Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 92 of 106
Found at i:35120715 original size:18 final size:18
Alignment explanation
Indices: 35120692--35120732 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
35120682 CCTTCTCTCT
35120692 TTCTTCTTCTTTTTTTTC
1 TTCTTCTTCTTTTTTTTC
35120710 TTCTTCTT-TTTTTTCTTC
1 TTCTTCTTCTTTTTT-TTC
35120728 TTCTT
1 TTCTT
35120733 TCCCTCTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTTCTTCTTTTTTTTC
Found at i:35120890 original size:13 final size:13
Alignment explanation
Indices: 35120866--35120899 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
35120856 CTATTCCTTC
35120866 TCTTTC-CTCTTG
1 TCTTTCTCTCTTG
35120878 TCTTTCTCTCTTG
1 TCTTTCTCTCTTG
35120891 TCTTT-TCTC
1 TCTTTCTCTC
35120900 CCTTTTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.32, G:0.06, T:0.62
Consensus pattern (13 bp):
TCTTTCTCTCTTG
Found at i:35121066 original size:3 final size:3
Alignment explanation
Indices: 35121058--35121099 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
35121048 CCCCCACTTA
35121058 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
35121100 TTTTATGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:35137226 original size:15 final size:15
Alignment explanation
Indices: 35137208--35137238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35137198 TCCACCACCG
*
35137208 TCGCCTCCTCCGCCA
1 TCGCCTCCGCCGCCA
35137223 TCGCCTCCGCCGCCA
1 TCGCCTCCGCCGCCA
35137238 T
1 T
35137239 GTCCACCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.58, G:0.16, T:0.19
Consensus pattern (15 bp):
TCGCCTCCGCCGCCA
Found at i:35149523 original size:51 final size:51
Alignment explanation
Indices: 35149448--35149604 Score: 269
Period size: 51 Copynumber: 3.1 Consensus size: 51
35149438 ATATGATCAG
* * *
35149448 ATTCATCTCCATAACCCTTGTTCTCTGCAGCATCATCCTTGCCAGTATGAT
1 ATTCATCTCCACAACCCTTATTCTCTGCAGCATCATCCTTGCCAGTTTGAT
*
35149499 ATTCATCTCCACAACCCTTTTTCTCTGCAGCATCATCCTTGCCAGTTTGAT
1 ATTCATCTCCACAACCCTTATTCTCTGCAGCATCATCCTTGCCAGTTTGAT
*
35149550 ATTCATCTCCACAACCCTTATTCCCTGCAGCATCATCCTTGCCAGTTTGAT
1 ATTCATCTCCACAACCCTTATTCTCTGCAGCATCATCCTTGCCAGTTTGAT
35149601 ATTC
1 ATTC
35149605 TCTGTAACCC
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (51 bp):
ATTCATCTCCACAACCCTTATTCTCTGCAGCATCATCCTTGCCAGTTTGAT
Found at i:35151395 original size:5 final size:5
Alignment explanation
Indices: 35151385--35151418 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
35151375 AGCTCCAAGA
*
35151385 TTTTC TTTTC TCTTC TTTTC TTTTGC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTT
35151419 CTGATCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:35151426 original size:20 final size:20
Alignment explanation
Indices: 35151385--35151427 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
35151375 AGCTCCAAGA
**
35151385 TTTTCTTTTCTCTTCTTTTC
1 TTTTCTTTTCTCTTCTGATC
35151405 TTTTGCTTTTCT-TTCTGATC
1 TTTT-CTTTTCTCTTCTGATC
35151425 TTT
1 TTT
35151428 CTGCCCTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTCTTTTCTCTTCTGATC
Found at i:35152422 original size:16 final size:16
Alignment explanation
Indices: 35152401--35152431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35152391 ACAATATACA
35152401 TAATTAATAAATAAAT
1 TAATTAATAAATAAAT
*
35152417 TAATTAATTAATAAA
1 TAATTAATAAATAAA
35152432 AAAATTTAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTAATAAATAAAT
Found at i:35156754 original size:14 final size:14
Alignment explanation
Indices: 35156735--35156779 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
35156725 TACTTAAATA
*
35156735 TATATTTTTATTTG
1 TATATTTATATTTG
35156749 TATATTTATATATT-
1 TATATTTATAT-TTG
*
35156763 TATATATATATTTG
1 TATATTTATATTTG
35156777 TAT
1 TAT
35156780 TCCTCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (14 bp):
TATATTTATATTTG
Found at i:35156760 original size:8 final size:8
Alignment explanation
Indices: 35156733--35156769 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
35156723 CTTACTTAAA
35156733 TATATATT
1 TATATATT
35156741 T-T-TATT
1 TATATATT
*
35156747 TGTATATT
1 TATATATT
35156755 TATATATT
1 TATATATT
35156763 TATATAT
1 TATATAT
35156770 ATATTTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 5 0.19
7 2 0.08
8 19 0.73
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (8 bp):
TATATATT
Found at i:35156789 original size:34 final size:35
Alignment explanation
Indices: 35156732--35156798 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
35156722 TCTTACTTAA
* **
35156732 ATATATATTTTTATTTGTATATTTATA-TATTTAT
1 ATATATATTTGTATTCCTATATTTATATTATTTAT
* *
35156766 ATATATATTTGTATTCCTCTATTTGTATTATTT
1 ATATATATTTGTATTCCTATATTTATATTATTT
35156799 TCTTATACCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 22 0.81
35 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (35 bp):
ATATATATTTGTATTCCTATATTTATATTATTTAT
Found at i:35158219 original size:34 final size:35
Alignment explanation
Indices: 35158149--35158219 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
35158139 TTTTAAAATC
* **
35158149 TTTATATTGAAAGGGTTTTTTCAAATCTCTTGGAA
1 TTTATATTAAAAGGGTTTTTTCAAAGATCTTGGAA
35158184 TTTATATTAAAAGGGTTTTTTCAGAAGAT-TT-GAA
1 TTTATATTAAAAGGGTTTTTTCA-AAGATCTTGGAA
35158218 TT
1 TT
35158220 CACTCTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 5 0.16
35 24 0.75
36 3 0.09
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (35 bp):
TTTATATTAAAAGGGTTTTTTCAAAGATCTTGGAA
Found at i:35162004 original size:18 final size:19
Alignment explanation
Indices: 35161970--35162005 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35161960 TATTTGGTTG
*
35161970 TTGTTGTTTTGTGGTCTTA
1 TTGTTGTTTTGTAGTCTTA
35161989 TTGTTG-TTTGTAGTCTT
1 TTGTTGTTTTGTAGTCTT
35162006 GGTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.06, C:0.06, G:0.25, T:0.64
Consensus pattern (19 bp):
TTGTTGTTTTGTAGTCTTA
Found at i:35168359 original size:2 final size:2
Alignment explanation
Indices: 35168354--35168392 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
35168344 TTAAAAAAAT
35168354 TA TA TA TA TA TA TA TA GTA -A CTA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA
35168393 AAAGAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 30 0.88
3 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:35175069 original size:3 final size:3
Alignment explanation
Indices: 35175061--35175086 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35175051 CTATGACAAG
35175061 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
35175087 ATATACTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:35175255 original size:2 final size:2
Alignment explanation
Indices: 35175250--35175339 Score: 98
Period size: 2 Copynumber: 46.5 Consensus size: 2
35175240 GGCCTAGGGG
* * *
35175250 GA GA GA GA CA GA GA GA CA GA GA GA GA GA GA GA GA GA G- GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
35175291 GA -A GA -A GA -A GA NGA GA GA CA GA GA GA CA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35175331 GA GA GA GA G
1 GA GA GA GA G
35175340 GGGAAGAGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
1 4 0.05
2 67 0.92
3 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35178980 original size:15 final size:15
Alignment explanation
Indices: 35178957--35178988 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35178947 GTGACAAGGG
35178957 TTACATGACTGAATA
1 TTACATGACTGAATA
*
35178972 TTACGTGACTGAATA
1 TTACATGACTGAATA
35178987 TT
1 TT
35178989 TGTTGAGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (15 bp):
TTACATGACTGAATA
Found at i:35178993 original size:102 final size:102
Alignment explanation
Indices: 35178766--35179005 Score: 295
Period size: 103 Copynumber: 2.3 Consensus size: 102
35178756 TTTATTTGGC
* * * * *
35178766 ATTAGGTGCCTGAATATTTGTTTAGCAGTGTGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
* * *
35178831 ATGTTGAGTGTTGCGTGACAGGTAATACGTGATTGAAT
66 ATGTTGAGCGTTGCGTGACAGGT-ATACATGACTGAAT
** * * * * *
35178869 ATTACCAGACTAAATATTTGTTGAGCATTACGTGAGTTCTTTATAGGCCTTACGTGGCTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
*
35178934 TTGTT-AGCGTTGCGTGACAAGGGT-TACATGACTGAAT
66 ATGTTGAGCGTTGCGTGAC-A-GGTATACATGACTGAAT
35178971 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGA
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGA
35179006 CTTATTTGTA
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
102 54 0.47
103 58 0.50
104 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (102 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
ATGTTGAGCGTTGCGTGACAGGTATACATGACTGAAT
Found at i:35179018 original size:102 final size:102
Alignment explanation
Indices: 35178766--35179021 Score: 300
Period size: 102 Copynumber: 2.5 Consensus size: 102
35178756 TTTATTTGGC
* * * * * *
35178766 ATTAGGTGCCTGAATATTTGTTTAGCAGTGTGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
* * *
35178831 ATGTTGAGTGTTGCGTGACAGGTAATACGTGATTGAAT
66 ATGTTGAGCGTTGCGTGACAGGT-ATACATGACTGAAT
** * * * *
35178869 ATTACCAGACTAAATATTTGTTGAGCATTACGTGAGTTCTTTATAGGCCTTACGTGGCTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
*
35178934 TTGTT-AGCGTTGCGTGACAAGGGT-TACATGACTGAAT
66 ATGTTGAGCGTTGCGTGAC-A-GGTATACATGACTGAAT
* * *
35178971 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACTTATTTGTAGGCATT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATT
35179022 GGGTGACTTT
Statistics
Matches: 127, Mismatches: 24, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
102 66 0.52
103 58 0.46
104 3 0.02
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.38
Consensus pattern (102 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
ATGTTGAGCGTTGCGTGACAGGTATACATGACTGAAT
Found at i:35179027 original size:22 final size:23
Alignment explanation
Indices: 35178985--35179030 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
35178975 CGTGACTGAA
*
35178985 TATTTGTTGAGCATTGCGTGACT
1 TATTTGTAGAGCATTGCGTGACT
*
35179008 TATTTGTAG-GCATTGGGTGACT
1 TATTTGTAGAGCATTGCGTGACT
35179030 T
1 T
35179031 TAGCTACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (23 bp):
TATTTGTAGAGCATTGCGTGACT
Found at i:35179637 original size:30 final size:30
Alignment explanation
Indices: 35179596--35179654 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
35179586 GGAGGTGCCT
* *
35179596 TTGAGTTTGAGGGACTAGTTGCACATATTC
1 TTGAGTGTGAGGGACCAGTTGCACATATTC
35179626 TTGAGTGTGAGGGACCAGTTGCACATATT
1 TTGAGTGTGAGGGACCAGTTGCACATATT
35179655 TCAGCAGGAT
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:0.24, C:0.14, G:0.29, T:0.34
Consensus pattern (30 bp):
TTGAGTGTGAGGGACCAGTTGCACATATTC
Found at i:35181109 original size:118 final size:111
Alignment explanation
Indices: 35180291--35181044 Score: 1017
Period size: 111 Copynumber: 6.7 Consensus size: 111
35180281 GGTGCGTGAC
* * *
35180291 TGACTTGTGCAATTC-TCGTGTTATTTTGAGGCTTTTGTTCAGCAGTTTTTTAGGCAATGCGTGA
1 TGACTTGTGCAATTCGT-GTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGA
* * * *
35180355 CTTGTTTTTATATATTGTGTTACCTGTTATAGCGAGAGTGGTGGCACG
64 CTGGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
* * * *
35180403 TGACTTGTGCAATTCATGTATTGTTTTGAGGCTTTTGTTCAGTAATTTTTTAGGCAATGCGTGAC
1 TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGAC
* *
35180468 TGGTTTTTATATATTGCGTTACCTATTGTAGCGAGAGTGGTGGTGCG
65 TGGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
* * * * *
35180515 TGACTTGTGCAATTCGTGTGTTGTTTTGAAGTTTTTGTTCAATAGTTTTTTAAGCTTGCGTGATT
1 TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* *
35180580 GGTTTTTATATATTGTGTTACCTGTTGTAGCGAGAGTGGTGGTGCG
66 GGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
* * * * *
35180626 TGACTTGTGCAATTCGTGTGTTGTTTTGAAGTTTTTGTTCAATAGTTTTTTAAGCTTGCGTGATT
1 TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
*
35180691 GGTTTTTATATATTGTGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
66 GGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
*
35180737 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
1 TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
*
35180802 GGTTTTTATATATTGCGTTACCTGTTGTAGCGTGAGTGGT-GCTGCG
66 GGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGC-GCG
* * * * *
35180848 TGACTTGTGCAATTTGTGTGTTCTTTAGAGGCTTTTGTTTAGTAGTTTTTTAGGCTTACGTGACT
1 TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * * * *
35180913 GATTTTTATATATTGCATGACCTGTTGTTATGTATTGCGAGATTGGTGGCACG
66 GGTTTTTATATATTGCGTTACC---TG-T-TGTA--GCGAGAGTGGTGGCGCG
* * * *
35180966 TGACTTGTACAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTTACT
1 TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
35181031 GGTTTTTATATATT
66 GGTTTTTATATATT
35181045 ACGTGACTTG
Statistics
Matches: 580, Mismatches: 52, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
110 2 0.00
111 340 0.59
112 148 0.26
113 1 0.00
114 2 0.00
115 1 0.00
116 4 0.01
118 80 0.14
119 2 0.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.46
Consensus pattern (111 bp):
TGACTTGTGCAATTCGTGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
GGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
Found at i:35181121 original size:118 final size:117
Alignment explanation
Indices: 35180291--35181130 Score: 826
Period size: 111 Copynumber: 7.4 Consensus size: 117
35180281 GGTGCGTGAC
* * * *
35180291 TGACTTGTGCAATTC-TCGTGTTATTTTGAGGCTTTTGTTCAGCAGTTTTTTAGGCAATGCGTGA
1 TGACTTGTGCAATTCAT-GTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGA
* * *
35180355 CTTGTTTTTATATATTGTGTTACCTG--TTA--TA--GCGAGAGTGGTGGCACG
64 CTGGTTTTTATATATTGCGTGACCTGTTTTATGTATTGCGAGAGTGGTGGCACG
* * * *
35180403 TGACTTGTGCAATTCATGTATTGTTTTGAGGCTTTTGTTCAGTAATTTTTTAGGCAATGCGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCGTGAC
* * **
35180468 TGGTTTTTATATATTGCGTTACC---TAT-TGTA--GCGAGAGTGGTGGTGCG
65 TGGTTTTTATATATTGCGTGACCTGTTTTATGTATTGCGAGAGTGGTGGCACG
* * * * * * *
35180515 TGACTTGTGCAATTCGTGTGTTGTTTTGAAGTTTTTGTTCAATAGTTTTTTAAGCTTGCGTGATT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * **
35180580 GGTTTTTATATATTGTGTTACCTG---T-TGTA--GCGAGAGTGGTGGTGCG
66 GGTTTTTATATATTGCGTGACCTGTTTTATGTATTGCGAGAGTGGTGGCACG
* * * * * * *
35180626 TGACTTGTGCAATTCGTGTGTTGTTTTGAAGTTTTTGTTCAATAGTTTTTTAAGCTTGCGTGATT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
35180691 GGTTTTTATATATTGTGTTACCTG---T-TGTA--GCGAGAGTGGTGGCGCG
66 GGTTTTTATATATTGCGTGACCTGTTTTATGTATTGCGAGAGTGGTGGCACG
*
35180737 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
35180802 GGTTTTTATATATTGCGTTACCTG---T-TGTA--GCGTGAGTGGT-GCTGCG
66 GGTTTTTATATATTGCGTGACCTGTTTTATGTATTGCGAGAGTGGTGGC-ACG
** * * *
35180848 TGACTTGTGCAATTTGTGTGTTCTTTAGAGGCTTTTGTTTAGTAGTTTTTTAGGCTTACGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * *
35180913 GATTTTTATATATTGCATGACCTGTTGTTATGTATTGCGAGATTGGTGGCACG
66 GGTTTTTATATATTGCGTGACCTGTT-TTATGTATTGCGAGAGTGGTGGCACG
* * * *
35180966 TGACTTGTACAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGATTGCGTTACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
* * * * *
35181031 GGTTTTTATATATTACGTGACTTGTTATTATATATTGTGAGAGCGGTGGCACG
66 GGTTTTTATATATTGCGTGACCTGTT-TTATGTATTGCGAGAGTGGTGGCACG
*** * * * *
35181084 TGACTTGTGCAATTCGCCTCTTGTTTAGGGGCGTTTGTTCACTAGTT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTT
35181131 ATTAGGCATT
Statistics
Matches: 646, Mismatches: 67, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
110 2 0.00
111 342 0.53
112 145 0.22
113 1 0.00
115 1 0.00
116 4 0.01
118 149 0.23
119 2 0.00
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.45
Consensus pattern (117 bp):
TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGTGACT
GGTTTTTATATATTGCGTGACCTGTTTTATGTATTGCGAGAGTGGTGGCACG
Found at i:35186559 original size:22 final size:23
Alignment explanation
Indices: 35186531--35186586 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
35186521 AAAATAGGTG
*
35186531 AGTCACGCG-TGCAAGATCAACT
1 AGTCACGCGATCCAAGATCAACT
* * *
35186553 AGTCACGCGATCCCATATCATCT
1 AGTCACGCGATCCAAGATCAACT
35186576 AGTCACGCGAT
1 AGTCACGCGAT
35186587 TCAATAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (23 bp):
AGTCACGCGATCCAAGATCAACT
Found at i:35186888 original size:94 final size:95
Alignment explanation
Indices: 35186714--35186890 Score: 205
Period size: 94 Copynumber: 1.9 Consensus size: 95
35186704 AGAATAAATA
* * * *
35186714 CTCACGCCATTCCATAATAATTAGTAACACGACTCCATATATATTACTCATGCGAGTCAATATCA
1 CTCACGCCATTCCATAATAACTAATAACACGACTCCATATATACTACTAATGCGAGTCAATATCA
* * *
35186779 ACTAGTAACGTGATTCTACAAAAAAGTCAT
66 AATACTAACGCGATTCTACAAAAAAGTCAT
* * * * *
35186809 CTCACGCGC-TTCCATATTAACTAATAACGCGA-TCGATATTTACTACTAATGGGAGTCAATATC
1 CTCACGC-CATTCCATAATAACTAATAACACGACTCCATATATACTACTAATGCGAGTCAATATC
* *
35186872 AAATACTCATGCGATTCTA
65 AAATACTAACGCGATTCTA
35186891 AATCTTAACT
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
94 40 0.60
95 26 0.39
96 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (95 bp):
CTCACGCCATTCCATAATAACTAATAACACGACTCCATATATACTACTAATGCGAGTCAATATCA
AATACTAACGCGATTCTACAAAAAAGTCAT
Found at i:35187061 original size:69 final size:70
Alignment explanation
Indices: 35186835--35187064 Score: 329
Period size: 70 Copynumber: 3.3 Consensus size: 70
35186825 TTAACTAATA
* * * *
35186835 ACGCGATCGATATTTACTACTAATGGGAGTCAATATCAAATACTCATGCGATTCTAAATCTTAAC
1 ACGCGATCCATATTTACTACTAACGGGAGTCAATATCAAATATTCACGCGATTCTAAATCTTAAC
* *
35186900 TAG-TA
66 -GGTTC
*
35186905 ATGCGATCCATATTTACTACTAACGGGAGTCAATATCAAATATTCACGCGATTCTAAATCTTAAC
1 ACGCGATCCATATTTACTACTAACGGGAGTCAATATCAAATATTCACGCGATTCTAAATCTTAAC
35186970 GGTTC
66 GGTTC
* * * * *
35186975 ACGTGATCCATAGTTACTACTAACGAGAGTCAATATCAAATATTTA-GTGATTCTAAATCTTAAC
1 ACGCGATCCATATTTACTACTAACGGGAGTCAATATCAAATATTCACGCGATTCTAAATCTTAAC
35187039 GGTTC
66 GGTTC
35187044 ACGCGATCCATATTTACTACT
1 ACGCGATCCATATTTACTACT
35187065 CACACGATTC
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
69 42 0.29
70 102 0.71
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (70 bp):
ACGCGATCCATATTTACTACTAACGGGAGTCAATATCAAATATTCACGCGATTCTAAATCTTAAC
GGTTC
Found at i:35208197 original size:2 final size:2
Alignment explanation
Indices: 35208190--35208240 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
35208180 TTTTAAATGA
*
35208190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35208232 AT AT GT AT A
1 AT AT AT AT A
35208241 GATAGGGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35218669 original size:82 final size:81
Alignment explanation
Indices: 35218533--35218691 Score: 239
Period size: 82 Copynumber: 2.0 Consensus size: 81
35218523 AGGGGCACCT
**
35218533 AGCAGTGTTTCTTTCTGATGACCAGCATTCTGGTATCAAATGGTAGTTAACTTGTAGATAACAAT
1 AGCAGTGTTTCTTTCTGATGACCAGCATTCTAATATCAAATGGTAGTTAACTTGTAGATAACAAT
*
35218598 CATAATTCAGGAGTCA
66 CAAAATTCAGGAGTCA
* * *
35218614 AGCAGTGTTTCTTTCGTGATTG-CCAGCATTCTAATGTCAATTGGTATTTAACTTGTAGATAACA
1 AGCAGTGTTTCTTTC-TGA-TGACCAGCATTCTAATATCAAATGGTAGTTAACTTGTAGATAACA
35218678 ATCAAAATTCAGGA
64 ATCAAAATTCAGGA
35218692 CTTCAAGAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
81 15 0.21
82 53 0.76
83 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (81 bp):
AGCAGTGTTTCTTTCTGATGACCAGCATTCTAATATCAAATGGTAGTTAACTTGTAGATAACAAT
CAAAATTCAGGAGTCA
Found at i:35219710 original size:485 final size:485
Alignment explanation
Indices: 35218801--35219770 Score: 1895
Period size: 485 Copynumber: 2.0 Consensus size: 485
35218791 TAATATCAAT
35218801 CCAACATAAATATAGCTACACTTTCCATGTATCAAACATTTCATGAAAATTGAGCCAAAAAACAA
1 CCAACATAAATATAGCTACACTTTCCATGTATCAAACATTTCATGAAAATTGAGCCAAAAAACAA
*
35218866 ATCATGAGAATGTTGACAATGCAATGAAACACAAGATTTTAGGTGAACAAGGTACCTCACCACTA
66 ATCATGAGAATGTTGACAATGCAATGAAACACAAGATTTTAGGTGAACAAGGTACCTCACCACCA
35218931 ACAAAGCAAAAGGGGTTAATATATTCCAAATGTAATTCAATGATTAGAAGATAAAACTTATATAA
131 ACAAAGCAAAAGGGGTTAATATATTCCAAATGTAATTCAATGATTAGAAGATAAAACTTATATAA
35218996 CTGTTGTGATATATTTTTATCTCTTCAAAATGATACTACAACTCCACAGACTAAAAAACACAAAC
196 CTGTTGTGATATATTTTTATCTCTTCAAAATGATACTACAACTCCACAGACTAAAAAACACAAAC
35219061 ACCCACACAAAATTTGGGTAAGAAGACAATAAAAAAAAACATGAAGCAAAAATTGAAACTTGATT
261 ACCCACACAAAATTTGGGTAAGAAGACAATAAAAAAAAACATGAAGCAAAAATTGAAACTTGATT
* *
35219126 GCACAGAGCTCTTTTGTCAAACTTTGTAATCATTAAGAGGGCATAATCAACTTTTCAGCTTTGTG
326 GCACAGAGCTCTTTTGTCAAAATTTGTAATCATTAAAAGGGCATAATCAACTTTTCAGCTTTGTG
35219191 ATAGTGAGAAGTCAACGTATATTTTACAAGACCCAGGATCACACAGGGACAACATACAATGTGAT
391 ATAGTGAGAAGTCAACGTATATTTTACAAGACCCAGGATCACACAGGGACAACATACAATGTGAT
35219256 CACTTCTGTTAGAGGAGAAGATGGAAAACA
456 CACTTCTGTTAGAGGAGAAGATGGAAAACA
35219286 CCAACATAAATATAGCTACACTTTCCATGTATCAAACATTTCATGAAAATTGAGCCAAAAAACAA
1 CCAACATAAATATAGCTACACTTTCCATGTATCAAACATTTCATGAAAATTGAGCCAAAAAACAA
35219351 ATCATGAGAATGTTGACAATGCAATGAAACACAAGATTTTAGGTGAACAAGGTACCTCACCACCA
66 ATCATGAGAATGTTGACAATGCAATGAAACACAAGATTTTAGGTGAACAAGGTACCTCACCACCA
35219416 ACAAAGCAAAAGGGGTTAATATATTCCAAATGTAATTCAATGATTAGAAGATAAAACTTATATAA
131 ACAAAGCAAAAGGGGTTAATATATTCCAAATGTAATTCAATGATTAGAAGATAAAACTTATATAA
*
35219481 CTGTTGTGATATATTTTTATCTCTTCAAAATGATACTACAACTCCACAGACTCAAAAACACAAAC
196 CTGTTGTGATATATTTTTATCTCTTCAAAATGATACTACAACTCCACAGACTAAAAAACACAAAC
*
35219546 ACCCACACAAAATTTGGGTAAGAAGACAATAAAAGAAAACATGAAGCAAAAATTGAAACTTGATT
261 ACCCACACAAAATTTGGGTAAGAAGACAATAAAAAAAAACATGAAGCAAAAATTGAAACTTGATT
35219611 GCACAGAGCTCTTTTGTCAAAATTTGTAATCATTAAAAGGGCATAATCAACTTTTCAGCTTTGTG
326 GCACAGAGCTCTTTTGTCAAAATTTGTAATCATTAAAAGGGCATAATCAACTTTTCAGCTTTGTG
35219676 ATAGTGAGAAGTCAACGTATATTTTACAAGACCCAGGATCACACAGGGACAACATACAATGTGAT
391 ATAGTGAGAAGTCAACGTATATTTTACAAGACCCAGGATCACACAGGGACAACATACAATGTGAT
35219741 CACTTCTGTTAGAGGAGAAGATGGAAAACA
456 CACTTCTGTTAGAGGAGAAGATGGAAAACA
35219771 AGAAAAGAAT
Statistics
Matches: 480, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
485 480 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (485 bp):
CCAACATAAATATAGCTACACTTTCCATGTATCAAACATTTCATGAAAATTGAGCCAAAAAACAA
ATCATGAGAATGTTGACAATGCAATGAAACACAAGATTTTAGGTGAACAAGGTACCTCACCACCA
ACAAAGCAAAAGGGGTTAATATATTCCAAATGTAATTCAATGATTAGAAGATAAAACTTATATAA
CTGTTGTGATATATTTTTATCTCTTCAAAATGATACTACAACTCCACAGACTAAAAAACACAAAC
ACCCACACAAAATTTGGGTAAGAAGACAATAAAAAAAAACATGAAGCAAAAATTGAAACTTGATT
GCACAGAGCTCTTTTGTCAAAATTTGTAATCATTAAAAGGGCATAATCAACTTTTCAGCTTTGTG
ATAGTGAGAAGTCAACGTATATTTTACAAGACCCAGGATCACACAGGGACAACATACAATGTGAT
CACTTCTGTTAGAGGAGAAGATGGAAAACA
Found at i:35229701 original size:14 final size:14
Alignment explanation
Indices: 35229682--35229716 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
35229672 ACGTACATAC
*
35229682 ATACATATATATGT
1 ATACATATATATAT
35229696 ATACATATATATAT
1 ATACATATATATAT
35229710 ATACATA
1 ATACATA
35229717 ACATAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:35235411 original size:2 final size:2
Alignment explanation
Indices: 35235406--35235431 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35235396 AAAACAAAAA
35235406 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
35235432 TCTACACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35247713 original size:9 final size:9
Alignment explanation
Indices: 35247699--35247723 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35247689 CTTTTGAGAA
35247699 AAAAAAAGG
1 AAAAAAAGG
35247708 AAAAAAAGG
1 AAAAAAAGG
35247717 AAAAAAA
1 AAAAAAA
35247724 TAGGAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:35247758 original size:21 final size:19
Alignment explanation
Indices: 35247695--35247758 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
35247685 TTTTCTTTTG
35247695 AGAAAAAAAAAGGAAAAAA
1 AGAAAAAAAAAGGAAAAAA
* *
35247714 AGGAAAAAAATAGGAAGATAA
1 A-GAAAAAAAAAGGAA-AAAA
35247735 AGAAAAAAAAGAGGAAAAGAA
1 AGAAAAAAAA-AGGAAAA-AA
35247756 AGA
1 AGA
35247759 GAGTGGGAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 14 0.38
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (19 bp):
AGAAAAAAAAAGGAAAAAA
Found at i:35249945 original size:90 final size:90
Alignment explanation
Indices: 35249721--35250045 Score: 280
Period size: 90 Copynumber: 3.6 Consensus size: 90
35249711 TACCCCATAA
* * * * * * *
35249721 TCTTG-TTTACCATCCA-TGGCTTCGGCATCGAACATGTCTTGTTGCTCGAGAGGCT-TCTTGTT
1 TCTTGTTTTACCAT-CAGTGGCTTCGGCACCAAACATGTCTCGTTACTCAAGAGGATCCCTT-TT
* *
35249783 ATGTAACCATTCAATTTTGCCTCGTAG
64 ATATAACCATTCAATTTTGCCCCGTAG
* * ** * ** * *
35249810 TCTTGTTTTACCATCAATGGCTTTGGTGCCAGATGTGTTTTGTTACTCAAGAGGATCCCTTTTAT
1 TCTTGTTTTACCATCAGTGGCTTCGGCACCAAACATGTCTCGTTACTCAAGAGGATCCCTTTTAT
35249875 ATAACCATTCAATTTTGCCCCGTAG
66 ATAACCATTCAATTTTGCCCCGTAG
* * ** * * * * *
35249900 TCTTGTTTTATCGTGGGTGGCTTTGGCATCAAACATGTCTCGTTACTTGAA-ATGATCCCTCTTA
1 TCTTGTTTTACCATCAGTGGCTTCGGCACCAAACATGTCTCGTTAC-TCAAGAGGATCCCTTTTA
** * *
35249964 TATAACCATTCGTTTTTACCCTGTAG
65 TATAACCATTCAATTTTGCCCCGTAG
* * *
35249990 TCTTGTTTTACCATCTAGTGGCTTCGACACCAAACGTGTCTCATTACTCAAGAGGA
1 TCTTGTTTTACCATC-AGTGGCTTCGGCACCAAACATGTCTCGTTACTCAAGAGGA
35250046 CCACATTAAT
Statistics
Matches: 184, Mismatches: 46, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
89 7 0.04
90 143 0.78
91 34 0.18
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (90 bp):
TCTTGTTTTACCATCAGTGGCTTCGGCACCAAACATGTCTCGTTACTCAAGAGGATCCCTTTTAT
ATAACCATTCAATTTTGCCCCGTAG
Found at i:35253106 original size:22 final size:22
Alignment explanation
Indices: 35253081--35253124 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
35253071 ACGAGATAAG
35253081 ACTTAAGTTGAATACAA-TAAAA
1 ACTTAA-TTGAATACAAGTAAAA
*
35253103 ACTTAATTGAATATAAGTAAAA
1 ACTTAATTGAATACAAGTAAAA
35253125 GAAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (22 bp):
ACTTAATTGAATACAAGTAAAA
Found at i:35270576 original size:2 final size:2
Alignment explanation
Indices: 35270569--35270612 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
35270559 NNNNNNNNTT
35270569 TA TA TA TA TA -A TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35270609 -A TA T
1 TA TA T
35270613 GCATAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35278632 original size:15 final size:17
Alignment explanation
Indices: 35278601--35278633 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
35278591 ATTTTGGTGC
35278601 AAAATTGAAATAAAGAG
1 AAAATTGAAATAAAGAG
35278618 AAAA-TGAAA-AAAGAG
1 AAAATTGAAATAAAGAG
35278633 A
1 A
35278634 TGGAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (17 bp):
AAAATTGAAATAAAGAG
Found at i:35279033 original size:74 final size:74
Alignment explanation
Indices: 35278906--35279055 Score: 176
Period size: 74 Copynumber: 2.0 Consensus size: 74
35278896 GGACTTAGTT
* * ** * *
35278906 TTGATCACGAACTTCACTTGATCTTTGCTTCTAGGGTCTTGGCAACTTGATCTTAATCGCAAACA
1 TTGATCAAGAACTTCACTTGATCTTCGCTTCTAGGGTCTTAACAACTTAATCTTAATCACAAACA
*
35278971 CTTGATATC
66 CTTGACATC
* * * * *
35278980 TTGATCAAGAATTTCGCTTGATCTTCGCTTC-AGATGTCTTAACGACTTAATCTTAATCACGAAC
1 TTGATCAAGAACTTCACTTGATCTTCGCTTCTAG-GGTCTTAACAACTTAATCTTAATCACAAAC
35279044 ACTTGACATC
65 ACTTGACATC
35279054 TT
1 TT
35279056 TGCTTTAAGG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
73 2 0.03
74 61 0.97
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (74 bp):
TTGATCAAGAACTTCACTTGATCTTCGCTTCTAGGGTCTTAACAACTTAATCTTAATCACAAACA
CTTGACATC
Found at i:35279154 original size:78 final size:78
Alignment explanation
Indices: 35279016--35279162 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 78
35279006 GCTTCAGATG
** * * *
35279016 TCTTAACGACTTAATCTTAATCACGAACACTTGACATCTTTGCTTTAAGGGCTTTGACGACTTGA
1 TCTTAACGACTTAATCTTAATCACGAACACTTGACATCTTCACTTCAAGGGCTTTCACGACTTAA
35279081 TCTTGATGAAGTA
66 TCTTGATGAAGTA
* * *
35279094 TCTTGACGACTTAATCTTAATCACGAACACTTGATATCTTCACTTCAA-GGATCTTCACGACTTA
1 TCTTAACGACTTAATCTTAATCACGAACACTTGACATCTTCACTTCAAGGGCT-TTCACGACTTA
35279158 ATCTT
65 ATCTT
35279163 TATCACGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 3 0.05
78 57 0.95
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (78 bp):
TCTTAACGACTTAATCTTAATCACGAACACTTGACATCTTCACTTCAAGGGCTTTCACGACTTAA
TCTTGATGAAGTA
Found at i:35282387 original size:23 final size:23
Alignment explanation
Indices: 35282361--35282406 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35282351 AGGTTACCAT
*
35282361 GTGGCATGTCATGATGCTGCCAC
1 GTGGCATGTCACGATGCTGCCAC
35282384 GTGGCATGTCACGATGCTGCCAC
1 GTGGCATGTCACGATGCTGCCAC
35282407 ATCATGTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.24
Consensus pattern (23 bp):
GTGGCATGTCACGATGCTGCCAC
Found at i:35285515 original size:18 final size:17
Alignment explanation
Indices: 35285469--35285518 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
35285459 TTAGTTAAAA
35285469 TAATAACTATTTTT-TT
1 TAATAACTATTTTTATT
* *
35285485 TAAAAAATCATTTTTATT
1 TAATAACT-ATTTTTATT
35285503 TAATATACTATTTTTA
1 TAATA-ACTATTTTTA
35285519 CTAAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 6 0.22
17 6 0.22
18 13 0.48
19 2 0.07
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATAACTATTTTTATT
Found at i:35295312 original size:5 final size:5
Alignment explanation
Indices: 35295302--35295331 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
35295292 GTGCATTTAA
35295302 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
35295332 GTGTTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35295669 original size:20 final size:20
Alignment explanation
Indices: 35295644--35295681 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35295634 CAACTCTCAT
35295644 AGTTCTCTAAAATTTTATCA
1 AGTTCTCTAAAATTTTATCA
*
35295664 AGTTCTCTGAAATTTTAT
1 AGTTCTCTAAAATTTTAT
35295682 TGGATTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (20 bp):
AGTTCTCTAAAATTTTATCA
Found at i:35303823 original size:2 final size:2
Alignment explanation
Indices: 35303816--35303843 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35303806 TCATATAAAA
35303816 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35303844 GGAGGGAGGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35331774 original size:38 final size:39
Alignment explanation
Indices: 35331713--35331790 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 39
35331703 AACAATTTTT
*
35331713 ATTATTCTTGTAATATTCTAGGCATTATTACAAAAAATA
1 ATTATTCTTGTAATATTATAGGCATTATTACAAAAAATA
*
35331752 ATTATT-TT-TAATAGTTATAGGCATTATTATAAAAAATA
1 ATTATTCTTGTAATA-TTATAGGCATTATTACAAAAAATA
35331790 A
1 A
35331791 AAATTTAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 5 0.14
38 25 0.69
39 6 0.17
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (39 bp):
ATTATTCTTGTAATATTATAGGCATTATTACAAAAAATA
Found at i:35333763 original size:15 final size:16
Alignment explanation
Indices: 35333744--35333781 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
35333734 AAAGGGTATT
*
35333744 AATAAAATGGAAAAGG
1 AATAAAATAGAAAAGG
*
35333760 -ATAAAATAGAAATGG
1 AATAAAATAGAAAAGG
35333775 AATAAAA
1 AATAAAA
35333782 ATAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (16 bp):
AATAAAATAGAAAAGG
Found at i:35333796 original size:22 final size:22
Alignment explanation
Indices: 35333771--35333814 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35333761 TAAAATAGAA
35333771 ATGGAATAAAAATAATAAATAT
1 ATGGAATAAAAATAATAAATAT
* * *
35333793 ATGGCATAAAAATGATTAATAT
1 ATGGAATAAAAATAATAAATAT
35333815 CAAAATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (22 bp):
ATGGAATAAAAATAATAAATAT
Found at i:35337176 original size:30 final size:30
Alignment explanation
Indices: 35337142--35337207 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
35337132 AATTATTGGT
*
35337142 TATAAAAATTTATTTGATTTAAAATAAAAA
1 TATAAAAATTTATTTAATTTAAAATAAAAA
35337172 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAATTTAAAATAAAAA
35337202 TATAAA
1 TATAAA
35337208 GGTAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATAAAAATTTATTTAATTTAAAATAAAAA
Found at i:35337217 original size:30 final size:30
Alignment explanation
Indices: 35337142--35337233 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
35337132 AATTATTGGT
** *
35337142 TATAAAAATTTATTTGATTTAAAATAAAAA
1 TATAAAAATAAATTTAATTTAAAATAAAAA
**
35337172 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATAAATTTAATTTAAAATAAAAA
** **
35337202 TATAAAGGTAAATTTAATAAAAATATAAAAA
1 TATAAAAATAAATTTAATTTAAA-ATAAAAA
35337233 T
1 T
35337234 TTATTTAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 46 0.85
31 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
TATAAAAATAAATTTAATTTAAAATAAAAA
Found at i:35337256 original size:13 final size:13
Alignment explanation
Indices: 35337238--35337262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35337228 AAAAATTTAT
35337238 TTAAATATTATAG
1 TTAAATATTATAG
35337251 TTAAATATTATA
1 TTAAATATTATA
35337263 ATTTTGATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTAAATATTATAG
Found at i:35350157 original size:58 final size:58
Alignment explanation
Indices: 35350083--35350196 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 58
35350073 AATCAAAGCC
*
35350083 TCTAGAAAGAAGATTAAAGCCTTTCCAAAGTGGATTCAAGAACAAATCACAAGACCTT
1 TCTAGAAAGAAGATTAAAGCCTCTCCAAAGTGGATTCAAGAACAAATCACAAGACCTT
* * * *
35350141 TCTAGAAGGAAGATTAAAGCCTCTCCAGAGTGGATTCAAGAACATATCGCAAGACC
1 TCTAGAAAGAAGATTAAAGCCTCTCCAAAGTGGATTCAAGAACAAATCACAAGACC
35350197 CTTGAGGCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (58 bp):
TCTAGAAAGAAGATTAAAGCCTCTCCAAAGTGGATTCAAGAACAAATCACAAGACCTT
Found at i:35350223 original size:41 final size:41
Alignment explanation
Indices: 35350175--35350284 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
35350165 CCAGAGTGGA
* *
35350175 TTCAAGAACATA-TCGCAAGACCCTTGAGGCAAAGTTCGGAG
1 TTCAAGAACA-AGTCGCAAGACCCTTGAAGCAAAGTTCGAAG
* * *
35350216 TTTAAGAACAAGTTGCAAGATCCTTGAAGCAAAGTTCGAAG
1 TTCAAGAACAAGTCGCAAGACCCTTGAAGCAAAGTTCGAAG
*
35350257 TTCAAGAACAAGTCGCAAGACCTTTGAA
1 TTCAAGAACAAGTCGCAAGACCCTTGAA
35350285 ATGAAATCTC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 1 0.02
41 58 0.98
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (41 bp):
TTCAAGAACAAGTCGCAAGACCCTTGAAGCAAAGTTCGAAG
Found at i:35350481 original size:41 final size:41
Alignment explanation
Indices: 35350402--35350481 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
35350392 ATTGTTCGTA
* **
35350402 AGAACAGGTCACAAGACGCTTGAAGCAAAGTTTGAAGTTTT
1 AGAACAAGTCACAAGACGCTTGAAGCAAAGTTCAAAGTTTT
* **
35350443 AGAACAAGTCGCAAGATTCTTGAAGCAAAGTTCAAAGTT
1 AGAACAAGTCACAAGACGCTTGAAGCAAAGTTCAAAGTT
35350482 CAAGACCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (41 bp):
AGAACAAGTCACAAGACGCTTGAAGCAAAGTTCAAAGTTTT
Found at i:35350493 original size:28 final size:28
Alignment explanation
Indices: 35350461--35350514 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
35350451 TCGCAAGATT
35350461 CTTGAAGCAAAGTTCAAAGTTCAAGACC
1 CTTGAAGCAAAGTTCAAAGTTCAAGACC
* *
35350489 CTTGAAGCCAAGTTCGAAGTTCAAGA
1 CTTGAAGCAAAGTTCAAAGTTCAAGA
35350515 ACAAGTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (28 bp):
CTTGAAGCAAAGTTCAAAGTTCAAGACC
Found at i:35350629 original size:34 final size:33
Alignment explanation
Indices: 35350582--35350649 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 33
35350572 GAAGTGAAAT
35350582 CTCCAAATGTTCATTCAAGATCAAGTCATAAGA
1 CTCCAAATGTTCATTCAAGATCAAGTCATAAGA
*
35350615 CTCCAAACTGTTCATTCAAGATTAAGTCATAAGA
1 CTCCAAA-TGTTCATTCAAGATCAAGTCATAAGA
35350649 C
1 C
35350650 CAAATCGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (33 bp):
CTCCAAATGTTCATTCAAGATCAAGTCATAAGA
Found at i:35350834 original size:47 final size:49
Alignment explanation
Indices: 35350733--35350868 Score: 170
Period size: 47 Copynumber: 2.8 Consensus size: 49
35350723 AAATCGATTC
* * * * * *
35350733 AGTCTCCAAATCG-TAAGTTCAAGAATAAGTTGCAAGACTCTTAAAGCGA
1 AGTCTCCAAATTGTTCA-TTCAAGAACAAGTTACAAGACCCCTAAAGCGA
* *
35350782 AGTCTCCAAATTGTTCATTCAAGATCAAG-T-CAAGACCCCTAAATCGA
1 AGTCTCCAAATTGTTCATTCAAGAACAAGTTACAAGACCCCTAAAGCGA
35350829 AGTCTCCAAATTGTTCATTCAAGAACAAGTTACAAGACCC
1 AGTCTCCAAATTGTTCATTCAAGAACAAGTTACAAGACCC
35350869 TTGAAGAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
47 42 0.55
48 2 0.03
49 30 0.39
50 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (49 bp):
AGTCTCCAAATTGTTCATTCAAGAACAAGTTACAAGACCCCTAAAGCGA
Found at i:35350970 original size:49 final size:49
Alignment explanation
Indices: 35350889--35351138 Score: 174
Period size: 49 Copynumber: 5.2 Consensus size: 49
35350879 TTAGAAGTTT
* * * * * *
35350889 AAGAACAAGTCACAAGATCCTCGAAGCAAAGTCTTCAAATCATTCGTTC
1 AAGATCAAGTCATAAGATCCTTGAAACGAAGTCTCCAAATCATTCGTTC
**
35350938 AAGATCAAGTCATAAGA-CCATTGAAACGAAGTCTCCAAATTGTTCGTTC
1 AAGATCAAGTCATAAGATCC-TTGAAACGAAGTCTCCAAATCATTCGTTC
* * * ** *
35350987 AAGTTCAAGTCATAAGATCCTTGAAACGAAATATCCAAATTTTTCATTC
1 AAGATCAAGTCATAAGATCCTTGAAACGAAGTCTCCAAATCATTCGTTC
* * * * **
35351036 AAGATTAAGT--TAAG-GCCTTTAAA-GAAAGGTTTCCAAATTGTTCGTTC
1 AAGATCAAGTCATAAGATCCTTGAAACG-AA-GTCTCCAAATCATTCGTTC
* * * * **
35351083 AAG-TTAAGGTCATAAGATTCTTTAAACGAAATCTCCAAATTGTTCG-TC
1 AAGATCAA-GTCATAAGATCCTTGAAACGAAGTCTCCAAATCATTCGTTC
35351131 AAG-TCAAG
1 AAGATCAAG
35351139 GCCTTTGAAG
Statistics
Matches: 166, Mismatches: 26, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
45 1 0.01
46 13 0.08
47 25 0.15
48 10 0.06
49 105 0.63
50 11 0.07
51 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (49 bp):
AAGATCAAGTCATAAGATCCTTGAAACGAAGTCTCCAAATCATTCGTTC
Found at i:35351084 original size:47 final size:47
Alignment explanation
Indices: 35350931--35351134 Score: 175
Period size: 49 Copynumber: 4.2 Consensus size: 47
35350921 CTTCAAATCA
* * *
35350931 TTCGTTCAAGATCAAGTCATAAGA-CCATTGAAACGAAGTCTCCAAATTG
1 TTCGTTCAAG-TTAAGT-ATAAGAGCC-TTGAAACGAAATATCCAAATTG
* *
35350980 TTCGTTCAAGTTCAAGTCATAAGATCCTTGAAACGAAATATCCAAATTT
1 TTCGTTCAAGTT-AAGT-ATAAGAGCCTTGAAACGAAATATCCAAATTG
* * *
35351029 TTCATTCAAGATTAAGT-TAAG-GCCTTTAAA-GAAAGGTTTCCAAATTG
1 TTCGTTCAAG-TTAAGTATAAGAGCCTTGAAACGAAA--TATCCAAATTG
** * *
35351076 TTCGTTCAAGTTAAGGTCATAAGATTCTTTAAACGAAATCTCCAAATTG
1 TTCGTTCAAGTTAA-GT-ATAAGAGCCTTGAAACGAAATATCCAAATTG
35351125 TTCG-TCAAGT
1 TTCGTTCAAGT
35351135 CAAGGCCTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 21
0.80 0.08 0.13
Matches are distributed among these distances:
45 4 0.03
46 11 0.08
47 24 0.18
48 7 0.05
49 71 0.54
50 11 0.08
51 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (47 bp):
TTCGTTCAAGTTAAGTATAAGAGCCTTGAAACGAAATATCCAAATTG
Found at i:35359819 original size:13 final size:12
Alignment explanation
Indices: 35359790--35359843 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
35359780 TTGTTTCTTA
*
35359790 TTTCTTCTTTTC
1 TTTCTTTTTTTC
35359802 TTTTCTTTTTTTGC
1 -TTTCTTTTTTT-C
35359816 TTTCTTATTTTTTC
1 TTTC-T-TTTTTTC
*
35359830 TTTTTTTTTTTC
1 TTTCTTTTTTTC
35359842 TT
1 TT
35359844 AAAACTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 9 0.25
13 15 0.42
14 6 0.17
15 6 0.17
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:35359833 original size:22 final size:24
Alignment explanation
Indices: 35359794--35359844 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
35359784 TTCTTATTTC
35359794 TTCTT-TTCTTTTCTTTTTTTGCT
1 TTCTTATTCTTTTCTTTTTTTGCT
*
35359817 TTCTTATT-TTTTCTTTTTTT-TT
1 TTCTTATTCTTTTCTTTTTTTGCT
35359839 TTCTTA
1 TTCTTA
35359845 AAACTACATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.27
23 17 0.65
24 2 0.08
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (24 bp):
TTCTTATTCTTTTCTTTTTTTGCT
Found at i:35362205 original size:14 final size:15
Alignment explanation
Indices: 35362181--35362210 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
35362171 GGAATAATAT
35362181 AATTACTTTTCCTCA
1 AATTACTTTTCCTCA
35362196 AATT-CTTTTCCTCA
1 AATTACTTTTCCTCA
35362210 A
1 A
35362211 GTTCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTACTTTTCCTCA
Found at i:35367605 original size:2 final size:2
Alignment explanation
Indices: 35367600--35367658 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
35367590 TTAAAAGAAA
* **
35367600 CT CT CT CT CT CT CT CT CT NT AA CT ACT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT
35367643 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
35367659 GAACAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.05, C:0.46, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:35382166 original size:29 final size:29
Alignment explanation
Indices: 35382134--35382194 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
35382124 ACTTTGTGAA
* *
35382134 TTTTTTCT-ATTTAATATTTTGTAAATAT
1 TTTTTTCTCAATTAATATTTTATAAATAT
* *
35382162 TTTTTTCTCAATTAGTATTTTATAAATAA
1 TTTTTTCTCAATTAATATTTTATAAATAT
35382191 TTTT
1 TTTT
35382195 CATTCTCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTTTCTCAATTAATATTTTATAAATAT
Found at i:35390445 original size:38 final size:38
Alignment explanation
Indices: 35390356--35390460 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 38
35390346 CACACTCGGC
* *
35390356 TCATGTACATCCCCCCACATCGTGCACGTAGCCGGCGCCA
1 TCATGTACATCCCCCCACATCGTGCAC--AACCAGCGCCA
* * *
35390396 TCATGTGCATCCCCCCACATCGTGCACAATCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACAACCAGCGCCA
** *
35390434 TTGTGTACAT-CCCCCACATTGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
35390461 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
37 16 0.29
38 14 0.25
40 26 0.46
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (38 bp):
TCATGTACATCCCCCCACATCGTGCACAACCAGCGCCA
Found at i:35398509 original size:18 final size:19
Alignment explanation
Indices: 35398480--35398519 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
35398470 TTGTTTATTG
35398480 TTTCATTTATTATATTTAT
1 TTTCATTTATTATATTTAT
*
35398499 TTTCA-TTATTATCTTTAT
1 TTTCATTTATTATATTTAT
35398517 TTT
1 TTT
35398520 TGTTGACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCATTTATTATATTTAT
Found at i:35399655 original size:61 final size:59
Alignment explanation
Indices: 35399511--35399657 Score: 204
Period size: 59 Copynumber: 2.5 Consensus size: 59
35399501 TTGAATATTC
* * *
35399511 TTTCCACTTGGGCTTCACCTTTTAGGCTATCTCATTCTTTTCCTCTTATTTTGGTTTTG
1 TTTCTACTTGGGCTTCACCTTTTGGGCTATCTCATTCTTTTCCTCTTATTTTGGTTTTA
* * *
35399570 TTTCTACTTGGGCTTCACCTTTTGGGCTATGTCATTCTTTTCCTTTTTTTTTTGGGTTTTA
1 TTTCTACTTGGGCTTCACCTTTTGGGCTATCTCATTCTTTTCC-TCTTATTTT-GGTTTTA
* *
35399631 TTTCTACTTAGGCTTCACCCTTTGGGC
1 TTTCTACTTGGGCTTCACCTTTTGGGC
35399658 AGCCCACTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 40 0.51
60 7 0.09
61 31 0.40
ACGTcount: A:0.10, C:0.22, G:0.16, T:0.52
Consensus pattern (59 bp):
TTTCTACTTGGGCTTCACCTTTTGGGCTATCTCATTCTTTTCCTCTTATTTTGGTTTTA
Found at i:35399725 original size:18 final size:17
Alignment explanation
Indices: 35399683--35399726 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
35399673 TTTCTTTCTT
*
35399683 TTCTTCATTCCTTTATC
1 TTCTTCTTTCCTTTATC
*
35399700 TT-TTCTTTCCTTTTTC
1 TTCTTCTTTCCTTTATC
35399716 TCTCTTCTTTC
1 T-TCTTCTTTC
35399727 TAAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 13 0.57
17 3 0.13
18 7 0.30
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTTCTTTCCTTTATC
Found at i:35410967 original size:29 final size:26
Alignment explanation
Indices: 35410923--35410985 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
35410913 AAAATTAATC
*
35410923 AAAATAAAAATGAAAAATAGACCAAAAAT
1 AAAATAAAAATGAAAAA-AGA--AAAAAA
35410952 AAAATAAAAA-GAAAAAAAGAAAAAAA
1 AAAATAAAAATG-AAAAAAGAAAAAAA
35410978 AAAATAAA
1 AAAATAAA
35410986 TAAATAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 13 0.41
28 4 0.12
29 15 0.47
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (26 bp):
AAAATAAAAATGAAAAAAGAAAAAAA
Found at i:35413275 original size:44 final size:46
Alignment explanation
Indices: 35413194--35413280 Score: 151
Period size: 44 Copynumber: 1.9 Consensus size: 46
35413184 ATATAAACAA
35413194 ATAGAATAGAAATGAAAAAAAATAAACAAATAAAAATAAAAATTAG
1 ATAGAATAGAAATGAAAAAAAATAAACAAATAAAAATAAAAATTAG
*
35413240 ATAGAATAGAAATG-AAAAAAA-AAACAAATATAAATAAAAAT
1 ATAGAATAGAAATGAAAAAAAATAAACAAATAAAAATAAAAAT
35413281 AATAATATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 19 0.47
45 7 0.17
46 14 0.35
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.17
Consensus pattern (46 bp):
ATAGAATAGAAATGAAAAAAAATAAACAAATAAAAATAAAAATTAG
Found at i:35414366 original size:24 final size:24
Alignment explanation
Indices: 35414338--35414400 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
35414328 TCCCATTGTG
*
35414338 ATTCCGTTGGAAATTTCCAACGAA
1 ATTCCTTTGGAAATTTCCAACGAA
35414362 ATTCCTTTGGAAATTTCCAACGAA
1 ATTCCTTTGGAAATTTCCAACGAA
35414386 ATTCCTTTGGAAATT
1 ATTCCTTTGGAAATT
35414401 CTTTTCAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (24 bp):
ATTCCTTTGGAAATTTCCAACGAA
Found at i:35415923 original size:19 final size:19
Alignment explanation
Indices: 35415868--35415926 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
35415858 ACCCGGCTCA
35415868 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* ****
35415887 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
35415906 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
35415925 TG
1 TG
35415927 CACACGGGTA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
18 4 0.14
19 20 0.71
20 4 0.14
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:35417345 original size:29 final size:30
Alignment explanation
Indices: 35417312--35417383 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
35417302 TCCGTTTGAA
35417312 ATTTCCAAC-AAAGTTTTT-GTTGAAAATGC
1 ATTTCCAACGAAA-TTTTTCGTTGAAAATGC
* * *
35417341 ATTTCCAGCGGAATTTTTCGTTGGAAATGC
1 ATTTCCAACGAAATTTTTCGTTGAAAATGC
*
35417371 GTTTCCAACGAAA
1 ATTTCCAACGAAA
35417384 ATTCTTTTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 13 0.37
30 22 0.63
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (30 bp):
ATTTCCAACGAAATTTTTCGTTGAAAATGC
Found at i:35419862 original size:30 final size:30
Alignment explanation
Indices: 35419828--35419886 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
35419818 ATTTTCATTG
35419828 TCATCTCATTCCATGTCATCTTCTTCATCT
1 TCATCTCATTCCATGTCATCTTCTTCATCT
* *
35419858 TCATCTCTTTGCATGTCATCTTCTTCATC
1 TCATCTCATTCCATGTCATCTTCTTCATC
35419887 CTCAATAAAG
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:0.15, C:0.32, G:0.05, T:0.47
Consensus pattern (30 bp):
TCATCTCATTCCATGTCATCTTCTTCATCT
Found at i:35421188 original size:22 final size:22
Alignment explanation
Indices: 35421162--35421207 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
35421152 CTCTTGTAAT
35421162 AAACTATTTGAAAACAAATAAC
1 AAACTATTTGAAAACAAATAAC
35421184 AAACTATTTGAAAACAAATAAC
1 AAACTATTTGAAAACAAATAAC
35421206 AA
1 AA
35421208 TTATAGTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (22 bp):
AAACTATTTGAAAACAAATAAC
Found at i:35430874 original size:83 final size:83
Alignment explanation
Indices: 35430749--35431055 Score: 490
Period size: 83 Copynumber: 3.7 Consensus size: 83
35430739 TCGCAATAAA
* *
35430749 AAGCCTCTGGTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGAGATTTGGGGAAAGTGAGCGATGC
1 AAGCCTCTGCTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGAGATTTGGGGAAAGTGAGCGACGC
*
35430814 ACGGAGATTGGCAGCGAC
66 ACGGAGATTGGCAGCAAC
* *
35430832 AAGCCTCTGCTCTCGGCATAAGAAGGGGAAGCAAAGTAGAGAGATTTGCGGAAAGTGAGCGACGC
1 AAGCCTCTGCTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGAGATTTGGGGAAAGTGAGCGACGC
35430897 ACGGAGATTGGCAGCAAC
66 ACGGAGATTGGCAGCAAC
* * * * *
35430915 AAACCTTTGCTCTCAGCACAAGAAGGGGAAGCAAAGTAGAGAGTTTTGGGGAAAGTGAGTGACGC
1 AAGCCTCTGCTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGAGATTTGGGGAAAGTGAGCGACGC
*
35430980 ACGGAGATTGGCAGCCAC
66 ACGGAGATTGGCAGCAAC
* *
35430998 AAGCCTCTACTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGA-ATTTGGGAAAAGTGAG
1 AAGCCTCTGCTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGAGATTTGGGGAAAGTGAG
35431056 TGAGGTACAT
Statistics
Matches: 205, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
82 14 0.07
83 191 0.93
ACGTcount: A:0.33, C:0.18, G:0.34, T:0.15
Consensus pattern (83 bp):
AAGCCTCTGCTCTCGGCACAAGAAGGGGAAGCAAAGTAGAGAGATTTGGGGAAAGTGAGCGACGC
ACGGAGATTGGCAGCAAC
Found at i:35431595 original size:220 final size:218
Alignment explanation
Indices: 35431290--35431718 Score: 709
Period size: 220 Copynumber: 1.9 Consensus size: 218
35431280 GGTATATTAT
35431290 TAAATTTATTATATATATTAATGACACAAATTATATGTTATAGTTTGATATATATTACAAAATTT
1 TAAATTTATTATATATATTAATGACACAAATTATATGTTATAGTTTGATATATATTACAAAATTT
* * *** *
35431355 GTATAATTACTTATCAATATAATTTTATAAAAAGTATG-ATA-ATAGCTAATAAAATTAATAACT
66 GTACAATTAATTATCAATATAATACCATAAAAAGTATGAATACATAACTAATAAAATTAATAACT
35431418 GTAATCATATAAATAAAATTTACTATAAGCTTACATATAAAACATATTAATATATATATGTAAGA
131 GTAATCATATAAATAAAA-TTACTATAAGCTTACATATAAAACATATT-A-ATATATATGTAAGA
35431483 TATTTTAATATCTCANATGTTATATAC
193 TATTTTAATATCTCA-ATGTTATATAC
*
35431510 TAAATTTATTGTATATATTAATGACACAAATTATATGTTATAGTTTGATATATATTACAAAATTT
1 TAAATTTATTATATATATTAATGACACAAATTATATGTTATAGTTTGATATATATTACAAAATTT
*
35431575 GTACAATTAATTATCAATATAATACCCTAAAAAGTATGATAATACATAACTAATAAAATTAATAA
66 GTACAATTAATTATCAATATAATACCATAAAAAGTATG--AATACATAACTAATAAAATTAATAA
35431640 CTGTAATCATATAAATAAAATTACTATAAGCTTACATATAAAACATATTAATATATATGTAAGAT
129 CTGTAATCATATAAATAAAATTACTATAAGCTTACATATAAAACATATTAATATATATGTAAGAT
*
35431705 GTTTTAATATCTCA
194 ATTTTAATATCTCA
35431719 TATACATACA
Statistics
Matches: 196, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
220 96 0.49
221 28 0.14
222 1 0.01
223 32 0.16
224 39 0.20
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (218 bp):
TAAATTTATTATATATATTAATGACACAAATTATATGTTATAGTTTGATATATATTACAAAATTT
GTACAATTAATTATCAATATAATACCATAAAAAGTATGAATACATAACTAATAAAATTAATAACT
GTAATCATATAAATAAAATTACTATAAGCTTACATATAAAACATATTAATATATATGTAAGATAT
TTTAATATCTCAATGTTATATAC
Found at i:35434080 original size:47 final size:47
Alignment explanation
Indices: 35434006--35434105 Score: 164
Period size: 47 Copynumber: 2.1 Consensus size: 47
35433996 TGATGTGGGA
*
35434006 TCCTATGAGAGATACAAGGGTCGAAGTAGACCCAGACTAGTGTAACAG
1 TCCT-TGAGAGATACAAGGGTCGAAGTAGACCCAAACTAGTGTAACAG
* *
35434054 TCCTTGAGAGATACAAGTGTCGAAGTAGACCCAAACTAGTGTAAGAG
1 TCCTTGAGAGATACAAGGGTCGAAGTAGACCCAAACTAGTGTAACAG
35434101 TCCTT
1 TCCTT
35434106 CTTCTTTAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 45 0.92
48 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (47 bp):
TCCTTGAGAGATACAAGGGTCGAAGTAGACCCAAACTAGTGTAACAG
Found at i:35443215 original size:20 final size:20
Alignment explanation
Indices: 35443186--35443234 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
35443176 TTAAAGTAAT
*
35443186 TTAAAATAAAATAACATAAA
1 TTAAACTAAAATAACATAAA
* *
35443206 TTAATCTAAAATAACTTAAA
1 TTAAACTAAAATAACATAAA
35443226 TTAAACTAA
1 TTAAACTAA
35443235 TCAACATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAACTAAAATAACATAAA
Found at i:35458051 original size:19 final size:20
Alignment explanation
Indices: 35458027--35458066 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
35458017 CCATTTGACT
35458027 TATTGGAGTATGATTT-AAG
1 TATTGGAGTATGATTTGAAG
35458046 TATTGGAGTATGATTTGAAG
1 TATTGGAGTATGATTTGAAG
35458066 T
1 T
35458067 TTAGAAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (20 bp):
TATTGGAGTATGATTTGAAG
Found at i:35462213 original size:22 final size:23
Alignment explanation
Indices: 35462183--35462229 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
35462173 ATATAGAGTT
35462183 ATTTGAGCTTAATT-TTGATAGTA
1 ATTTGAGCTTAATTCTTG-TAGTA
35462206 ATTT-AGCTTAATTCTTGTAGTA
1 ATTTGAGCTTAATTCTTGTAGTA
35462228 AT
1 AT
35462230 GTACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (23 bp):
ATTTGAGCTTAATTCTTGTAGTA
Found at i:35466971 original size:29 final size:26
Alignment explanation
Indices: 35466915--35466973 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
35466905 TTTAGTTGAT
35466915 TTAGGATTTTTTTTCTTCTATTTAGA
1 TTAGGATTTTTTTTCTTCTATTTAGA
* *
35466941 TTAGGA-TTCTTTTCTTCT-TTT-TA
1 TTAGGATTTTTTTTCTTCTATTTAGA
35466964 TTAGGATTTT
1 TTAGGATTTT
35466974 ATTACTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 7 0.24
24 5 0.17
25 11 0.38
26 6 0.21
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.63
Consensus pattern (26 bp):
TTAGGATTTTTTTTCTTCTATTTAGA
Found at i:35471360 original size:26 final size:25
Alignment explanation
Indices: 35471319--35471369 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
35471309 GTCCCCTCAT
*
35471319 TCTTTTTTTTTTCTTTCCTTCTTTC
1 TCTTTTTTTTTGCTTTCCTTCTTTC
*
35471344 TCTTTTTTTCTTGCTTTTCTTCTTTC
1 TCTTTTTTT-TTGCTTTCCTTCTTTC
35471370 CTTATCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (25 bp):
TCTTTTTTTTTGCTTTCCTTCTTTC
Found at i:35471415 original size:37 final size:38
Alignment explanation
Indices: 35471338--35471417 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 38
35471328 TTTCTTTCCT
* *
35471338 TCTTTCTCTTTTTTTCTTGCTTTTCTTCTTTCCTTATC
1 TCTTTCTCTTTTTTTCTTGCTTTCCTTCCTTCCTTATC
35471376 TCTTTCTCTTTTTGTT-TT-CTTTCCTTCCTTCTCTT-TC
1 TCTTTCTCTTTTT-TTCTTGCTTTCCTTCCTTC-CTTATC
35471413 TCTTT
1 TCTTT
35471418 TCAGCTTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
37 18 0.47
38 18 0.47
39 2 0.05
ACGTcount: A:0.01, C:0.28, G:0.03, T:0.69
Consensus pattern (38 bp):
TCTTTCTCTTTTTTTCTTGCTTTCCTTCCTTCCTTATC
Found at i:35471441 original size:63 final size:59
Alignment explanation
Indices: 35471322--35471534 Score: 179
Period size: 63 Copynumber: 3.5 Consensus size: 59
35471312 CCCTCATTCT
* * *
35471322 TTTTTTTTTCTTTCCTTCTTTCTCTT-T-TTTTCTTGCTTTTCTTCTTTCCTTATCTCTTTCTC
1 TTTTTTTTTCTTTCCTTCCTTCTCTTCTCTTTTC--GCTTTTCTTCCTTCC--CTCTCTTT-TC
* *
35471384 TTTTTGTTTTCTTTCCTTCCTTCTCTTTCTCTTTTCAGCTTTCCTTCCTTCCCTCTCTTTTG
1 TTTTT-TTTTCTTTCCTTCCTTCTC-TTCTCTTTTC-GCTTTTCTTCCTTCCCTCTCTTTTC
* *
35471446 TTTTTCTCTTCCTTTCCTTCCTTCTC-TCTC-TTTCGACTTTTTTTCCTTCCCT-T-TTTT-
1 TTTTT-T-TTTCTTTCCTTCCTTCTCTTCTCTTTTCG-CTTTTCTTCCTTCCCTCTCTTTTC
* * *
35471503 TTTTTTTCTATTTCCTTCTTTCTCTTTCTCTT
1 TTTTTTTTTCTTTCCTTCCTTCTC-TTCTCTT
35471535 CCTTACTAGC
Statistics
Matches: 128, Mismatches: 14, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
55 14 0.11
56 1 0.01
57 9 0.07
58 5 0.04
59 2 0.02
60 18 0.14
61 4 0.03
62 12 0.09
63 42 0.33
64 2 0.02
65 14 0.11
66 5 0.04
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (59 bp):
TTTTTTTTTCTTTCCTTCCTTCTCTTCTCTTTTCGCTTTTCTTCCTTCCCTCTCTTTTC
Found at i:35471509 original size:59 final size:57
Alignment explanation
Indices: 35471380--35471534 Score: 172
Period size: 59 Copynumber: 2.6 Consensus size: 57
35471370 CTTATCTCTT
*
35471380 TCTCTTTTTGTTTTCTTTCCTTCCTTCTCTTTCTCTTTTCAGCTTTCCTTCCTTCCC
1 TCTCTTTTTTTTTTCTTTCCTTCCTTCTCTTTCTCTTTTCAGCTTTCCTTCCTTCCC
* **
35471437 TCTCTTTTGTTTTTCTCTTCCTTTCCTTC-CTTCTCTCTCTTTC-GACTTTTTTTCCTTCCC
1 TCTCTTTTTTTTTTCT-TTCC-TTCCTTCTCTT-TCTCT-TTTCAG-CTTTCCTTCCTTCCC
* *
35471497 T-TTTTTTTTTTTTCTATTTCCTTCTTTCTCTTTCTCTT
1 TCTCTTTTTTTTTTC--TTTCCTTCCTTCTCTTTCTCTT
35471535 CCTTACTAGC
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
57 14 0.17
58 8 0.10
59 35 0.42
60 25 0.30
61 1 0.01
ACGTcount: A:0.02, C:0.32, G:0.03, T:0.64
Consensus pattern (57 bp):
TCTCTTTTTTTTTTCTTTCCTTCCTTCTCTTTCTCTTTTCAGCTTTCCTTCCTTCCC
Found at i:35471604 original size:33 final size:34
Alignment explanation
Indices: 35471549--35471636 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 34
35471539 ACTAGCGTCT
* *
35471549 TTTCCTTCTCTT-TCTCTC-TTTTTTTGCTTTT-C
1 TTTCCTTCT-TTCCCTCTCTTTTTTTTTCTTTTCC
35471581 -TTCCTTGC-TTCCCTCTCTTTTTTTTTCTTTTCC
1 TTTCCTT-CTTTCCCTCTCTTTTTTTTTCTTTTCC
*
35471614 TTTCCTTCTTTCTCTCTCTTTTT
1 TTTCCTTCTTTCCCTCTCTTTTT
35471637 AGCTTTCCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
30 2 0.04
31 11 0.23
32 13 0.28
33 2 0.04
34 19 0.40
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (34 bp):
TTTCCTTCTTTCCCTCTCTTTTTTTTTCTTTTCC
Found at i:35471628 original size:30 final size:30
Alignment explanation
Indices: 35471547--35471664 Score: 120
Period size: 32 Copynumber: 3.9 Consensus size: 30
35471537 TTACTAGCGT
35471547 CTTTTCCTT-C-TCTTTCTCTCTTTTTTTG
1 CTTTTCCTTCCTTCTTTCTCTCTTTTTTTG
* *
35471575 CTTTT-CTTCCTTGCTTCCCTCTCTTTTTTTTT
1 CTTTTCCTTCCTT-CTT-TCTCTC-TTTTTTTG
*
35471607 CTTTTCCTTTCCTTCTTTCTCTCTCTTTTTAG
1 CTTTTCC-TTCCTTCTTTCTCTCT-TTTTTTG
35471639 C-TTTCCTTCCTTCATTT-TCTCTTTTT
1 CTTTTCCTTCCTTC-TTTCTCTCTTTTT
35471665 CTTCCTTCTC
Statistics
Matches: 76, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
27 3 0.04
28 6 0.08
29 5 0.07
30 15 0.20
31 14 0.18
32 23 0.30
33 4 0.05
34 6 0.08
ACGTcount: A:0.02, C:0.31, G:0.03, T:0.65
Consensus pattern (30 bp):
CTTTTCCTTCCTTCTTTCTCTCTTTTTTTG
Found at i:35472330 original size:24 final size:24
Alignment explanation
Indices: 35472301--35472346 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
35472291 TTTTTTATTT
35472301 ATTTATTCATTTATCA-ATTTTTTG
1 ATTTATTCATTTA-CATATTTTTTG
35472325 ATTTATTCATTTACATATTTTT
1 ATTTATTCATTTACATATTTTT
35472347 ATTAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTATTCATTTACATATTTTTTG
Found at i:35475720 original size:31 final size:27
Alignment explanation
Indices: 35475660--35475723 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
35475650 TAATTTTTAA
* *
35475660 TTATAATTTATTTATTTTTAGTTGTTT
1 TTATAATTAATTTATTTTTAGTAGTTT
35475687 TTATAATTAATTTATTTTTGAGTGAGTTAT
1 TTATAATTAATTTATTTTT-AGT-AGTT-T
35475717 TT-TAATT
1 TTATAATT
35475724 TTGTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 18 0.56
28 3 0.09
29 8 0.25
30 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (27 bp):
TTATAATTAATTTATTTTTAGTAGTTT
Found at i:35475739 original size:20 final size:21
Alignment explanation
Indices: 35475716--35475754 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
35475706 GAGTGAGTTA
*
35475716 TTTTAATTTTG-TATTATTCT
1 TTTTAATTTAGTTATTATTCT
*
35475736 TTTTAGTTTAGTTATTATT
1 TTTTAATTTAGTTATTATT
35475755 TATTAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTTAATTTAGTTATTATTCT
Found at i:35475997 original size:16 final size:15
Alignment explanation
Indices: 35475978--35476020 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
35475968 TTATTTATTT
35475978 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
35475994 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
35476010 TGAGTTATTTT
1 TTAGTTATTTT
35476021 AATTTTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:35476040 original size:20 final size:21
Alignment explanation
Indices: 35476017--35476055 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35476007 AAGTGAGTTA
*
35476017 TTTTAATTTTGT-ATTATTCT
1 TTTTAATTTAGTCATTATTCT
35476037 TTTTAATTTAGTCATTATT
1 TTTTAATTTAGTCATTATT
35476056 TATTAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTAATTTAGTCATTATTCT
Found at i:35476135 original size:301 final size:300
Alignment explanation
Indices: 35475587--35476177 Score: 1038
Period size: 301 Copynumber: 2.0 Consensus size: 300
35475577 CGTCTTTAGC
* *
35475587 TGATAATTTTATTTTATAGAATTATTTTATTCTAATTTTGTTATTAAATATTAGCTAAGTCCTTA
1 TGATAATTCTATTTTATAGAATTATTTTATTCTAATTTTGTTATTAAATATTAGCTAAGTCCTCA
* * *
35475652 ATTTTTAATTATAATTTATTTATTTTTAGTTGTTTTTATAATTAATTTATTTTTGAGTGAGTTAT
66 ATTTTCAATTATAATTTATTTATTTTTAGTTATTTTTATAATTAATTTATTTTTAAGTGAGTTAT
* * *
35475717 TTTAATTTTGTATTATTCTTTTTAGTTTAGTTATTATTTATTAGTTTTTTATATTTTTCATAGGA
131 TTTAATTTTGTATTATTCTTTTTAATTTAGTCATTATTTATTAGTTTTTTATATTTTTCATAAGA
* *
35475782 ATAAAAGAATTGGGCTTAATTTTGGAAAGTGAGATGTTGAAAGACCCGAAAGTCTACTTGCATAT
196 ATAAAAGAATTGAGCTTAATTTTGGAAAGTGAGATGTTGAAAGACCCGAAAGTCTACTTGCATAG
35475847 ACTTCAGTGTTTTGGCGATAACTCAAGCTACAGAGAGGTG
261 ACTTCAGTGTTTTGGCGATAACTCAAGCTACAGAGAGGTG
35475887 TGATAATTCTATTTTATAGAATTATTTTATTCTAATTTTTGTTATTAAATATTAGCTAAGTCCTC
1 TGATAATTCTATTTTATAGAATTATTTTATTCTAA-TTTTGTTATTAAATATTAGCTAAGTCCTC
*
35475952 AATTTTCAATTATAATTTATTTATTTTTAGTTATTTTTATAATTAGTTTATTTTTAAGTGAGTTA
65 AATTTTCAATTATAATTTATTTATTTTTAGTTATTTTTATAATTAATTTATTTTTAAGTGAGTTA
35476017 TTTTAATTTTGTATTATTCTTTTTAATTTAGTCATTATTTATTAGTTTTTTATATTTTTCATAAG
130 TTTTAATTTTGTATTATTCTTTTTAATTTAGTCATTATTTATTAGTTTTTTATATTTTTCATAAG
* * *
35476082 AATCAAAGAATTGAGCTTAATTTTGGAAAGTGAGATGTTGAAAGACTCGAAAGTCTGCTTGCATA
195 AATAAAAGAATTGAGCTTAATTTTGGAAAGTGAGATGTTGAAAGACCCGAAAGTCTACTTGCATA
*
35476147 GACTTCAGTGTTTTGGCGATAACTCGAGCTA
260 GACTTCAGTGTTTTGGCGATAACTCAAGCTA
35476178 TAGAACTCCA
Statistics
Matches: 275, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
300 34 0.12
301 241 0.88
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (300 bp):
TGATAATTCTATTTTATAGAATTATTTTATTCTAATTTTGTTATTAAATATTAGCTAAGTCCTCA
ATTTTCAATTATAATTTATTTATTTTTAGTTATTTTTATAATTAATTTATTTTTAAGTGAGTTAT
TTTAATTTTGTATTATTCTTTTTAATTTAGTCATTATTTATTAGTTTTTTATATTTTTCATAAGA
ATAAAAGAATTGAGCTTAATTTTGGAAAGTGAGATGTTGAAAGACCCGAAAGTCTACTTGCATAG
ACTTCAGTGTTTTGGCGATAACTCAAGCTACAGAGAGGTG
Found at i:35478082 original size:14 final size:14
Alignment explanation
Indices: 35478063--35478089 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35478053 CAAAATCAAT
35478063 TAATTAACTAAAAC
1 TAATTAACTAAAAC
35478077 TAATTAACTAAAA
1 TAATTAACTAAAA
35478090 TTTAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:35489067 original size:50 final size:49
Alignment explanation
Indices: 35488955--35489067 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 49
35488945 ATGTAAAAAG
* * *
35488955 ACAAATTATGCTATGGTAAAAATAATAAACAATAATGGATAAATAGTTAA
1 ACAAATT-TGTTATGATAAAAATAACAAACAATAATGGATAAATAGTTAA
* * * * *
35489005 ATAGACTTTGTTATGATAAAAATAACACACAGTAATGTATAAATAGTTAA
1 ACA-AATTTGTTATGATAAAAATAACAAACAATAATGGATAAATAGTTAA
35489055 ACAAATTGTGTTA
1 ACAAATT-TGTTA
35489068 ATTTATATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
49 3 0.06
50 45 0.88
51 3 0.06
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (49 bp):
ACAAATTTGTTATGATAAAAATAACAAACAATAATGGATAAATAGTTAA
Found at i:35490507 original size:22 final size:22
Alignment explanation
Indices: 35490479--35490560 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
35490469 ACTTAATCAC
35490479 TACGTGACTGATTTTTAGGCAT
1 TACGTGACTGATTTTTAGGCAT
* *
35490501 TACGTGATTG-GTTTTAGGCAT
1 TACGTGACTGATTTTTAGGCAT
* *
35490522 TGCATGACT-AGTTTTTAGGCAT
1 TACGTGACTGA-TTTTTAGGCAT
* *
35490544 TGCGTGATTGATTTTTA
1 TACGTGACTGATTTTTA
35490561 AGTAATGCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
21 16 0.33
22 32 0.65
23 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (22 bp):
TACGTGACTGATTTTTAGGCAT
Found at i:35490598 original size:23 final size:22
Alignment explanation
Indices: 35490572--35490683 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 22
35490562 GTAATGCCTA
35490572 AGTCACACAATGCTTTACTAACT
1 AGTCACACAATGCTTTA-TAACT
* *
35490595 AGTCACACAATGCCTTAATAACA
1 AGTCACACAATG-CTTTATAACT
** *
35490618 AGTCACGTAATGC-CTATCAACT
1 AGTCACACAATGCTTTAT-AACT
* *
35490640 AGTCACACAAAGCTTAATCAGAAACT
1 AGTCACACAATGCTT--T-A-TAACT
*
35490666 AGTCACACAATGCCTTAT
1 AGTCACACAATGCTTTAT
35490684 CAAAAACTAG
Statistics
Matches: 67, Mismatches: 15, Indels: 15
0.69 0.15 0.15
Matches are distributed among these distances:
21 2 0.03
22 14 0.21
23 27 0.40
24 5 0.07
25 1 0.01
26 18 0.27
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (22 bp):
AGTCACACAATGCTTTATAACT
Found at i:35490702 original size:26 final size:25
Alignment explanation
Indices: 35490591--35490867 Score: 187
Period size: 26 Copynumber: 11.6 Consensus size: 25
35490581 ATGCTTTACT
* *
35490591 AACTAGTCACACAATGCCT-T-AAT
1 AACTAGTCACGCAATGCCTATCAAA
* *
35490614 AACAAGTCACGTAATGCCTATC---
1 AACTAGTCACGCAATGCCTATCAAA
* * * *
35490636 AACTAGTCACACAAAGCTTAATCAGA
1 AACTAGTCACGCAATGCCT-ATCAAA
*
35490662 AACTAGTCACACAATGCCTTATCAAA
1 AACTAGTCACGCAATGCC-TATCAAA
*
35490688 AACTAGACACGCAATGCC---C-AA
1 AACTAGTCACGCAATGCCTATCAAA
** * *
35490709 AGTTAGTCATGCAATACCTATC---
1 AACTAGTCACGCAATGCCTATCAAA
*
35490731 AACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCC-TATCAAA
* *
35490757 AACAAGTCATGCAATGCC--T-AAA
1 AACTAGTCACGCAATGCCTATCAAA
**
35490779 GTC-AGTCACGCAATGCCTATC---
1 AACTAGTCACGCAATGCCTATCAAA
* *
35490800 AACTAGTCGCGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCC-TATCAAA
35490826 AACTAGTCACGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCC-TATCAAA
35490852 AACTAGTCACGCAATG
1 AACTAGTCACGCAATG
35490868 ACCAAAGTTT
Statistics
Matches: 199, Mismatches: 33, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
21 29 0.15
22 45 0.23
23 29 0.15
24 2 0.01
26 93 0.47
27 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.22
Consensus pattern (25 bp):
AACTAGTCACGCAATGCCTATCAAA
Found at i:35490844 original size:69 final size:69
Alignment explanation
Indices: 35490662--35490844 Score: 276
Period size: 69 Copynumber: 2.7 Consensus size: 69
35490652 CTTAATCAGA
* * * * * *
35490662 AACTAGTCACACAATGCCTTATCAAAAACTAGACACGCAATGCCCAAAGTTAGTCATGCAATACC
1 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTAAAGTCAGTCACGCAATACC
35490727 TATC
66 TATC
* * *
35490731 AACTAGTCACGCAATGCCTTATCAGAAACAAGTCATGCAATGCCTAAAGTCAGTCACGCAATGCC
1 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTAAAGTCAGTCACGCAATACC
35490796 TATC
66 TATC
*
35490800 AACTAGTCGCGCAATGCCTTATCAGAAACTAGTCACGCAATGCCT
1 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCT
35490845 TATCAAAAAC
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 102 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.22
Consensus pattern (69 bp):
AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTAAAGTCAGTCACGCAATACC
TATC
Found at i:35490881 original size:21 final size:21
Alignment explanation
Indices: 35490857--35490896 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35490847 TCAAAAACTA
*
35490857 GTCACGCAATGACCAAAGTTT
1 GTCACGAAATGACCAAAGTTT
*
35490878 GTCACGAAATGTCCAAAGT
1 GTCACGAAATGACCAAAGT
35490897 CAGTCACACA
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:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
GTCACGAAATGACCAAAGTTT
Found at i:35490902 original size:21 final size:21
Alignment explanation
Indices: 35490856--35490903 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
35490846 ATCAAAAACT
* *
35490856 AGTCACGCAATGACCAAAGTT
1 AGTCACGAAATGACCAAAGTC
* *
35490877 TGTCACGAAATGTCCAAAGTC
1 AGTCACGAAATGACCAAAGTC
35490898 AGTCAC
1 AGTCAC
35490904 ACAATGCCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTCACGAAATGACCAAAGTC
Found at i:35490909 original size:21 final size:21
Alignment explanation
Indices: 35490856--35490909 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
35490846 ATCAAAAACT
* *
35490856 AGTCACGCAATGACCAAAGTT
1 AGTCACACAATGACCAAAGTC
* *
35490877 TGTCACGA-AATGTCCAAAGTC
1 AGTCAC-ACAATGACCAAAGTC
35490898 AGTCACACAATG
1 AGTCACACAATG
35490910 CCTAAAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
AGTCACACAATGACCAAAGTC
Found at i:35491141 original size:60 final size:60
Alignment explanation
Indices: 35491028--35491153 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
35491018 AATGAATATG
* * * *
35491028 AATGCTCAAAATGTTCAAAAGTTTTTCTTCATATACCAAAAATCACTCTAAAATGCTTAAA
1 AATGCTCAAAACGCTCAAAAGTTTTTCTTAATATACCAAAAATCACTCCAAAATGC-TAAA
* * * *
35491089 AATGCTCAAAACGCTCACAAG-TTTTCTTAATGTATCAAAAA-CTACTCCAAAATGCTCAA
1 AATGCTCAAAACGCTCAAAAGTTTTTCTTAATATACCAAAAATC-ACTCCAAAATGCTAAA
35491148 AATGCT
1 AATGCT
35491154 TAAACGTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 10 0.18
60 28 0.50
61 18 0.32
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (60 bp):
AATGCTCAAAACGCTCAAAAGTTTTTCTTAATATACCAAAAATCACTCCAAAATGCTAAA
Found at i:35494454 original size:17 final size:17
Alignment explanation
Indices: 35494424--35494456 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35494414 TTCTTGATAA
35494424 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
35494441 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
35494457 TTTTATTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:35494661 original size:29 final size:28
Alignment explanation
Indices: 35494629--35494772 Score: 153
Period size: 29 Copynumber: 5.0 Consensus size: 28
35494619 AAATATATTA
* * *
35494629 TCTTGTCTAAATTTGAGACAAATATGTAT
1 TCTTGTCTAAA-TTAAGACAAACATGTTT
* * *
35494658 TCTTGTCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
*
35494688 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
35494717 TTTTGTCTAAATTAAGATCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
* *
35494746 TCTTATCTAAATTAAGACAAACTTGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
35494773 AAAGCTGCCA
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
28 25 0.26
29 49 0.50
30 14 0.14
31 10 0.10
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:35494709 original size:59 final size:58
Alignment explanation
Indices: 35494607--35494767 Score: 173
Period size: 59 Copynumber: 2.7 Consensus size: 58
35494597 TCTTGTCCGT
* * * * *
35494607 AATTAAGGCAAAAAATATATTATCTTGTCTAAATTTGAGACAAATATGTATTCTTGTCTA
1 AATTAAGACAAAAAATAT-TTTTCTTGTCTAAA-TTAAGACAAACATATATTCTTGTCTA
* * *
35494667 GATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTTTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATATATTCTTGTCTA
* * *
35494726 AATTAAGATC-AAACAT-GTTTTCTTATCTAAATTAAGACAAAC
1 AATTAAGA-CAAAAAATATTTTTCTTGTCTAAATTAAGACAAAC
35494768 TTGTTAAAGC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 15 0.17
58 9 0.10
59 42 0.48
60 21 0.24
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (58 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATATATTCTTGTCTA
Found at i:35500137 original size:2 final size:2
Alignment explanation
Indices: 35500114--35500168 Score: 65
Period size: 2 Copynumber: 26.5 Consensus size: 2
35500104 AATATCATTC
* * *
35500114 AT AT AG AT AC AT AT AA AT AT AT AT AGT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
35500157 AT GAT AT AT AT A
1 AT -AT AT AT AT A
35500169 ANTAATTCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 41 0.91
3 4 0.09
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:35500146 original size:19 final size:20
Alignment explanation
Indices: 35500114--35500169 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
35500104 AATATCATTC
*
35500114 ATATAGATACATATAAATAT
1 ATATAGATATATATAAATAT
*
35500134 ATATAG-TATATATATATAT
1 ATATAGATATATATAAATAT
35500153 ATATATGATATATATAA
1 ATATA-GATATATATAA
35500170 NTAATTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.52
20 7 0.23
21 8 0.26
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATAGATATATATAAATAT
Found at i:35500150 original size:17 final size:16
Alignment explanation
Indices: 35500114--35500168 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
35500104 AATATCATTC
* * *
35500114 ATATAGATACATATAA
1 ATATATATATATATAT
35500130 ATATATATAGTATATAT
1 ATATATATA-TATATAT
35500147 ATATATATATATGATAT
1 ATATATATATAT-ATAT
35500164 ATATA
1 ATATA
35500169 ANTAATTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.32
17 23 0.68
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (16 bp):
ATATATATATATATAT
Found at i:35502020 original size:29 final size:28
Alignment explanation
Indices: 35501896--35502064 Score: 122
Period size: 29 Copynumber: 5.7 Consensus size: 28
35501886 TTAGGACAAC
* * *
35501896 TCTTGTCCATAATTAAGATAAAAAATATTTT
1 TCTTGTCTA-AATTAAGA-CAAACATA-TTT
* * * * *
35501927 ATCTTGTCTAAATTTGAGATAAATATGTAT
1 -TCTTGTCTAAA-TTAAGACAAACATATTT
* * * *
35501957 TCTTATCTAGATTAAGATAAAAAATATTTT
1 TCTTGTCTAAATTAAGA-CAAACATA-TTT
*
35501987 TCTTGTTTTAAATTAAGACAAACATATTT
1 TCTTG-TCTAAATTAAGACAAACATATTT
* *
35502016 TCTTGTCTAGATTAAGATCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
35502045 TCTTGTCTAAATTAAGACAA
1 TCTTGTCTAAATTAAGACAA
35502065 GCATGTTAAA
Statistics
Matches: 110, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
28 18 0.16
29 48 0.44
30 14 0.13
31 17 0.15
32 13 0.12
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:35502025 original size:59 final size:58
Alignment explanation
Indices: 35501907--35502064 Score: 192
Period size: 59 Copynumber: 2.7 Consensus size: 58
35501897 CTTGTCCATA
* * * *
35501907 ATTAAGATAAAAAATATTTTATCTTGTCTAAATTTGAGATAAATATGTATTCTTATCTAG
1 ATTAAGATAAAAAATATTTT-TCTTGTCTAAA-TTAAGACAAACATATATTCTTATCTAG
* * *
35501967 ATTAAGATAAAAAATATTTTTCTTGTTTTAAATTAAGACAAACATATTTTCTTGTCTAG
1 ATTAAGATAAAAAATATTTTTCTTG-TCTAAATTAAGACAAACATATATTCTTATCTAG
* * *
35502026 ATTAAGATCAAACAT-GTTTTCTTGTCTAAATTAAGACAA
1 ATTAAGATAAAAAATATTTTTCTTGTCTAAATTAAGACAA
35502065 GCATGTTAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 14 0.16
58 8 0.09
59 39 0.45
60 25 0.29
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (58 bp):
ATTAAGATAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATATATTCTTATCTAG
Found at i:35503208 original size:2 final size:2
Alignment explanation
Indices: 35503201--35503235 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
35503191 ATTCCTAAAG
* *
35503201 AC AC AC AC AC AC AC AC AT AC GC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
35503236 AACGCATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.46, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:35503227 original size:18 final size:18
Alignment explanation
Indices: 35503204--35503241 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
35503194 CCTAAAGACA
*
35503204 CACACACACACACATACG
1 CACACACACACACAAACG
35503222 CACACACACACACAAACG
1 CACACACACACACAAACG
35503240 CA
1 CA
35503242 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.45, G:0.05, T:0.03
Consensus pattern (18 bp):
CACACACACACACAAACG
Found at i:35503246 original size:2 final size:2
Alignment explanation
Indices: 35503241--35503289 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
35503231 ACACAAACGC
35503241 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
35503283 AT AT AT A
1 AT AT AT A
35503290 AAGATTTAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35505099 original size:42 final size:43
Alignment explanation
Indices: 35505044--35505144 Score: 161
Period size: 42 Copynumber: 2.4 Consensus size: 43
35505034 ATCAATTGTG
* *
35505044 TTTTTGCTCCCTTTTTATATATAACGTGGTA-TTTTTTTCCTA
1 TTTTTGCTTCCTTTTTATATATAACGGGGTATTTTTTTTCCTA
*
35505086 TTTTTTCTTCCTTTTTATATATAACGGGGTATTTTTTTTCCTA
1 TTTTTGCTTCCTTTTTATATATAACGGGGTATTTTTTTTCCTA
35505129 TTTTTGC-TCCTTTTTA
1 TTTTTGCTTCCTTTTTA
35505145 GTTGTCTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 37 0.69
43 17 0.31
ACGTcount: A:0.15, C:0.16, G:0.09, T:0.60
Consensus pattern (43 bp):
TTTTTGCTTCCTTTTTATATATAACGGGGTATTTTTTTTCCTA
Found at i:35518192 original size:29 final size:29
Alignment explanation
Indices: 35518131--35518194 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
35518121 TAAATTTTTT
**
35518131 AAAAATTACACTTTTACCCCTGTAAAGTG
1 AAAAATTACACTTTTACCCCTAAAAAGTG
* *
35518160 AAAAATTACATTTTTACCCC-AAAAATTG
1 AAAAATTACACTTTTACCCCTAAAAAGTG
35518188 AAAAATT
1 AAAAATT
35518195 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCTAAAAAGTG
Found at i:35524888 original size:2 final size:2
Alignment explanation
Indices: 35524881--35524911 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35524871 TTACTTCTTA
35524881 AT AT AT 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 AT AT AT A
35524912 GTGAGCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35529649 original size:73 final size:74
Alignment explanation
Indices: 35529538--35529701 Score: 222
Period size: 73 Copynumber: 2.2 Consensus size: 74
35529528 CAAACACGAT
* * * * * *
35529538 AGAATTTAAGCCCAATTTAAGTAGGACCAAGATGTGTAAACTAGTTAAGTTGGTGTGAAAAAA-A
1 AGAATTTCAGTCCAA-TTAAGTAGCACCAACATGTGTAAACCAGTTAAATTGGTGTGAAAAAATA
35529602 AAAAAGAGAG
65 AAAAAGAGAG
* *
35529612 AGAATTTCAGTCCAATTAATTAGCACCAACTTGTGTAAACCAGTTAAATTGGTGTGAAAAAATAA
1 AGAATTTCAGTCCAATTAAGTAGCACCAACATGTGTAAACCAGTTAAATTGGTGTGAAAAAATAA
*
35529677 AAGAGAGAG
66 AAAAGAGAG
*
35529686 AGAATTTCAATCCAAT
1 AGAATTTCAGTCCAAT
35529702 AAAACTAGCA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 41 0.52
74 38 0.48
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.25
Consensus pattern (74 bp):
AGAATTTCAGTCCAATTAAGTAGCACCAACATGTGTAAACCAGTTAAATTGGTGTGAAAAAATAA
AAAAGAGAG
Found at i:35529811 original size:62 final size:62
Alignment explanation
Indices: 35529709--35530552 Score: 895
Period size: 62 Copynumber: 13.6 Consensus size: 62
35529699 AATAAAACTA
* * * *
35529709 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATAAAAAGAGTTTAAGTCAAATTTAGTTC
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * ** * *
35529771 GCATCCAAGATATTTAAATCCAATTATGTTGGCATGAAAAGAATTTAAGCTTAATTTAGCTA
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * *
35529833 GCATCCAAGATATTTAAGTCCAATCATGTTGGCATGAAAAGAATTTAAGCCCAATTTAGCTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * *
35529895 GCATCCAAGATGTTTAAGTCCAATCATGTTGGCATGGAAAGAGTTTTAGCTCAATTTAGTTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * * * * * *
35529957 GCATCCAAGATGTTTAAGTCCAGTTAGGTTGGCATGAAAAGATTTTTAGCTCAATATAGCTA
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * * ** *
35530019 GCATCCAAGATGTTTAAGTCTAGTTATGTTGGCACGAAAAGAATTTAAGCCCAATTTAACTA
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * ** * * *
35530081 GCATCCAAGATGTTCAAGTCCAGTTATAATCGCA-CAATGAA-AGTTTAAGCCCCAA-ATAGTTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAA--AAGAGTTTAAG-CCCAATTTAGTTG
* * * * *
35530143 TCATCCAAAATGTTTAAGTCCAACTATGTTGGCATAAAAAGATTTTAAGCCCAATTTAGTTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * * * * *
35530205 GCATCCAAGATATTTAAATCCATTTATGTTTGCATAAAAACACTTTAAGCCCAATTTAGTTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
** * * * * *
35530267 GCATCCAAGATGTTTAAGTTTAGTTATGTTGGCACGAAAAGAGTTTAAGCTCAATTTAGCTA
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * * * * * * * **
35530329 GCAT-CAAGATGTTTTAGTCCAGTTGTGTTAGCGTAAAAAAACTTTAAGCCCAATATAACTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * *
35530390 GCTTCGAAGATGTTTAAGTCCAATTATGTTGGCACGAAAAGAGTTTAAACCCAATTTAGTTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
* * * * * *
35530452 GCATCCAAGATGTTCAAGTCTAGTTATGTTGGCACGAAAAGAATTTAAGCCTAATTTAGTTG
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
*
35530514 GCATCCAAGATGTTTAAGTCCAATTATGTTAGCATGAAA
1 GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAA
35530553 GATTTTTAGT
Statistics
Matches: 653, Mismatches: 122, Indels: 14
0.83 0.15 0.02
Matches are distributed among these distances:
61 55 0.08
62 589 0.90
63 9 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (62 bp):
GCATCCAAGATGTTTAAGTCCAATTATGTTGGCATGAAAAGAGTTTAAGCCCAATTTAGTTG
Found at i:35533884 original size:62 final size:61
Alignment explanation
Indices: 35533688--35533889 Score: 199
Period size: 62 Copynumber: 3.3 Consensus size: 61
35533678 ATTATAGCTA
*
35533688 GCATCCAAGATGTTTAAGTCCAGCTATGTTGGCATGAAAAAAGTTTAAGCTTAATTTAACTT-
1 GCATCCAAGATGTTTAAGTCCAGTTATGTTGGCAT-AAAAAAGTTTAAGCTTAATTTAA-TTG
* * * * ** * * * * *
35533750 CCATCCATGATGTTCAAGTCTAGTTATAATGGAACGAAGAGAGTTTAAGCTCAATTTAATTG
1 GCATCCAAGATGTTTAAGTCCAGTTATGTTGGCA-TAAAAAAGTTTAAGCTTAATTTAATTG
** * * *
35533812 TTATCTAAGATATTTAAGTCCAGTTATGTTGGCATAAAAATACTTTAAGCTTAATTTAATTG
1 GCATCCAAGATGTTTAAGTCCAGTTATGTTGGCATAAAAA-AGTTTAAGCTTAATTTAATTG
*
35533874 GCATCCAAGATTTTTA
1 GCATCCAAGATGTTTA
35533890 TGTCTAGTGG
Statistics
Matches: 106, Mismatches: 31, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
61 5 0.05
62 101 0.95
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (61 bp):
GCATCCAAGATGTTTAAGTCCAGTTATGTTGGCATAAAAAAGTTTAAGCTTAATTTAATTG
Done.