Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 126 of 318
Found at i:39174019 original size:23 final size:23
Alignment explanation
Indices: 39173950--39174085 Score: 94
Period size: 23 Copynumber: 5.8 Consensus size: 23
39173940 ATGGTAATAA
* *
39173950 TAATAAATAGTAATAATAATACAT
1 TAATAAA-AATAATAATAATAAAT
* * *
39173974 TAATAAGAATAATGATAGTAAAT
1 TAATAAAAATAATAATAATAAAT
* * *
39173997 TAATAATAACAATAATAA-AAAA
1 TAATAAAAATAATAATAATAAAT
*
39174019 TAATAGAAAATAATAATAATAAAC
1 TAATA-AAAATAATAATAATAAAT
* * * * *
39174043 TAAGGAATAATAAAAATACTAACAA
1 TAA-TAAAAATAATAATAATAA-AT
*
39174068 TAATATAAATAATAATAA
1 TAATAAAAATAATAATAA
39174086 AAACAACAAG
Statistics
Matches: 85, Mismatches: 23, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
22 8 0.09
23 37 0.44
24 35 0.41
25 5 0.06
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (23 bp):
TAATAAAAATAATAATAATAAAT
Found at i:39174898 original size:17 final size:16
Alignment explanation
Indices: 39174878--39174918 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
39174868 AGATTTGAAA
39174878 CGAAAACAAAAAGAGAT
1 CGAAAA-AAAAAGAGAT
39174895 CGAAAAAAAAAGAGA-
1 CGAAAAAAAAAGAGAT
*
39174910 AGAAAAAAA
1 CGAAAAAAA
39174919 CCAAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 9 0.39
17 6 0.26
ACGTcount: A:0.73, C:0.07, G:0.17, T:0.02
Consensus pattern (16 bp):
CGAAAAAAAAAGAGAT
Found at i:39180568 original size:3 final size:3
Alignment explanation
Indices: 39180560--39180654 Score: 181
Period size: 3 Copynumber: 31.7 Consensus size: 3
39180550 TTTGGTAACC
*
39180560 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
39180608 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
39180655 AGTAGTGTAG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:39191497 original size:25 final size:25
Alignment explanation
Indices: 39191434--39191509 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
39191424 ATGTTAACAA
39191434 AATATTCAAAAT-ATATTTTAT-ATT
1 AATATT-AAAATAATATTTTATAATT
*
39191458 AATATTAATATTAATATTTTATAATT
1 AATATTAA-AATAATATTTTATAATT
*
39191484 AA-ATTTAAAATAATATATTTGTAATT
1 AATA-TTAAAATAATAT-TTTATAATT
39191510 TTTTTATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.05
24 8 0.18
25 17 0.39
26 17 0.39
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
AATATTAAAATAATATTTTATAATT
Found at i:39192368 original size:20 final size:21
Alignment explanation
Indices: 39192340--39192386 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
39192330 AAAGCCATAT
*
39192340 GAAACAGAAAGAA-AAAAAGA
1 GAAAGAGAAAGAAGAAAAAGA
**
39192360 GAAAGAGAAAGAAGAAAGGGA
1 GAAAGAGAAAGAAGAAAAAGA
39192381 GAAAGA
1 GAAAGA
39192387 AGGTTCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (21 bp):
GAAAGAGAAAGAAGAAAAAGA
Found at i:39200378 original size:22 final size:22
Alignment explanation
Indices: 39200353--39200404 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
39200343 CCAACTTAAT
* *
39200353 AATTAATTTAATTATAAAATTA
1 AATTAAATTAATTAAAAAATTA
*
39200375 AATTAAATTACTTAAAAAATTA
1 AATTAAATTAATTAAAAAATTA
39200397 AATCTAAA
1 AAT-TAAA
39200405 AACAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTAAATTAATTAAAAAATTA
Found at i:39201544 original size:22 final size:21
Alignment explanation
Indices: 39201516--39201559 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
39201506 AATCTGAGTT
*
39201516 TGCTTCTTGGCACAGGTTTTTC
1 TGCTTCTTGGCAC-GGTGTTTC
39201538 TGCTTCTTGGCACGGTGTTTC
1 TGCTTCTTGGCACGGTGTTTC
39201559 T
1 T
39201560 TCCATACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.07, C:0.23, G:0.25, T:0.45
Consensus pattern (21 bp):
TGCTTCTTGGCACGGTGTTTC
Found at i:39205820 original size:50 final size:50
Alignment explanation
Indices: 39205737--39206019 Score: 293
Period size: 50 Copynumber: 5.6 Consensus size: 50
39205727 CTAGTACGCA
* * ** *
39205737 TAGTAGCCTACACTTAGTACTACATACACGACCTAGCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * *
39205787 TAGTATCCTACACTTAGTACTACACACGTGACCTAACTATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * * ***
39205837 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACGTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTGGTACACG
*
39205888 TAGTAGCCTGCACTTAGTACTACAC-CTGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACAC-GTGACCTAACAATCTGGTACACG
* * *
39205938 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-AA-CTGTCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTG--GT--ACACG
* *
39205990 TAGTAGCCTACACATAGTACTACACACGTG
1 TAGTAGCCTGCACTTAGTACTACACACGTG
39206020 TTCTCACTGC
Statistics
Matches: 195, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
48 3 0.02
49 2 0.01
50 119 0.61
51 40 0.21
52 31 0.16
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
Found at i:39205911 original size:101 final size:101
Alignment explanation
Indices: 39205787--39205968 Score: 294
Period size: 101 Copynumber: 1.8 Consensus size: 101
39205777 CTGGTACACG
* * *
39205787 TAGTATCCTACACTTAGTACTACACAC-GTGACCTAACTATCTGATACACGTAGTAGCCTGCACT
1 TAGTAGCCTACACTTAGTACTACAC-CTGCGACCTAACAATCTGATACACGTAGTAGCCTGCACT
39205851 TAGTACTACACACGTGATCGAAGCTATCGGGTACGTA
65 TAGTACTACACACGTGATCGAAGCTATCGGGTACGTA
* *
39205888 TAGTAGCCTGCACTTAGTACTACACCTGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTACACTTAGTACTACACCTGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTT
*
39205953 AGTACTACACATGTGA
66 AGTACTACACACGTGA
39205969 CCTAAAACTG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
100 1 0.01
101 73 0.99
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTACACTTAGTACTACACCTGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTT
AGTACTACACACGTGATCGAAGCTATCGGGTACGTA
Found at i:39205969 original size:151 final size:152
Alignment explanation
Indices: 39205716--39206019 Score: 423
Period size: 151 Copynumber: 2.0 Consensus size: 152
39205706 CACCCTTGTA
* * *
39205716 ATCGAAGCTCTCTAGTACGCATAGTAGCCTACACTTAGTACTACATACACGACCTAGCAATCTGG
1 ATCGAAGCTATCGAGTACGCATAGTAGCCTACACTTAGTACTACATACACGACCTAACAATCTGG
* * *
39205781 TACACGTAGTATCCTACACTTAGTACTACACACGTGACCT-AACTATCTGATACACGTAGTAGCC
66 TACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAAACTATCTGAAACACATAGTAGCC
* *
39205845 TGCACTTAGTACTACACACGTG
131 TACACATAGTACTACACACGTG
* * * * *
39205867 ATCGAAGCTATCGGGTACGTATAGTAGCCTGCACTTAGTACTACA-CCTGCGACCTAACAATCTG
1 ATCGAAGCTATCGAGTACGCATAGTAGCCTACACTTAGTACTACATAC-ACGACCTAACAATCTG
* * * *
39205931 GTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAAAACTGTCTTAAACACATAGTAG
65 GTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCT-AAACTATCTGAAACACATAGTAG
39205996 CCTACACATAGTACTACACACGTG
129 CCTACACATAGTACTACACACGTG
39206020 TTCTCACTGC
Statistics
Matches: 133, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
150 1 0.01
151 92 0.69
153 40 0.30
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (152 bp):
ATCGAAGCTATCGAGTACGCATAGTAGCCTACACTTAGTACTACATACACGACCTAACAATCTGG
TACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAAACTATCTGAAACACATAGTAGCC
TACACATAGTACTACACACGTG
Found at i:39208778 original size:20 final size:18
Alignment explanation
Indices: 39208753--39208796 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
39208743 TGGGCCGAGG
*
39208753 ACACGGGTGTGTCCAGAGCC
1 ACACGGGCGTGT-CAGA-CC
*
39208773 ACACGGGCGTGTGAGACC
1 ACACGGGCGTGTCAGACC
39208791 ACACGG
1 ACACGG
39208797 CCTACCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.23, C:0.30, G:0.36, T:0.11
Consensus pattern (18 bp):
ACACGGGCGTGTCAGACC
Found at i:39210485 original size:13 final size:13
Alignment explanation
Indices: 39210452--39210485 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
39210442 AATATATTTA
*
39210452 AACCCAAGTACCC
1 AACCCAATTACCC
39210465 AACCCAATTACCC
1 AACCCAATTACCC
39210478 AACCCAAT
1 AACCCAAT
39210486 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.41, C:0.44, G:0.03, T:0.12
Consensus pattern (13 bp):
AACCCAATTACCC
Found at i:39210841 original size:21 final size:21
Alignment explanation
Indices: 39210815--39210854 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39210805 TTTTGAGGTA
*
39210815 TTTTATAATCTTATTTAATAT
1 TTTTATAATCATATTTAATAT
*
39210836 TTTTATAATGATATTTAAT
1 TTTTATAATCATATTTAAT
39210855 TATATTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTATAATCATATTTAATAT
Found at i:39217101 original size:29 final size:30
Alignment explanation
Indices: 39217062--39217127 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 30
39217052 GAAGGAAAGG
39217062 AAAA-TAA-GTTGTGTTTAGGGTTTG-AAA
1 AAAATTAAGGTTGTGTTTAGGGTTTGAAAA
39217089 AAAATTAAGGTTGTGTTTAGGGTTTGAAAA
1 AAAATTAAGGTTGTGTTTAGGGTTTGAAAA
39217119 AAAATTAAG
1 AAAATTAAG
39217128 AGATTGTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 4 0.11
28 3 0.08
29 17 0.47
30 12 0.33
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATTAAGGTTGTGTTTAGGGTTTGAAAA
Found at i:39220454 original size:47 final size:47
Alignment explanation
Indices: 39220339--39220527 Score: 191
Period size: 47 Copynumber: 3.9 Consensus size: 47
39220329 TGCACATAGT
* ** * *
39220339 CACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTACAC-GGAT
1 CACATATCAC--ACCGATGCCATAGCCCAGATATGGTCTTATACAGGAG
* * *
39220387 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGAG
* * *
39220434 CACATATCACACCGATGCCATATCCCGGATATGGTCTTATACGGGAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGAG
* *
39220481 CACATATCACATCTCCTCGAAGCCATAGCCCAGCTATGGTCTTATAC
1 CACATATCACA----C-CGATGCCATAGCCCAGATATGGTCTTATAC
39220528 GGAAATCACA
Statistics
Matches: 119, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 26 0.22
47 56 0.47
48 10 0.08
51 1 0.01
52 26 0.22
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (47 bp):
CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGAG
Found at i:39220523 original size:99 final size:94
Alignment explanation
Indices: 39220320--39220527 Score: 222
Period size: 93 Copynumber: 2.1 Consensus size: 94
39220310 CATAGTAAAA
** *
39220320 CTATGGTCTTGCACATAGTCACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTACACGG
1 CTATGGTCTTATACATAGTCACATATCACA-ACCGAGGCCATAGCCCAGACATGGTCTTACACGG
* * *
39220385 ATCACATATCACACTGATGCCATATCCCAG
65 AGCACATATCACACTGAAGCCATAGCCCAG
* * * * * *
39220415 ATATGGTCTTATACAGTAG-CACATATCAC-ACCGATGCCATATCCCGGATATGGTCTTATACGG
1 CTATGGTCTTATACA-TAGTCACATATCACAACCGAGGCCATAGCCCAGACATGGTCTTACAC-G
39220478 GAGCACATATCACATCTCCTCGAAGCCATAGCCCAG
64 GAGCACATATCACA----CT-GAAGCCATAGCCCAG
39220514 CTATGGTCTTATAC
1 CTATGGTCTTATAC
39220528 GGAAATCACA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
93 26 0.28
94 14 0.15
95 22 0.24
96 3 0.03
98 2 0.02
99 26 0.28
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (94 bp):
CTATGGTCTTATACATAGTCACATATCACAACCGAGGCCATAGCCCAGACATGGTCTTACACGGA
GCACATATCACACTGAAGCCATAGCCCAG
Found at i:39235052 original size:30 final size:31
Alignment explanation
Indices: 39234998--39235064 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
39234988 TAATTTAATC
*
39234998 AATTTTAATTTTTGTATTTTTTGAAATATTT-
1 AATTTTAATTTTTGTATCTTTTGAAAT-TTTA
39235029 AATTTT-ATTCTTTGTA-CTTTTGAAATTTTA
1 AATTTTAATT-TTTGTATCTTTTGAAATTTTA
39235059 AATTTT
1 AATTTT
39235065 TAGTCATGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 3 0.09
30 18 0.55
31 12 0.36
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (31 bp):
AATTTTAATTTTTGTATCTTTTGAAATTTTA
Found at i:39237681 original size:28 final size:23
Alignment explanation
Indices: 39237649--39237714 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 23
39237639 TTTGTCCATT
*
39237649 TATTTTATAAAATTTATTTATTTA
1 TATTTTATAAAATTTA-ATATTTA
*
39237673 TTTTAATTTATCAAAATTTAATATTTA
1 ---TATTTTAT-AAAATTTAATATTTA
39237700 TATTTTATAAAATTT
1 TATTTTATAAAATTT
39237715 TATAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 7 0.20
24 7 0.20
27 13 0.37
28 8 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTATAAAATTTAATATTTA
Found at i:39237682 original size:27 final size:27
Alignment explanation
Indices: 39237647--39237700 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
39237637 TTTTTGTCCA
* *
39237647 TTTATTTTAT-AAAATTTATTTATTTAT
1 TTTAATTTATCAAAATTTA-ATATTTAT
39237674 TTTAATTTATCAAAATTTAATATTTAT
1 TTTAATTTATCAAAATTTAATATTTAT
39237701 ATTTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTAATTTATCAAAATTTAATATTTAT
Found at i:39247215 original size:3 final size:3
Alignment explanation
Indices: 39247207--39247235 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39247197 ATACACACAA
39247207 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39247236 ACCATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39251050 original size:20 final size:19
Alignment explanation
Indices: 39251002--39251041 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
39250992 TTGTTATTTT
39251002 AAAG-ATTAAATGTAGAGA
1 AAAGAATTAAATGTAGAGA
* *
39251020 AAAGAATTAAATTTAGGGA
1 AAAGAATTAAATGTAGAGA
39251039 AAA
1 AAA
39251042 TACATTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (19 bp):
AAAGAATTAAATGTAGAGA
Found at i:39252140 original size:44 final size:43
Alignment explanation
Indices: 39252087--39252172 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 43
39252077 AAAATAGAAG
*
39252087 TTGTGATAATTATACATTTAAAAATAATTATAATTTAATATTAT
1 TTGTGATAATTAAACATTTAAAAATAATTATAATTTAA-ATTAT
*
39252131 TTGTGATAATTAAATATTTAAAAATAATTATAATTTAAATTA
1 TTGTGATAATTAAACATTTAAAAATAATTATAATTTAAATTA
39252173 CAATTATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 4 0.10
44 36 0.90
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.47
Consensus pattern (43 bp):
TTGTGATAATTAAACATTTAAAAATAATTATAATTTAAATTAT
Found at i:39252159 original size:18 final size:17
Alignment explanation
Indices: 39252136--39252169 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39252126 ATTATTTGTG
39252136 ATAATTAAATATTTAAAA
1 ATAATTAAA-ATTTAAAA
*
39252154 ATAATTATAATTTAAA
1 ATAATTAAAATTTAAA
39252170 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATTTAAAA
Found at i:39257847 original size:25 final size:25
Alignment explanation
Indices: 39257819--39257869 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
39257809 TTCCTTATAA
**
39257819 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
39257844 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
39257869 A
1 A
39257870 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:39257868 original size:12 final size:12
Alignment explanation
Indices: 39257822--39257869 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
39257812 CTTATAAACT
39257822 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
39257834 TTCTATTAGGACT
1 TTAAATTAGGA-A
39257847 TTAAATTAGGAA
1 TTAAATTAGGAA
*
39257859 TTAGATTAGGA
1 TTAAATTAGGA
39257870 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:39262514 original size:25 final size:25
Alignment explanation
Indices: 39262486--39262536 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
39262476 TTCCTTATAA
**
39262486 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
39262511 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
39262536 A
1 A
39262537 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:39262535 original size:12 final size:12
Alignment explanation
Indices: 39262489--39262536 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
39262479 CTTATAAACT
39262489 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
39262501 TTCTATTAGGACT
1 TTAAATTAGGA-A
39262514 TTAAATTAGGAA
1 TTAAATTAGGAA
*
39262526 TTAGATTAGGA
1 TTAAATTAGGA
39262537 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:39267308 original size:21 final size:21
Alignment explanation
Indices: 39267282--39267322 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39267272 ATCTGCTCAA
* *
39267282 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
39267303 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
39267323 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:39273229 original size:19 final size:19
Alignment explanation
Indices: 39273205--39273245 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
39273195 AGTAAAATAT
*
39273205 TTTCCAGAAAATAATTTAC
1 TTTCCAAAAAATAATTTAC
*
39273224 TTTCCAAAAAATGATTTAC
1 TTTCCAAAAAATAATTTAC
39273243 TTT
1 TTT
39273246 TCTGGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTCCAAAAAATAATTTAC
Found at i:39277043 original size:6 final size:6
Alignment explanation
Indices: 39277023--39277060 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
39277013 GGGACGCAAT
*
39277023 GAAGG- GAAGGA GAAGGG GAAGGA GAAGGA GAAGGA GAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAA
39277061 AGCGTTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:39281186 original size:32 final size:32
Alignment explanation
Indices: 39281120--39281187 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
39281110 TTTTTGTTAA
* * *
39281120 TGTTGGATTCTGAAATTTTAGTTTATTATGTT
1 TGTTGGATTCTAAAATTTTAGTCTATGATGTT
39281152 TGTTGGATTCTAAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATGTT
39281184 TGTT
1 TGTT
39281188 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATGTT
Found at i:39281213 original size:27 final size:27
Alignment explanation
Indices: 39281183--39281255 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
39281173 TGTCTTGATT
39281183 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
39281210 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
39281242 TTGTTGGATATTGA
1 TTGTTAGATATTGA
39281256 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:39281235 original size:32 final size:32
Alignment explanation
Indices: 39281196--39281256 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
39281186 TTAGATATTG
39281196 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
39281228 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
39281257 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:39282269 original size:22 final size:22
Alignment explanation
Indices: 39282238--39282286 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
39282228 GGACAATGTT
39282238 GTTATAATGTGCTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
* *
39282260 GTTATCATGTGGTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
39282282 GTTAT
1 GTTAT
39282287 GCACTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (22 bp):
GTTATAATGTGCTGTAATATTA
Found at i:39282299 original size:22 final size:22
Alignment explanation
Indices: 39282209--39282299 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
39282199 TAATGTGGTG
39282209 TAATATTAGTTATGCACT-TGGA
1 TAATATTAGTTAT-CACTGTGGA
* * *
39282231 CAATGTT-GTTAT-AATGTGCTG-
1 TAATATTAGTTATCACTGTG--GA
*
39282252 TAATATTAGTTATCA-TGTGGTG
1 TAATATTAGTTATCACTGTGG-A
39282274 TAATATTAGTTATGCACT-TGGA
1 TAATATTAGTTAT-CACTGTGGA
39282296 TAAT
1 TAAT
39282300 GTTGTTGTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 10 0.19
22 32 0.59
23 6 0.11
24 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (22 bp):
TAATATTAGTTATCACTGTGGA
Found at i:39282769 original size:14 final size:14
Alignment explanation
Indices: 39282747--39282790 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
39282737 CCAGAAAAGT
* *
39282747 AAATCATTTTTCAG
1 AAATTATTTTCCAG
39282761 AAATTATTTTCCAG
1 AAATTATTTTCCAG
39282775 AAATTATTTTCC-G
1 AAATTATTTTCCAG
39282788 AAA
1 AAA
39282791 AATATTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:39282796 original size:14 final size:14
Alignment explanation
Indices: 39282747--39282798 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
39282737 CCAGAAAAGT
*
39282747 AAATCATTTTTCAGA
1 AAAT-ATTTTCCAGA
*
39282762 AATTATTTTCCAGA
1 AAATATTTTCCAGA
*
39282776 AATTATTTTCC-GAA
1 AAATATTTTCCAG-A
39282790 AAATATTTT
1 AAATATTTT
39282799 ACCTGCAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 1 0.03
14 29 0.88
15 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (14 bp):
AAATATTTTCCAGA
Found at i:39282962 original size:11 final size:11
Alignment explanation
Indices: 39282946--39282981 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39282936 TCAATCTAAT
39282946 TTGATTAGTGA
1 TTGATTAGTGA
39282957 TTGATT--TG-
1 TTGATTAGTGA
39282965 TTGATTAGTGA
1 TTGATTAGTGA
39282976 TTGATT
1 TTGATT
39282982 TGTTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (11 bp):
TTGATTAGTGA
Found at i:39282968 original size:19 final size:19
Alignment explanation
Indices: 39282946--39282985 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
39282936 TCAATCTAAT
39282946 TTGATTAGTGATTGATTTG
1 TTGATTAGTGATTGATTTG
39282965 TTGATTAGTGATTGATTTG
1 TTGATTAGTGATTGATTTG
39282984 TT
1 TT
39282986 TTGTTTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (19 bp):
TTGATTAGTGATTGATTTG
Found at i:39283678 original size:16 final size:16
Alignment explanation
Indices: 39283639--39283669 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39283629 GACCCGTCTC
39283639 AAATATATTATATTAT
1 AAATATATTATATTAT
*
39283655 AAAAATATTATATTA
1 AAATATATTATATTA
39283670 ATTATATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATATTATATTAT
Found at i:39284672 original size:17 final size:19
Alignment explanation
Indices: 39284650--39284686 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
39284640 AATTATTATC
39284650 TAACTTT-TTTAAA-ATTT
1 TAACTTTCTTTAAATATTT
39284667 TAACTTTCTTTAAATATTT
1 TAACTTTCTTTAAATATTT
39284686 T
1 T
39284687 TTAGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
TAACTTTCTTTAAATATTT
Found at i:39284911 original size:23 final size:22
Alignment explanation
Indices: 39284873--39284915 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
39284863 ATTCAACTCG
39284873 ACTCGAATTCGAAACTCAAATA
1 ACTCGAATTCGAAACTCAAATA
39284895 ACTC-AATTCGATTAACTCAAA
1 ACTCGAATTCGA--AACTCAAA
39284916 ATTCGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (22 bp):
ACTCGAATTCGAAACTCAAATA
Found at i:39287501 original size:24 final size:24
Alignment explanation
Indices: 39287474--39287525 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39287464 TTAGTAAGTC
*
39287474 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39287498 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39287522 AAAT
1 AAAT
39287526 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39289469 original size:24 final size:24
Alignment explanation
Indices: 39289442--39289493 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39289432 TTAGTAAGTC
*
39289442 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39289466 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39289490 AAAT
1 AAAT
39289494 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39296587 original size:16 final size:17
Alignment explanation
Indices: 39296556--39296588 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39296546 TTCATAAGTA
39296556 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
39296573 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
39296589 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:39296775 original size:44 final size:44
Alignment explanation
Indices: 39296725--39296815 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
39296715 CTATTTTGTA
39296725 CATACATTTCCATATGACCAGTTCTTGTAAACATTTCACACAAC
1 CATACATTTCCATATGACCAGTTCTTGTAAACATTTCACACAAC
39296769 CATACATTTCCATATGACCAGTTCTTGTAAACATTTCACACAAC
1 CATACATTTCCATATGACCAGTTCTTGTAAACATTTCACACAAC
39296813 CAT
1 CAT
39296816 TTCATATAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (44 bp):
CATACATTTCCATATGACCAGTTCTTGTAAACATTTCACACAAC
Found at i:39297027 original size:46 final size:46
Alignment explanation
Indices: 39296913--39297277 Score: 570
Period size: 46 Copynumber: 8.0 Consensus size: 46
39296903 TTATCTTTGA
* ** ***
39296913 CATGATGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
39296958 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
39297004 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
39297050 CTTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
39297096 CGTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
39297142 CCTGTTGCCATGGTATCTTTCAACCACGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
39297188 CATGTTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
39297234 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
39297278 TTCAGAAAGC
Statistics
Matches: 297, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 35 0.12
46 262 0.88
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:39301231 original size:18 final size:18
Alignment explanation
Indices: 39301195--39301231 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39301185 TGTAATATAT
*
39301195 TTCAAAATTCACTATTAA
1 TTCAAAATTCACTAATAA
*
39301213 TTCAAAATTCTCTAATAA
1 TTCAAAATTCACTAATAA
39301231 T
1 T
39301232 CCTTATCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (18 bp):
TTCAAAATTCACTAATAA
Found at i:39302139 original size:16 final size:17
Alignment explanation
Indices: 39302108--39302140 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39302098 TTCATAAGTA
39302108 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
39302125 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
39302141 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:39302478 original size:46 final size:46
Alignment explanation
Indices: 39302426--39302785 Score: 454
Period size: 46 Copynumber: 7.8 Consensus size: 46
39302416 TTTGACATGA
* *** * **
39302426 TGCCATGGTGTCTTTCAACCATGGTCTTGTTCATTTCATGTTACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
* ** *** *
39302472 TGCCATGGTATCTTTTAACCATGGTCTTATTCA-TTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
* * **
39302517 TGCCATGGTATCTTTCAACCATGGTCTTACGCATTTTATATCCTGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
*
39302563 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCT-TGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT-TATGT
* **
39302609 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCCTGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
* *
39302655 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
*
39302701 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
* *
39302747 TACCATGGTGTCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
39302786 TTCAGAAAGC
Statistics
Matches: 286, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
45 37 0.13
46 249 0.87
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATGT
Found at i:39302644 original size:92 final size:92
Alignment explanation
Indices: 39302421--39302785 Score: 500
Period size: 92 Copynumber: 4.0 Consensus size: 92
39302411 TTATCTTTGA
* * *** * * *
39302421 CATGATGCCATGGTGTCTTTCAACCATGGTCTTGTTCATTTCATGTTAC-ATTGCCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-ATCCTGTTGCCATGGTATCT
* ** ***
39302485 TTTAACCATGGTCTTATTCA-TTCCCGT
65 TTCAACCATGGTCTTACACATTTCATAT
* *
39302512 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACGCATTTTATATCCTGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCCTGTTGCCATGGTATCTT
*
39302577 TCAACCATGGTCTTACACATTTTATAT
66 TCAACCATGGTCTTACACATTTCATAT
* *
39302604 CTTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCCTGTTGCCATGGTATCTT
*
39302669 TCAACTATGGTCTTACACATTTCATAT
66 TCAACCATGGTCTTACACATTTCATAT
* * *
39302696 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTACCATGGTGTCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCCTGTTGCCATGGTATCTT
39302761 TCAACCATGGTCTTACACATTTCAT
66 TCAACCATGGTCTTACACATTTCAT
39302786 TTCAGAAAGC
Statistics
Matches: 246, Mismatches: 26, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
90 2 0.01
91 69 0.28
92 175 0.71
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (92 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCCTGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATAT
Found at i:39305840 original size:101 final size:101
Alignment explanation
Indices: 39305702--39305904 Score: 291
Period size: 101 Copynumber: 2.0 Consensus size: 101
39305692 CACAGCTCTG
* * * *
39305702 CCATGGTCTTACGTTCATAGTGCTATAACTCAGTTATGGTCTTATCATCAGAATG-TCGTAGCCC
1 CCATGGTCATAAGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCT-GTAGCCC
39305766 AACTATAGTCTTACATATAAACACTATCATGGACCAA
65 AACTATAGTCTTACATATAAACACTATCATGGACCAA
*
39305803 CCATGGTCATAAGTTCATAGTGCCATAACCCAGTTATGGTTTTATCATCAGAATGCTGTAGCCCA
1 CCATGGTCATAAGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCTGTAGCCCA
* * * * * *
39305868 GCTATGGTCTTACATATATACATTGTCATGGTCCAA
66 ACTATAGTCTTACATATAAACACTATCATGGACCAA
39305904 C
1 C
39305905 TGTGGTTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 89 0.99
102 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (101 bp):
CCATGGTCATAAGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCTGTAGCCCA
ACTATAGTCTTACATATAAACACTATCATGGACCAA
Found at i:39308157 original size:13 final size:12
Alignment explanation
Indices: 39308131--39308163 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
39308121 TTCTAAATTT
39308131 AAAAAATT-ATA
1 AAAAAATTAATA
39308142 AAAAAATTAATA
1 AAAAAATTAATA
39308154 AAAATAATTA
1 AAAA-AATTA
39308164 TGAGCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 7 0.35
13 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAAATTAATA
Found at i:39308158 original size:10 final size:11
Alignment explanation
Indices: 39308131--39308164 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
39308121 TTCTAAATTT
39308131 AAAAAATTATA
1 AAAAAATTATA
39308142 AAAAAATTAATA
1 AAAAAATT-ATA
39308154 AAAATAATTAT
1 AAAA-AATTAT
39308165 GAGCTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 9 0.43
13 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:39308977 original size:50 final size:50
Alignment explanation
Indices: 39308902--39309008 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 50
39308892 CCATGGCAAC
* *
39308902 AAGTGATAAGTGATAGTTTCGGCTACATTTATCTGATCAAGAACAAGTGA
1 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGAACAAGTGA
*
39308952 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGAACAAGTGA
39309002 AAGTGAT
1 AAGTGAT
39309009 CAAGGACAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (50 bp):
AAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGAACAAGTGA
Found at i:39309012 original size:20 final size:20
Alignment explanation
Indices: 39308987--39309028 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39308977 CACTTATCTA
39308987 ATCAAGGACAAGTGAAAGTG
1 ATCAAGGACAAGTGAAAGTG
39309007 ATCAAGGACAAGTGAAAGTG
1 ATCAAGGACAAGTGAAAGTG
39309027 AT
1 AT
39309029 AAGTGATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.29, T:0.17
Consensus pattern (20 bp):
ATCAAGGACAAGTGAAAGTG
Found at i:39309049 original size:70 final size:71
Alignment explanation
Indices: 39308935--39309078 Score: 227
Period size: 70 Copynumber: 2.0 Consensus size: 71
39308925 TACATTTATC
* *
39308935 TGATCAAGAACAAGTGAAAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGGACAAGT
1 TGATCAAGAACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAAT
39309000 GA-AAG
66 GACAAG
* * * *
39309005 TGATCAAGGACAAGTGAAAGTGATAAGTGATAGCTTCGGTTACACTTATCTGATCAATGACAAAT
1 TGATCAAGAACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAAT
39309070 GACAAG
66 GACAAG
39309076 TGA
1 TGA
39309079 AAAGTGGTAG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 61 0.91
71 6 0.09
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (71 bp):
TGATCAAGAACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAAT
GACAAG
Found at i:39309118 original size:31 final size:31
Alignment explanation
Indices: 39309074--39309191 Score: 137
Period size: 31 Copynumber: 3.8 Consensus size: 31
39309064 ACAAATGACA
39309074 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * *
39309105 AATGAAAATTGGTAGCTTCAGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * * * * *
39309136 AGTGAAAAATGATAGCTTCGGTTGCTTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* *
39309167 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCAGCTAC
39309192 AAGTCACAAG
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:39313805 original size:22 final size:23
Alignment explanation
Indices: 39313768--39313810 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39313758 TTTTATGTCA
**
39313768 ATTTTTTTATTTTTCT-TTAATT
1 ATTTTTTTATAATTCTATTAATT
39313790 ATTTTTTTATAATTCTATTAA
1 ATTTTTTTATAATTCTATTAA
39313811 AAATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTTTTATAATTCTATTAATT
Found at i:39316650 original size:23 final size:23
Alignment explanation
Indices: 39316619--39316663 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
39316609 AGTTGTCCAA
* **
39316619 TTTTTCTTTTCTGTTCTTCTTTC
1 TTTTCCTTTTCTAATCTTCTTTC
39316642 TTTTCCTTTTCTAATCTTCTTT
1 TTTTCCTTTTCTAATCTTCTTT
39316664 TTTCTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTCCTTTTCTAATCTTCTTTC
Found at i:39323296 original size:30 final size:30
Alignment explanation
Indices: 39323253--39323311 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39323243 CTTAACAAGC
39323253 AAATGCCTCTAAAATAATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* *
39323283 AAATGGCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
39323312 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:39331199 original size:16 final size:17
Alignment explanation
Indices: 39331170--39331202 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39331160 AAATATATAA
39331170 TAAAATTATAGTTAAAT
1 TAAAATTATAGTTAAAT
39331187 TAAAATT-TAGTTAAAT
1 TAAAATTATAGTTAAAT
39331203 GTTTAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAAATTATAGTTAAAT
Found at i:39336330 original size:19 final size:19
Alignment explanation
Indices: 39336306--39336344 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39336296 AGTATGTTCT
39336306 TGAGTTAAATTACAAGTTG
1 TGAGTTAAATTACAAGTTG
39336325 TGAGTTAAATTACAAGTTG
1 TGAGTTAAATTACAAGTTG
39336344 T
1 T
39336345 ACAAGTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (19 bp):
TGAGTTAAATTACAAGTTG
Found at i:39339725 original size:12 final size:12
Alignment explanation
Indices: 39339708--39339735 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39339698 ATGGTGGAAT
39339708 GATGTTTTAGAA
1 GATGTTTTAGAA
39339720 GATGTTTTAGAA
1 GATGTTTTAGAA
39339732 GATG
1 GATG
39339736 GCTGATACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (12 bp):
GATGTTTTAGAA
Found at i:39342102 original size:32 final size:32
Alignment explanation
Indices: 39342061--39342124 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
39342051 ATGGTAGTTT
39342061 TCACCAGCAAAAACGGTGGTAGTGAAAAACTC
1 TCACCAGCAAAAACGGTGGTAGTGAAAAACTC
*
39342093 TCACCAGCAAAAACGGTGGTGGTGAAAAACTC
1 TCACCAGCAAAAACGGTGGTAGTGAAAAACTC
39342125 ATGTTTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (32 bp):
TCACCAGCAAAAACGGTGGTAGTGAAAAACTC
Found at i:39343543 original size:49 final size:48
Alignment explanation
Indices: 39343447--39343786 Score: 200
Period size: 49 Copynumber: 7.0 Consensus size: 48
39343437 ATCTTTCATG
* * ** **
39343447 AAAATAATAACCTTGCTCCCAAATGCATAGGGGAAGAATTATAGAAGGT
1 AAAATAATAACCTTGCTCTCAAATGCAT-GGGGGAGGCTTACGGAAGGT
*
39343496 AAAATAATAACATTGCTCTCAAATGCATGTGGGGAGGCTTACGGAAGGT
1 AAAATAATAACCTTGCTCTCAAATGCATG-GGGGAGGCTTACGGAAGGT
* * * * * * * * *
39343545 AGAATGATAACCCTACTCTCAGATGTATGGGGGAAGCTTGCGAAAGGT
1 AAAATAATAACCTTGCTCTCAAATGCATGGGGGAGGCTTACGGAAGGT
* * * * * * *
39343593 AAAATAATAACCTTGTTCCCAGACGTATGGGAGGAGACTTACGAAAGGT
1 AAAATAATAACCTTGCTCTCAAATGCATGGG-GGAGGCTTACGGAAGGT
* ** * * * * *
39343642 AGTAAACAATAACCCAGCTCTTAGACGTATGGGGGAGGCTTATGGAAGGT
1 A--AAATAATAACCTTGCTCTCAAATGCATGGGGGAGGCTTACGGAAGGT
* * * * * *
39343692 AGAGTAATAACCTTGCTCCCATACAT--ATGAAGGGAGACTTATGGAAGGT
1 AAAATAATAACCTTGCTCTCA-A-ATGCATG-GGGGAGGCTTACGGAAGGT
* * * * * *
39343741 ATAATAATAACCCTACTCCCTAATGCAT-GGAGAGGCTTACGGAAGG
1 AAAATAATAACCTTGCTCTCAAATGCATGGGGGAGGCTTACGGAAGG
39343787 CTCAATGTCT
Statistics
Matches: 226, Mismatches: 56, Indels: 20
0.75 0.19 0.07
Matches are distributed among these distances:
47 16 0.07
48 58 0.26
49 112 0.50
50 16 0.07
51 24 0.11
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (48 bp):
AAAATAATAACCTTGCTCTCAAATGCATGGGGGAGGCTTACGGAAGGT
Found at i:39343728 original size:99 final size:97
Alignment explanation
Indices: 39343491--39343758 Score: 238
Period size: 99 Copynumber: 2.7 Consensus size: 97
39343481 AGAATTATAG
* * * * * * * **
39343491 AAGGTAAAATAATAACATTGCTCTCA-A-ATGCATGTGGGGAGGCTTACGGAAGGTAGAATGATA
1 AAGGTAAAATAATAACCTTGCTCCCAGACAT--ATGAGAGGAGACTTACGAAAGGTATAACAATA
* *
39343554 ACCCTACTCTCAGATGTATGGGGGAAGCTTGCGA
64 ACCCTACTCTCAGACGTATGGGGGAAGCTTACGA
* * *
39343588 AAGGTAAAATAATAACCTTGTTCCCAGACGTATGGGAGGAGACTTACGAAAGGTAGTAAACAATA
1 AAGGTAAAATAATAACCTTGCTCCCAGACATATGAGAGGAGACTTACGAAAGGTA-T-AACAATA
* * * *
39343653 ACCC-AGCTCTTAGACGTATGGGGGAGGCTTATGG
64 ACCCTA-CTCTCAGACGTATGGGGGAAGCTTACGA
* * * * * *
39343687 AAGGTAGAGTAATAACCTTGCTCCCATACATATGA-AGGGAGACTTATGGAAGGTATAATAATAA
1 AAGGTAAAATAATAACCTTGCTCCCAGACATATGAGA-GGAGACTTACGAAAGGTATAACAATAA
39343751 CCCTACTC
65 CCCTACTC
39343759 CCTAATGCAT
Statistics
Matches: 138, Mismatches: 26, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
97 56 0.41
98 5 0.04
99 77 0.56
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (97 bp):
AAGGTAAAATAATAACCTTGCTCCCAGACATATGAGAGGAGACTTACGAAAGGTATAACAATAAC
CCTACTCTCAGACGTATGGGGGAAGCTTACGA
Found at i:39344493 original size:9 final size:9
Alignment explanation
Indices: 39344476--39344512 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39344466 TGAGTTTTCG
39344476 AATTCGAAT
1 AATTCGAAT
*
39344485 AACTCGAAT
1 AATTCGAAT
39344494 AATTCGAAT
1 AATTCGAAT
39344503 AATTCGAAT
1 AATTCGAAT
39344512 A
1 A
39344513 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39345189 original size:86 final size:86
Alignment explanation
Indices: 39345099--39345272 Score: 312
Period size: 86 Copynumber: 2.0 Consensus size: 86
39345089 ATTAAAATTG
*
39345099 AATTATTAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATCAATTTCACATTTTA
1 AATTATTAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
39345164 TCTTTAAAATAACTTTTATTA
66 TCTTTAAAATAACTTTTATTA
* * *
39345185 AATTATTAATTATGTCATAAAATATTCGTGTTAAAATTTTGTATTGGTATAAATTTTACATTTTA
1 AATTATTAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
39345250 TCTTTAAAATAACTTTTATTA
66 TCTTTAAAATAACTTTTATTA
39345271 AA
1 AA
39345273 AAACCACATT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.48
Consensus pattern (86 bp):
AATTATTAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
TCTTTAAAATAACTTTTATTA
Found at i:39346871 original size:25 final size:25
Alignment explanation
Indices: 39346824--39346871 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39346814 ATGTTGTTCG
*
39346824 AATATTGCATTGTTAATGATGTCTA
1 AATATTGCATTATTAATGATGTCTA
* * *
39346849 AATATTGTATTATTGATGCTGTC
1 AATATTGCATTATTAATGATGTC
39346872 CGAATCAGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (25 bp):
AATATTGCATTATTAATGATGTCTA
Found at i:39347282 original size:6 final size:6
Alignment explanation
Indices: 39347271--39347298 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39347261 TGTGATTTAA
39347271 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
39347299 CTTTTCAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:39347901 original size:15 final size:15
Alignment explanation
Indices: 39347871--39347920 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
39347861 TATAAATTAT
39347871 ATAATAT-ATA-AAA
1 ATAATATAATATAAA
39347884 ATAATATAATATAAA
1 ATAATATAATATAAA
* *
39347899 ATATTATAAATTTAAA
1 ATAATAT-AATATAAA
39347915 A-AATAT
1 ATAATAT
39347921 TCTAGACTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 7 0.23
14 3 0.10
15 13 0.42
16 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATATAATATAAA
Found at i:39348445 original size:3 final size:3
Alignment explanation
Indices: 39348437--39348464 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39348427 CCATACTAGT
39348437 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39348465 TTAAGAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39349751 original size:21 final size:21
Alignment explanation
Indices: 39349727--39349791 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
39349717 AATTAAATTT
39349727 TAAAATTTTGATGGATGTTCA
1 TAAAATTTTGATGGATGTTCA
* *
39349748 TAAAA-ATTGAT--ATGATT-T
1 TAAAATTTTGATGGATG-TTCA
39349766 TAAAATTTTGATGGATGTTCA
1 TAAAATTTTGATGGATGTTCA
39349787 TAAAA
1 TAAAA
39349792 ATTGATATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (21 bp):
TAAAATTTTGATGGATGTTCA
Found at i:39349777 original size:39 final size:39
Alignment explanation
Indices: 39349723--39349804 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
39349713 ATTCAATTAA
39349723 ATTTTAAAATTTTGATGGATGTTCATAAAAATTGATATG
1 ATTTTAAAATTTTGATGGATGTTCATAAAAATTGATATG
39349762 ATTTTAAAATTTTGATGGATGTTCATAAAAATTGATATG
1 ATTTTAAAATTTTGATGGATGTTCATAAAAATTGATATG
39349801 ATTT
1 ATTT
39349805 GATTTGCATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (39 bp):
ATTTTAAAATTTTGATGGATGTTCATAAAAATTGATATG
Found at i:39350478 original size:70 final size:70
Alignment explanation
Indices: 39350375--39350515 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
39350365 TTTTTAAATA
*
39350375 TATAATTACTGTTTAATAGTTAGTTTTTATTTAAATTAAATTTAAAATATATAAACATAATAATT
1 TATAATTACTGTTTAATAGTTAGTTTTTATTTAAATTAAATTTAAAATATATAAACATAATAATA
39350440 ATTAT
66 ATTAT
*
39350445 TATAATTACTGTTTAATAGTTAGTTTTTATTTAAATTTAATTTAAAATATATAAACATAATAATA
1 TATAATTACTGTTTAATAGTTAGTTTTTATTTAAATTAAATTTAAAATATATAAACATAATAATA
39350510 ATTAT
66 ATTAT
39350515 T
1 T
39350516 TTTTATAAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (70 bp):
TATAATTACTGTTTAATAGTTAGTTTTTATTTAAATTAAATTTAAAATATATAAACATAATAATA
ATTAT
Found at i:39353183 original size:14 final size:16
Alignment explanation
Indices: 39353149--39353185 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39353139 TTTGTAATAT
*
39353149 AAATTTAGCACTTATA
1 AAATTTAGCACGTATA
39353165 AAATTTAGCA-GTA-A
1 AAATTTAGCACGTATA
39353179 AAATTTA
1 AAATTTA
39353186 TTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (16 bp):
AAATTTAGCACGTATA
Found at i:39354210 original size:2 final size:2
Alignment explanation
Indices: 39354205--39354229 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39354195 AATATCACAC
39354205 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39354230 CCACTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39355138 original size:37 final size:35
Alignment explanation
Indices: 39355072--39355143 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
39355062 AATTTTATTA
* *
39355072 AAAAAAACTGAATTACAAAAGTAAAAAAAGTAAAG
1 AAAAAAACTGAATTACAAAAGAAAAAAAAGAAAAG
*
39355107 AAAAAAACTGTAAATTGCAAAA-AAAAGAAAAGAAAAG
1 AAAAAAACTG--AATTACAAAAGAAAA-AAAAGAAAAG
39355144 CTTCCACGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 10 0.32
36 3 0.10
37 18 0.58
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.12
Consensus pattern (35 bp):
AAAAAAACTGAATTACAAAAGAAAAAAAAGAAAAG
Found at i:39355840 original size:29 final size:30
Alignment explanation
Indices: 39355808--39355866 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
39355798 TTTAGTCTAA
*
39355808 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
* *
39355837 TGTGCAATTTTATATATGAAATTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
39355867 GATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTTTATACATGAAACTTTGATTT
Found at i:39359025 original size:30 final size:30
Alignment explanation
Indices: 39358927--39359025 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 30
39358917 CTAACTCCCA
*
39358927 TAATTCCCTATTAGATCAATG-AGAGTTCTC
1 TAATTCCCTATTAGATCAA-GAATAGTTCTC
* * *
39358957 TAATTCCCTATTAGGTCGAGAACACATTATTATCTC
1 TAATTCCCTATTAGATC---AAGA-A-TAGT-TCTC
*
39358993 TAATTCCCTATTAGATTAAGAATAGTTCTC
1 TAATTCCCTATTAGATCAAGAATAGTTCTC
39359023 TAA
1 TAA
39359026 CAACTTACTA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
30 23 0.43
31 3 0.06
32 1 0.02
33 5 0.09
34 1 0.02
35 2 0.04
36 19 0.35
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (30 bp):
TAATTCCCTATTAGATCAAGAATAGTTCTC
Found at i:39359060 original size:66 final size:66
Alignment explanation
Indices: 39358927--39359063 Score: 150
Period size: 66 Copynumber: 2.1 Consensus size: 66
39358917 CTAACTCCCA
*** * * * * *
39358927 TAATTCCCTATTAGATCAATGAGAGTTCTCTAATTCCCTATTAGGTCGAGAACACATTATTATCT
1 TAATTCCCTATTAGATCAATGAGAGTTCTCTAACAACCTACTAGGTCGAGAAAAAAGTATTACCT
39358992 C
66 C
* * * *
39358993 TAATTCCCTATTAGATTAA-GAATAGTTCTCTAACAACTTACTAGGTCGAGAAAAAAGTGTTACC
1 TAATTCCCTATTAGATCAATG-AGAGTTCTCTAACAACCTACTAGGTCGAGAAAAAAGTATTACC
39359057 TC
65 TC
39359059 TAATT
1 TAATT
39359064 TTCTATTGGG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
65 1 0.02
66 57 0.98
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (66 bp):
TAATTCCCTATTAGATCAATGAGAGTTCTCTAACAACCTACTAGGTCGAGAAAAAAGTATTACCT
C
Found at i:39361767 original size:40 final size:40
Alignment explanation
Indices: 39361723--39361833 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
39361713 TGAGTTACCA
* * *
39361723 TAGTGAATCAGGAACAAGTCCTATCCACTTTATATAT-TTC
1 TAGTGAATCAGGAATAAATCCTATTCACTTTA-ATATCTTC
* * *
39361763 TAGTGAATCAGGAATAAATCCTATTCGCTTTAATTTCTTT
1 TAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTTC
39361803 TAGTGAATCAGGAATAAATCCTATTCACTTT
1 TAGTGAATCAGGAATAAATCCTATTCACTTT
39361834 TAATTCTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
39 3 0.05
40 60 0.95
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (40 bp):
TAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTTC
Found at i:39362720 original size:16 final size:18
Alignment explanation
Indices: 39362694--39362732 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
39362684 TAAACCCCAA
39362694 TTTCTCCTTTTT-CTTTC
1 TTTCTCCTTTTTCCTTTC
39362711 TTTC-CCTTTTTCCTTTC
1 TTTCTCCTTTTTCCTTTC
39362728 TTTCT
1 TTTCT
39362733 TTCTCCCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCTCCTTTTTCCTTTC
Found at i:39362966 original size:8 final size:8
Alignment explanation
Indices: 39362945--39362981 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
39362935 TTACTTTATT
39362945 TAAT-TAA
1 TAATATAA
*
39362952 TATTATAA
1 TAATATAA
39362960 TAATATAA
1 TAATATAA
39362968 TAATATAA
1 TAATATAA
39362976 TAATAT
1 TAATAT
39362982 TTACTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 3 0.11
8 24 0.89
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TAATATAA
Found at i:39366745 original size:21 final size:20
Alignment explanation
Indices: 39366713--39366751 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39366703 TTTGCCAAGA
*
39366713 TTAGATTAAATTTTTATATG
1 TTAGATTAAATTTGTATATG
*
39366733 TTAGAATTTAATTTGTATA
1 TTAG-ATTAAATTTGTATA
39366752 ACTATTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (20 bp):
TTAGATTAAATTTGTATATG
Found at i:39367827 original size:9 final size:9
Alignment explanation
Indices: 39367801--39367843 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
39367791 AATTGAAAAA
39367801 GAATAATTT
1 GAATAATTT
*
39367810 -TATAATTT
1 GAATAATTT
*
39367818 GAACAATTT
1 GAATAATTT
39367827 GAATAATTT
1 GAATAATTT
39367836 GAATAATT
1 GAATAATT
39367844 GATTGGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (9 bp):
GAATAATTT
Found at i:39370394 original size:22 final size:20
Alignment explanation
Indices: 39370357--39370397 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
39370347 TAAAGTTAAA
39370357 AAATTATAAAAGAAAAAATT
1 AAATTATAAAAGAAAAAATT
*
39370377 AAATTACTCAAAATAAAAAAT
1 AAATTA-T-AAAAGAAAAAAT
39370398 AGGGACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATTATAAAAGAAAAAATT
Found at i:39373579 original size:19 final size:19
Alignment explanation
Indices: 39373555--39373592 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39373545 ACAAGGAACA
39373555 GTAGAATAATCCATATTTG
1 GTAGAATAATCCATATTTG
39373574 GTAGAATAATCCATATTTG
1 GTAGAATAATCCATATTTG
39373593 ATATGGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
GTAGAATAATCCATATTTG
Found at i:39387034 original size:23 final size:23
Alignment explanation
Indices: 39386995--39387048 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
39386985 AATAACAATG
**
39386995 AAGAAGAAA-AAAGAAGATTAGAA
1 AAGAA-AAAGAAAGAAGAACAGAA
*
39387018 AAGGAAAAGAAAGAAGAACAGAA
1 AAGAAAAAGAAAGAAGAACAGAA
39387041 AAGAAAAA
1 AAGAAAAA
39387049 TTGGACAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAGAACAGAA
Found at i:39389846 original size:22 final size:23
Alignment explanation
Indices: 39389816--39389858 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39389806 CAATATATTT
**
39389816 TTAATAGAATTATAAAAAAATAA
1 TTAATAGAAAAATAAAAAAATAA
39389839 TTAA-AGAAAAATAAAAAAAT
1 TTAATAGAAAAATAAAAAAAT
39389859 TGACATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (23 bp):
TTAATAGAAAAATAAAAAAATAA
Found at i:39400270 original size:44 final size:49
Alignment explanation
Indices: 39400195--39400299 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 49
39400185 CGGGGGGTGA
*
39400195 AAATGTGTAAGACCATGGTTGAAAGACACCATGGTA-ACCATG-ATA-T-
1 AAATGTGT-AGACCATGGTTGAAAGACACCATGGCACACCATGAATACTG
*
39400241 AAATGTGTAGACCATGG-TGAAAGATACCATGGCACGACCATGAATACTG
1 AAATGTGTAGACCATGGTTGAAAGACACCATGGCAC-ACCATGAATACTG
39400290 AAATGTGTAG
1 AAATGTGTAG
39400300 GAATCCATGG
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
44 15 0.29
45 9 0.17
46 14 0.27
47 3 0.06
48 1 0.02
49 10 0.19
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (49 bp):
AAATGTGTAGACCATGGTTGAAAGACACCATGGCACACCATGAATACTG
Found at i:39405204 original size:45 final size:46
Alignment explanation
Indices: 39405131--39405228 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 46
39405121 GCTTTCTGAA
*
39405131 ATGAGAATGTGTAAGA-CATGGTTGAAAGACACCATGG-AACATGAT
1 ATGA-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
39405176 ATGAAATGTGTAAGACTATGGTTGAAAGATACCA-GG-AA-AT-AT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
39405218 ATGAAATGTGT
1 ATGAAATGTGT
39405229 GACCGTGGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
42 13 0.26
43 2 0.04
44 15 0.30
45 20 0.40
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:39405306 original size:46 final size:44
Alignment explanation
Indices: 39405249--39405510 Score: 306
Period size: 46 Copynumber: 5.9 Consensus size: 44
39405239 GCAACTGGAT
39405249 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACACGA
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA-GA
39405294 CATGAAATGTGTAAGAACCATGGTTGAAAGATACCATGGCAACAAGA
1 -ATGAAATGTGTAAG-ACCATGGTTGAAAGATACCATGGCAAC-AGA
39405341 ATGAAAATGTGTAAGACCATGGTTGAAAGATA-CATGGCAACAGA
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGA
*
39405385 TAT-AAAAGTG-AA-A-CATGGTT-AAAGATACC-TGGCAACAGGA
1 -ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA-GA
* *
39405425 TATAAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGA
1 -ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA-GA
* * **
39405471 AAGGAATGAATAAGACCATGGTTG-AAGAGTACCGATGGCA
1 ATGAAATGTGTAAGACCATGGTTGAAAGA-TACC-ATGGCA
39405511 TCATGTCAAA
Statistics
Matches: 194, Mismatches: 8, Indels: 28
0.84 0.03 0.12
Matches are distributed among these distances:
39 15 0.08
40 13 0.07
41 6 0.03
42 4 0.02
43 7 0.04
44 14 0.07
45 44 0.23
46 50 0.26
47 40 0.21
48 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Consensus pattern (44 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGA
Found at i:39405675 original size:41 final size:43
Alignment explanation
Indices: 39405614--39405700 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 43
39405604 GTTATATGAA
39405614 ATGGTTGTGTGAAATGTTTACAAGAA-TGGTCATATGGAATGT
1 ATGGTTGTGTGAAATGTTTACAAGAACTGGTCATATGGAATGT
39405656 ATGGTTGT-TGAAATGTTTACAAGAACTGGTCATATGGAATGT
1 ATGGTTGTGTGAAATGTTTACAAGAACTGGTCATATGGAATGT
39405698 ATG
1 ATG
39405701 TAACAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 17 0.39
42 27 0.61
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.36
Consensus pattern (43 bp):
ATGGTTGTGTGAAATGTTTACAAGAACTGGTCATATGGAATGT
Found at i:39405857 original size:16 final size:17
Alignment explanation
Indices: 39405838--39405871 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39405828 ATGATGGAGC
39405838 AATGAAAT-ATTGATAT
1 AATGAAATGATTGATAT
39405854 AATGAAATGATTGATAT
1 AATGAAATGATTGATAT
39405871 A
1 A
39405872 TACTTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (17 bp):
AATGAAATGATTGATAT
Found at i:39417546 original size:23 final size:22
Alignment explanation
Indices: 39417517--39417559 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
39417507 TTTTTCGAAT
39417517 TTTGAGTTAATCGAATT-GAGTTA
1 TTTGAGTT--TCGAATTCGAGTTA
39417540 TTTGAGTTTCGAATTCGAGT
1 TTTGAGTTTCGAATTCGAGT
39417560 CGAGTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (22 bp):
TTTGAGTTTCGAATTCGAGTTA
Found at i:39417780 original size:17 final size:19
Alignment explanation
Indices: 39417747--39417783 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
39417737 AAAATTCTAA
39417747 AAAATATTTAAAGAAAGTT
1 AAAATATTTAAAGAAAGTT
39417766 AAAAT-TTTAAA-AAAGTT
1 AAAATATTTAAAGAAAGTT
39417783 A
1 A
39417784 GATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAATATTTAAAGAAAGTT
Found at i:39419461 original size:19 final size:19
Alignment explanation
Indices: 39419437--39419475 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39419427 CTATAAACAA
39419437 AACAAATCAATCACTAATC
1 AACAAATCAATCACTAATC
39419456 AACAAATCAATCACTAATC
1 AACAAATCAATCACTAATC
39419475 A
1 A
39419476 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (19 bp):
AACAAATCAATCACTAATC
Found at i:39429835 original size:30 final size:30
Alignment explanation
Indices: 39429799--39429897 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
39429789 CTAGCCTTTG
*
39429799 CCACCACCAACTCCACTAGCTACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
39429829 CCACCACCAACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
39429859 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
39429889 CCACCACCA
1 CCACCACCA
39429898 CTTGTACCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:39430472 original size:25 final size:26
Alignment explanation
Indices: 39430444--39430514 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
39430434 ATTCTAAATT
*
39430444 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
* *
39430469 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATTAATA
*
39430494 CTATATTATTTATATATATAT
1 CTATATTATGTATATATATAT
39430515 ATTTTTTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 2 0.05
25 35 0.92
26 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.54
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:39430513 original size:29 final size:28
Alignment explanation
Indices: 39430473--39430583 Score: 97
Period size: 29 Copynumber: 4.0 Consensus size: 28
39430463 ATTATACTAT
39430473 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATACTATATTA
* ** *
39430502 TTTATATATATATATTTTTTAC-ATGTTA
1 TTTATGTATATAT-TTTAATACTATATTA
39430530 TCTTATGTATATATTTTAAT--TATATTA
1 T-TTATGTATATATTTTAATACTATATTA
* * *
39430557 TGTATGTAT-T-TTTTTACACTATATTA
1 TTTATGTATATATTTTAATACTATATTA
39430583 T
1 T
39430584 GTACATATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
24 5 0.08
25 1 0.02
26 15 0.23
27 6 0.09
28 10 0.15
29 29 0.44
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTATGTATATATTTTAATACTATATTA
Found at i:39430517 original size:14 final size:14
Alignment explanation
Indices: 39430454--39430518 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
39430444 CTATATTACG
*
39430454 TATATATATAT-TA
1 TATATATTTATATA
*
39430467 TACTAT-TTTATGTA
1 TA-TATATTTATATA
*
39430481 TATATCTTTA-ATA
1 TATATATTTATATA
39430494 CTATATTATTTATATA
1 -TATA-TATTTATATA
39430510 TATATATTT
1 TATATATTT
39430519 TTTACATGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
13 11 0.26
14 20 0.47
15 9 0.21
16 3 0.07
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (14 bp):
TATATATTTATATA
Found at i:39430557 original size:22 final size:22
Alignment explanation
Indices: 39430527--39430568 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39430517 TTTTTACATG
*
39430527 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
39430549 TTATATTATGTATGTATTTT
1 TTATATTATGTATATATTTT
39430569 TTTACACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:39430562 original size:26 final size:26
Alignment explanation
Indices: 39430533--39430586 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39430523 CATGTTATCT
*
39430533 TATGTATATATTTTA-ATTATATTATG
1 TATGTAT-TATTTTACACTATATTATG
*
39430559 TATGTATTTTTTTACACTATATTATG
1 TATGTATTATTTTACACTATATTATG
39430585 TA
1 TA
39430587 CATATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (26 bp):
TATGTATTATTTTACACTATATTATG
Found at i:39430602 original size:20 final size:20
Alignment explanation
Indices: 39430577--39430635 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
39430567 TTTTTACACT
39430577 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
39430597 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
39430620 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
39430636 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:39430618 original size:48 final size:48
Alignment explanation
Indices: 39430514--39430620 Score: 110
Period size: 48 Copynumber: 2.2 Consensus size: 48
39430504 TATATATATA
* * * * *
39430514 TATTTTTTACATGTTATCTTATGTATATATTTTAATTATATTATGTATG
1 TATTTTTTACA-GCTATATTATGTACATATTTTAATTATATCACGTATG
*
39430563 TATTTTTTTACA-CTATATTATGTACATATTTTTAA-TATTATCACGTATT
1 TA-TTTTTTACAGCTATATTATGTACATA-TTTTAATTA-TATCACGTATG
39430612 TATTTTTTA
1 TATTTTTTA
39430621 TATATGTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
48 22 0.45
49 18 0.37
50 9 0.18
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (48 bp):
TATTTTTTACAGCTATATTATGTACATATTTTAATTATATCACGTATG
Found at i:39430772 original size:16 final size:15
Alignment explanation
Indices: 39430748--39430782 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
39430738 TAATTATTAT
39430748 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
39430764 TATTTTAATATTTTA
1 TATTCTAATATTTTA
39430779 TATT
1 TATT
39430783 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:39436542 original size:16 final size:17
Alignment explanation
Indices: 39436521--39436554 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39436511 ATTAAAAGTA
39436521 AAGGAAAGATT-TTTAC
1 AAGGAAAGATTGTTTAC
*
39436537 AAGGAAAGGTTGTTTAC
1 AAGGAAAGATTGTTTAC
39436554 A
1 A
39436555 GAGAGGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
AAGGAAAGATTGTTTAC
Found at i:39438219 original size:18 final size:18
Alignment explanation
Indices: 39438196--39438230 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39438186 TATTAATATA
39438196 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCCTGATTG
*
39438214 GGAGTAAATCCTTGATT
1 GGAGTAAATCCCTGATT
39438231 AGGATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
GGAGTAAATCCCTGATTG
Found at i:39438439 original size:18 final size:19
Alignment explanation
Indices: 39438406--39438441 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39438396 AATTTCCTTT
39438406 ATTGAAATATTAGTTTAGA
1 ATTGAAATATTAGTTTAGA
*
39438425 ATTGATATA-TAGTTTAG
1 ATTGAAATATTAGTTTAG
39438442 TTTCAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (19 bp):
ATTGAAATATTAGTTTAGA
Found at i:39440304 original size:10 final size:10
Alignment explanation
Indices: 39440288--39440318 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39440278 TTTAAAACTC
39440288 ATTTTAAATG
1 ATTTTAAATG
*
39440298 TTTTTAAATG
1 ATTTTAAATG
39440308 ATTTTAAATG
1 ATTTTAAATG
39440318 A
1 A
39440319 CTTAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
ATTTTAAATG
Found at i:39441058 original size:21 final size:21
Alignment explanation
Indices: 39441007--39441058 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
39440997 TTAAATATTT
39441007 ATTTTA-AATATGAATTTAAA
1 ATTTTATAATATGAATTTAAA
*
39441027 A-TTTCTAATAT-ATATTTAAA
1 ATTTTATAATATGA-ATTTAAA
39441047 ATTTTATAATAT
1 ATTTTATAATAT
39441059 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 14 0.52
21 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTTATAATATGAATTTAAA
Found at i:39441060 original size:17 final size:18
Alignment explanation
Indices: 39441020--39441073 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
39441010 TTAAATATGA
39441020 ATTTAAAATTTCTAATATAT
1 ATTTAAAATTT-T-ATATAT
39441040 ATTTAAAATTTTATA-AT
1 ATTTAAAATTTTATATAT
**
39441057 ATTTTTAATTTTATATA
1 ATTTAAAATTTTATATA
39441074 ATTAACATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.48
18 4 0.13
19 1 0.03
20 11 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAAAATTTTATATAT
Found at i:39441704 original size:125 final size:126
Alignment explanation
Indices: 39441590--39441868 Score: 339
Period size: 129 Copynumber: 2.2 Consensus size: 126
39441580 GGTAAATCGA
* * * *
39441590 AACCCAGCACGTAGGGCACGTTTTCTCGAATTCCCAAACGTTAAACATTGTCTT-GTTTT-AGAA
1 AACCCAGCACGTAGGGCACGATTCCCCGAATTCCCAAAC-TTAAACATTGCCTTCGTTTTAAGAA
39441653 TTTAGAAAACATGAGTGAAA-TTCTAAAGGAATATTCGATTATTTGAACAAACGAGAAATTGC
65 TTTAGAAAACATGAGTGAAATTTC-AAAGGAATATTCGATTATTTGAACAAACGAGAAATTGC
* * * ** *
39441715 AACCCAGCTCGATAGGGCACGATTCCCCGAATTTCCATACTTCGACGTTGCCTTCGTTTTAAAGA
1 AACCCAGCACG-TAGGGCACGATTCCCCGAATTCCCAAACTTAAACATTGCCTTCGTTTT-AAGA
** * * *
39441780 ATTTTTAAAACATGAGTGAAATTTCAAAAGAATATTCGATCATTTTGAATAAACGAGAAATTGC
64 ATTTAGAAAACATGAGTGAAATTTCAAAGGAATATTCGATTA-TTTGAACAAACGAGAAATTGC
*
39441844 AACCCAGCACGGTAGGACACGATTC
1 AACCCAGCAC-GTAGGGCACGATTC
39441869 TTCGAATTTC
Statistics
Matches: 130, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
125 20 0.15
126 28 0.22
128 37 0.28
129 44 0.34
130 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (126 bp):
AACCCAGCACGTAGGGCACGATTCCCCGAATTCCCAAACTTAAACATTGCCTTCGTTTTAAGAAT
TTAGAAAACATGAGTGAAATTTCAAAGGAATATTCGATTATTTGAACAAACGAGAAATTGC
Found at i:39446704 original size:16 final size:17
Alignment explanation
Indices: 39446683--39446720 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
39446673 TTAAAATTAG
* *
39446683 TTTTT-ATATTTTTATT
1 TTTTTAATAATTTAATT
39446699 TTTTTAATAATTTAATT
1 TTTTTAATAATTTAATT
39446716 TTTTT
1 TTTTT
39446721 GAGTGAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTAATAATTTAATT
Found at i:39446705 original size:29 final size:31
Alignment explanation
Indices: 39446653--39446710 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
39446643 TTAATGAAGT
39446653 TTTTCTATATTTTGTATTTGTTAA-AATTAG
1 TTTTCTATATTTTGTATTTGTTAATAATTAG
*
39446683 TTTT-TATATTTT-TATTTTTTTAATAATT
1 TTTTCTATATTTTGTA-TTTGTTAATAATT
39446711 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 15 0.60
30 8 0.32
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (31 bp):
TTTTCTATATTTTGTATTTGTTAATAATTAG
Found at i:39452213 original size:24 final size:24
Alignment explanation
Indices: 39452186--39452232 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
39452176 ATTTCAACGC
39452186 TGGAAGAATATCAGTTGATAGGTG
1 TGGAAGAATATCAGTTGATAGGTG
39452210 TGGAAGAATATCAGTTGATAGGT
1 TGGAAGAATATCAGTTGATAGGT
39452233 CCCAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (24 bp):
TGGAAGAATATCAGTTGATAGGTG
Found at i:39456713 original size:11 final size:11
Alignment explanation
Indices: 39456685--39456714 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39456675 GATAGAAATA
*
39456685 ATTATTATATG
1 ATTATTTTATG
39456696 ATTATTTTATG
1 ATTATTTTATG
39456707 ATTATTTT
1 ATTATTTT
39456715 GAGGTCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
ATTATTTTATG
Found at i:39463516 original size:14 final size:14
Alignment explanation
Indices: 39463490--39463519 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39463480 TGAAAATATC
*
39463490 TTTCAGAAAATAAT
1 TTTCAAAAAATAAT
39463504 TTTCAAAAAATAAT
1 TTTCAAAAAATAAT
39463518 TT
1 TT
39463520 ATTTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (14 bp):
TTTCAAAAAATAAT
Done.