----TTTTAAAAATAAAATCGGA
*
3978162 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTAAAAATAAAATCGGA
* * *
3978213 GATGGAATATCCCTGATT
1 GTTGGAGTATCCCCGATT
3978231 GCGGAGAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
51 33 0.54
54 1 0.02
55 27 0.44
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAATCGGA
Found at i:3980047 original size:10 final size:10
Alignment explanation
Indices: 3980034--3980063 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3980024 CAATGGAATA
3980034 GTGTTTTTTT
1 GTGTTTTTTT
3980044 GTGTTTTTTT
1 GTGTTTTTTT
3980054 G-GTTTTTTT
1 GTGTTTTTTT
3980063 G
1 G
3980064 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:3980614 original size:33 final size:33
Alignment explanation
Indices: 3980576--3980642 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3980566 AAAATTTCCA
***
3980576 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3980609 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3980642 A
1 A
3980643 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3980615 original size:13 final size:13
Alignment explanation
Indices: 3980597--3980622 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3980587 ACAAAGATCC
3980597 ATGTATCGATACA
1 ATGTATCGATACA
3980610 ATGTATCGATACA
1 ATGTATCGATACA
3980623 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3980686 original size:19 final size:19
Alignment explanation
Indices: 3980662--3980716 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
3980652 CAGTAGCTAA
*
3980662 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
3980681 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
3980700 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3980717 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:3980805 original size:21 final size:21
Alignment explanation
Indices: 3980779--3980818 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3980769 GGAATGTATC
3980779 ACAAATGTATCGATACATTCT
1 ACAAATGTATCGATACATTCT
3980800 ACAAATGTATCGATACATT
1 ACAAATGTATCGATACATT
3980819 TGAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
ACAAATGTATCGATACATTCT
Found at i:3981661 original size:55 final size:55
Alignment explanation
Indices: 3981577--3982093 Score: 520
Period size: 55 Copynumber: 9.3 Consensus size: 55
3981567 AAAGCGTATT
* *
3981577 CTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTC
*
3981632 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTC
*
3981687 CTGCTCTTT---GA--GG---ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTC
** *
3981734 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTC
* * **
3981789 CTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGG-GATC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG-TC
* * **
3981844 CTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATC
1 CTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTGTC
** * * *
3981905 CTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAATAGGC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG-GT-GTC
** *
3981961 GTCTCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTC
1 --CT-GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG-----GTGTC
** * * *
3982023 CCACTCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTC
3982078 CTGCTCTTTGAGGACT
1 CTGCTCTTTGAGGACT
3982094 AAAAAGCGGA
Statistics
Matches: 401, Mismatches: 34, Indels: 54
0.82 0.07 0.11
Matches are distributed among these distances:
47 41 0.10
50 4 0.01
52 4 0.01
54 4 0.01
55 197 0.49
56 9 0.02
58 2 0.00
59 64 0.16
60 53 0.13
61 21 0.05
62 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTC
Found at i:3981722 original size:102 final size:103
Alignment explanation
Indices: 3981599--3982098 Score: 405
Period size: 102 Copynumber: 4.5 Consensus size: 103
3981589 GACTAAAAAG
*
3981599 TGCCACCAACTCGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAAC
*
3981664 TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGA-G-GA
65 TTGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGACGAGA
*
3981701 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAAC
* * *
3981766 TTGTGTGGGCTTCGAA-AGGGGTCCTGCTCTTTGGGGACTGAAAAA
65 TTGTGTGGGCTT-TAAGAGGCGTCCTGCTCTTT---GAC-G--AGA
** * *
3981811 TGCCACCAACTTGTGTGGGCTTCGAAAGG-GATCCTGCTCTTTGGGGACTGAAAGGTGCCACCAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGTG-TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAA
* * *
3981875 CTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGG
64 CTTGTGTGGGCTTT---AAG---AGGCGTCCTGCTCTTT---GAC-G-AGA
* * * **
3981926 TGCCACCAACTTGGGTGGGCTTTAAAAGAATAGGCGTCTCGCTCTTTGAGGACTGAAGGTGCCAC
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-GT-GTC--CT-GCTCTTTGAGGACTGAAAATGCCAC
* ** *
3981991 CAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCCACTCTTTGAGGACTGAAAAA
61 CAACTTGTGTGGGCTTT--AAG---AGGCGTCCTGCTCTTT---GAC-G--AGA
* * *
3982045 TGCCACCAACTTGTATGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTAAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAAA
3982099 GCGGAAGGAG
Statistics
Matches: 337, Mismatches: 36, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
102 90 0.27
103 2 0.01
105 2 0.01
107 1 0.00
109 5 0.01
110 68 0.20
112 2 0.01
114 16 0.05
115 29 0.09
116 20 0.06
117 3 0.01
118 29 0.09
119 54 0.16
120 16 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (103 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAAATGCCACCAACT
TGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGACGAGA
Found at i:3986644 original size:20 final size:20
Alignment explanation
Indices: 3986621--3986693 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3986611 ACAACTCAAA
3986621 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3986641 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3986662 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3986682 GTATCGATACAT
1 GTATCGATACAT
3986694 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3986672 original size:41 final size:42
Alignment explanation
Indices: 3986621--3986715 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
3986611 ACAACTCAAA
*
3986621 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3986662 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3986704 GTATCGATACAT
1 GTATCGATACAT
3986716 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:3986772 original size:13 final size:13
Alignment explanation
Indices: 3986754--3986779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3986744 TACAGCAAGT
3986754 ATGTATCGATACA
1 ATGTATCGATACA
3986767 ATGTATCGATACA
1 ATGTATCGATACA
3986780 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3990862 original size:15 final size:15
Alignment explanation
Indices: 3990842--3990880 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3990832 TAAAAATGTC
*
3990842 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3990857 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
3990872 CCAAATGAA
1 CAAAATGAA
3990881 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3992966 original size:20 final size:21
Alignment explanation
Indices: 3992888--3992965 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
3992878 ATGTCCAAAA
*
3992888 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
3992908 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
3992932 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
3992953 TGTATCGATACAT
1 TGTATCGATACAT
3992966 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:3992970 original size:13 final size:13
Alignment explanation
Indices: 3992952--3992990 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3992942 ACATTTTTTG
3992952 TTGTATCGATACA
1 TTGTATCGATACA
3992965 TTGTATCGATACA
1 TTGTATCGATACA
*
3992978 CTGTATCGATACA
1 TTGTATCGATACA
3992991 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3994837 original size:18 final size:16
Alignment explanation
Indices: 3994796--3994841 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
3994786 AATTACTTGA
3994796 TTAAGGGGGAGATTTT
1 TTAAGGGGGAGATTTT
3994812 TTAAGGGGGAGATTTT
1 TTAAGGGGGAGATTTT
3994828 TTAAACGGGGGAGA
1 TT-AA-GGGGGAGA
3994842 CAAAGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 18 0.64
17 2 0.07
18 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.39, T:0.30
Consensus pattern (16 bp):
TTAAGGGGGAGATTTT
Found at i:3995471 original size:20 final size:20
Alignment explanation
Indices: 3995448--3995520 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3995438 ACAACTCAAA
3995448 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3995468 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3995489 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3995509 GTATCGATACAT
1 GTATCGATACAT
3995521 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3995499 original size:41 final size:42
Alignment explanation
Indices: 3995448--3995542 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
3995438 ACAACTCAAA
*
3995448 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3995489 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3995531 GTATCGATACAT
1 GTATCGATACAT
3995543 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:3995599 original size:13 final size:13
Alignment explanation
Indices: 3995581--3995606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3995571 TACAGCAAGT
3995581 ATGTATCGATACA
1 ATGTATCGATACA
3995594 ATGTATCGATACA
1 ATGTATCGATACA
3995607 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3998826 original size:17 final size:17
Alignment explanation
Indices: 3998804--3998837 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3998794 ACATCGATTC
*
3998804 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
3998821 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
3998838 CTTACCTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:4005544 original size:28 final size:28
Alignment explanation
Indices: 4005488--4005564 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
4005478 GGAATTAAGC
* **
4005488 CGGGGTTGGAGTATCCCCTCA-GAGGTAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
4005516 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
** * *
4005544 CAAGATTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
4005565 TGTGAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4005712 original size:52 final size:51
Alignment explanation
Indices: 4005549--4005722 Score: 192
Period size: 51 Copynumber: 3.4 Consensus size: 51
4005539 AATAACAAGA
* * * * *
4005549 TTGGAGTATCCTCGATT-GTGAAAAAATTGCTGATTTTGGAAGTAAAATCGGAG
1 TTGGAGTATCCCCGATTAG-GGAAAAATTG-TG-TTTTAGAAATAAAATCGGGG
* * *
4005602 TTGGAGTATCCCCGATTAAAGG-AAATTTGGTGTTTTAAAAATAAAATC-GGG
1 TTGGAGTATCCCCGATT-AGGGAAAAATT-GTGTTTTAGAAATAAAATCGGGG
*
4005653 TTGGAGTATCCCCGATTAGGGAAAAATTAGTGTTTTAGCAATAAAATCGGGG
1 TTGGAGTATCCCCGATTAGGGAAAAATT-GTGTTTTAGAAATAAAATCGGGG
4005705 TTGGAGTATCCCCGATTA
1 TTGGAGTATCCCCGATTA
4005723 TGAGAAATCA
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
50 3 0.03
51 41 0.40
52 34 0.33
53 23 0.22
54 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTAGGGAAAAATTGTGTTTTAGAAATAAAATCGGGG
Found at i:4005740 original size:51 final size:49
Alignment explanation
Indices: 4005582--4005768 Score: 180
Period size: 51 Copynumber: 3.7 Consensus size: 49
4005572 AAATTGCTGA
* * * *
4005582 TTTTGGAAGTAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAATTTGGTG
1 TTTTAGAA-TAAAATCGGGGTTGGAGTATCCCCGATTAGA-GAAA-TTAGTG
* *
4005634 TTTTAAAAATAAAATC-GGGTTGGAGTATCCCCGATTAGGGAAAAATTAGTG
1 TTTT-AGAATAAAATCGGGGTTGGAGTATCCCCGATTA--GAGAAATTAGTG
* * *
4005685 TTTTAGCAATAAAATCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA
1 TTTTAG-AATAAAATCGGGGTTGGAGTATCCCCGATTA-GAGAAATTAGTG
*
4005736 TTTTAAGAAT-AAAGCAGGGGTTGGAGTATCCCC
1 TTTT-AGAATAAAATC-GGGGTTGGAGTATCCCC
4005769 TCGAAAATAA
Statistics
Matches: 115, Mismatches: 13, Indels: 15
0.80 0.09 0.10
Matches are distributed among these distances:
50 5 0.04
51 70 0.61
52 37 0.32
53 3 0.03
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (49 bp):
TTTTAGAATAAAATCGGGGTTGGAGTATCCCCGATTAGAGAAATTAGTG
Found at i:4005814 original size:27 final size:27
Alignment explanation
Indices: 4005752--4005826 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
4005742 GAATAAAGCA
4005752 GGGGTTGGAGTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTAT-CCC-CGATAAATAAC
* *
4005780 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATAAATAAC
4005807 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
4005827 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 3 0.07
27 28 0.64
28 13 0.30
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATAAATAAC
Found at i:4005908 original size:263 final size:264
Alignment explanation
Indices: 4005437--4005933 Score: 698
Period size: 263 Copynumber: 1.9 Consensus size: 264
4005427 TCGAAAATAA
** * *
4005437 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATTAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
** *
4005502 CCCCTCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGATTGGAGTATCCTCGATTG
66 CCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACAAGATTGGAGTATCCCCGATTG
** * * *
4005567 TGAAAAAATTGCTGATTTTGGAAGTAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAATTTGG
131 TGAAAAAATTGCTGATTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAG
* *
4005632 TGTTTTAAAAATAAAATCGG-GTTGGAGTATCCCCGATTAGGGAAAAATTAGTGTTTTAGCAATA
196 TGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTAGGGAAAAATTAGTGTTTTAGCAATA
4005696 AAAT
261 AAAT
*
4005700 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
* ** *
4005765 CCCCTC-GAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATT
66 CCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATGAAATAACAAGATTGGAGTATCCCCGATT
* * * *
4005828 GTGAAAAATTTG-TGTTTTTTTTAAAAATACAATCGGAGTTGGAGTATCCCCGATTATA-GAAAA
130 GTGAAAAAATTGCTG---ATTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAA
* *
4005891 TTAGTGTTTTGAAAATAAAATCGGAGATGGAATATTCCCGATT
192 TTAGTGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATT
4005934 GCGGAGAATT
Statistics
Matches: 204, Mismatches: 25, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
261 2 0.01
262 34 0.17
263 118 0.58
264 50 0.25
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (264 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
CCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACAAGATTGGAGTATCCCCGATTG
TGAAAAAATTGCTGATTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAG
TGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTAGGGAAAAATTAGTGTTTTAGCAATA
AAAT
Found at i:4007751 original size:10 final size:10
Alignment explanation
Indices: 4007738--4007767 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4007728 CAATGGAATA
4007738 GTGTTTTTTT
1 GTGTTTTTTT
4007748 GTGTTTTTTT
1 GTGTTTTTTT
4007758 G-GTTTTTTT
1 GTGTTTTTTT
4007767 G
1 G
4007768 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:4008320 original size:13 final size:13
Alignment explanation
Indices: 4008302--4008327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4008292 ACAAAGATCC
4008302 ATGTATCGATACA
1 ATGTATCGATACA
4008315 ATGTATCGATACA
1 ATGTATCGATACA
4008328 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4008323 original size:33 final size:33
Alignment explanation
Indices: 4008281--4008347 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4008271 AAAATTTCCA
***
4008281 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4008314 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4008347 A
1 A
4008348 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4008391 original size:19 final size:18
Alignment explanation
Indices: 4008367--4008434 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4008357 CAGTAGCTAA
4008367 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4008386 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4008401 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4008418 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4008435 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4008407 original size:13 final size:13
Alignment explanation
Indices: 4008389--4008413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4008379 ACAATACTTA
4008389 TGTATCGATACAT
1 TGTATCGATACAT
4008402 TGTATCGATACA
1 TGTATCGATACA
4008414 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4008411 original size:32 final size:32
Alignment explanation
Indices: 4008370--4008432 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4008360 TAGCTAATTA
*
4008370 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4008402 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4008433 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4008496 original size:21 final size:22
Alignment explanation
Indices: 4008470--4008527 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
4008460 GTTGGGACCC
*
4008470 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
4008491 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
4008512 TGTATCGATACATTTG
1 TGTATCGATACATTTG
4008528 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:4009305 original size:55 final size:54
Alignment explanation
Indices: 4009221--4009744 Score: 560
Period size: 55 Copynumber: 9.4 Consensus size: 54
4009211 ATAAAGCGTA
* * *
4009221 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
4009276 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
*
4009331 TCCTGCTCTTTGA-G---G---ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
4009378 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
4009433 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
4009488 TCTTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
** * *
4009549 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* ** *
4009608 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* *
4009667 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
4009722 TCCTGCTCTTTGAGGACTAAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
4009745 GCGAAAGGAG
Statistics
Matches: 421, Mismatches: 24, Indels: 49
0.85 0.05 0.10
Matches are distributed among these distances:
47 42 0.10
48 3 0.01
50 1 0.00
52 1 0.00
54 11 0.03
55 204 0.48
56 8 0.02
59 77 0.18
60 48 0.11
61 20 0.05
64 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:4009365 original size:102 final size:106
Alignment explanation
Indices: 4009245--4009744 Score: 476
Period size: 102 Copynumber: 4.5 Consensus size: 106
4009235 GACTAAAAAG
* *
4009245 TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAAC
*
4009310 TTGTGTGGGCTTT-AAG-AGGTGTCCTGCTCTTTGA-G-G-A
65 TTGTGTGGGCTTTAAAGAAGGCGTCCTGCTCTTTGAGGAGAA
*
4009347 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAAC
* *
4009412 TTGTGTGGGCTTCGAAAG--GG-GTCCTGCTCTTTGGGGACTGAAAAA
65 TTGTGTGGGCTT-TAAAGAAGGCGTCCTGCTCTTTGAGGA--G---AA
* * * * *
4009457 TGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCTTGCTCTTTGGGGACTGAAAGGTGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAA-ATGCCACCAAC
* *
4009522 TTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAA
65 TTGTGTGGGCTTT--AAAG--AAGGCGTCCTGCTCTTTGAGGA--GAA
* * * **
4009570 GGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCC
1 --TGCCACCAACTTGTGTGGGCTTT----G-AAAGGCGTCCTGCTCTTTGAGGACTGAAAATGCC
* *
4009635 ACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCCGCTCTTTGAGGACTGAAAAA
59 ACCAACTTGTGTGGGCTTT-AAAG--AAGGCGTCCTGCTCTTTGAGGA--G---AA
* *
4009691 TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTAAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAA
4009745 GCGAAAGGAG
Statistics
Matches: 339, Mismatches: 31, Indels: 44
0.82 0.07 0.11
Matches are distributed among these distances:
102 88 0.26
103 3 0.01
104 3 0.01
106 1 0.00
109 4 0.01
110 68 0.20
111 4 0.01
113 2 0.01
114 25 0.07
115 22 0.06
116 18 0.05
118 29 0.09
119 47 0.14
120 23 0.07
121 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (106 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAATGCCACCAACT
TGTGTGGGCTTTAAAGAAGGCGTCCTGCTCTTTGAGGAGAA
Found at i:4009622 original size:59 final size:60
Alignment explanation
Indices: 4009492--4009718 Score: 359
Period size: 59 Copynumber: 3.8 Consensus size: 60
4009482 AAGGGGTCTT
* *
4009492 GCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGCATCCC
* *
4009553 GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCC
1 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCC
* *
4009612 GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCC
1 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCC
**
4009671 GCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
4009719 GCGTCCTGCT
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
59 86 0.55
60 56 0.36
61 14 0.09
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (60 bp):
GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCATCCC
Found at i:4015952 original size:28 final size:28
Alignment explanation
Indices: 4015912--4015983 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
4015902 GGAATAAAGC
**
4015912 CGGGGTTGGAGTATCCCCTCA-GAGGTAA
1 CGGGGTTGGAGTATCCCC-CATGAAATAA
*
4015940 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCCATGAAATAA
*
4015968 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
4015984 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAATAA
Found at i:4016104 original size:52 final size:52
Alignment explanation
Indices: 4015971--4016359 Score: 220
Period size: 52 Copynumber: 7.4 Consensus size: 52
4015961 GAAATAACGA
* * ** *
4015971 GGTTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTG-TTTTAAAAATAAAATCGG
* * * ***
4016024 AGCTGGAGTATCCTCGACTAAAGG-AAAATTGGTGTTTTAAAAATAAAATCGG
1 GGTTGGAGTATCCCCGA-TTGTGGAAAAATTGGTGTTTTAAAAATAAAATCGG
* **
4016076 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTAAAAATAAAATCGG
* * *** * * *
4016128 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTAAGAAT-AAAGCAGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTAAAAATAAAATC-GG
* * * **** *
4016179 GGTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGGAGTATCCCCAATGATTAA-CGG
1 GGTTGGAGTATCCCCGATTGTGGAAA-AA-----TTGGTGTTTTAAAAAT-A-AAATCGG
* * *
4016234 GGTTGGAGTATCCCCGATTGTGAAAAAATTGTGTTTTTTTTAAAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTG-G--TGTTTTAAAAATAAAATCGG
* * * * *
4016289 AGTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTAAAAATAAAATCGG
* * *
4016340 AGATGGAATATCCCCGATTG
1 GGTTGGAGTATCCCCGATTG
4016360 CTAAGAATTG
Statistics
Matches: 254, Mismatches: 61, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 4 0.02
51 70 0.28
52 74 0.29
53 29 0.11
54 17 0.07
55 39 0.15
56 6 0.02
57 2 0.01
58 3 0.01
59 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTAAAAATAAAATCGG
Found at i:4016239 original size:27 final size:28
Alignment explanation
Indices: 4016177--4016248 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
4016167 GAATAAAGCA
**
4016177 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCAAGGAAATAAC
* *
4016205 GGGGTTGGAGTATCCCCAATG-ATTAAC
1 GGGGTTGGAGTATCCCCAAGGAAATAAC
4016232 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
4016249 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCAAGGAAATAAC
Found at i:4016294 original size:55 final size:51
Alignment explanation
Indices: 4016235--4016359 Score: 144
Period size: 51 Copynumber: 2.4 Consensus size: 51
4016225 GATTAACGGG
4016235 GTTGGAGTATCCCCGATTGTGAAAAAATT-GTGTTTTTTTTAAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGT-AAAAAATTAGTG----TTTTAAAAATAAAATCAGA
* * * *
4016290 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTAAAAATAAAATCAGA
* *
4016341 GATGGAATATCCCCGATTG
1 GTTGGAGTATCCCCGATTG
4016360 CTAAGAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
51 33 0.53
54 7 0.11
55 22 0.35
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTAAAAATAAAATCAGA
Found at i:4016333 original size:264 final size:264
Alignment explanation
Indices: 4015861--4016359 Score: 750
Period size: 264 Copynumber: 1.9 Consensus size: 264
4015851 ACGAAAATAA
** *
4015861 CGGGGTTGGAGCATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGCATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
** * *
4015926 CCCCTCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCCCGATTG
** * *
4015991 TGAAAAAATTGGTGTTTTTGGAAATAAAATCAGAGCTGGAGTATCCTCGACTAAAGGAAAATTGG
131 TGAAAAAATTGGTGTTTTTAAAAATAAAATCAGAGCTGGAGTATCCCCGACTAAAGGAAAATTAG
* * *
4016056 TGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
196 TGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
4016121 AAAT
261 AAAT
* *
4016125 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
1 CGGGGTTGGAGCATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
* * *
4016190 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG-ATTAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCCCGATTG
* * * *
4016254 TGAAAAAATTGTGTTTTTTTTAAAAATAAAATCAGAGTTGGAGTATCCCCGATTATA-GAAAATT
131 TGAAAAAATTG-G-TGTTTTTAAAAATAAAATCAGAGCTGGAGTATCCCCGACTAAAGGAAAATT
*
4016318 AGTGTTTTGAAAATAAAATCGGAGATGGAATATCCCCGATTG
194 AGTGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTG
4016360 CTAAGAATTG
Statistics
Matches: 209, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
263 36 0.17
264 137 0.66
265 36 0.17
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (264 bp):
CGGGGTTGGAGCATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
CCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCCCGATTG
TGAAAAAATTGGTGTTTTTAAAAATAAAATCAGAGCTGGAGTATCCCCGACTAAAGGAAAATTAG
TGTTTTAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
AAAT
Found at i:4018175 original size:10 final size:10
Alignment explanation
Indices: 4018162--4018191 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4018152 TAATGGAATA
4018162 GTGTTTTTTT
1 GTGTTTTTTT
4018172 GTGTTTTTTT
1 GTGTTTTTTT
4018182 G-GTTTTTTT
1 GTGTTTTTTT
4018191 G
1 G
4018192 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:4018744 original size:13 final size:13
Alignment explanation
Indices: 4018726--4018751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4018716 ACAAAGATCC
4018726 ATGTATCGATACA
1 ATGTATCGATACA
4018739 ATGTATCGATACA
1 ATGTATCGATACA
4018752 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4018747 original size:33 final size:33
Alignment explanation
Indices: 4018705--4018771 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4018695 AAAATTTCCA
***
4018705 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4018738 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4018771 A
1 A
4018772 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4018815 original size:19 final size:18
Alignment explanation
Indices: 4018791--4018858 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4018781 CAGTAGCTAA
4018791 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4018810 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4018825 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4018842 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4018859 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4018831 original size:13 final size:13
Alignment explanation
Indices: 4018813--4018837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4018803 ACAATACTTA
4018813 TGTATCGATACAT
1 TGTATCGATACAT
4018826 TGTATCGATACA
1 TGTATCGATACA
4018838 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4018835 original size:32 final size:32
Alignment explanation
Indices: 4018794--4018856 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4018784 TAGCTAATTA
*
4018794 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4018826 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4018857 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4018920 original size:21 final size:22
Alignment explanation
Indices: 4018894--4018951 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
4018884 GTTGGGACCC
*
4018894 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
4018915 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
4018936 TGTATCGATACATTTG
1 TGTATCGATACATTTG
4018952 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:4020591 original size:98 final size:97
Alignment explanation
Indices: 4020373--4020612 Score: 243
Period size: 98 Copynumber: 2.5 Consensus size: 97
4020363 AATTTTATTT
* * *
4020373 ATCGGGGATACTCCAACCCTATTCCTCTAAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
1 ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
* * *
4020438 GTTTAAATCTTATTCTCACTTAAATTATCACC
66 CTTGAAATCTTATTCTCACCTAAATTATCACC
* * * * * * * *
4020470 ATCGGTGCCACTTCAACCTCATTCCTTTGAGGGGATACTCCAA-CTCCGTTTTTAAA-ACTTGTT
1 ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCT-CGCTTTTAAACAC--ATC
** **
4020533 AAGACTTGAAA-CTTATTCTTGCCTAAATTATCATT
63 AA-ACTTGAAATCTTATTCTCACCTAAATTATCACC
* *
4020568 GTCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCTAACC
1 ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACC
4020613 CCATTTTTCA
Statistics
Matches: 113, Mismatches: 25, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
96 4 0.04
97 44 0.39
98 58 0.51
99 7 0.06
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (97 bp):
ATCGGGGACACTCCAACCCCATTCCTCTGAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
CTTGAAATCTTATTCTCACCTAAATTATCACC
Found at i:4034488 original size:91 final size:91
Alignment explanation
Indices: 4034275--4034470 Score: 374
Period size: 91 Copynumber: 2.2 Consensus size: 91
4034265 ATTATTCAAA
* *
4034275 GTATCGATACATATGCAATTGTATTAATACATAAAGGTTGACTTAAGCTACCAAGGTCAAAACCC
1 GTATCGATACATATGCAATTGTATCAATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
4034340 TTAAATGTATCGATACACACCTAGAT
66 TTAAATGTATCGATACACACCTAGAT
4034366 GTATCGATACATATGCAATTGTATCAATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
1 GTATCGATACATATGCAATTGTATCAATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
4034431 TTAAATGTATCGATACACACCTAGAT
66 TTAAATGTATCGATACACACCTAGAT
4034457 GTATCGATACATAT
1 GTATCGATACATAT
4034471 TACTTAGTAT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 103 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (91 bp):
GTATCGATACATATGCAATTGTATCAATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
TTAAATGTATCGATACACACCTAGAT
Found at i:4034505 original size:19 final size:20
Alignment explanation
Indices: 4034457--4034527 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
4034447 ACACCTAGAT
4034457 GTATCGATACATATTACTTA
1 GTATCGATACATATTACTTA
* *
4034477 GTATCGATACATGTT-CTTG
1 GTATCGATACATATTACTTA
* *
4034496 GTATCAATACATATTGAATTA
1 GTATCGATACATATT-ACTTA
4034517 -TATCGATACAT
1 GTATCGATACAT
4034528 GAATCTGGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 16 0.38
20 24 0.57
21 2 0.05
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (20 bp):
GTATCGATACATATTACTTA
Found at i:4034601 original size:21 final size:20
Alignment explanation
Indices: 4034577--4034630 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
4034567 TTACTGTGCA
*
4034577 TGTATCGATACATACTTGAAT
1 TGTATCGATACATA-GTGAAT
*
4034598 TGTATCGATACATAGTGCAT
1 TGTATCGATACATAGTGAAT
*
4034618 TATATCGATACAT
1 TGTATCGATACAT
4034631 TGAGCCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAGTGAAT
Found at i:4036221 original size:15 final size:15
Alignment explanation
Indices: 4036200--4036238 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
4036190 GTCAACCATC
4036200 AATGATGATGAAGA-
1 AATGATGATGAAGAT
*
4036214 AGATGATGATGATGAT
1 A-ATGATGATGAAGAT
4036230 AATGATGAT
1 AATGATGAT
4036239 AAAGTTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (15 bp):
AATGATGATGAAGAT
Found at i:4036793 original size:21 final size:21
Alignment explanation
Indices: 4036752--4036802 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4036742 GTTAATAAAG
* *
4036752 AATTAACCAATAAGAATAACA
1 AATTAACTAATAAGAACAACA
4036773 AATTAACTAATGAA-AACAACA
1 AATTAACTAAT-AAGAACAACA
*
4036794 AATTGACTA
1 AATTAACTA
4036803 GGAAAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.22
Consensus pattern (21 bp):
AATTAACTAATAAGAACAACA
Found at i:4042066 original size:19 final size:19
Alignment explanation
Indices: 4042022--4042077 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4042012 CTGCCAGTTT
**
4042022 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
4042042 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
4042061 CATGTATCGATATAATG
1 CATGTATCGATACAATG
4042078 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:4049094 original size:15 final size:15
Alignment explanation
Indices: 4049076--4049110 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4049066 TGAGTCATTT
4049076 TCATCATTATCATCA
1 TCATCATTATCATCA
* *
4049091 TCATCCTTATCTTCA
1 TCATCATTATCATCA
4049106 TCATC
1 TCATC
4049111 TTTAATGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:4057174 original size:50 final size:50
Alignment explanation
Indices: 4057099--4057307 Score: 190
Period size: 50 Copynumber: 4.2 Consensus size: 50
4057089 GCCATGTTGA
* * *
4057099 AAGTCCACACTAGCTAACACTTGATAAAGAGGTTAAGCCCTATAGAATCT
1 AAGTCCACACTAGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
* * * * *
4057149 AAGTCCACACTAGCTAGCATTTGATAAGGAAGCTAA-TCCTATAGAGTCA
1 AAGTCCACACTAGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
* * * ** * * *
4057198 AAGTCTATACAAGCT-GACACCTAAATAGGGAGGTTAAGCCCTGTAGACTCT
1 AAGTCCACACTAGCTAG-CA-CTTGATAAGGAGGTTAAGCCCTATAGAGTCT
* * *
4057249 AAGCCCACA-TAAGCTAGCACCTGATATGGAGGTTAAGCCCTATAGAGTCT
1 AAGTCCACACT-AGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
*
4057299 AAGTGCACA
1 AAGTCCACA
4057308 ATGTAGACAC
Statistics
Matches: 121, Mismatches: 33, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
48 1 0.01
49 24 0.20
50 74 0.61
51 21 0.17
52 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (50 bp):
AAGTCCACACTAGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
Found at i:4060270 original size:148 final size:149
Alignment explanation
Indices: 4060100--4060374 Score: 344
Period size: 148 Copynumber: 1.9 Consensus size: 149
4060090 TTTTTCGTCC
* * * * *
4060100 AATAAAAATTATCACCTAAATTT-TTGGAATTTCTAATATT-CTCATGGGTATCCATGAGGGTAT
1 AATAAAAATTATCACCTAAATTTCTTAGAATTTCCAATATTCCT-ATAGGCATCCATAAGGGTAT
* ** *
4060163 GAAAAATTTTTAAAACT-TTTCATATCTTTTCGGTTCTCCATTAAGGTATGAAATG-AATTTTTT
65 G-AAAATTTTCAAAACTCTTT-ATATCTTTTCAATCCTCCATTAAGGTATGAAATGAAATTTTTT
4060226 GGGAAATAAAAAAATTAAATTA
128 GGGAAATAAAAAAATTAAATTA
* *
4060248 AATAAAAATTATGATCC-CAATTTCTTAGAATTTCCAATATTCCTATAGGCATCCATAAGGGTAT
1 AATAAAAATTATCA-CCTAAATTTCTTAGAATTTCCAATATTCCTATAGGCATCCATAAGGGTAT
* * * *
4060312 GAAAATTTTCAAAACTCTTTGTGTCTTTTCAATCCTTCATTAAGTTATGAAATGAAATTTTTT
65 GAAAATTTTCAAAACTCTTTATATCTTTTCAATCCTCCATTAAGGTATGAAATGAAATTTTTT
4060375 AGAAAAACAA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
148 59 0.55
149 46 0.43
150 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (149 bp):
AATAAAAATTATCACCTAAATTTCTTAGAATTTCCAATATTCCTATAGGCATCCATAAGGGTATG
AAAATTTTCAAAACTCTTTATATCTTTTCAATCCTCCATTAAGGTATGAAATGAAATTTTTTGGG
AAATAAAAAAATTAAATTA
Found at i:4062256 original size:13 final size:13
Alignment explanation
Indices: 4062238--4062263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4062228 TACAGCAAGT
4062238 ATGTATCGATACA
1 ATGTATCGATACA
4062251 ATGTATCGATACA
1 ATGTATCGATACA
4062264 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4064511 original size:21 final size:21
Alignment explanation
Indices: 4064478--4064522 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4064468 TTGCAAGTTG
*
4064478 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
4064500 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
4064520 AAA
1 AAA
4064523 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4068450 original size:20 final size:20
Alignment explanation
Indices: 4068371--4068450 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
4068361 AATGTCCAAA
*
4068371 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
4068391 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
4068416 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
4068436 TTGTATCGATACATT
1 ATGTATCGATACATT
4068451 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:4068454 original size:13 final size:13
Alignment explanation
Indices: 4068436--4068474 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4068426 ACATTTTTCT
4068436 TTGTATCGATACA
1 TTGTATCGATACA
4068449 TTGTATCGATACA
1 TTGTATCGATACA
*
4068462 CTGTATCGATACA
1 TTGTATCGATACA
4068475 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4071028 original size:13 final size:13
Alignment explanation
Indices: 4071010--4071035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4071000 TACAGCAAGT
4071010 ATGTATCGATACA
1 ATGTATCGATACA
4071023 ATGTATCGATACA
1 ATGTATCGATACA
4071036 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4072456 original size:45 final size:44
Alignment explanation
Indices: 4072391--4072485 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
4072381 TTATAGAGTC
** * * * *
4072391 AAAGTCCATATTAGTTGGCACTTATTAGAGAGGTTAAACCCTAT
1 AAAGTCCATATTAACTGGCACCTAATAAAGAGGTTAAACACTAT
* *
4072435 AGAAGTCCGTATTAACTGGCACCTAATAAAGAGGTTAAGCACTAT
1 A-AAGTCCATATTAACTGGCACCTAATAAAGAGGTTAAACACTAT
4072480 AAAGTC
1 AAAGTC
4072486 AAAAGTCTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 6 0.14
45 36 0.86
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (44 bp):
AAAGTCCATATTAACTGGCACCTAATAAAGAGGTTAAACACTAT
Found at i:4072576 original size:50 final size:50
Alignment explanation
Indices: 4072107--4072581 Score: 175
Period size: 50 Copynumber: 9.6 Consensus size: 50
4072097 ACAATAATTA
* * ** * *
4072107 GCACCTAATTAGG-AGGTTAAGCTCTATAGAGTTTAAGTCCACACAAATTG
1 GCACTTAA-TAGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
* * * * * * * * *
4072157 GCATCTT-ATAGGGAGCTTAAGCCTTATAGAGTCTATGTCCATACAAGCTA
1 GCA-CTTAATAGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
* * * * * ** * *
4072207 GCACCTAATAGGAAAGTTAAGCCTTGTAGAGTCTAAGTCTGCACAAGCTG
1 GCACTTAATAGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
* * * ** * * *** *
4072257 GCTCCTGATA-GAGAGGTTAAGCATTGTAGAGTAAAAAGTCCATGTTAGCTG
1 GCACTTAATAGGA-AGGTTAAGCCCTATAGAGT-CAAAGTCCACACTAGTTG
* * ** * *
4072308 ACACCTT-ATAAGAACATTAAGTCCTATATAGTCAAAGTCCACACTAGTTG
1 GCA-CTTAATAGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
* * * * *
4072358 GCA-TCTGATAAGGAA-GTTAAGTCTTATAGAGTCAAAGTCCATATTAGTTG
1 GCACT-TAAT-AGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
* * ** * **
4072408 GCACTTATTA-GAGAGGTTAAACCCTAT--AG---AAGTCCGTATTAACTG
1 GCACTTAATAGGA-AGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
* * * * * * *
4072453 GCACCTAATA-AAGAGGTTAAGCACTATAAAGTCAAAAGTCTACACTAGCTA
1 GCACTTAATAGGA-AGGTTAAGCCCTATAGAGTC-AAAGTCCACACTAGTTG
** * * *
4072504 GCACTTGTTAGGAAGGTAAAGCCCTATGGAGTCTAAGTCCACACTAGTTG
1 GCACTTAATAGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
*
4072554 GCACTTAATAGGAAGGTTAAGCCTTATA
1 GCACTTAATAGGAAGGTTAAGCCCTATA
4072582 AATAAAAAGT
Statistics
Matches: 315, Mismatches: 90, Indels: 40
0.71 0.20 0.09
Matches are distributed among these distances:
45 35 0.11
47 2 0.01
48 5 0.02
49 11 0.03
50 191 0.61
51 66 0.21
52 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (50 bp):
GCACTTAATAGGAAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGTTG
Found at i:4072665 original size:48 final size:50
Alignment explanation
Indices: 4072567--4072680 Score: 151
Period size: 48 Copynumber: 2.3 Consensus size: 50
4072557 CTTAATAGGA
* *
4072567 AGGTTAAGCCTTATAAATAAAAAGTCCAATTTAGTTAGCACTTGGGAAGG
1 AGGTTAAGCCCTATAAATAAAAAGTCCAATTAAGTTAGCACTTGGGAAGG
* * * *
4072617 AGGTTAAGCCCT-TAGATAGAAAGTCCAATTAATTTA-CACTTGGTAAGG
1 AGGTTAAGCCCTATAAATAAAAAGTCCAATTAAGTTAGCACTTGGGAAGG
*
4072665 AGGTTAAGCCTTATAA
1 AGGTTAAGCCCTATAA
4072681 GGAAAGTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
48 22 0.40
49 22 0.40
50 11 0.20
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (50 bp):
AGGTTAAGCCCTATAAATAAAAAGTCCAATTAAGTTAGCACTTGGGAAGG
Found at i:4076915 original size:52 final size:52
Alignment explanation
Indices: 4076845--4076965 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
4076835 GAAAATTTAT
*
4076845 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
4076897 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
4076949 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
4076966 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:4076978 original size:52 final size:51
Alignment explanation
Indices: 4076845--4076985 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
4076835 GAAAATTTAT
4076845 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
4076897 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
4076949 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
4076986 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:4076992 original size:13 final size:13
Alignment explanation
Indices: 4076974--4076998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4076964 CAAAGATCAG
4076974 TGTATCGATACAA
1 TGTATCGATACAA
4076987 TGTATCGATACA
1 TGTATCGATACA
4076999 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4077082 original size:13 final size:13
Alignment explanation
Indices: 4077064--4077088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4077054 CAAAAAAATA
4077064 TGTATCGATACAT
1 TGTATCGATACAT
4077077 TGTATCGATACA
1 TGTATCGATACA
4077089 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4077084 original size:33 final size:33
Alignment explanation
Indices: 4077042--4077108 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4077032 AGTAGCTTAA
4077042 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
4077075 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
4077108 A
1 A
4077109 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:4082907 original size:78 final size:78
Alignment explanation
Indices: 4082825--4082973 Score: 203
Period size: 78 Copynumber: 1.9 Consensus size: 78
4082815 AAACCAAACT
* * *
4082825 TTTAAGATTATTTTAGTATTTTTGCATTAAA-ATCAAGCATTT-AGCATTAGTTTTGCATTTTTA
1 TTTAAGATCATTTTAGTATTTTTGCATTAAACCT-AAGCATTTAAG-ATTAGTTTTGCACTTTTA
*
4082888 TCTCAAAATCGAACA
64 TATCAAAATCGAACA
* * *
4082903 TTTAAGGTCATTTTAGTATTTTTGCATTAAACCTAATCCTTTAAGATTAGTTTTGCACTTTTATA
1 TTTAAGATCATTTTAGTATTTTTGCATTAAACCTAAGCATTTAAGATTAGTTTTGCACTTTTATA
4082968 TCAAAA
66 TCAAAA
4082974 CCAAGCCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 59 0.95
79 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (78 bp):
TTTAAGATCATTTTAGTATTTTTGCATTAAACCTAAGCATTTAAGATTAGTTTTGCACTTTTATA
TCAAAATCGAACA
Found at i:4084122 original size:43 final size:43
Alignment explanation
Indices: 4084061--4084159 Score: 171
Period size: 43 Copynumber: 2.3 Consensus size: 43
4084051 TACTTTTCAT
*
4084061 AATGTATCGATACATGCATTTTAAATTTATAACCGTTGGGCAC
1 AATGTATCGATACATGCATTTGAAATTTATAACCGTTGGGCAC
*
4084104 AATGTATCGATACATGCATTTGAAATTTATAGCCGTTGGGCAC
1 AATGTATCGATACATGCATTTGAAATTTATAACCGTTGGGCAC
*
4084147 AATGTACCGATAC
1 AATGTATCGATAC
4084160 TTTTCACTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (43 bp):
AATGTATCGATACATGCATTTGAAATTTATAACCGTTGGGCAC
Found at i:4085238 original size:20 final size:20
Alignment explanation
Indices: 4085213--4085264 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
4085203 TACAAGCAAT
*
4085213 GTATCGATACAATCTATCAA
1 GTATCGATACAATCTACCAA
* * *
4085233 GTATCGATACATTGTACCAT
1 GTATCGATACAATCTACCAA
4085253 GTATCGATACAA
1 GTATCGATACAA
4085265 ACAGTGGTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
GTATCGATACAATCTACCAA
Found at i:4085337 original size:19 final size:19
Alignment explanation
Indices: 4085293--4085348 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
4085283 TTTCCAATCT
**
4085293 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
4085313 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
4085332 CATGTATCGATACAATG
1 CATGTATCGATACAATG
4085349 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:4085351 original size:13 final size:13
Alignment explanation
Indices: 4085333--4085359 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4085323 TACAATGAAC
4085333 ATGTATCGATACA
1 ATGTATCGATACA
4085346 ATGTATCGATACA
1 ATGTATCGATACA
4085359 A
1 A
4085360 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4085947 original size:21 final size:22
Alignment explanation
Indices: 4085903--4085979 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
4085893 AGTTATCATT
* *
4085903 TTTCTCCCCCTCAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
4085925 TTTCTCCCCTTTAATCAAA-AA
1 TTTCTCCCCCTTAATCAAAGAA
*
4085946 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
4085968 TTTCTCCCCCTT
1 TTTCTCCCCCTT
4085980 TGTCAAATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
21 20 0.41
22 29 0.59
ACGTcount: A:0.26, C:0.35, G:0.03, T:0.36
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:4092587 original size:13 final size:13
Alignment explanation
Indices: 4092569--4092593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4092559 CATATTTCTT
4092569 TGTATCGATACAC
1 TGTATCGATACAC
4092582 TGTATCGATACA
1 TGTATCGATACA
4092594 TGATCTTACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:4095131 original size:10 final size:10
Alignment explanation
Indices: 4095112--4095142 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4095102 GTATCGATAC
4095112 ATGAACAGTG
1 ATGAACAGTG
*
4095122 ATGAATAGTG
1 ATGAACAGTG
4095132 ATGAACAGTG
1 ATGAACAGTG
4095142 A
1 A
4095143 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:4095355 original size:21 final size:21
Alignment explanation
Indices: 4095329--4095369 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4095319 GTCAACCTTG
4095329 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
4095350 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
4095370 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:4100199 original size:13 final size:13
Alignment explanation
Indices: 4100177--4100211 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4100167 AAGGATCTTA
*
4100177 GTATCAATACATT
1 GTATCGATACATT
4100190 GTATCGATACATT
1 GTATCGATACATT
*
4100203 GTATGGATA
1 GTATCGATA
4100212 TAAGGGCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:4102140 original size:28 final size:27
Alignment explanation
Indices: 4102098--4102183 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
4102088 ATTGTTTTGG
**
4102098 AAACAAAAAGGGGGAGAGATATTTTTT
1 AAACAAAAAAAGGGAGAGATATTTTTT
*** * *
4102125 AAATTTGAAAAAGGGAAAGAT-TGTTTTGG
1 AAA-CAAAAAAAGGGAGAGATAT-TTTT-T
4102154 AAACAAAAAAAGGGAGAGATATTTTTT
1 AAACAAAAAAAGGGAGAGATATTTTTT
4102181 AAA
1 AAA
4102184 AGGAAAACAT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
27 7 0.16
28 32 0.74
29 4 0.09
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (27 bp):
AAACAAAAAAAGGGAGAGATATTTTTT
Found at i:4102142 original size:56 final size:56
Alignment explanation
Indices: 4102040--4102183 Score: 200
Period size: 56 Copynumber: 2.5 Consensus size: 56
4102030 TTTTTGCTAT
*
4102040 AACAAAAAGGGGGAGAAAT-TTTTTGAAATAAATTTGAAAAAAGGAAAAATTGTTTTGGA
1 AACAAAAAGGGGGAGAGATATTTTT----TAAATTTGAAAAAAGGAAAAATTGTTTTGGA
* *
4102099 AACAAAAAGGGGGAGAGATATTTTTTAAATTTGAAAAAGGGAAAGATTGTTTTGGA
1 AACAAAAAGGGGGAGAGATATTTTTTAAATTTGAAAAAAGGAAAAATTGTTTTGGA
**
4102155 AACAAAAAAAGGGAGAGATATTTTTTAAA
1 AACAAAAAGGGGGAGAGATATTTTTTAAA
4102184 AGGAAAACAT
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
56 56 0.71
59 18 0.23
60 5 0.06
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (56 bp):
AACAAAAAGGGGGAGAGATATTTTTTAAATTTGAAAAAAGGAAAAATTGTTTTGGA
Found at i:4102241 original size:44 final size:45
Alignment explanation
Indices: 4102148--4102235 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
4102138 GGAAAGATTG
4102148 TTTTGGAAACAAAAAAAGGGAGAGATATTTTTTAAAAGGAAAACA
1 TTTTGGAAACAAAAAAAGGGAGAGATATTTTTTAAAAGGAAAACA
*
4102193 TTTTGGAAAC-AAAAAGGGGAAGAGATATTTTTTAAAAGGAAAA
1 TTTTGGAAACAAAAAAAGGG-AGAGATATTTTTTAAAAGGAAAA
4102236 TTTTTGTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 8 0.20
45 33 0.80
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (45 bp):
TTTTGGAAACAAAAAAAGGGAGAGATATTTTTTAAAAGGAAAACA
Found at i:4102920 original size:13 final size:13
Alignment explanation
Indices: 4102902--4102958 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
4102892 CATATTGCTT
4102902 TGTATCGATACAC
1 TGTATCGATACAC
4102915 TGTATCGATACATGATC
1 TGTATCGATAC---A-C
4102932 TTTGTATCGATACAC
1 --TGTATCGATACAC
4102947 TGTATCGATACA
1 TGTATCGATACA
4102959 TGATCTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 1 0.03
16 2 0.05
17 1 0.03
19 11 0.29
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:4102939 original size:19 final size:19
Alignment explanation
Indices: 4102915--4102977 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
4102905 ATCGATACAC
4102915 TGTATCGATACATGATCTT
1 TGTATCGATACATGATCTT
4102934 TGTATCGATAC---A-C--
1 TGTATCGATACATGATCTT
4102947 TGTATCGATACATGATCTT
1 TGTATCGATACATGATCTT
4102966 TGTATCGATACA
1 TGTATCGATACA
4102978 CAGCGAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 1 0.03
16 2 0.05
17 1 0.03
19 23 0.61
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGATCTT
Found at i:4102940 original size:32 final size:32
Alignment explanation
Indices: 4102883--4102978 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
4102873 AAGCCCAGAA
4102883 GTATCGATACAT-ATTGCTTTGTATCGATACACT
1 GTATCGATACATGA-T-CTTTGTATCGATACACT
4102916 GTATCGATACATGATCTTTGTATCGATACACT
1 GTATCGATACATGATCTTTGTATCGATACACT
4102948 GTATCGATACATGATCTTTGTATCGATACAC
1 GTATCGATACATGATCTTTGTATCGATACAC
4102979 AGCGAATTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
32 48 0.77
33 13 0.21
34 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (32 bp):
GTATCGATACATGATCTTTGTATCGATACACT
Found at i:4106209 original size:20 final size:20
Alignment explanation
Indices: 4106161--4106219 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
4106151 AAAAGCCCAA
4106161 AATGTATCGATACAATTGTAAG
1 AATGTATCGATAC-ATT-TAAG
* **
4106183 CATGTATCGATACATTTACT
1 AATGTATCGATACATTTAAG
4106203 AATGTATCGATACATTT
1 AATGTATCGATACATTT
4106220 TCTTGGGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 18 0.55
21 3 0.09
22 12 0.36
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTTAAG
Found at i:4106266 original size:20 final size:20
Alignment explanation
Indices: 4106241--4106296 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
4106231 TGCAGGGTAG
4106241 TTATGTATCGATACATTCAC
1 TTATGTATCGATACATTCAC
* *
4106261 TTATGTATCGATTCATTTAC
1 TTATGTATCGATACATTCAC
* *
4106281 TGTTTATATCGATACA
1 T-TATGTATCGATACA
4106297 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (20 bp):
TTATGTATCGATACATTCAC
Found at i:4108291 original size:19 final size:20
Alignment explanation
Indices: 4108247--4108300 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
4108237 CTGCCAGTTT
* **
4108247 CATGTATTGATACAATTGTG
1 CATGTATCGATACAATTGAA
4108267 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
4108286 CATGTATCGATACAA
1 CATGTATCGATACAA
4108301 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:4108920 original size:30 final size:30
Alignment explanation
Indices: 4108879--4109022 Score: 175
Period size: 30 Copynumber: 4.8 Consensus size: 30
4108869 GCTTTCGTTT
4108879 AAAAA-TTTCTCCCCCTTGATAATCATTTA
1 AAAAATTTTCTCCCCCTTGATAATCATTTA
*
4108908 AAAAATTTTCTCCCCCTTGATAATCGTTTTAA
1 AAAAATTTTCTCCCCCTTGATAATC-ATTT-A
* **
4108940 AAAAATTTTCT-ACCCTTGATAAAAAATTTA
1 AAAAATTTTCTCCCCCTTGAT-AATCATTTA
* * *
4108970 AAAGATTTTCTCCCCCTTGAGAATCGTTTA
1 AAAAATTTTCTCCCCCTTGATAATCATTTA
*
4109000 AAAAATTTTCTCCTCCTTGATAA
1 AAAAATTTTCTCCCCCTTGATAA
4109023 AAAATTTATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
29 5 0.05
30 56 0.58
31 21 0.22
32 14 0.15
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAAATTTTCTCCCCCTTGATAATCATTTA
Found at i:4108978 original size:62 final size:61
Alignment explanation
Indices: 4108873--4109030 Score: 207
Period size: 62 Copynumber: 2.6 Consensus size: 61
4108863 ATTAAGGCTT
* * ** *
4108873 TCGTTT-AAAAA-TTTCTCCCCCTTGAT-AATCATTTAAAAAATTTTCTCCCCCTTGATAA
1 TCGTTTAAAAAATTTTCTACTCCTTGATAAAAAATTTAAAAAATTTTCTCCCCCTTGAGAA
*
4108931 TCGTTTTAAAAAAATTTTCTAC-CCTTGATAAAAAATTTAAAAGATTTTCTCCCCCTTGAGAA
1 TCG-TTT-AAAAAATTTTCTACTCCTTGATAAAAAATTTAAAAAATTTTCTCCCCCTTGAGAA
*
4108993 TCGTTTAAAAAATTTTCTCCTCCTTGATAAAAAATTTA
1 TCGTTTAAAAAATTTTCTACTCCTTGATAAAAAATTTA
4109031 TTTTCAAACA
Statistics
Matches: 88, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
58 3 0.03
59 3 0.03
60 13 0.15
61 32 0.36
62 37 0.42
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (61 bp):
TCGTTTAAAAAATTTTCTACTCCTTGATAAAAAATTTAAAAAATTTTCTCCCCCTTGAGAA
Found at i:4111055 original size:23 final size:23
Alignment explanation
Indices: 4111028--4111074 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4111018 TTCAAAAATA
*
4111028 TGGCACAAATTAATATCAAATCT
1 TGGCAAAAATTAATATCAAATCT
*
4111051 TGGCAAAAATTAATATCGAATCT
1 TGGCAAAAATTAATATCAAATCT
4111074 T
1 T
4111075 ACCCTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (23 bp):
TGGCAAAAATTAATATCAAATCT
Found at i:4117099 original size:13 final size:13
Alignment explanation
Indices: 4117081--4117105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4117071 CAATTCATCA
4117081 TGTATCGATACAT
1 TGTATCGATACAT
4117094 TGTATCGATACA
1 TGTATCGATACA
4117106 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4117116 original size:33 final size:32
Alignment explanation
Indices: 4117061--4117125 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
4117051 TTTGAAGTAA
*
4117061 TGTATCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTCA-CATGTATCAATACAT
4117094 TGTATCGATACAATGTGC-CATGTATCAATACA
1 TGTATCGATACAAT-T-CACATGTATCAATACA
4117126 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAATTCACATGTATCAATACAT
Found at i:4117874 original size:32 final size:33
Alignment explanation
Indices: 4117814--4117876 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
4117804 GGCCCAGAAG
*
4117814 TATCGATACATATTGCTTTGTATCGATACACTA
1 TATCGATACATATTGCTTGGTATCGATACACTA
4117847 TATCGATACATGA-T-CTTGGTATCGATACAC
1 TATCGATACAT-ATTGCTTGGTATCGATACAC
4117877 AACGACTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (33 bp):
TATCGATACATATTGCTTGGTATCGATACACTA
Found at i:4122298 original size:38 final size:41
Alignment explanation
Indices: 4122256--4122346 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
4122246 TTATAACAAA
**
4122256 AAGGGAGAGAG-AT-T-ATTGTTTATTGGT-AAGAACGTATT
1 AAGGGAGAGAGTATGTAATTGTTTAAAGGTGAA-AACGTATT
* *
4122294 AAGGGAAAGAGTTTGTAATTGTTTAAAGGTGAAAACGTATT
1 AAGGGAGAGAGTATGTAATTGTTTAAAGGTGAAAACGTATT
*
4122335 AAGGGGGAGAGT
1 AAGGGAGAGAGT
4122347 TTGCATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 10 0.23
39 1 0.02
40 1 0.02
41 29 0.67
42 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.32, T:0.30
Consensus pattern (41 bp):
AAGGGAGAGAGTATGTAATTGTTTAAAGGTGAAAACGTATT
Found at i:4125424 original size:20 final size:20
Alignment explanation
Indices: 4125401--4125473 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4125391 ACAATTCAAA
4125401 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4125421 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4125442 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4125462 GTATCGATACAT
1 GTATCGATACAT
4125474 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4125445 original size:21 final size:21
Alignment explanation
Indices: 4125419--4125494 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
4125409 ACATGTTGCA
4125419 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4125440 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
4125460 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
4125481 TTGTATCGATACAT
1 ATGTATCGATACAT
4125495 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4125452 original size:41 final size:41
Alignment explanation
Indices: 4125401--4125494 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
4125391 ACAATTCAAA
*
4125401 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
4125442 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4125483 GTATCGATACAT
1 GTATCGATACAT
4125495 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:4125551 original size:13 final size:13
Alignment explanation
Indices: 4125533--4125558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4125523 TACAGCAAGT
4125533 ATGTATCGATACA
1 ATGTATCGATACA
4125546 ATGTATCGATACA
1 ATGTATCGATACA
4125559 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4129641 original size:15 final size:15
Alignment explanation
Indices: 4129621--4129651 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4129611 TAAAAATGTC
*
4129621 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4129636 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4129651 C
1 C
4129652 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Done.