Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 133 of 292
Found at i:39493329 original size:103 final size:103
Alignment explanation
Indices: 39493150--39493358 Score: 355
Period size: 103 Copynumber: 2.0 Consensus size: 103
39493140 GCAAGCTGAA
*
39493150 GTCTTTGAGCTGTAAAATAAAATCATAGCCAAGTTATGCATTTCTTCAAATTTCAGACAAATGGA
1 GTCTTTGAGCTGTAAAACAAAATCATAGCCAAGTTATGCATTTCTTCAAATTTCAGACAAATGGA
* * * *
39493215 TCTCAGGAGTCCAAGAGTATTAGACTCGAGTTTGCATG
66 TCTAAAGAGTCCAAGAGTATTAGACTCGAGATTGAATG
* *
39493253 GTCTTTGAGCTGTAAAACAAAATCATAGCCAAGTTATGCGTTTCTTCAAATTTCAGATAAATGGA
1 GTCTTTGAGCTGTAAAACAAAATCATAGCCAAGTTATGCATTTCTTCAAATTTCAGACAAATGGA
39493318 TCTAAAGAGTCCAAGAGTATTAGACTCGAGATTGAATG
66 TCTAAAGAGTCCAAGAGTATTAGACTCGAGATTGAATG
39493356 GTC
1 GTC
39493359 ACTGAATTTC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (103 bp):
GTCTTTGAGCTGTAAAACAAAATCATAGCCAAGTTATGCATTTCTTCAAATTTCAGACAAATGGA
TCTAAAGAGTCCAAGAGTATTAGACTCGAGATTGAATG
Found at i:39494090 original size:15 final size:15
Alignment explanation
Indices: 39494070--39494099 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39494060 TCTACTAAAA
39494070 AATGGGCAAATTAGT
1 AATGGGCAAATTAGT
39494085 AATGGGCAAATTAGT
1 AATGGGCAAATTAGT
39494100 CTCTATACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
AATGGGCAAATTAGT
Found at i:39499652 original size:16 final size:17
Alignment explanation
Indices: 39499631--39499668 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
39499621 TTCTATATGG
*
39499631 ATTTTACT-TTTATTTT
1 ATTTTACTATATATTTT
39499647 ATTTTACTACTATATTTT
1 ATTTTACTA-TATATTTT
39499665 ATTT
1 ATTT
39499669 AAATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTACTATATATTTT
Found at i:39500028 original size:20 final size:21
Alignment explanation
Indices: 39499991--39500032 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
39499981 ATTATTTTGT
39499991 AATTAAAAAGAGAAATAAATA
1 AATTAAAAAGAGAAATAAATA
*
39500012 AATTAAATAGA-AAATAAATA
1 AATTAAAAAGAGAAATAAATA
39500032 A
1 A
39500033 TAATTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AATTAAAAAGAGAAATAAATA
Found at i:39500106 original size:20 final size:21
Alignment explanation
Indices: 39500069--39500110 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
39500059 ATTATTTTGT
39500069 AATTAAAAAGAGAAATAAATA
1 AATTAAAAAGAGAAATAAATA
*
39500090 AATTAAATAGA-AAATAAATA
1 AATTAAAAAGAGAAATAAATA
39500110 A
1 A
39500111 TAATTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AATTAAAAAGAGAAATAAATA
Found at i:39500172 original size:20 final size:20
Alignment explanation
Indices: 39500147--39500187 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
39500137 ATTATTTTGT
39500147 AATTAAA-AGAGAAATAAATA
1 AATTAAATAGA-AAATAAATA
39500167 AATTAAATAGAAAATAAATA
1 AATTAAATAGAAAATAAATA
39500187 A
1 A
39500188 TAATTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (20 bp):
AATTAAATAGAAAATAAATA
Found at i:39500182 original size:155 final size:156
Alignment explanation
Indices: 39499960--39500271 Score: 617
Period size: 155 Copynumber: 2.0 Consensus size: 156
39499950 AACTTATCAC
39499960 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
1 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
39500025 ATAAATAATAATTTTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATA
66 ATAAATAATAATTTTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATA
39500090 AATTAAATAGAAAATAAATAATAATT
131 AATTAAATAGAAAATAAATAATAATT
39500116 TTGAATATATAATTAAATTTTATTATTTTGTAATT-AAAAGAGAAATAAATAAATTAAATAGAAA
1 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
39500180 ATAAATAATAATTTTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATA
66 ATAAATAATAATTTTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATA
39500245 AATTAAATAGAAAATAAATAATAATT
131 AATTAAATAGAAAATAAATAATAATT
39500271 T
1 T
39500272 AAAATTTGCT
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 121 0.78
156 35 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (156 bp):
TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
ATAAATAATAATTTTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATA
AATTAAATAGAAAATAAATAATAATT
Found at i:39500201 original size:77 final size:78
Alignment explanation
Indices: 39499960--39500271 Score: 617
Period size: 78 Copynumber: 4.0 Consensus size: 78
39499950 AACTTATCAC
39499960 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
1 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
39500025 ATAAATAATAATT
66 ATAAATAATAATT
39500038 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
1 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
39500103 ATAAATAATAATT
66 ATAAATAATAATT
39500116 TTGAATATATAATTAAATTTTATTATTTTGTAATT-AAAAGAGAAATAAATAAATTAAATAGAAA
1 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
39500180 ATAAATAATAATT
66 ATAAATAATAATT
39500193 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
1 TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
39500258 ATAAATAATAATT
66 ATAAATAATAATT
39500271 T
1 T
39500272 AAAATTTGCT
Statistics
Matches: 233, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
77 77 0.33
78 156 0.67
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (78 bp):
TTGAATATATAATTAAATTTTATTATTTTGTAATTAAAAAGAGAAATAAATAAATTAAATAGAAA
ATAAATAATAATT
Found at i:39500261 original size:20 final size:21
Alignment explanation
Indices: 39500224--39500265 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
39500214 ATTATTTTGT
39500224 AATTAAAAAGAGAAATAAATA
1 AATTAAAAAGAGAAATAAATA
*
39500245 AATTAAATAGA-AAATAAATA
1 AATTAAAAAGAGAAATAAATA
39500265 A
1 A
39500266 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AATTAAAAAGAGAAATAAATA
Found at i:39500704 original size:30 final size:31
Alignment explanation
Indices: 39500670--39500732 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
39500660 ACTTGTTTTA
*
39500670 TTGTTAA-TTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
* *
39500700 TTGTTAATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
39500731 TT
1 TT
39500733 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.62
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGGCAT
Found at i:39505481 original size:18 final size:19
Alignment explanation
Indices: 39505455--39505502 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
39505445 TGAATTTCAC
*
39505455 AATTCGAATAACTTT-AAT
1 AATTTGAATAACTTTAAAT
39505473 AATTTGAATAA-TTTAAAT
1 AATTTGAATAACTTTAAAT
*
39505491 AATTTAAATAAC
1 AATTTGAATAAC
39505503 AAATTGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (19 bp):
AATTTGAATAACTTTAAAT
Found at i:39505482 original size:9 final size:9
Alignment explanation
Indices: 39505461--39505501 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
39505451 TCACAATTCG
39505461 AATAACTTT-
1 AATAA-TTTA
*
39505470 AATAATTTG
1 AATAATTTA
39505479 AATAATTTA
1 AATAATTTA
39505488 AATAATTTA
1 AATAATTTA
39505497 AATAA
1 AATAA
39505502 CAAATTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 3 0.10
9 27 0.90
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
AATAATTTA
Found at i:39505610 original size:18 final size:19
Alignment explanation
Indices: 39505582--39505622 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
39505572 AACTACAAAA
39505582 AAAAGTTCAAAATAATTT-T
1 AAAAGTTCAAAAT-ATTTAT
39505601 AAAA-TTCAAAATATTTAT
1 AAAAGTTCAAAATATTTAT
39505619 AAAA
1 AAAA
39505623 AATTTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAGTTCAAAATATTTAT
Found at i:39505659 original size:27 final size:27
Alignment explanation
Indices: 39505613--39505705 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 27
39505603 AATTCAAAAT
*
39505613 ATTTATAAAAAAT-T-TCAAAATTTATA
1 ATTT-TAAAAAATATATAAAAATTTATA
* *
39505639 TTTTTAAAAAATATATAAAAATATAAAATA
1 ATTTTAAAAAATATATAAAAAT-T--TATA
* *
39505669 ATTCT-AAAAATATATAAAAAATTTAAA
1 ATTTTAAAAAATATAT-AAAAATTTATA
39505696 ATTTTAAAAA
1 ATTTTAAAAA
39505706 TTTTCTAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 8 0.15
26 4 0.08
27 12 0.23
28 5 0.10
29 11 0.21
30 12 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTTTAAAAAATATATAAAAATTTATA
Found at i:39505660 original size:10 final size:10
Alignment explanation
Indices: 39505645--39505688 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
39505635 TATATTTTTA
39505645 AAAAATATAT
1 AAAAATATAT
39505655 AAAAATATA-
1 AAAAATATAT
*
39505664 AAATAAT-TCT
1 AAA-AATATAT
39505674 AAAAATATAT
1 AAAAATATAT
39505684 AAAAA
1 AAAAA
39505689 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATATAT
Found at i:39505676 original size:19 final size:19
Alignment explanation
Indices: 39505643--39505696 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
39505633 TTTATATTTT
39505643 TAAAAAATATATAAAAATATA
1 TAAAAAAT-T-TAAAAATATA
*
39505664 -AAATAATTCTAAAAATATA
1 TAAAAAATT-TAAAAATATA
39505683 TAAAAAATTTAAAA
1 TAAAAAATTTAAAA
39505697 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAAATTTAAAAATATA
Found at i:39505685 original size:21 final size:18
Alignment explanation
Indices: 39505643--39505696 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
39505633 TTTATATTTT
*
39505643 TAAAAAATATATAAAAATA
1 TAAAAAATTTA-AAAAATA
39505662 TAAAATAATTCTAAAAATATA
1 TAAAA-AATT-TAAAAA-ATA
39505683 TAAAAAATTTAAAA
1 TAAAAAATTTAAAA
39505697 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 10 0.32
20 11 0.35
21 10 0.32
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAATTTAAAAAATA
Found at i:39506713 original size:22 final size:22
Alignment explanation
Indices: 39506687--39506735 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
39506677 ATATTGATAC
39506687 ATATAAAATATATT-TTTTAATT
1 ATATAAAAT-TATTATTTTAATT
*
39506709 ATAT--AATTATTATTTTATTT
1 ATATAAAATTATTATTTTAATT
39506729 ATATAAA
1 ATATAAA
39506736 TAAAAGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.17
20 14 0.61
22 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATAAAATTATTATTTTAATT
Found at i:39509187 original size:16 final size:16
Alignment explanation
Indices: 39509168--39509199 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39509158 AATTGTTTTA
39509168 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
39509184 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
39509200 ACTCCATTCT
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:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:39509478 original size:50 final size:50
Alignment explanation
Indices: 39509403--39509686 Score: 333
Period size: 50 Copynumber: 5.7 Consensus size: 50
39509393 AAGCTCTCTA
*
39509403 GTACACATAGTAGCCTCCACTTAGTACTACACATGCT-ACCTATCAATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATG-TGACCTATCAATCTG
* * *
39509453 GTACACGTAGTAGCCTGCACTTAGTACTACAC-TCGTGACTTATCCATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACAT-GTGACCTATCAATCTG
* * * * ** * *
39509503 ATACACGTAGTAGCCTGCACTTAGTACTATACACGTGATCGAAGTTAA-CGG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATCTG
* *
39509554 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCCG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTG
* * *
39509604 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTAACCTAATC-ATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-ATCAATCTG
*
39509654 ATACACATAGTAGCCTGCACTTAGTACTACACA
1 GTACACATAGTAGCCTGCACTTAGTACTACACA
39509687 CATGATCGAA
Statistics
Matches: 199, Mismatches: 28, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
49 5 0.03
50 152 0.76
51 40 0.20
52 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (50 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTG
Found at i:39509682 original size:151 final size:151
Alignment explanation
Indices: 39509403--39509716 Score: 479
Period size: 151 Copynumber: 2.1 Consensus size: 151
39509393 AAGCTCTCTA
* *
39509403 GTACACATAGTAGCCTCCACTTAGTACTACACATGCTACCTATCAATCTGGTACACGTAGTAGCC
1 GTACGCATAGTAGCCTCCACTTAGTACTACACATGCTACCTATCAATCCGGTACACGTAGTAGCC
* * * * *
39509468 TGCACTTAGTACTACACTCGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTAT
66 TGCACTTAGTACTACACACGTAACTAATCCATCTGATACACATAGTAGCCTGCACTTAGTACTAC
* **
39509533 ACACGTGATCGAAGTTAACGG
131 ACACATGATCGAAACTAACGG
*
39509554 GTACGCATAGTAGCCTGCACTTAGTACTACACATG-TGACCTATCAATCCGGTACACGTAGTAGC
1 GTACGCATAGTAGCCTCCACTTAGTACTACACATGCT-ACCTATCAATCCGGTACACGTAGTAGC
39509618 CTGCACTTAGTACTACACACGTAACCTAAT-CATCTGATACACATAGTAGCCTGCACTTAGTACT
65 CTGCACTTAGTACTACACACGTAA-CTAATCCATCTGATACACATAGTAGCCTGCACTTAGTACT
*
39509682 ACACACATGATCGAAACTATCGG
129 ACACACATGATCGAAACTAACGG
*
39509705 GTAAGCATAGTA
1 GTACGCATAGTA
39509717 TGTAATATCC
Statistics
Matches: 148, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
150 1 0.01
151 143 0.97
152 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (151 bp):
GTACGCATAGTAGCCTCCACTTAGTACTACACATGCTACCTATCAATCCGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTAACTAATCCATCTGATACACATAGTAGCCTGCACTTAGTACTAC
ACACATGATCGAAACTAACGG
Found at i:39509716 original size:101 final size:99
Alignment explanation
Indices: 39509403--39509687 Score: 347
Period size: 101 Copynumber: 2.8 Consensus size: 99
39509393 AAGCTCTCTA
* * *
39509403 GTACACATAGTAGCCTCCACTTAGTACTACACATGCTACCT-ATCAATCTGGTACACGTAGTAGC
1 GTACACATAGTAGCCTGCACTTAGTACTACACACG-TACCTAATC-ATCTGGTACACATAGTAGC
* * * *
39509467 CTGCACTTAGTACTACACTCGTGACTTATCCATCTG
64 CTGCACTTAGTACTACACACGTGACCTATCAATCCG
* * * * * * * * *
39509503 ATACACGTAGTAGCCTGCACTTAGTACTATACACGTGATCGAAGTTAACGGGTACGCATAGTAGC
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGT-ACCTAA-TCATCTGGTACACATAGTAGC
*
39509568 CTGCACTTAGTACTACACATGTGACCTATCAATCCG
64 CTGCACTTAGTACTACACACGTGACCTATCAATCCG
* *
39509604 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTAACCTAATCATCTGATACACATAGTAGCC
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGT-ACCTAATCATCTGGTACACATAGTAGCC
39509669 TGCACTTAGTACTACACAC
65 TGCACTTAGTACTACACAC
39509688 ATGATCGAAA
Statistics
Matches: 154, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
99 1 0.01
100 67 0.44
101 85 0.55
102 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (99 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACACGTACCTAATCATCTGGTACACATAGTAGCCT
GCACTTAGTACTACACACGTGACCTATCAATCCG
Found at i:39511056 original size:46 final size:46
Alignment explanation
Indices: 39511006--39511181 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
39510996 TGGTTGAGCA
39511006 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39511052 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
39511097 CATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
39511145 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39511182 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 61 0.55
47 28 0.25
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39511162 original size:93 final size:93
Alignment explanation
Indices: 39511003--39511174 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
39510993 GGATGGTTGA
39511003 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
39511068 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
39511096 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC-CGAACTCGTTGAG
39511160 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
39511175 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 1 0.01
93 75 0.99
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39514659 original size:15 final size:16
Alignment explanation
Indices: 39514623--39514652 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39514613 ACATATCATT
39514623 TATTTCATTATATCAA
1 TATTTCATTATATCAA
39514639 TATTTCA-TATATCA
1 TATTTCATTATATCA
39514653 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:39515523 original size:35 final size:35
Alignment explanation
Indices: 39515483--39515553 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
39515473 CTTGTTTATA
*
39515483 ACCTTACCACATCCTGGTCACTTAATGAACACATC
1 ACCTTACCACATCCTGGTCACATAATGAACACATC
39515518 ACCTTACCACATCCTGGTCACATAATGAACACATC
1 ACCTTACCACATCCTGGTCACATAATGAACACATC
39515553 A
1 A
39515554 TTCACATAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.08, T:0.24
Consensus pattern (35 bp):
ACCTTACCACATCCTGGTCACATAATGAACACATC
Found at i:39522212 original size:46 final size:45
Alignment explanation
Indices: 39522162--39522337 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
39522152 TGGTTGAGCA
39522162 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
39522208 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
39522253 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
39522301 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39522338 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:39522318 original size:93 final size:93
Alignment explanation
Indices: 39522159--39522330 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
39522149 GGATGGTTGA
* *
39522159 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39522224 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
39522252 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39522317 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
39522331 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39523765 original size:52 final size:51
Alignment explanation
Indices: 39523638--39523771 Score: 166
Period size: 52 Copynumber: 2.6 Consensus size: 51
39523628 TGGGGGCGTT
* *
39523638 ACATAGTAGCCTACACTTAGTACTACACATG-CTACCTAACAATCTGGTAC
1 ACATAGTAGCCTGCACTTAGTACTACACATGTCTACCTAACAATCTGGAAC
* * *
39523688 ACGTAGTAGCCTGCATTTAGTACTACACATGTC-ACCTAA-AACTGTCTTGAAC
1 ACATAGTAGCCTGCACTTAGTACTACACATGTCTACCTAACAA---TCTGGAAC
*
39523740 ACATAGTAGCCTGCACATAGTACTACACATGT
1 ACATAGTAGCCTGCACTTAGTACTACACATGT
39523772 TTTCTCACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
49 2 0.03
50 34 0.47
51 1 0.01
52 35 0.49
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (51 bp):
ACATAGTAGCCTGCACTTAGTACTACACATGTCTACCTAACAATCTGGAAC
Found at i:39526759 original size:15 final size:15
Alignment explanation
Indices: 39526735--39526793 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
39526725 ATAGACAACA
* *
39526735 AGAAAACCAAGATTG
1 AGAAATCCAAGATAG
*
39526750 AGAAGTCCAAGATAG
1 AGAAATCCAAGATAG
39526765 AGAAATCCAAGATA-
1 AGAAATCCAAGATAG
39526779 AGGAAATCCAAGATA
1 A-GAAATCCAAGATA
39526794 CAATATCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 1 0.03
15 38 0.97
ACGTcount: A:0.53, C:0.14, G:0.20, T:0.14
Consensus pattern (15 bp):
AGAAATCCAAGATAG
Found at i:39536116 original size:29 final size:29
Alignment explanation
Indices: 39536074--39536131 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39536064 TCTTTAGTGT
39536074 TCAATACAAATTCAAGGTAGGCTTCATAC
1 TCAATACAAATTCAAGGTAGGCTTCATAC
39536103 TCAATACAAATTCAAGGTAGGCTTCATAC
1 TCAATACAAATTCAAGGTAGGCTTCATAC
39536132 CCTTTCCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (29 bp):
TCAATACAAATTCAAGGTAGGCTTCATAC
Found at i:39543204 original size:180 final size:180
Alignment explanation
Indices: 39542884--39543226 Score: 508
Period size: 180 Copynumber: 1.9 Consensus size: 180
39542874 GAGCTACGAA
* ** *
39542884 ACTCCAAATTAAGATCCGTTAATTTTCTATGAAACTAAACTCATATATATTCTTACCAGAAAATT
1 ACTCCAAATTAAGAACCACTAATTTTCTATGAAACTAAACTCAAATATATTCTTACCAGAAAATT
* *
39542949 TTTAGAATTTTTGGTTTATCCAATTAGTACAGTATATTCATTAAAGATACCCCTAATTCACTATC
66 TTCAGAATTTTTAGTTTATCCAATTAGTACAGTATATTCATTAAAGATACCCCTAATTCACTATC
*
39543014 TGATAGTTCCGACCTCTCTTCACTAAAAATTATTTATTTCATGGTAATGG
131 TGACAGTTCCGACCTCTCTTCACTAAAAATTATTTATTTCATGGTAATGG
* * *
39543064 ACTCCAAATTAAGAACCACTAATTTTCTCA-GAACCTAGACTCAAATATATTCTTACCATAAAAT
1 ACTCCAAATTAAGAACCACTAATTTTCT-ATGAAACTAAACTCAAATATATTCTTACCAGAAAAT
* * * ** *
39543128 TTTCAGAATTTTTAGTTTTTCCAATTAGTACAGTTTATTCATTAAAGATACCTCTGTTTCACTGT
65 TTTCAGAATTTTTAGTTTATCCAATTAGTACAGTATATTCATTAAAGATACCCCTAATTCACTAT
**
39543193 CTTCCAGTTCCGACCTCTCTTCACTAAAAATTAT
130 CTGACAGTTCCGACCTCTCTTCACTAAAAATTAT
39543227 ATATCTTATG
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
180 143 0.99
181 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (180 bp):
ACTCCAAATTAAGAACCACTAATTTTCTATGAAACTAAACTCAAATATATTCTTACCAGAAAATT
TTCAGAATTTTTAGTTTATCCAATTAGTACAGTATATTCATTAAAGATACCCCTAATTCACTATC
TGACAGTTCCGACCTCTCTTCACTAAAAATTATTTATTTCATGGTAATGG
Found at i:39543587 original size:16 final size:16
Alignment explanation
Indices: 39543568--39543599 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39543558 AATTGTTTTA
39543568 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
39543584 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
39543600 ACTCCATTCT
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:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:39543868 original size:50 final size:50
Alignment explanation
Indices: 39543810--39544296 Score: 471
Period size: 50 Copynumber: 9.7 Consensus size: 50
39543800 CTGGTACGCA
* * *
39543810 TAGTAGCCTGCACTTAGTACCACACATGCGACCTATCAATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACG
* * * * *
39543860 TAGTAGCCTACACTTAGTACTACATACGTGACTTATCCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACG
** * * * * *
39543910 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAATCTGATACACG
* * ** *
39543961 TAGTAGCCGGCACTTAGTACTACACATGCAACCTATCAATC-CAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGA-TACACG
* *
39544011 TAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACG
* * ** * ** *
39544061 TAGTAGCCTGCACTTAGTACTACATATGTGATCGAAGTTAATGGGTATGCA--
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAATCTG-ATACACG
* * * * *
39544112 TAGTAGCCTACAGTTAGTACTACACATGTGACCTATCAATC-CAGTAAACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGA-TACACG
* *
39544162 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACG
* * * * * * *
39544212 TAGTAGCTTGCACTTAGTACTACACATGCGACCTAACAATCTGGTATAGG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACG
*
39544262 TAGTAGCCTGTACTTAGTACTACACACGTGACCTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTA
39544297 AAACTGTCTT
Statistics
Matches: 351, Mismatches: 74, Indels: 24
0.78 0.16 0.05
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 7 0.02
50 265 0.75
51 66 0.19
52 6 0.02
53 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACG
Found at i:39544065 original size:151 final size:151
Alignment explanation
Indices: 39543802--39544237 Score: 694
Period size: 151 Copynumber: 2.9 Consensus size: 151
39543792 GAAGGTCTCT
* *
39543802 GGTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCTATCAAT-CTGATACACGTAGTAG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCAG-TACACGTAGTAG
* * *
39543866 CCTACACTTAGTACTACATACGTGACTTATCCATCTAATACACGTAGTAGCCTGCACTTAGTACT
65 CCTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACT
39543931 ACACACGTGATCGAAGTTAACG
130 ACACACGTGATCGAAGTTAACG
* *
39543953 GGTACGCATAGTAGCCGGCACTTAGTACTACACATGCAACCTATCAATCCAGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCAGTACACGTAGTAGC
39544018 CTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
* * *
39544083 CATATGTGATCGAAGTTAATG
131 CACACGTGATCGAAGTTAACG
* * * * *
39544104 GGTATGCATAGTAGCCTACAGTTAGTACTACACATGTGACCTATCAATCCAGTAAACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCAGTACACGTAGTAGC
* * *
39544169 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCTTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
39544234 CACA
131 CACA
39544238 TGCGACCTAA
Statistics
Matches: 263, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 261 0.99
152 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCAGTACACGTAGTAGC
CTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
CACACGTGATCGAAGTTAACG
Found at i:39544116 original size:101 final size:98
Alignment explanation
Indices: 39543801--39544296 Score: 402
Period size: 101 Copynumber: 5.0 Consensus size: 98
39543791 CGAAGGTCTC
* * * *
39543801 TGGTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCTATCAATCTGATACACGTAGTAG
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACGTAGTAG
* * * *
39543866 CCTACACTTAGTACTACATACGTGACTTATCCATC
66 CCTGCACTTAGTACTACATATGTGACCTAT-CA-A
** * ** * * * * *
39543901 TAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACGCATAGT
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAATCTGATACACGTAGT
* * **
39543965 AGCCGGCACTTAGTACTACACATGCAACCTATCAA
64 AGCCTGCACTTAGTACTACATATGTGACCTATCAA
* * * *
39544000 TCCAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGT
1 T--GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACGTAGT
** *
39544065 AGCCTGCACTTAGTACTACATATGTGATCGAAGTTAA
64 AGCCTGCACTTAGTACTACATATGTGA-CCTA-TCAA
** * * * * *
39544102 TGGGTATGCATAGTAGCCTACAGTTAGTACTACACATGTGACCTATCAATC-CAGTAAACGTAGT
1 T-GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGA-TACACGTAGT
* * * *
39544166 AGCCTGCACTTAGTACTACACACGTGACCTAACCATC
64 AGCCTGCACTTAGTACTACATATGTGACCT-ATCA-A
* * * * * * * * *
39544203 TGATACACGTAGTAGCTTGCACTTAGTACTACACATGCGACCTAACAATCTGGTATAGGTAGTAG
1 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACGTAGTAG
* * *
39544268 CCTGTACTTAGTACTACACACGTGACCTA
66 CCTGCACTTAGTACTACATATGTGACCTA
39544297 AAACTGTCTT
Statistics
Matches: 314, Mismatches: 71, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
99 4 0.01
100 150 0.48
101 153 0.49
102 7 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (98 bp):
TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGATACACGTAGTAG
CCTGCACTTAGTACTACATATGTGACCTATCAA
Found at i:39544168 original size:201 final size:200
Alignment explanation
Indices: 39543810--39544293 Score: 528
Period size: 201 Copynumber: 2.4 Consensus size: 200
39543800 CTGGTACGCA
* *
39543810 TAGTAGCCTGCACTTAGTACCACACATGCGACCTATCAATCTGATACACGTAGTAGCCTACACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGCCTGCACTT
** * *
39543875 AGTACTACATACGTGACTTATCCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
66 AGTACTACATACGTGACGAATCAATCTAATACAC-TAGTAGCCTACACTTAGTACTACACACGTG
* * ** ** * *
39543940 ATCGAAGTTAACGGGTACGCATAGTAGCCGGCACTTAGTACTACACATGCAACCTATCAATCCAG
130 ATCCAAGTCAACCAGTAAACATAGTAGCCGGCACTTAGTACTACACACGCAACCTAACAAT-CAG
39544005 -TACACG
194 ATACACG
* * * *
39544011 TAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGCCTGCACTT
* * * * * *
39544076 AGTACTACATATGTGATCGAAGTTAATGGGT-ATGCA-TAGTAGCCTACAGTTAGTACTACACAT
66 AGTACTACATACGTGA-CGAA-TCAAT--CTAATACACTAGTAGCCTACACTTAGTACTACACAC
* * * ** *
39544139 GTGA-CCTA-TCAATCCAGTAAACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCAT
127 GTGATCCAAGTCAA-CCAGTAAACATAGTAGCCGGCACTTAGTACTACACACGCAACCTAACAAT
*
39544202 CTGATACACG
191 CAGATACACG
* * * * * *
39544212 TAGTAGCTTGCACTTAGTACTACACATGCGACCTAACAATCTGGTATAGGTAGTAGCCTGTACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGCCTGCACTT
*
39544277 AGTACTACACACGTGAC
66 AGTACTACATACGTGAC
39544294 CTAAAACTGT
Statistics
Matches: 234, Mismatches: 43, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
200 6 0.03
201 190 0.81
202 30 0.13
203 3 0.01
204 4 0.02
205 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (200 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGCCTGCACTT
AGTACTACATACGTGACGAATCAATCTAATACACTAGTAGCCTACACTTAGTACTACACACGTGA
TCCAAGTCAACCAGTAAACATAGTAGCCGGCACTTAGTACTACACACGCAACCTAACAATCAGAT
ACACG
Found at i:39544336 original size:151 final size:151
Alignment explanation
Indices: 39543802--39544296 Score: 552
Period size: 151 Copynumber: 3.3 Consensus size: 151
39543792 GAAGGTCTCT
* * * * * * *
39543802 GGTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCTATCAAT-CTG-ATACACGTAGTA
1 GGTATGCATAGTAGCCTACACTTAGTACTACACACGTGACCTATAAATCCAGTA-ACACGTAGTA
* * * * *
39543865 GCCTACACTTAGTACTACATACGTGACTTATCCATCTAATACACGTAGTAGCCTGCACTTAGTAC
65 GCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTAC
* * * * *
39543930 TACACACGTGATCGAAGTTAACG
130 TACACATGCGACCGAAG-CAATG
* ** * ** *
39543953 GGTACGCATAGTAGCCGGCACTTAGTACTACACATGCAACCTATCAATCCAGT-ACACGTAGTAG
1 GGTATGCATAGTAGCCTACACTTAGTACTACACACGTGACCTATAAATCCAGTAACACGTAGTAG
* *
39544017 CCTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACT
66 CCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACT
* * * *
39544082 ACATATGTGATCGAAGTTAATG
131 ACACATGCGACCGAAG-CAATG
* * *
39544104 GGTATGCATAGTAGCCTACAGTTAGTACTACACATGTGACCTATCAATCCAGTAA-ACGTAGTAG
1 GGTATGCATAGTAGCCTACACTTAGTACTACACACGTGACCTATAAATCCAGTAACACGTAGTAG
*
39544168 CCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCTTGCACTTAGTACT
66 CCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACT
* *
39544233 ACACATGCGACCTAA-CAATCT
131 ACACATGCGACCGAAGCAAT-G
* **
39544254 GGTATAG-GTAGTAGCCTGTACTTAGTACTACACACGTGACCTA
1 GGTAT-GCATAGTAGCCTACACTTAGTACTACACACGTGACCTA
39544297 AAACTGTCTT
Statistics
Matches: 309, Mismatches: 30, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
149 3 0.01
150 36 0.12
151 267 0.86
152 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (151 bp):
GGTATGCATAGTAGCCTACACTTAGTACTACACACGTGACCTATAAATCCAGTAACACGTAGTAG
CCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACT
ACACATGCGACCGAAGCAATG
Found at i:39544722 original size:19 final size:20
Alignment explanation
Indices: 39544694--39544740 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
39544684 AAGAACATGT
39544694 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
39544715 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
39544734 TATATAT
1 TATATAT
39544741 ACTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:39554317 original size:30 final size:30
Alignment explanation
Indices: 39554265--39554323 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39554255 CAAAAATCAT
* * *
39554265 ACTTTTACAAATTTTCATTTTGACCCCTAA
1 ACTTTCACAAATTTACACTTTGACCCCTAA
*
39554295 ACTTTCACATATTTACACTTTGACCCCTA
1 ACTTTCACAAATTTACACTTTGACCCCTA
39554324 GGCTCGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.03, T:0.41
Consensus pattern (30 bp):
ACTTTCACAAATTTACACTTTGACCCCTAA
Found at i:39555313 original size:3 final size:3
Alignment explanation
Indices: 39555283--39555338 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
39555273 GAGAGAAAGG
* * *
39555283 AGA AG- AGA AAA ATA AGA AAA AG- AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
39555329 AGA AGA AGA A
1 AGA AGA AGA A
39555339 AGAAAGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:39555579 original size:27 final size:27
Alignment explanation
Indices: 39555549--39555601 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
39555539 TAGGATTATG
39555549 TTATAAATTGTTGTGATTAGTTTAGTT
1 TTATAAATTGTTGTGATTAGTTTAGTT
*
39555576 TTATAAATTGTTGTGTTTAGTTTAGT
1 TTATAAATTGTTGTGATTAGTTTAGT
39555602 ATTTGGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.57
Consensus pattern (27 bp):
TTATAAATTGTTGTGATTAGTTTAGTT
Found at i:39555948 original size:50 final size:49
Alignment explanation
Indices: 39555894--39556051 Score: 129
Period size: 50 Copynumber: 3.1 Consensus size: 49
39555884 TAATTTTATG
39555894 GTTATTTTATTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTA
1 GTTATTTT-TTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTA
* * * * * * * **** * *
39555944 GTTATGTGTTTT-GTGATTTTTTAGTAATGTATTTAAAAAAAAATAATTTTATA
1 GTTAT-T-TTTTAGTAATTTATGA-TTAGGT-TATATAAATTGTTAGTGTT-TA
39555997 GTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTA
1 GTTATTTT-TTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTA
39556047 GTTAT
1 GTTAT
39556052 GTGTTTTGTG
Statistics
Matches: 75, Mismatches: 26, Indels: 14
0.65 0.23 0.12
Matches are distributed among these distances:
50 20 0.27
51 20 0.27
52 20 0.27
53 15 0.20
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (49 bp):
GTTATTTTTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTA
Found at i:39556001 original size:103 final size:102
Alignment explanation
Indices: 39555854--39556075 Score: 394
Period size: 103 Copynumber: 2.2 Consensus size: 102
39555844 TAGGGTATTA
*
39555854 TGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATGGTTATTTTATTAGTAATTTATGATT
1 TGATTTTTTAGTAATGT-ATTTAAAAAAAATAATTTTATAGTTATTTTATTAGTAATTTATGATT
39555919 AGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTG
65 AGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTG
*
39555957 TGATTTTTTAGTAATGTATTTAAAAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATT
1 TGATTTTTTAGTAATGTATTT-AAAAAAAATAATTTTATAGTTATTTTATTAGTAATTTATGATT
39556022 AGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTG
65 AGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTG
39556060 TGATTTTTT--TAATGTA
1 TGATTTTTTAGTAATGTA
39556076 ATTCTTATAT
Statistics
Matches: 116, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
101 7 0.06
102 4 0.03
103 105 0.91
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (102 bp):
TGATTTTTTAGTAATGTATTTAAAAAAAATAATTTTATAGTTATTTTATTAGTAATTTATGATTA
GGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTG
Found at i:39556094 original size:103 final size:103
Alignment explanation
Indices: 39555789--39556104 Score: 392
Period size: 103 Copynumber: 3.0 Consensus size: 103
39555779 TTATAGTTAT
* * * * * *
39555789 TTATTTTGTTAATAATTTATGGGATTAGG-T-TACAAATTGTTAGTATTTAGTGGTTTAGGGTAT
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTATATAAATTGTTAGTGTTTAGT--TAT-GTGTTT
* *
39555852 TATGATTTTTTAGTAATGTAA-TTTAAAAAAAATAATTTTATGG
61 TGTGATTTTTTA-TAATGTAATTTTAAAAAAAATAATTTTATAG
*
39555895 TTATTTTATTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTGTGA
*
39555960 TTTTTTAGTAATGT-ATTTAAAAAAAAATAATTTTATAG
66 TTTTTTA-TAATGTAATTTTAAAAAAAATAATTTTATAG
39555998 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTGTGA
* * **
39556063 TTTTTT-TAATGTAATTCTTATATAATGTAATTTTATA-
66 TTTTTTATAATGTAATT-TTAAAAAAAATAATTTTATAG
39556100 TTATT
1 TTATT
39556105 ATTTATTCAT
Statistics
Matches: 189, Mismatches: 16, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
101 6 0.03
102 9 0.05
103 127 0.67
104 9 0.05
105 1 0.01
106 37 0.20
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.53
Consensus pattern (103 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTGTGA
TTTTTTATAATGTAATTTTAAAAAAAATAATTTTATAG
Found at i:39556100 original size:15 final size:16
Alignment explanation
Indices: 39556069--39556100 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39556059 GTGATTTTTT
39556069 TAATGTAATTCTTATA
1 TAATGTAATTCTTATA
39556085 TAATGTAATT-TTATA
1 TAATGTAATTCTTATA
39556100 T
1 T
39556101 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TAATGTAATTCTTATA
Found at i:39558437 original size:46 final size:44
Alignment explanation
Indices: 39558287--39558497 Score: 183
Period size: 46 Copynumber: 4.6 Consensus size: 44
39558277 TCACTTGTGT
* * * *
39558287 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA-
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTAC--GA-GAC
* * *
39558333 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCAAC-ATTGAGAC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTA-CGAGAC
* * * *
39558379 GAGTACTAGTGTAAGACATGTTTGGGACATGCATCAGCTTCGAGAT
1 GAG--CCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGAC
*
39558425 GTAAGCCAGTGTAAGACATGTCTGGGACATGCATTAGCTACGAGAC
1 G--AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGAC
* *
39558471 GTGCCAGTGTAAGACCATGTTTGGGAC
1 GAGCCAGTGTAAGA-CATGTCTGGGAC
39558498 GTGGCATCGG
Statistics
Matches: 135, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
44 12 0.09
45 13 0.10
46 66 0.49
47 26 0.19
48 18 0.13
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (44 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGAC
Found at i:39565979 original size:24 final size:24
Alignment explanation
Indices: 39565951--39565996 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39565941 TGACTTAATT
39565951 TCATTACACCATCCAA-TTCATATA
1 TCATTACA-CATCCAATTTCATATA
* *
39565975 TCATTTCACATTCAATTTCATA
1 TCATTACACATCCAATTTCATA
39565997 GTCTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (24 bp):
TCATTACACATCCAATTTCATATA
Found at i:39568029 original size:46 final size:46
Alignment explanation
Indices: 39567976--39568232 Score: 172
Period size: 46 Copynumber: 5.5 Consensus size: 46
39567966 TTGCGTGTGT
39567976 TAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGA-TATGAGAGC
** * * * *
39568022 TAGTGTAAGACCATGTCTAGGG-CATGGCATC-GGTATTGAGACGAGGGC
1 TAGTGTAAGA-CATGTCT-GGGACAT-GCATCAGCCA-CGATATGAGAGC
* * * * *
39568070 TAGTGTAAGACATGTCTGGAACATGCATCGGCCTCGAGACGTA-AGC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGATATG-AGAGC
* * ** * *
39568116 CAATGTAAGACATGTCTGGGACATGCATTGGCTACGA-ATGATAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGATATGAGAGC
* * *
39568161 CAGTGTAAGACCATGTCTGGGACATGGCATCAACTTGA-GATAT--GAGC
1 TAGTGTAAGA-CATGTCTGGGACAT-GCATCAGC--CACGATATGAGAGC
39568208 TAGTGTAAGACCATGTCT-GGACATG
1 TAGTGTAAGA-CATGTCTGGGACATG
39568233 GCATTTGCAC
Statistics
Matches: 171, Mismatches: 26, Indels: 29
0.76 0.12 0.13
Matches are distributed among these distances:
44 1 0.01
45 15 0.09
46 76 0.44
47 49 0.29
48 26 0.15
49 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGATATGAGAGC
Found at i:39574078 original size:50 final size:50
Alignment explanation
Indices: 39574019--39574119 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
39574009 GTGGTTACCG
39574019 AGAGAGTGGGGCCAGTTGCTTACCAATTGGATTTACCACTAAAATTGGAA
1 AGAGAGTGGGGCCAGTTGCTTACCAATTGGATTTACCACTAAAATTGGAA
* *
39574069 AGAGAGTGGGGCCTGTTGCTTACCGATTGGATTTACCACTAAAATTGGAA
1 AGAGAGTGGGGCCAGTTGCTTACCAATTGGATTTACCACTAAAATTGGAA
39574119 A
1 A
39574120 AGATTCACTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (50 bp):
AGAGAGTGGGGCCAGTTGCTTACCAATTGGATTTACCACTAAAATTGGAA
Found at i:39575297 original size:27 final size:26
Alignment explanation
Indices: 39575273--39575380 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 26
39575263 TAGAATACTT
39575273 TAGTTTACTAAAATTACCAAAATACCCC
1 TAGTTT-CTAAAATTACCAAAATA-CCC
*
39575301 TAGTTTGTAAAATTACCAAAATACCC
1 TAGTTTCTAAAATTACCAAAATACCC
* * * *
39575327 TTGGTTTGTGAAATTACCGAAATACCC
1 -TAGTTTCTAAAATTACCAAAATACCC
* *
39575354 TCAATTTGTAAAATTACCAAAATACCC
1 T-AGTTTCTAAAATTACCAAAATACCC
39575381 CTGAATTACA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.06
27 60 0.86
28 6 0.09
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (26 bp):
TAGTTTCTAAAATTACCAAAATACCC
Found at i:39575403 original size:54 final size:54
Alignment explanation
Indices: 39575283--39575408 Score: 141
Period size: 54 Copynumber: 2.3 Consensus size: 54
39575273 TAGTTTACTA
* * ** **
39575283 AAATTACCA-AAATACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTG
1 AAATTA-CAGAAATACCCTC-AATTTGTAAAATTACCAAAATACCCCTGAATTGAC
*
39575337 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGAATT-AC
1 AAATTACAGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGAATTGAC
39575390 AAAGTTACAGAAATACCCT
1 AAA-TTACAGAAATACCCT
39575409 TGACTTTCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
53 4 0.07
54 56 0.92
55 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (54 bp):
AAATTACAGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGAATTGAC
Found at i:39575458 original size:27 final size:27
Alignment explanation
Indices: 39575419--39575470 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
39575409 TGACTTTCTA
39575419 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
39575446 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
39575471 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:39575568 original size:27 final size:27
Alignment explanation
Indices: 39575523--39575614 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
39575513 TACCCCTATT
*
39575523 AGGTAAA-AGACCGTAAAGCCCCTGTA
1 AGGTAAAGTGACCGTAAAGCCCCTGTA
*
39575549 GGGTAAAGTGACCGTAAAGCCCCTGTA
1 AGGTAAAGTGACCGTAAAGCCCCTGTA
*
39575576 AGGTAACGTGACCGTAATA-CCCCTGTA
1 AGGTAAAGTGACCGTAA-AGCCCCTGTA
* *
39575603 TGGTAAAATGAC
1 AGGTAAAGTGAC
39575615 GAATATGCCC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
26 6 0.11
27 50 0.88
28 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
AGGTAAAGTGACCGTAAAGCCCCTGTA
Found at i:39576806 original size:25 final size:24
Alignment explanation
Indices: 39576773--39576820 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
39576763 TTATAACATG
* * *
39576773 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
39576797 AAAAGTGACCATTATACCCCTAGG
1 AAAA-TGACCATTATACCCCTAGG
39576821 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:39576882 original size:20 final size:20
Alignment explanation
Indices: 39576857--39576927 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
39576847 ATTTTGATAA
*
39576857 ACATGATATGTATAATATGC
1 ACATGATATGTATGATATGC
* *
39576877 ACATGACATGTATGATGTGC
1 ACATGATATGTATGATATGC
39576897 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
39576917 ACATGAGATGT
1 ACATGATATGT
39576928 TCATAAATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39577029 original size:24 final size:24
Alignment explanation
Indices: 39576972--39577124 Score: 229
Period size: 24 Copynumber: 6.4 Consensus size: 24
39576962 GGAGGAAGTG
39576972 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
39576996 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
39577019 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
39577043 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
39577067 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
39577090 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
39577114 TAAAAGAGGCT
1 CAAAAG-GGCT
39577125 AGGCCTCCAG
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
23 44 0.37
24 71 0.60
25 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:39577041 original size:47 final size:47
Alignment explanation
Indices: 39576972--39577124 Score: 227
Period size: 47 Copynumber: 3.2 Consensus size: 47
39576962 GGAGGAAGTG
39576972 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
39577019 CAAAAGGGCTTATGCCCTAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
* *
39577067 -TAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTAT
*
39577114 TAAAAGAGGCT
1 CAAAAG-GGCT
39577125 AGGCCTCCAG
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
47 65 0.68
48 26 0.27
49 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (47 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:39577088 original size:71 final size:71
Alignment explanation
Indices: 39576972--39577124 Score: 261
Period size: 71 Copynumber: 2.1 Consensus size: 71
39576962 GGAGGAAGTG
*
39576972 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
39577037 AGTTAT
66 AGTTAT
* *
39577043 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
39577108 AGTTAT
66 AGTTAT
*
39577114 TAAAAGAGGCT
1 CAAAAG-GGCT
39577125 AGGCCTCCAG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 73 0.95
72 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (71 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
AGTTAT
Found at i:39579082 original size:29 final size:30
Alignment explanation
Indices: 39579049--39579106 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
39579039 AAATCGATTT
*
39579049 TCAA-GTATAGGGGGAAAATGGTCATTTTG
1 TCAAGGTATAAGGGGAAAATGGTCATTTTG
*
39579078 TCAAGGTCTAAGGGGAAAATGGTCATTTT
1 TCAAGGTATAAGGGGAAAATGGTCATTTT
39579107 ACTTAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (30 bp):
TCAAGGTATAAGGGGAAAATGGTCATTTTG
Found at i:39579610 original size:47 final size:47
Alignment explanation
Indices: 39579456--39579667 Score: 161
Period size: 47 Copynumber: 4.5 Consensus size: 47
39579446 TGCGTGAGCT
* * * *
39579456 AGTGTAAGA-CATGTCTAGGACATGTATCGGCCAC-ATTATGAGAG-C
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGA-GATGAGAGTC
* ** * * * *
39579501 TAGCGTAAGACCATGTCCAGGACATGGCATCGGC-ATTGAGACGAGGGTG
1 -AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTA-CGAGATGAGAGTC
* *
39579550 AGTGTATGA-CATGTCTGGGACATGCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGAGAGTC
* * *
39579596 AGTGTAAGACCATGT-TAGGGACATGGCATCGACT-TGAGAT-ATGAGCC
1 AGTGTAAGACCATGTCT-GGGACAT-GCATCGGCTACGAGATGA-GAGTC
39579643 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
39579668 GCATTGGCAC
Statistics
Matches: 133, Mismatches: 22, Indels: 22
0.75 0.12 0.12
Matches are distributed among these distances:
46 35 0.26
47 69 0.52
48 28 0.21
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGAGAGTC
Found at i:39579657 original size:94 final size:95
Alignment explanation
Indices: 39579450--39579667 Score: 232
Period size: 94 Copynumber: 2.3 Consensus size: 95
39579440 GTCACTTGCG
* * * *
39579450 TGAGCTAGTGTAAGACATGTCTAGGACATGTATCGGCCACATTATGAGAGCTAGCGTAAGACCAT
1 TGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCTAGCGTAAGACCAT
*
39579515 GTCCAGGACATGGCATCGGCATTGAGACGA
66 GTCCAGGACATGGCATCGACATTGAGACGA
* ** * * * *
39579545 -GGGTGAGTGTATGACATGTCTGGGACATGCATCGGCTACGA-GATGATAG-TCAGTGTAAGACC
1 TGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGAGCT-AGCGTAAGACC
* *
39579607 ATGT-TAGGGACATGGCATCGAC-TTGAGA-TA
64 ATGTCCA-GGACATGGCATCGACATTGAGACGA
39579637 TGAGCCAGTGTAAGACCATGTCTGGGACATG
1 TGAGCCAGTGTAAGA-CATGTCTGGGACATG
39579668 GCATTGGCAC
Statistics
Matches: 101, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
92 1 0.01
93 18 0.18
94 81 0.80
95 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (95 bp):
TGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCTAGCGTAAGACCAT
GTCCAGGACATGGCATCGACATTGAGACGA
Found at i:39579668 original size:47 final size:47
Alignment explanation
Indices: 39579505--39579671 Score: 173
Period size: 47 Copynumber: 3.6 Consensus size: 47
39579495 GAGAGCTAGC
** * * *
39579505 GTAAGACCATGTCCAGGACATGGCATCGGCATTGAGACGA-GGGTGAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGA-TATGAGTCAGT
* *
39579553 GTATGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGAT-AGTCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCT-TGAGAT-ATGAGTCAGT
* *
39579599 GTAAGACCATGT-TAGGGACATGGCATCGACTTGAGATATGAGCCAGT
1 GTAAGACCATGTCT-GGGACATGGCATCGGCTTGAGATATGAGTCAGT
39579646 GTAAGACCATGTCTGGGACATGGCAT
1 GTAAGACCATGTCTGGGACATGGCAT
39579672 TGGCACCTTA
Statistics
Matches: 100, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
45 1 0.01
46 26 0.26
47 59 0.59
48 14 0.14
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.23
Consensus pattern (47 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATATGAGTCAGT
Found at i:39582551 original size:7 final size:7
Alignment explanation
Indices: 39582536--39582573 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
39582526 TCATCAAAGC
*
39582536 AAAACAA
1 AAAATAA
39582543 AAAATAA
1 AAAATAA
39582550 AAAATAA
1 AAAATAA
39582557 AAAA-ATA
1 AAAATA-A
39582564 AAAATAA
1 AAAATAA
39582571 AAA
1 AAA
39582574 GAGAAGGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 1 0.04
7 26 0.93
8 1 0.04
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAATAA
Found at i:39582568 original size:14 final size:15
Alignment explanation
Indices: 39582541--39582573 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
39582531 AAAGCAAAAC
39582541 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
39582556 AAAAAAT-AAAAATA
1 AAAAAATAAAAAATA
39582570 AAAA
1 AAAA
39582574 GAGAAGGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:39585586 original size:47 final size:46
Alignment explanation
Indices: 39585517--39585644 Score: 177
Period size: 47 Copynumber: 2.8 Consensus size: 46
39585507 TATGTGTGCT
*
39585517 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGA-AATTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACAA-GAA-CC
* * * * *
39585564 AGTGTAAGACATATCTGGGACATGCATCAGCATTGAGACGAGAACT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACAAGAACC
39585610 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCG
39585645 CGGTAGATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
46 33 0.46
47 37 0.52
48 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACAAGAACC
Found at i:39585628 original size:46 final size:47
Alignment explanation
Indices: 39585514--39585835 Score: 192
Period size: 49 Copynumber: 6.8 Consensus size: 47
39585504 TGATATGTGT
* *
39585514 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGAAATTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGAAATGAA
* * * *
39585561 GCCAGTGTAAGACATATCTGGGACATGCATCAGCATTGAGACGA-GAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGA-AATGAA
* * *
39585608 -CTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGGTAGAT-AA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCG-AG-AAATGAA
* * * ** * ** *
39585655 GCTAGTGTAAGACCTGTCTAGGACATGGCGTTGGC-T-TA-TCATG-T
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCATCGAGAAATGAA
* * * * * *
39585699 GTTAGTGTAAGACCTGTCTGGGACATGGCATCGAG-ACCAATAGATGAGA
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATC-AGCATCGAGAAATGA-A
* * * * ** *
39585748 GCCAGTGTAAGACCTGTCTGGGACATAGCATCGGCCTCGCTATATGAAA
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCATCGAGAAATG-AA
* *
39585797 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCATC
39585836 TTAACCCATG
Statistics
Matches: 216, Mismatches: 43, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
44 30 0.14
45 1 0.00
46 34 0.16
47 47 0.22
48 27 0.12
49 53 0.25
50 24 0.11
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGAAATGAA
Found at i:39588101 original size:40 final size:40
Alignment explanation
Indices: 39588041--39588224 Score: 232
Period size: 40 Copynumber: 4.6 Consensus size: 40
39588031 TATTCGAATG
*
39588041 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
39588081 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* *
39588121 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
39588161 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
39588201 ATATCCGAGCTAAGA-CTCGAAGGC
1 ATATCCGGGCTAAGATC-CGAAGGC
39588225 CTTGTGCGAG
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 3 0.02
40 121 0.95
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:39588174 original size:80 final size:80
Alignment explanation
Indices: 39588041--39588260 Score: 270
Period size: 80 Copynumber: 2.8 Consensus size: 80
39588031 TATTCGAATG
* * *
39588041 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGACTATATCCGGGCTAAGATCCCGAAGGC
* *
39588105 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
39588121 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGACTATATCCGGGCTAAGATCCCGAAGGC
*
39588185 ATTTATGCTAGTGACC
65 ATTTATGCGAGTGACC
* * * * **
39588201 ATATCCGAGCTAAGACTCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGACTATATCCGGGCTAAGATCCCGAAG
39588261 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
78 14 0.11
79 20 0.16
80 90 0.73
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGACTATATCCGGGCTAAGATCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:39596210 original size:40 final size:40
Alignment explanation
Indices: 39596118--39596334 Score: 234
Period size: 39 Copynumber: 5.5 Consensus size: 40
39596108 TATTCGAATG
* *
39596118 ATATCCGGGCTAAG-TCCCGAA-GCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
39596157 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
39596197 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
39596237 ATAT-CGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * * **
39596276 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
39596315 ATATCC-GGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGATCCGAAG
39596335 ATACTTGGGT
Statistics
Matches: 151, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
37 7 0.05
38 6 0.04
39 68 0.45
40 68 0.45
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:39596249 original size:79 final size:78
Alignment explanation
Indices: 39596118--39596334 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 78
39596108 TATTCGAATG
* * *
39596118 ATATCCGGGCTAAGTCCCGAA-GCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGACTATAT-CGGGCTAAGATCCGAAGGCA
* *
39596182 TTTGTGCGAGTTG-CT
64 TTTATGCGAG-TGACC
*
39596197 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCGGGCTAAG-TCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGACTATATCGGGCTAAGAT-CCGAAGGCA
*
39596261 TTTATGCTAGTGACC
64 TTTATGCGAGTGACC
* * ** *
39596276 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAA-ATCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGACTATATCGGGCTAAGATCCGAAG
39596335 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
77 6 0.05
78 25 0.21
79 70 0.58
80 19 0.16
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (78 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGACTATATCGGGCTAAGATCCGAAGGCATT
TATGCGAGTGACC
Found at i:39604367 original size:19 final size:19
Alignment explanation
Indices: 39604343--39604388 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
39604333 ACATGGACAC
39604343 TTTTATTTGTTAATTTTGT
1 TTTTATTTGTTAATTTTGT
39604362 TTTTATTTGTTAATTTTGT
1 TTTTATTTGTTAATTTTGT
*
39604381 CTTTATTT
1 TTTTATTT
39604389 ACTGGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (19 bp):
TTTTATTTGTTAATTTTGT
Found at i:39608989 original size:50 final size:48
Alignment explanation
Indices: 39608859--39609326 Score: 312
Period size: 48 Copynumber: 9.8 Consensus size: 48
39608849 CCATGGCGAA
**
39608859 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAGGAT
* * **
39608907 ATGTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCAACACAGGTAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CAGG-AT
* **
39608955 ATGAGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAGGAT
* * * *
39609003 A-G-GTG-TCAGTGTAAGACCATGTTTGGGACATGCCATCGGTACC-GATAT
1 ATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGG--CCAG-GAT
* * ** *
39609051 ATGAGAGCCAATGTAAGACCATGTCTAAGACATGGCATCAGCGTCA--AT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-G-GCCAGGAT
* * * * **
39609099 ATGTGAGCCAGTGTAAGACTATGTCTGGGACATGGCATAGGCCTTGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAGGAT
* * * ** * *
39609147 AT--GTGTTAGTGAAAGACCATGAT-TGGGACATGGTGTCTGCACTGGTAT
1 ATGAGAGCTAGTGTAAGACCATG-TCTGGGACATGGCATCGGC-CAGG-AT
* * ***
39609195 ATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAGGAT
* * * * * * * * *
39609243 ATGTGAGCCAGTGTAAGACCATGTTTGGAATATGGCACCGG-TATTGTT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-GGAT
* * *
39609291 ATGAAAGCTAGTGTAAAACCATGTCTAGGACATGGC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGC
39609327 TTCGACATGA
Statistics
Matches: 326, Mismatches: 71, Indels: 46
0.74 0.16 0.10
Matches are distributed among these distances:
45 1 0.00
46 91 0.28
47 9 0.03
48 129 0.40
49 7 0.02
50 87 0.27
51 1 0.00
52 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (48 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAGGAT
Found at i:39609003 original size:96 final size:96
Alignment explanation
Indices: 39608859--39609136 Score: 367
Period size: 96 Copynumber: 2.9 Consensus size: 96
39608849 CCATGGCGAA
*
39608859 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGTCAGTGTAAGAC
1 ATGAGAGCTAATGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGTCAGTGTAAGAC
*
39608924 CATGTCTGGGACATGGCATCAACACAGGTAT
66 CATGTCTGGGACATGGCATCAACACAGATAT
* *
39608955 ATGAGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATAGGTGTCAGTGTAAGAC
1 ATGAGAGCTAATGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGTCAGTGTAAGAC
* * *** *
39609020 CATGTTTGGGACATGCCATCGGTACCGATAT
66 CATGTCTGGGACATGGCATCAACACAGATAT
* ** * * ** *
39609051 ATGAGAGCCAATGTAAGACCATGTCTAAGACATGGCATCAGCGTCAATATGTGAGCCAGTGTAAG
1 ATGAGAGCTAATGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGT--GTCAGTGTAAG
*
39609116 ACTATGTCTGGGACATGGCAT
64 ACCATGTCTGGGACATGGCAT
39609137 AGGCCTTGAT
Statistics
Matches: 158, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
96 130 0.82
98 28 0.18
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (96 bp):
ATGAGAGCTAATGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGTCAGTGTAAGAC
CATGTCTGGGACATGGCATCAACACAGATAT
Found at i:39609135 original size:144 final size:143
Alignment explanation
Indices: 39608916--39609266 Score: 450
Period size: 144 Copynumber: 2.4 Consensus size: 143
39608906 TATGTGTCAG
* * * * *
39608916 TGTAAGACCATGTCTGGGACATGGCATCAACACAGGTATATGAGAGCTACTGTAAGACCATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATCAGCTCA---ATATGTGAGCCAGTGTAAGACCATGTCT
* * * *
39608981 GGGACATGGCATCGGCCTTGATAGGTGTCAGTGTAAGACCATGTTTGGGACATGCCATCGGTACC
63 GGGACATGGCATAGGCCTTGATAGGTGTCAGTGAAAGACCATGATTGGGACATGCCATCGGCACC
39609046 GATATATGAGAGCCAA
128 GATATATGAGAGCCAA
** *
39609062 TGTAAGACCATGTCTAAGACATGGCATCAGCGTCAATATGTGAGCCAGTGTAAGACTATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCAGC-TCAATATGTGAGCCAGTGTAAGACCATGTCTGG
* * *** * * *
39609127 GACATGGCATAGGCCTTGATATGTGTTAGTGAAAGACCATGATTGGGACATGGTGTCTGCACTGG
65 GACATGGCATAGGCCTTGATAGGTGTCAGTGAAAGACCATGATTGGGACATGCCATCGGCACCGA
*
39609192 TATATGAGAGCCAG
130 TATATGAGAGCCAA
* *
39609206 TGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATGTGAGCCAGTGTAAGACCATGT
1 TGTAAGACCATGTCTGGGACATGGCATCAG-CTCAATATGTGAGCCAGTGTAAGACCATGT
39609267 TTGGAATATG
Statistics
Matches: 177, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
144 146 0.82
145 1 0.01
146 28 0.16
147 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (143 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCTCAATATGTGAGCCAGTGTAAGACCATGTCTGGG
ACATGGCATAGGCCTTGATAGGTGTCAGTGAAAGACCATGATTGGGACATGCCATCGGCACCGAT
ATATGAGAGCCAA
Found at i:39609294 original size:96 final size:97
Alignment explanation
Indices: 39608859--39609326 Score: 348
Period size: 96 Copynumber: 4.9 Consensus size: 97
39608849 CCATGGCGAA
* * * * *
39608859 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATAT--GTGTCAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAGCCAGTGTAAG
** *
39608922 ACCATGTCTGGGACATGGCATC-AACACAGGTAT
66 ACCATGTCTGGGACATGGCATCGGCCTCA-G-AT
* * * * * *
39608955 ATGAGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATA-G-GTGTCAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAGCCAGTGTAAG
* * * *
39609018 ACCATGTTTGGGACATGCCATCGGTACC-GATAT
66 ACCATGTCTGGGACATGGCATCGG--CCTCAGAT
* * * * ** *
39609051 ATGAGAGCCAATGTAAGACCATGTCT-AAGACATGGCATCAGCGTCAATATGTGAGCCAGTGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGA-ACATGGCATCGGCATTGATATGAGAGCCAGTGTAA
* * *
39609115 GACTATGTCTGGGACATGGCATAGGCCT-TGAT
65 GACCATGTCTGGGACATGGCATCGGCCTCAGAT
* ** * * ** * *
39609147 AT--GTGTTAGTGAAAGACCATGAT-TGGGACATGGTGTCTGCACTGGTATATGAGAGCCAGTGT
1 ATGAGAGCCAGTGTAAGACCATG-TCTGGAACATGGCATCGGCA-TTG-ATATGAGAGCCAGTGT
*
39609209 AAGACCATGTTTGGGACATGGCATCGGCCTCA-AT
63 AAGACCATGTCTGGGACATGGCATCGGCCTCAGAT
* * * * * * * * *
39609243 ATGTGAGCCAGTGTAAGACCATGTTTGGAATATGGCACCGGTATTGTTATGAAAGCTAGTGTAAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAGCCAGTGTAAG
*
39609308 ACCATGTCTAGGACATGGC
66 ACCATGTCTGGGACATGGC
39609327 TTCGACATGA
Statistics
Matches: 297, Mismatches: 59, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
94 25 0.08
95 2 0.01
96 207 0.70
97 4 0.01
98 58 0.20
99 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (97 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAGCCAGTGTAAG
ACCATGTCTGGGACATGGCATCGGCCTCAGAT
Found at i:39609314 original size:240 final size:240
Alignment explanation
Indices: 39608863--39609326 Score: 628
Period size: 240 Copynumber: 1.9 Consensus size: 240
39608853 GGCGAAATGA
* * *
39608863 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGTCAGTGTAAGACCATG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATAGGCCTTGATATGTGTCAGTGAAAGACCATG
*
39608928 TCTGGGACATGGCATCAACACAGGTATATGAGAGCTACTGTAAGACCATGTCTGGGACATGGCAT
66 TCTGGGACATGGCATCAACACAGGTATATGAGAGCCACTGTAAGACCATGTCTGGGACATGGCAT
** * * * * *
39608993 CGGCCTTGATAGGTGTCAGTGTAAGACCATGTTTGGGACATGCCATCGGTACCGATATATGAGAG
131 CGGCCTCAATAGGAGCCAGTGTAAGACCATGTTTGGAACATGCCACCGGTACCGATATATGAAAG
*
39609058 CCAATGTAAGACCATGTCTAAGACATGGCATCAGCGTCAATATGT
196 CCAATGTAAAACCATGTCTAAGACATGGCATCAGCGTCAATATGT
* *
39609103 GAGCCAGTGTAAGACTATGTCTGGGACATGGCATAGGCCTTGATATGTGTTAGTGAAAGACCATG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATAGGCCTTGATATGTGTCAGTGAAAGACCATG
** ** * * *
39609168 AT-TGGGACATGGTGTCTGCACTGGTATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCA
66 -TCTGGGACATGGCATCAACACAGGTATATGAGAGCCACTGTAAGACCATGTCTGGGACATGGCA
* * **
39609232 TCGGCCTCAATATGTGAGCCAGTGTAAGACCATGTTTGGAATATGGCACCGGTATTG-T-TATGA
130 TCGGCCTCAATA-G-GAGCCAGTGTAAGACCATGTTTGGAACATGCCACCGGTACCGATATATGA
* * *
39609295 AAGCTAGTGTAAAACCATGTCTAGGACATGGC
193 AAGCCAATGTAAAACCATGTCTAAGACATGGC
39609327 TTCGACATGA
Statistics
Matches: 193, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
240 156 0.81
241 3 0.02
242 34 0.18
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (240 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATAGGCCTTGATATGTGTCAGTGAAAGACCATG
TCTGGGACATGGCATCAACACAGGTATATGAGAGCCACTGTAAGACCATGTCTGGGACATGGCAT
CGGCCTCAATAGGAGCCAGTGTAAGACCATGTTTGGAACATGCCACCGGTACCGATATATGAAAG
CCAATGTAAAACCATGTCTAAGACATGGCATCAGCGTCAATATGT
Found at i:39617659 original size:25 final size:26
Alignment explanation
Indices: 39617631--39617690 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 26
39617621 AGTCCTATTT
39617631 GTGTTAT--AAACAACTTTTATGAATG
1 GTGTTATGAAAAC-ACTTTTATGAATG
39617656 GTGTTAGCATGAAAACACTTTTATGAATG
1 GTGTT---ATGAAAACACTTTTATGAATG
39617685 GTGTTA
1 GTGTTA
39617691 CAGACACTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
25 5 0.17
26 1 0.03
28 2 0.07
29 18 0.60
30 4 0.13
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (26 bp):
GTGTTATGAAAACACTTTTATGAATG
Found at i:39624452 original size:40 final size:40
Alignment explanation
Indices: 39624405--39624588 Score: 262
Period size: 40 Copynumber: 4.6 Consensus size: 40
39624395 TTCGGACAAG
* *
39624405 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
39624445 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
39624485 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
39624525 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
39624565 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
39624589 CATTCGAATA
Statistics
Matches: 127, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 125 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:39627865 original size:40 final size:40
Alignment explanation
Indices: 39627816--39627967 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
39627806 ACAACCACAA
* * *** *
39627816 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
*
39627856 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
* *
39627896 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATC-ACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC
* * *
39627936 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
39627968 CATTCAAATG
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
39 2 0.02
40 92 0.96
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
Found at i:39635846 original size:40 final size:39
Alignment explanation
Indices: 39635797--39635947 Score: 160
Period size: 40 Copynumber: 3.8 Consensus size: 39
39635787 ACAACCACAA
* * ** *
39635797 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT-AAAACTC
*
39635837 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAAAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAAAACTC
* * *
39635876 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-AACTC
* * *
39635916 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
39635948 CATTCAAATG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
39 36 0.38
40 59 0.62
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAAAACTC
Found at i:39640231 original size:35 final size:35
Alignment explanation
Indices: 39640186--39640269 Score: 141
Period size: 35 Copynumber: 2.4 Consensus size: 35
39640176 TCTTCGGAGC
39640186 CATTGGTGTGTTTCAGATGGATTAACTCTTTTGAG
1 CATTGGTGTGTTTCAGATGGATTAACTCTTTTGAG
* *
39640221 CATTGGTGTGTTTCGGATGGATTAGCTCTTTTGAG
1 CATTGGTGTGTTTCAGATGGATTAACTCTTTTGAG
39640256 CATCTGGTGTGTTT
1 CAT-TGGTGTGTTT
39640270 ATGTTGGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 36 0.78
36 10 0.22
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (35 bp):
CATTGGTGTGTTTCAGATGGATTAACTCTTTTGAG
Found at i:39644265 original size:49 final size:47
Alignment explanation
Indices: 39644102--39644274 Score: 163
Period size: 48 Copynumber: 3.6 Consensus size: 47
39644092 GATAAGATGC
* **
39644102 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTAGCA-C-ATCAAAGT
1 CGATGCCATGTCCCAGACA-GGTCTTACACTGGCT-TCATCTATC-GGGT
* * * *
39644150 CGATGCCATGTCCCAGACAGGTTTTACATTGACTTCATATATCGAGG-
1 CGATGCCATGTCCCAGACAGGTCTTACACTGGCTTCATCTATCG-GGT
* * *
39644197 CTGATGTCGTGTCCCAGACAGGTTTTACACTGGCTCTCATCTATCGGTGT
1 C-GATGCCATGTCCCAGACAGGTCTTACACTGGCT-TCATCTATCGG-GT
*
39644247 CGATGCCATGTCCTAGACAGGTCTTACA
1 CGATGCCATGTCCCAGACAGGTCTTACA
39644275 GTAACACACA
Statistics
Matches: 102, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
46 2 0.02
47 13 0.13
48 53 0.52
49 33 0.32
50 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGGCTTCATCTATCGGGT
Found at i:39644366 original size:141 final size:138
Alignment explanation
Indices: 39644154--39644412 Score: 308
Period size: 141 Copynumber: 1.9 Consensus size: 138
39644144 CAAAGTCGAT
* * * * *
39644154 GCCATGTCCCAGACAGGTTTTACATTGACTTCATATATCGAGGCTGATGTCGTGTCCCAGACAGG
1 GCCATGTCCCAGACAGGTCTTACATAGACTTCATATATCGAGGCTAATGTCATGTCCCAAACAGG
* * ** *
39644219 TTTTACACTGGCTCTCATCTATCGGTGTCGATGCCATGTCCTAGACAGGTCTTACAGTAACACAC
66 TCTTACACTAGCTCTCATC--TCAATGCCGATG-CATGTCCTAGACAGGTCTTACAGTAACACAC
39644284 AACAAGCTAAC
128 AACAAGCTAAC
* *
39644295 GCCATGTCCTAGACAGGTCTTACACTAG-CTT-GTATATCTTGAGGCTAATG-CATGTCCCAAAC
1 GCCATGTCCCAGACAGGTCTTACA-TAGACTTCATATATC--GAGGCTAATGTCATGTCCCAAAC
* * *
39644357 ATGTCTTACACTAGCTCTCGTCTCAATGCCGATGCATGTCCTAGACATGTCTTACA
63 AGGTCTTACACTAGCTCTCATCTCAATGCCGATGCATGTCCTAGACAGGTCTTACA
39644413 CTGGCTCTCA
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
138 21 0.21
139 9 0.09
140 6 0.06
141 53 0.53
142 11 0.11
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (138 bp):
GCCATGTCCCAGACAGGTCTTACATAGACTTCATATATCGAGGCTAATGTCATGTCCCAAACAGG
TCTTACACTAGCTCTCATCTCAATGCCGATGCATGTCCTAGACAGGTCTTACAGTAACACACAAC
AAGCTAAC
Found at i:39644405 original size:46 final size:45
Alignment explanation
Indices: 39644342--39644465 Score: 153
Period size: 46 Copynumber: 2.7 Consensus size: 45
39644332 CTTGAGGCTA
* * *
39644342 ATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAA-T-GCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTC--AT-AAGTGGCCG
* *
39644388 ATGCATGTCCTAGACATGTCTTACACTGGCTCTCATAATGTGGTCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAA-GTGGCCG
39644434 ATGCATGTCCCAGACATGTCTTACACTGGCTC
1 ATGCATGTCCCAGACATGTCTTACACTGGCTC
39644466 ATATACCACC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
43 2 0.03
44 1 0.01
45 1 0.01
46 65 0.94
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAAGTGGCCG
Found at i:39645223 original size:29 final size:29
Alignment explanation
Indices: 39645181--39645239 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
39645171 TAAAATTCAG
* *
39645181 CAAACAACATAAATCTTTTCATGGCAAAT
1 CAAACAACATAAATATTTTCATGGAAAAT
39645210 CAAACAACATAAATATTTTCATGGAAAAT
1 CAAACAACATAAATATTTTCATGGAAAAT
39645239 C
1 C
39645240 CCTATACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (29 bp):
CAAACAACATAAATATTTTCATGGAAAAT
Found at i:39652501 original size:2 final size:2
Alignment explanation
Indices: 39652496--39652535 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39652486 GCTATATATA
*
39652496 TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39652536 GCACTTAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:39654769 original size:70 final size:69
Alignment explanation
Indices: 39654671--39654887 Score: 226
Period size: 68 Copynumber: 3.1 Consensus size: 69
39654661 ATAGTAGCCC
* * * * * *
39654671 GTCGGGACAGTAAACACTGGGAAACATAAGGTGTAAGACCGTAGTTGGGCTATGGCCACCCAGTG
1 GTCGAGACAGTAAA-AATGAGAAACATAAGGTGTAAGACCATAGTTGGACTATGGCCA-CTAGTG
39654736 TAGTCT
64 TAGTCT
* *
39654742 GTCGAGACAGTAAAAATGAGAAACATAAGGTGTAAGGCCATAGTTGGACTATGGCCTCTAGTGTA
1 GTCGAGACAGTAAAAATGAGAAACATAAGGTGTAAGACCATAGTTGGACTATGGCCACTAGTGTA
39654807 GT-T
66 GTCT
* * ** * * *
39654810 CATC-AGGATAGTAAAACA--AGAAATGTAAGGTGTATGACCATAGTTAGACTATAGCCACTAGT
1 -GTCGA-GACAGTAAAA-ATGAGAAACATAAGGTGTAAGACCATAGTTGGACTATGGCCACTAGT
39654872 GTAGTCT
63 GTAGTCT
39654879 GTCGAGACA
1 GTCGAGACA
39654888 ATAATACAGG
Statistics
Matches: 122, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
68 49 0.40
69 22 0.18
70 38 0.31
71 13 0.11
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (69 bp):
GTCGAGACAGTAAAAATGAGAAACATAAGGTGTAAGACCATAGTTGGACTATGGCCACTAGTGTA
GTCT
Found at i:39655051 original size:54 final size:54
Alignment explanation
Indices: 39654908--39655053 Score: 157
Period size: 54 Copynumber: 2.6 Consensus size: 54
39654898 GTTGTATTGT
* * * *
39654908 GTAAGACCATAGCTGAAAGATGTTATCGTATCAAGAGATGAAATGAAAATAAAATGA
1 GTAAGACCATGGCTGAAAGATGTTATGGCATC---ATATGAAATGAAAATAAAATGA
* *** * * *
39654965 GTAAGACCATGGCTAAAAGACACTATGACATCATATGAATTGACAATAAAATGA
1 GTAAGACCATGGCTGAAAGATGTTATGGCATCATATGAAATGAAAATAAAATGA
*
39655019 GTAAGACCATGGTTGAAAGATGTTATGGCATCATA
1 GTAAGACCATGGCTGAAAGATGTTATGGCATCATA
39655054 GAGAGTTTGA
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
54 48 0.67
57 24 0.33
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (54 bp):
GTAAGACCATGGCTGAAAGATGTTATGGCATCATATGAAATGAAAATAAAATGA
Found at i:39659192 original size:29 final size:29
Alignment explanation
Indices: 39659150--39659277 Score: 179
Period size: 28 Copynumber: 4.5 Consensus size: 29
39659140 GAAAGCATGT
39659150 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39659179 ATATGAATGTGATTTGGGCC-CATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39659207 ATACGAATGTGATTTGGGCCT-ATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * * *
39659235 ATACGAATGTGATTTTGGCCTAATAGACC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39659264 ATATGAATGAGATT
1 ATATGAATGTGATT
39659278 AGGTCATATG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
28 53 0.59
29 37 0.41
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:39659266 original size:57 final size:57
Alignment explanation
Indices: 39659154--39659277 Score: 169
Period size: 57 Copynumber: 2.2 Consensus size: 57
39659144 GCATGTATAT
* * * *
39659154 GAATGTGATTTGGGCCTAATGGGCCATATGAATGTGATTTGGGCCCATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATACGAATGTGATTTGGGCCAATAGACCATAC
* *
39659211 GAATGTGATTTGGGCCT-ATGGGCCATACGAATGTGATTTTGGCCTAATAGACCATAT
1 GAATGTGATTTGGGCCTAATGGGCCATACGAATGTGATTTGGGCC-AATAGACCATAC
*
39659268 GAATGAGATT
1 GAATGTGATT
39659278 AGGTCATATG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 25 0.42
57 34 0.58
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (57 bp):
GAATGTGATTTGGGCCTAATGGGCCATACGAATGTGATTTGGGCCAATAGACCATAC
Found at i:39668094 original size:42 final size:42
Alignment explanation
Indices: 39668048--39668144 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
39668038 TCCTCACCTA
*
39668048 TGTAACTCACTGAGTAGCC-CTACACGCCCATGTGCCAGGCCG
1 TGTAACTCACTGAGTAGCCAC-ACACACCCATGTGCCAGGCCG
* * * *
39668090 TGTAACTCTCTGAGTTGCCACACACACCCGTGTGCTAGGCCG
1 TGTAACTCACTGAGTAGCCACACACACCCATGTGCCAGGCCG
39668132 TGTAACTCACTGA
1 TGTAACTCACTGA
39668145 CTTGAATACT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.23
Consensus pattern (42 bp):
TGTAACTCACTGAGTAGCCACACACACCCATGTGCCAGGCCG
Found at i:39669255 original size:42 final size:42
Alignment explanation
Indices: 39669208--39669294 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
39669198 TCACACAAGT
*
39669208 TGTGGGTCGGAATGTAAGCTACACGATGCTGCTCTCATGAGC
1 TGTGGGTCGGAATGTAAGCTACACGATGCTGCTCACATGAGC
39669250 TGTGGGTCGGAATGTAAGCTACACGATGCTGCTCACATGAGC
1 TGTGGGTCGGAATGTAAGCTACACGATGCTGCTCACATGAGC
39669292 TGT
1 TGT
39669295 AAGGAATCCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (42 bp):
TGTGGGTCGGAATGTAAGCTACACGATGCTGCTCACATGAGC
Found at i:39683686 original size:2 final size:2
Alignment explanation
Indices: 39683679--39683706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39683669 AACTACATTA
39683679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39683707 GAATTGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39683962 original size:47 final size:46
Alignment explanation
Indices: 39683851--39684021 Score: 158
Period size: 46 Copynumber: 3.7 Consensus size: 46
39683841 ACTTGTGTGA
*
39683851 GCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCACATT--ATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGG---CATTGAATGAGT
* * *
39683897 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCATTGAAACGAGT
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTG-AATGAGT
* *
39683945 GCTAGTGTAAGA-TATGTCTGGGACATGCATCGGC-TATGAGATGTGT
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCAT-TGA-ATGAGT
*
39683991 -C-AGTGTAAGACCATGCCTGGGACATGGCATC
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATC
39684022 CGCACAAATA
Statistics
Matches: 105, Mismatches: 11, Indels: 18
0.78 0.08 0.13
Matches are distributed among these distances:
44 9 0.09
45 19 0.18
46 29 0.28
47 27 0.26
48 21 0.20
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAATGAGT
Found at i:39691106 original size:31 final size:31
Alignment explanation
Indices: 39691068--39691131 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
39691058 CCTTTTCATA
39691068 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
39691099 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
39691130 TT
1 TT
39691132 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:39691374 original size:24 final size:24
Alignment explanation
Indices: 39691323--39691441 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
39691313 GCTTTATCAT
*
39691323 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
39691348 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
39691372 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
39691395 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
39691419 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
39691442 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:39691402 original size:47 final size:48
Alignment explanation
Indices: 39691323--39691441 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
39691313 GCTTTATCAT
*
39691323 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
39691372 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
39691419 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
39691442 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:39691516 original size:20 final size:20
Alignment explanation
Indices: 39691491--39691551 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
39691481 TTATGATTAC
39691491 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
39691511 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
39691531 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
39691551 A
1 A
39691552 CCACATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:39691626 original size:25 final size:25
Alignment explanation
Indices: 39691594--39691641 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39691584 ATACATAAAC
* * *
39691594 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
39691619 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
39691642 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:39693713 original size:13 final size:13
Alignment explanation
Indices: 39693695--39693719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39693685 GGAAGAAATT
39693695 ATAGAAGATTTGC
1 ATAGAAGATTTGC
39693708 ATAGAAGATTTG
1 ATAGAAGATTTG
39693720 TAATCTTAGA
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:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (13 bp):
ATAGAAGATTTGC
Found at i:39693759 original size:24 final size:23
Alignment explanation
Indices: 39693714--39693767 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
39693704 TTGCATAGAA
*
39693714 GATTTGT-AATCTTAGAATATTT
1 GATTTGTAAATCTTAGAAGATTT
*
39693736 GATTCTGTAAATCTTAGGAGATTT
1 GATT-TGTAAATCTTAGAAGATTT
*
39693760 AATTTGTA
1 GATTTGTA
39693768 GATTGTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (23 bp):
GATTTGTAAATCTTAGAAGATTT
Found at i:39695182 original size:7 final size:7
Alignment explanation
Indices: 39695170--39695202 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
39695160 TAAAACAATT
39695170 ATAAAAA
1 ATAAAAA
39695177 ATAAAAA
1 ATAAAAA
39695184 ATAAAAA
1 ATAAAAA
39695191 A-ACAAAA
1 ATA-AAAA
39695198 ATAAA
1 ATAAA
39695203 TAAGCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (7 bp):
ATAAAAA
Found at i:39695235 original size:11 final size:11
Alignment explanation
Indices: 39695221--39695252 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
39695211 TTATAAACAT
39695221 ATAAAATATAA
1 ATAAAATATAA
39695232 ATAAAATA-AA
1 ATAAAATATAA
39695242 ATAAAA-ATAA
1 ATAAAATATAA
39695252 A
1 A
39695253 GATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 11 0.55
11 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:39695532 original size:21 final size:20
Alignment explanation
Indices: 39695508--39695576 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 20
39695498 ACATAAAATT
39695508 TATAAACAAAATATATAATGA
1 TATAAACAAAATATATAAT-A
* *
39695529 TATAGACAATATGATAGATAATA
1 TATAAACAA-A--ATATATAATA
*
39695552 TATAAA-ATAATATAT-ATA
1 TATAAACAAAATATATAATA
39695570 TAGTAAA
1 TA-TAAA
39695577 ATATATGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.13
19 9 0.23
21 9 0.23
22 2 0.05
23 6 0.15
24 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (20 bp):
TATAAACAAAATATATAATA
Found at i:39695596 original size:7 final size:7
Alignment explanation
Indices: 39695517--39695627 Score: 57
Period size: 7 Copynumber: 14.9 Consensus size: 7
39695507 TTATAAACAA
39695517 AATATAT
1 AATATAT
39695524 AATGATAT
1 AAT-ATAT
*
39695532 AGACAATAT
1 A-A-TATAT
* *
39695541 GATAGAT
1 AATATAT
39695548 AATATAT
1 AATATAT
39695555 AA-A-AT
1 AATATAT
39695560 AATATAT
1 AATATAT
*
39695567 ATATAGTAA
1 A-ATA-TAT
39695576 AATATATGT
1 AATATA--T
39695585 AATATA-
1 AATATAT
39695591 ATATATAAT
1 A-ATAT-AT
*
39695600 AATGTAT
1 AATATAT
39695607 AATAATAT
1 AAT-ATAT
*
39695615 AATAAAT
1 AATATAT
39695622 AATATA
1 AATATA
39695628 CAAAGATAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
5 4 0.05
6 3 0.04
7 35 0.44
8 22 0.28
9 15 0.19
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (7 bp):
AATATAT
Found at i:39695607 original size:10 final size:10
Alignment explanation
Indices: 39695517--39695627 Score: 61
Period size: 10 Copynumber: 10.6 Consensus size: 10
39695507 TTATAAACAA
39695517 AATATATAAT
1 AATATATAAT
* * *
39695527 GATATA-GAC
1 AATATATAAT
39695536 AATATGATAGAT
1 AATAT-ATA-AT
39695548 AATATATAA-
1 AATATATAAT
39695557 AATA-AT-AT
1 AATATATAAT
39695565 ATATATAGTAA-
1 A-ATATA-TAAT
39695576 AATATATGTAATAT
1 AATATA--T-A-AT
39695590 AATATATAAT
1 AATATATAAT
*
39695600 AATGTATAAT
1 AATATATAAT
39695610 AATATAATAAAT
1 AATAT-AT-AAT
39695622 AATATA
1 AATATA
39695628 CAAAGATAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
7 1 0.01
8 3 0.04
9 12 0.15
10 28 0.35
11 11 0.14
12 17 0.22
13 1 0.01
14 6 0.08
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
AATATATAAT
Found at i:39695618 original size:30 final size:30
Alignment explanation
Indices: 39695542--39695627 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
39695532 AGACAATATG
*
39695542 ATAG-ATAAT-ATATAAAATAATATAT-AT
1 ATAGTATAATAATATAATATAATATATAAT
* *
39695569 ATAGTAAAATATATGTAATATAATATATAAT
1 ATAGTATAATA-ATATAATATAATATATAAT
39695600 A-ATGTATAATAATATAATA-AATAATATA
1 ATA-GTATAATAATATAATATAAT-ATATA
39695628 CAAAGATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.08
28 4 0.08
29 3 0.06
30 27 0.56
31 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (30 bp):
ATAGTATAATAATATAATATAATATATAAT
Found at i:39697312 original size:43 final size:44
Alignment explanation
Indices: 39697222--39697351 Score: 192
Period size: 43 Copynumber: 3.0 Consensus size: 44
39697212 AGCTGAAATG
*
39697222 TTCGATCTACTCTCT-GACAATACAGAGACGCCAAATCTGCTATC
1 TTCGATCTGCTCTCTAG-CAATACAGAGACGCCAAATCTGCTATC
*
39697266 TTCGATCTGCTCTCTAGCAATACA-AGATGCCAAATCTGCTATC
1 TTCGATCTGCTCTCTAGCAATACAGAGACGCCAAATCTGCTATC
* * *
39697309 TTCGACCGGCTCTCTAACAATACAGAGACGCCAAATCTGCTAT
1 TTCGATCTGCTCTCTAGCAATACAGAGACGCCAAATCTGCTAT
39697352 TGTGACAGCC
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
43 39 0.50
44 38 0.49
45 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (44 bp):
TTCGATCTGCTCTCTAGCAATACAGAGACGCCAAATCTGCTATC
Found at i:39699063 original size:40 final size:40
Alignment explanation
Indices: 39699004--39699211 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
39698994 CAATTGAATG
* * * * *
39699004 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * * * *
39699044 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * *
39699084 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * * *
39699124 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAACTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * * **
39699164 ATATCCGGGCTAAGATCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
39699204 ATATCCGG
1 ATATCCGG
39699212 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
Found at i:39705789 original size:68 final size:70
Alignment explanation
Indices: 39705717--39705914 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
39705707 ACACCCTGTA
* * * *
39705717 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
39705779 ATAAAT
65 ATAAAT
*
39705785 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
39705850 ATAAAT
65 ATAAAT
*
39705856 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
39705915 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:39705828 original size:41 final size:41
Alignment explanation
Indices: 39705783--39705900 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
39705773 TGAAAGATAA
39705783 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
39705824 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
39705854 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
39705895 ATGTAG
1 ATGTAG
39705901 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:39705840 original size:71 final size:71
Alignment explanation
Indices: 39705751--39705914 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
39705741 GAGATGTATC
39705751 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39705816 AGGACA
66 AGGACA
39705822 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39705887 AGGACA
66 AGGACA
39705893 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39705915 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39713356 original size:68 final size:70
Alignment explanation
Indices: 39713284--39713481 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
39713274 ACACCCTGTA
* * * *
39713284 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
39713346 ATAAAT
65 ATAAAT
*
39713352 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
39713417 ATAAAT
65 ATAAAT
*
39713423 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
39713482 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:39713395 original size:41 final size:41
Alignment explanation
Indices: 39713350--39713467 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
39713340 TGAAAGATAA
39713350 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
39713391 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
39713421 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
39713462 ATGTAG
1 ATGTAG
39713468 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:39713407 original size:71 final size:71
Alignment explanation
Indices: 39713318--39713481 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
39713308 GAGATGTATC
39713318 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39713383 AGGACA
66 AGGACA
39713389 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39713454 AGGACA
66 AGGACA
39713460 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39713482 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39728097 original size:40 final size:40
Alignment explanation
Indices: 39728052--39728218 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
39728042 CGGAATATAA
39728052 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
39728092 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
39728132 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
39728172 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
39728211 CCGGATAT
1 CCGGATAT
39728219 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:39731098 original size:39 final size:40
Alignment explanation
Indices: 39731014--39731162 Score: 180
Period size: 39 Copynumber: 3.8 Consensus size: 40
39731004 TCGAATGATG
* * ** *
39731014 TCCGGGCTAAG-TCCCAAGGC-TTTGTGCTGAGTGACCATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGC-GAGTTCCCAAA
*
39731053 TTCGGACTAAGATCCGAAGGCATTTGT-CGAGTTCCCAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCCAAA
39731092 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCCAAA
** *
39731132 TCCGGGTTAAG-TCCCAAGGCATTTGTGCGAG
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAG
39731163 CTATTATAAC
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 62 0.64
40 30 0.31
41 5 0.05
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCCAAA
Found at i:39739137 original size:40 final size:40
Alignment explanation
Indices: 39739080--39739231 Score: 202
Period size: 40 Copynumber: 3.8 Consensus size: 40
39739070 TCGAATGATG
* ** *
39739080 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGAGTGACCATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTCCCAAA
39739120 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTCCCAAA
39739160 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTCCCAAA
**
39739200 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAG
39739232 CTATTATAAC
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
39 1 0.01
40 94 0.91
41 8 0.08
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTCCCAAA
Found at i:39739245 original size:40 final size:40
Alignment explanation
Indices: 39739080--39739271 Score: 187
Period size: 40 Copynumber: 4.8 Consensus size: 40
39739070 TCGAATGATG
*
39739080 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGAG-TGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGCT-ACCAAA
* * *
39739120 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACCAAA
* * *
39739160 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACCAAA
* **
39739200 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCA-AA
* * *
39739241 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
39739272 TCGCTATATC
Statistics
Matches: 134, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
39 1 0.01
40 122 0.91
41 11 0.08
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCAAA
Done.