Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 183 of 198
Found at i:57008086 original size:42 final size:42
Alignment explanation
Indices: 57008027--57008112 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
57008017 GATTAGAAGA
*
57008027 GTTCAGAGATTTCTTTGACTTCGAGTCGATGAGACACTAGAT
1 GTTCAGAGATTTCTTTGACTTCGAGTCAATGAGACACTAGAT
*
57008069 GTTCAGAGATTTCTTTGACTTCGAGTCAATGAGACACTGGAT
1 GTTCAGAGATTTCTTTGACTTCGAGTCAATGAGACACTAGAT
57008111 GT
1 GT
57008113 CAATTTACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
GTTCAGAGATTTCTTTGACTTCGAGTCAATGAGACACTAGAT
Found at i:57015250 original size:24 final size:24
Alignment explanation
Indices: 57015216--57015267 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
57015206 TTTCTAGAAG
* *
57015216 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
57015240 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
57015264 ATTT
1 ATTT
57015268 GACTTTATTT
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:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:57016240 original size:26 final size:26
Alignment explanation
Indices: 57016211--57016260 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
57016201 GATCAACTTA
57016211 TTCAAACAGAGGTAAAACTTGTAACC
1 TTCAAACAGAGGTAAAACTTGTAACC
*
57016237 TTCAAACATAGGTAAAACTTGTAA
1 TTCAAACAGAGGTAAAACTTGTAA
57016261 GTTCTGCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (26 bp):
TTCAAACAGAGGTAAAACTTGTAACC
Found at i:57019718 original size:24 final size:24
Alignment explanation
Indices: 57019655--57019706 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
57019645 TTTCTAGAAG
* * *
57019655 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
57019679 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
57019703 ATTT
1 ATTT
57019707 GACTTTGATT
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:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:57036126 original size:23 final size:23
Alignment explanation
Indices: 57036100--57036197 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
57036090 ATAAGTGCCA
*
57036100 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57036123 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57036146 CACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57036168 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57036191 CACTGAT
1 CACTGAT
57036198 CAATAACAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
22 22 0.31
23 50 0.69
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:57036165 original size:45 final size:46
Alignment explanation
Indices: 57036100--57036197 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
57036090 ATAAGTGCCA
*
57036100 CACTGATATGTAGCCAAAGCTACCACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
*
57036146 CACTGA-ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
57036191 CACTGAT
1 CACTGAT
57036198 CAATAACAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (46 bp):
CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
Found at i:57041438 original size:23 final size:23
Alignment explanation
Indices: 57041412--57041509 Score: 180
Period size: 23 Copynumber: 4.3 Consensus size: 23
57041402 ATAAGTGCCA
57041412 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57041435 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57041458 CACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57041480 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57041503 CACTGAT
1 CACTGAT
57041510 CAATAACAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
22 22 0.30
23 51 0.70
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:57041477 original size:45 final size:46
Alignment explanation
Indices: 57041412--57041509 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 46
57041402 ATAAGTGCCA
*
57041412 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
57041458 CACTGA-ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
57041503 CACTGAT
1 CACTGAT
57041510 CAATAACAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 44 0.88
46 6 0.12
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (46 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
Found at i:57043578 original size:11 final size:11
Alignment explanation
Indices: 57043564--57043643 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 11
57043554 ATTTTTTTAA
57043564 TTTTAAAATAT
1 TTTTAAAATAT
57043575 TTTTAAAATATTT
1 TTTTAAAATA--T
** *
57043588 TTTTATTATTT
1 TTTTAAAATAT
57043599 TAATTTAAAAATAT
1 T--TTT-AAAATAT
57043613 TTTTAAAATACT
1 TTTTAAAATA-T
*
57043625 TTTTTAAA-A-
1 TTTTAAAATAT
57043634 TTTTAAAATA
1 TTTTAAAATA
57043644 AATTTTTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
9 7 0.13
10 1 0.02
11 19 0.35
12 11 0.20
13 11 0.20
14 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:57043600 original size:38 final size:38
Alignment explanation
Indices: 57043544--57043639 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
57043534 TAAATATATT
* *
57043544 TATTTTTTATATTTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTT-TATTATTTTAATTTAAAAATATTTTTAAAA
57043583 TATTTTTTTATTATTTTAATTTAAAAATATTTTTAAAA
1 TATTTTTTTATTATTTTAATTTAAAAATATTTTTAAAA
* **
57043621 TACTTTTTTAAAATTTTAA
1 TATTTTTTTATTATTTTAA
57043640 AATAAATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
38 44 0.85
39 8 0.15
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (38 bp):
TATTTTTTTATTATTTTAATTTAAAAATATTTTTAAAA
Found at i:57046394 original size:19 final size:19
Alignment explanation
Indices: 57046370--57046461 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
57046360 AATCATATCT
57046370 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
57046389 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
** *
57046408 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
57046427 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
57046446 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
57046462 CCTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:57046428 original size:38 final size:38
Alignment explanation
Indices: 57046347--57046461 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 38
57046337 AAATTAAATC
* *
57046347 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTACATATCATA
* *
57046389 TCTAAGATTACATATCATATCTAAGATTATATATTATA
1 TCTAAGATTACATATCATATCTAAGATTACATATCATA
* *
57046427 TCTAAGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTACATATC
57046462 CCTGAAGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
38 47 0.72
41 7 0.11
42 11 0.17
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTACATATCATA
Found at i:57051821 original size:20 final size:20
Alignment explanation
Indices: 57051787--57051828 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
57051777 AACTATTTAA
** *
57051787 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
57051807 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
57051827 AT
1 AT
57051829 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:57052263 original size:19 final size:19
Alignment explanation
Indices: 57052223--57052266 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
57052213 CTTCTTTTTC
*
57052223 TGTTCGAGTTCCATTTGCG
1 TGTTCGAGTTCCATTCGCG
* *
57052242 TGTTCGAGTTCCGTTCGTG
1 TGTTCGAGTTCCATTCGCG
57052261 TGTTCG
1 TGTTCG
57052267 TCTGTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.20, G:0.30, T:0.43
Consensus pattern (19 bp):
TGTTCGAGTTCCATTCGCG
Found at i:57055960 original size:6 final size:6
Alignment explanation
Indices: 57055949--57055983 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
57055939 GTGCTAATTC
57055949 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGGTG
1 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGGTG
57055984 CAGGAGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.17
Consensus pattern (6 bp):
AGGTGA
Found at i:57062211 original size:72 final size:72
Alignment explanation
Indices: 57062060--57062202 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
57062050 TCTCGGATTT
* * * * *
57062060 AAAAACAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGACCGTTTAAA
1 AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAAACCATTTAAA
57062125 ACTTGAG
66 ACTTGAG
* *
57062132 AAAAAAAGGGATCATGCTCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAAATCATTT-AA
1 AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAAACCATTTAAA
57062196 ACTTGAG
66 ACTTGAG
57062203 TTTGAAAAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 9 0.14
72 55 0.86
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (72 bp):
AAAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAAACCATTTAAA
ACTTGAG
Found at i:57062832 original size:27 final size:26
Alignment explanation
Indices: 57062797--57062858 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
57062787 GTATGTGTAT
*
57062797 ATATATATATATATATGAAAATA-AAAA
1 ATATATATAGAT-TAT-AAAATATAAAA
* *
57062824 ATGTATATAGATTATAGAATATAAAA
1 ATATATATAGATTATAAAATATAAAA
57062850 ATATATATA
1 ATATATATA
57062859 AGTATGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 15 0.50
27 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (26 bp):
ATATATATAGATTATAAAATATAAAA
Found at i:57063005 original size:9 final size:9
Alignment explanation
Indices: 57062966--57063012 Score: 53
Period size: 8 Copynumber: 5.3 Consensus size: 9
57062956 TAAATGAATA
*
57062966 AATAATAAT
1 AATATTAAT
57062975 AATA-TAAT
1 AATATTAAT
57062983 AATA-TAAT
1 AATATTAAT
57062991 AATATTAAT
1 AATATTAAT
*
57063000 AGTATTAAAT
1 AATATT-AAT
57063010 AAT
1 AAT
57063013 TAATTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
8 16 0.47
9 13 0.38
10 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
AATATTAAT
Found at i:57063014 original size:17 final size:18
Alignment explanation
Indices: 57062962--57063016 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
57062952 AGTATAAATG
57062962 AATAA-ATAATAATAATAT
1 AATAATATAATAATAAT-T
57062980 AATAATATAATAAT-ATT
1 AATAATATAATAATAATT
* *
57062997 AATAGTATTA-AATAATT
1 AATAATATAATAATAATT
57063014 AAT
1 AAT
57063017 TTTAATAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 7 0.21
19 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATAATATAATAATAATT
Found at i:57071778 original size:17 final size:16
Alignment explanation
Indices: 57071758--57071792 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
57071748 ATTATCATAC
*
57071758 TTATTCTTATTATTGTA
1 TTATTATTATTATT-TA
57071775 TTATTATTATTATTTA
1 TTATTATTATTATTTA
57071791 TT
1 TT
57071793 TGTTTTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:57072734 original size:11 final size:11
Alignment explanation
Indices: 57072718--57072756 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
57072708 TATATAAATA
57072718 TATAAATTAAT
1 TATAAATTAAT
*
57072729 TATAAAGTATAT
1 TATAAATTA-AT
57072741 TATTAAATTAAT
1 TA-TAAATTAAT
57072753 TATA
1 TATA
57072757 TTATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:57074203 original size:23 final size:22
Alignment explanation
Indices: 57074177--57074220 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
57074167 AGCCCAGATT
57074177 CCTAACCCAAATCAAAACTAAAC
1 CCTAACCCAAAT-AAAACTAAAC
* *
57074200 CCTAGCCCAACTAAAACTAAA
1 CCTAACCCAAATAAAACTAAA
57074221 AATTATTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.50, C:0.34, G:0.02, T:0.14
Consensus pattern (22 bp):
CCTAACCCAAATAAAACTAAAC
Found at i:57074555 original size:16 final size:16
Alignment explanation
Indices: 57074522--57074576 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 16
57074512 TACTTACTTT
57074522 TTTTGATCTATTTATTTTA
1 TTTT-ATCT-TTT-TTTTA
57074541 TTTTATCTTTTTTTTTA
1 TTTTATC-TTTTTTTTA
*
57074558 TTTT-TCTTTTTTTCA
1 TTTTATCTTTTTTTTA
57074573 TTTT
1 TTTT
57074577 TCTGTTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 9 0.26
18 6 0.18
19 5 0.15
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTATCTTTTTTTTA
Found at i:57074556 original size:17 final size:17
Alignment explanation
Indices: 57074522--57074570 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
57074512 TACTTACTTT
*
57074522 TTTTGATCTATTTATTTTA
1 TTTT-ATCT-TTTTTTTTA
57074541 TTTTATCTTTTTTTTTA
1 TTTTATCTTTTTTTTTA
57074558 TTTT-TCTTTTTTT
1 TTTTATCTTTTTTT
57074571 CATTTTTCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 9 0.31
17 12 0.41
18 4 0.14
19 4 0.14
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTATCTTTTTTTTTA
Found at i:57074577 original size:15 final size:14
Alignment explanation
Indices: 57074536--57074579 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 14
57074526 GATCTATTTA
57074536 TTTTATTTTATCTTTTT
1 TTTTATTTT-TC--TTT
57074553 TTTTATTTTTCTTT
1 TTTTATTTTTCTTT
57074567 TTTTCATTTTTCT
1 TTTT-ATTTTTCT
57074580 GTTATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.27
15 8 0.31
16 2 0.08
17 9 0.35
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTATTTTTCTTT
Found at i:57080336 original size:44 final size:44
Alignment explanation
Indices: 57080265--57080352 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
57080255 TGTCGAGTGG
* * *
57080265 CAAATGTTGACTCTAATGTAGTTGTTGATTGTGGGTGTATCTGT
1 CAAATGTTAACTATAATGTAGTCGTTGATTGTGGGTGTATCTGT
*
57080309 CAAATGTTAACTATAATGTGGTCGTTGATTGTGGGTGTATCTGT
1 CAAATGTTAACTATAATGTAGTCGTTGATTGTGGGTGTATCTGT
57080353 TGATAAGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (44 bp):
CAAATGTTAACTATAATGTAGTCGTTGATTGTGGGTGTATCTGT
Found at i:57087515 original size:27 final size:27
Alignment explanation
Indices: 57087485--57087549 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
57087475 TTTTTTTTCT
*
57087485 TTTTATTCTTTTTTTATTC-TTCCTTCC
1 TTTT-TTCTTTTCTTATTCTTTCCTTCC
* * *
57087512 TTTTTCACGTTTCTTATTCTTTCCTTTC
1 TTTTT-TCTTTTCTTATTCTTTCCTTCC
57087540 TTTTTTCTTT
1 TTTTTTCTTT
57087550 ATCTGTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 17 0.57
28 12 0.40
ACGTcount: A:0.06, C:0.22, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTTCTTTTCTTATTCTTTCCTTCC
Found at i:57089450 original size:2 final size:2
Alignment explanation
Indices: 57089443--57089467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57089433 TGGTGCCTTT
57089443 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
57089468 GCTTTAAGAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57095049 original size:17 final size:18
Alignment explanation
Indices: 57095014--57095050 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
57095004 GCTACAAAAC
*
57095014 AAAATGAAGAAATAGAAG
1 AAAATGAAGAAAAAGAAG
57095032 AAAATGAA-AAAAAGAAG
1 AAAATGAAGAAAAAGAAG
57095049 AA
1 AA
57095051 GCTATTGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (18 bp):
AAAATGAAGAAAAAGAAG
Found at i:57096021 original size:17 final size:15
Alignment explanation
Indices: 57095991--57096026 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
57095981 TTTAAAATTT
57095991 TAAAAATATAAAATA
1 TAAAAATATAAAATA
57096006 TAAAATATATTAAAATA
1 TAAAA-ATA-TAAAATA
57096023 TAAA
1 TAAA
57096027 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 3 0.16
17 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATATAAAATA
Found at i:57097092 original size:26 final size:26
Alignment explanation
Indices: 57097049--57097112 Score: 121
Period size: 25 Copynumber: 2.5 Consensus size: 26
57097039 TATTATGGAG
57097049 TGTTTTATTTTGAATTTTTTTAAAAT
1 TGTTTTATTTTGAATTTTTTTAAAAT
57097075 TG-TTTATTTTGAATTTTTTTAAAAT
1 TGTTTTATTTTGAATTTTTTTAAAAT
57097100 TGTTTTATTTTGA
1 TGTTTTATTTTGA
57097113 TAAAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 25 0.68
26 12 0.32
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (26 bp):
TGTTTTATTTTGAATTTTTTTAAAAT
Found at i:57098411 original size:16 final size:15
Alignment explanation
Indices: 57098390--57098422 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
57098380 CAAAGAAAAA
57098390 AATAAAATAAATCAAT
1 AATAAAATAAAT-AAT
57098406 AATAAAATAAATAAT
1 AATAAAATAAATAAT
57098421 AA
1 AA
57098423 CAATGATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAAATAAATAAT
Found at i:57098426 original size:21 final size:20
Alignment explanation
Indices: 57098388--57098437 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
57098378 ATCAAAGAAA
*
57098388 AAAATAAAATAAATCAATAAT
1 AAAAT-AAATAAAACAATAAT
*
57098409 AAAATAAATAATAACAATGAT
1 AAAATAAATAA-AACAATAAT
57098430 AACAATAA
1 AA-AATAA
57098438 TAGTTCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATAAATAAAACAATAAT
Found at i:57098621 original size:4 final size:4
Alignment explanation
Indices: 57098606--57098722 Score: 64
Period size: 4 Copynumber: 29.2 Consensus size: 4
57098596 ATTTGTAATA
* * *
57098606 AAAT ACAT AAAT AAAT AAAT -AAT -AAT AGAT ATAAT -AAT AAAT ATAGT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT A-AAT
* * * * * **
57098653 AAAAG AAAA AACAA AAAT AAAA AACAA AAAT AAAT GTAT AAAT --AT AAAT
1 -AAAT AAAT AA-AT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT
57098702 AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT A
57098723 CAAAGAAACA
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
2 2 0.02
3 9 0.10
4 64 0.72
5 13 0.15
6 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:57098644 original size:22 final size:21
Alignment explanation
Indices: 57098602--57098716 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 21
57098592 TGCAATTTGT
57098602 AATAAAATACATAAATAAATA
1 AATAAAATACATAAATAAATA
*
57098623 AATAATAATAGATATAAT-AATA
1 AATAA-AATACATA-AATAAATA
* * * * * *
57098645 AATATAGTAAAAGAAAAAACAAA
1 AATAAAAT-ACATAAATAA-ATA
* * *
57098668 AATAAAAAACAAAAATAAATG
1 AATAAAATACATAAATAAATA
* *
57098689 TATAAATATAAATAAATAAATA
1 AATAAA-ATACATAAATAAATA
57098711 AATAAA
1 AATAAA
57098717 TAAATACAAA
Statistics
Matches: 67, Mismatches: 21, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
21 15 0.22
22 42 0.63
23 10 0.15
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (21 bp):
AATAAAATACATAAATAAATA
Found at i:57098674 original size:13 final size:13
Alignment explanation
Indices: 57098653--57098686 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
57098643 TAAATATAGT
*
57098653 AAAAGAAAAAACA
1 AAAATAAAAAACA
57098666 AAAATAAAAAACA
1 AAAATAAAAAACA
57098679 AAAATAAA
1 AAAATAAA
57098687 TGTATAAATA
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:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAATAAAAAACA
Found at i:57100457 original size:130 final size:130
Alignment explanation
Indices: 57100271--57100606 Score: 361
Period size: 130 Copynumber: 2.5 Consensus size: 130
57100261 TTTAATTCGG
* * * * *
57100271 TCCACTGCAACTTCAGGGAGATAGGATTAGTATCTTCAATATGCTCCACTGCAACTTTAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGATTAGTAACTTCAACATGCTCAACTGCAACTTCAGGGAGA
* * * *
57100336 TAAGGTTTGCTATGATTTGCTTTACTGCAACTTCAAAGAGATAAGATTTGCTATTTTCAATCTGC
66 TAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGCCATTTTCAATCTGC
* * *
57100401 TCCACTGCAACTTTAGGGAGATAAGACTT-GTAACTTCAACCTGCTCAACTGTAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGA-TTAGTAACTTCAACATGCTCAACTGCAACTTCAGGGAG
* * *
57100465 ATAATGTTTGTTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCCATTTATAGCTTC
65 ATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGCCA--T-T---TTC
*
57100530 AATCTGT
124 AATCTGC
* * ** * * * *
57100537 TCCACTGCAACTTCAAGGAAATAAGATTCTCTATCTTTAGTC-TGCTCCACTGCAACTTCAGGGA
1 TCCACTGCAACTTCAGGGAGATAAGATT-AGTAACTTCA-ACATGCTCAACTGCAACTTCAGGGA
57100601 GATAAG
64 GATAAG
57100607 ACTTATAACT
Statistics
Matches: 170, Mismatches: 26, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
130 100 0.59
131 2 0.01
132 1 0.01
133 1 0.01
135 2 0.01
136 32 0.19
137 31 0.18
138 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (130 bp):
TCCACTGCAACTTCAGGGAGATAAGATTAGTAACTTCAACATGCTCAACTGCAACTTCAGGGAGA
TAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGCCATTTTCAATCTGC
Found at i:57100590 original size:181 final size:181
Alignment explanation
Indices: 57100359--57100845 Score: 762
Period size: 181 Copynumber: 2.7 Consensus size: 181
57100349 GATTTGCTTT
* * * *
57100359 ACTGCAACTTCAAAGAGATAAGATT-TGCTAT-TTTCAATCTGCTCCACTGCAACTTTAGGGAGA
1 ACTGCAACTTCAAGGAAATAAGATTCT-CTATCTTT-AGTCTGCTCCACTGCAACTTCAGGGAGA
* * *
57100422 TAAGACTTGTAACTTCAACCTGCTCAACTGTAACTTCAGGGAGATAATGTTTGTTATGATCTGCT
64 TAAGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGCTATGATCTGCT
*
57100487 CTACTGCAACTTCAGAGAGATAAGATCTGCCATTTATAGCTTCAATCTGTTCC
129 CTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTTCC
57100540 ACTGCAACTTCAAGGAAATAAGATTCTCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAAGGAAATAAGATTCTCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
* * * *
57100605 AGACTTATAACTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGCTATGATTTGCTCT
66 AGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGCTATGATCTGCTCT
* *
57100670 ACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCC
131 ACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTTCC
* * * * *
57100721 ACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGTGAGATA
1 ACTGCAACTTCAAGGAAATAAGATTCTCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
*
57100786 AGACTAGTAACTTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGCTATGATCT
66 AGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGCTATGATCT
57100846 TTAATCCATC
Statistics
Matches: 280, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
181 276 0.99
182 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (181 bp):
ACTGCAACTTCAAGGAAATAAGATTCTCTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
AGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGCTATGATCTGCTCT
ACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTTCC
Found at i:57100830 original size:44 final size:44
Alignment explanation
Indices: 57100271--57100831 Score: 304
Period size: 44 Copynumber: 12.6 Consensus size: 44
57100261 TTTAATTCGG
* * * *
57100271 TCCACTGCAACTTCAGGGAGATAGGATTAGTATCTTCAATATGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAATCTGC
* * ** * *
57100315 TCCACTGCAACTTTAGGGAGATAAG-GT--TTGCTAT-GATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAGTAACT-TCAATCTGC
** ** * * **
57100356 TTTACTGCAACTTCAAAGAGATAAGATTTGCTATTTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAG-TAACTTCAATCTGC
* * *
57100401 TCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAATCTGC
* * * * * *
57100445 TCAACTGTAACTTCAGGGAGATAATG-TTTGTTA--T-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAA-GACTAGTAACTTCAATCTGC
* * * *
57100486 TCTACTGCAACTTCAGAGAGATAAGATCTGCCATTTATAGCTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA-CT---A-GTA-A-CTTCAATCTGC
* * * * * *
57100537 TCCACTGCAACTTCAAGGAAATAAGATTCT-CTATCTTTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA--CTAGTAACTTCAATCTGC
*
57100582 TCCACTGCAACTTCAGGGAGATAAGACTTA-TAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGAC-TAGTAACTTCAATCTGC
* * ** * *
57100626 TCCACTGCAACTTCAGAGAGATAAG-GT--TTGCTAT-GATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAGTAACT-TCAATCTGC
* * * * *
57100667 TCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA-C--T-A-GTA-A-CTTCAATCTGC
* * * * * *
57100718 TCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAG-TAACTTCAATCTGC
* *
57100763 TCCACTGCAACTTCAGTGAGATAAGACTAGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAATCTGC
*
57100807 TCCACTGTAACTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
57100832 GTTTGCTATG
Statistics
Matches: 391, Mismatches: 92, Indels: 68
0.71 0.17 0.12
Matches are distributed among these distances:
40 1 0.00
41 84 0.21
42 6 0.02
43 2 0.01
44 130 0.33
45 99 0.25
46 1 0.00
47 5 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 56 0.14
52 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAATCTGC
Found at i:57103582 original size:43 final size:43
Alignment explanation
Indices: 57103486--57103599 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
57103476 CTCTTACAAA
* * * *
57103486 GCCAACGTTCCAGACGGGGTCTTACATGTAATCACATATCGAT
1 GCCAACGTCCCAGACAGGGTCTTACACGTAAACACATATCGAT
* * *
57103529 G-CTACTGTCCCAGATAGGGTCTTACACGTAAACACA-AGTCGGT
1 GCCAAC-GTCCCAGACAGGGTCTTACACGTAAACACATA-TCGAT
*
57103572 GCCAACGTCCCAGACATGGTCTTACACG
1 GCCAACGTCCCAGACAGGGTCTTACACG
57103600 ATAACATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 4 0.07
43 51 0.88
44 3 0.05
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (43 bp):
GCCAACGTCCCAGACAGGGTCTTACACGTAAACACATATCGAT
Found at i:57104494 original size:11 final size:12
Alignment explanation
Indices: 57104479--57104507 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
57104469 TATGTTTATG
57104479 TTATTAACATTA
1 TTATTAACATTA
57104491 -TATTAACATTA
1 TTATTAACATTA
57104502 TTATTA
1 TTATTA
57104508 TTTTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTAACATTA
Found at i:57105400 original size:19 final size:19
Alignment explanation
Indices: 57105379--57105450 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
57105369 AGCCTCTCCT
57105379 TTTTCTTTTCTCATTTC-T-
1 TTTTCTTTT-TCATTTCTTC
57105397 TTTTCTTTTTTC-TTTCATTC
1 TTTTC-TTTTTCATTTC-TTC
*
57105417 TTTTCTTTTTCATTTTTTC
1 TTTTCTTTTTCATTTCTTC
*
57105436 TTTTCTGTTTCATTT
1 TTTTCTTTTTCATTT
57105451 TTTAATTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.09
18 7 0.15
19 28 0.60
20 8 0.17
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTTCATTTCTTC
Found at i:57105408 original size:13 final size:14
Alignment explanation
Indices: 57105392--57105439 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 14
57105382 TCTTTTCTCA
57105392 TTTCTTTTTC-TTT
1 TTTCTTTTTCATTT
57105405 TTTC--TTTCATTCT
1 TTTCTTTTTCATT-T
57105418 TTTCTTTTTCATTT
1 TTTCTTTTTCATTT
57105432 TTTCTTTT
1 TTTCTTTT
57105440 CTGTTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.13
12 2 0.06
13 9 0.29
14 9 0.29
15 7 0.23
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTCATTT
Found at i:57105409 original size:20 final size:19
Alignment explanation
Indices: 57105384--57105426 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
57105374 CTCCTTTTTC
57105384 TTTTC-TCATTTCTTTTTCTT
1 TTTTCTTCA-TTC-TTTTCTT
57105404 TTTTCTTTCATTCTTTTCTT
1 TTTTC-TTCATTCTTTTCTT
57105424 TTT
1 TTT
57105427 CATTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 15 0.71
21 3 0.14
22 3 0.14
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTCATTCTTTTCTT
Found at i:57105418 original size:33 final size:33
Alignment explanation
Indices: 57105381--57105453 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
57105371 CCTCTCCTTT
*
57105381 TTCTTTTCTCATTTC-TTTTTCTTTTTTCTTTCA
1 TTCTTTTCT-ATTTCATTTTTCTTTTCTCTTTCA
* *
57105414 TTCTTTTCTTTTTCATTTTTTCTTTTCTGTTTCA
1 TTCTTTTCTATTTCA-TTTTTCTTTTCTCTTTCA
57105448 TT-TTTT
1 TTCTTTT
57105454 AATTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 4 0.11
33 13 0.37
34 18 0.51
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.75
Consensus pattern (33 bp):
TTCTTTTCTATTTCATTTTTCTTTTCTCTTTCA
Found at i:57105440 original size:13 final size:12
Alignment explanation
Indices: 57105378--57105441 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 12
57105368 TAGCCTCTCC
57105378 TTTTTCTTTTCT
1 TTTTTCTTTTCT
**
57105390 CATTTCTTTTTCT
1 TTTTTC-TTTTCT
57105403 TTTTTC-TTTCAT
1 TTTTTCTTTTC-T
57105415 TCTTTTCTTTTTCAT
1 T-TTTTC-TTTTC-T
57105430 TTTTTCTTTTCT
1 TTTTTCTTTTCT
57105442 GTTTCATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 4 0.09
12 7 0.16
13 20 0.47
14 5 0.12
15 7 0.16
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:57105451 original size:26 final size:24
Alignment explanation
Indices: 57105378--57105461 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 24
57105368 TAGCCTCTCC
57105378 TTTTTCTTTTCTCATTTCTTTTTC-T
1 TTTTTCTTTTCT--TTTCTTTTTCAT
57105403 TTTTTCTTTCATTCTTTTCTTTTTCAT
1 TTTTTC-TT--TTCTTTTCTTTTTCAT
*
57105430 TTTTTCTTTTCTGTTTCATTTTTTAAT
1 TTTTTCTTTTCT-TTTC--TTTTTCAT
57105457 TTTTT
1 TTTTT
57105462 TAAAAATAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
24 4 0.08
25 10 0.20
26 14 0.27
27 19 0.37
28 4 0.08
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTCTTTTCTTTTCTTTTTCAT
Found at i:57105460 original size:34 final size:34
Alignment explanation
Indices: 57105396--57105460 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
57105386 TTCTCATTTC
* *
57105396 TTTTTCTTTTTTCTTTCATTCTTTTCTTTTTCAT
1 TTTTTCTTTTCTCTTTCATTCTTTTATTTTTCAT
*
57105430 TTTTTCTTTTCTGTTTCATT-TTTTAATTTTT
1 TTTTTCTTTTCTCTTTCATTCTTTT-ATTTTT
57105461 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.77
Consensus pattern (34 bp):
TTTTTCTTTTCTCTTTCATTCTTTTATTTTTCAT
Found at i:57110479 original size:16 final size:15
Alignment explanation
Indices: 57110458--57110490 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
57110448 TCAAAGAAAA
57110458 AATAAAATAAATCAAT
1 AATAAAATAAAT-AAT
57110474 AATAAAATAAATAAT
1 AATAAAATAAATAAT
57110489 AA
1 AA
57110491 CAATGATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAAATAAATAAT
Found at i:57110494 original size:21 final size:21
Alignment explanation
Indices: 57110456--57110509 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
57110446 AATCAAAGAA
*
57110456 AAAATAAAATAA-ATCAATAAT
1 AAAAT-AAATAATAACAATAAT
*
57110477 AAAATAAATAATAACAATGAT
1 AAAATAAATAATAACAATAAT
57110498 AACAAT-AATAAT
1 AA-AATAAATAAT
57110510 TCTAATGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.21
21 20 0.69
22 3 0.10
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAAATAATAACAATAAT
Found at i:57111326 original size:12 final size:12
Alignment explanation
Indices: 57111309--57111334 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57111299 CTCTCCAGAA
57111309 TCCGGCCAGGGG
1 TCCGGCCAGGGG
57111321 TCCGGCCAGGGG
1 TCCGGCCAGGGG
57111333 TC
1 TC
57111335 ACCGCACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.46, T:0.12
Consensus pattern (12 bp):
TCCGGCCAGGGG
Found at i:57113179 original size:151 final size:151
Alignment explanation
Indices: 57112905--57113192 Score: 452
Period size: 151 Copynumber: 1.9 Consensus size: 151
57112895 AAATTGTGAA
* *
57112905 TAATGTGGATTCGGGCGCTGGTCATAAGTTCTACCCGTGGCTGAGTATACTGGCATATGTTGCGG
1 TAATGTGAACTCGGGCGCTGGTCATAAGTTCTACCCGTGGCTGAGTATACTGGCATATGTTGCGG
* * * * *
57112970 ATACCTGACAGCTTGTGTGAGCAGCACTGAGTAGTAACGAATGACTGATAGTTTGTGTGAGCAGG
66 ATACCTGACAGCTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAGA
57113035 CCCGTGATGCAAAACTATGAT
131 CCCGTGATGCAAAACTATGAT
* * * *
57113056 TAATGTGAACTCGGGTGCTGGTCTTAAGTTCTACCTGTGGCT-AGGTATACTGGCATATGTTGGG
1 TAATGTGAACTCGGGCGCTGGTCATAAGTTCTACCCGTGGCTGA-GTATACTGGCATATGTTGCG
*
57113120 GATACCTGACAGCTTGTGTGAGCAGCACTGAGTAGTAATAAAAGACTGACAGCTTGTGTGAGCAG
65 GATACCTGACAGCTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAG
57113185 ACCCGTGA
130 ACCCGTGA
57113193 AAGTGAATAG
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
150 1 0.01
151 123 0.99
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (151 bp):
TAATGTGAACTCGGGCGCTGGTCATAAGTTCTACCCGTGGCTGAGTATACTGGCATATGTTGCGG
ATACCTGACAGCTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACTGACAGCTTGTGTGAGCAGA
CCCGTGATGCAAAACTATGAT
Found at i:57119058 original size:42 final size:42
Alignment explanation
Indices: 57118933--57119051 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 42
57118923 GCGTTTACAG
* *
57118933 AAAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
* * *
57118975 AAAAAACGCCACCACTAAAGATCATGTTCTTTAGCGGCGCTTGGT
1 AAAAAACG---CCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
*
57119020 AAAAAACGCCGCTATAGATCATGTTCTTTAGC
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGC
57119052 AACGCTTTCA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
42 29 0.43
45 38 0.57
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
Found at i:57119527 original size:21 final size:21
Alignment explanation
Indices: 57119503--57119572 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
57119493 GCTTCTCTCG
* *
57119503 CTGCTTCTCGCGCTGCAGCCT
1 CTGCTTCTCTCGCTGTAGCCT
*
57119524 CTGCTTCTCTCGCCGTAGCCT
1 CTGCTTCTCTCGCTGTAGCCT
*
57119545 CTGCTTCCCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGTAGCCT
57119566 CTGCTTC
1 CTGCTTC
57119573 CATCGTTGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.04, C:0.43, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGTAGCCT
Found at i:57119573 original size:21 final size:21
Alignment explanation
Indices: 57119503--57119592 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
57119493 GCTTCTCTCG
* *
57119503 CTGCTTCTCGCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
* * *
57119524 CTGCTTCTCTCGCCGTAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
*
57119545 CTGCTTCCCTCGCTGTAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
* * *
57119566 CTGCTTCCATCGTTGCCGCCT
1 CTGCTTCCCTCGCTGCAGCCT
57119587 CTGCTT
1 CTGCTT
57119593 TAAGTTGTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.04, C:0.42, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCT
Found at i:57122509 original size:365 final size:365
Alignment explanation
Indices: 57121839--57122555 Score: 1182
Period size: 365 Copynumber: 2.0 Consensus size: 365
57121829 TGCATCGACA
* *
57121839 TTTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAATGGCACCGTTTTA
1 TTTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTA
* *
57121904 TAAAAATATAAGGAAACATTCTGGCGTTTTCCCAAACACGGCACAATTAATATATTATCGAACAG
66 TAAAAATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACAG
* * * * *
57121969 GCGTCGTTTTCAGTAAATTTTGTACATCCTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTC
131 ACGCCGTTTTCAGAAAATTTTATACATCCTTGCGGCGTTTATAATAAAACGCCACTAAAAGATTC
* * *
57122034 CATCCTTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTATGGCGCTTTTAGGAA
196 CATCCTTCAACTGAAACGGCACCGTTTTCGCAAAGTTCAAATATTATTTACGGCGCTTTTAGAAA
* * * * *
57122099 AAACGCCACAGCTAAAATTTATTCCCTAAGTCGAAACGACGCCGTATCGGTAAATGTAATAAATA
261 AAACGCCACAACTAAAACTTATTCCCTAAGCCGAAACGACGCCGTATCGATAAATGCAATAAATA
57122164 TTTGTGGCTTTTTTTATCAAAACGCCGGTAATGTCTACCT
326 TTTGTGGCTTTTTTTATCAAAACGCCGGTAATGTCTACCT
**
57122204 TTTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGTGCCATTTTA
1 TTTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTA
*
57122269 TAAAAATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCG
66 TAAAAATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACAG
*
57122334 ACGCCGTTTTCAGAAAATTTTATACATCCTTGCGGCGTTTATAATAAAACGCCACTAAAATATTC
131 ACGCCGTTTTCAGAAAATTTTATACATCCTTGCGGCGTTTATAATAAAACGCCACTAAAAGATTC
* * ** *
57122399 CATCCTTCAATTGAAACGGCACCGTTTTGGCAAAGTTTTAATATTATTTACGGCGCTTTTCGAAA
196 CATCCTTCAACTGAAACGGCACCGTTTTCGCAAAGTTCAAATATTATTTACGGCGCTTTTAGAAA
* *
57122464 AAACGCCACAACTTAAACTTATTCCCTAAGCCGAAACGACGCCGTATCGATAAATGCAATAAATT
261 AAACGCCACAACTAAAACTTATTCCCTAAGCCGAAACGACGCCGTATCGATAAATGCAATAAATA
57122529 TTTGTGGCTTTTTTTATCAAAACGCCG
326 TTTGTGGCTTTTTTTATCAAAACGCCG
57122556 CTAAATCTTA
Statistics
Matches: 324, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
365 324 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (365 bp):
TTTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTA
TAAAAATATAAGGAAACATTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACAG
ACGCCGTTTTCAGAAAATTTTATACATCCTTGCGGCGTTTATAATAAAACGCCACTAAAAGATTC
CATCCTTCAACTGAAACGGCACCGTTTTCGCAAAGTTCAAATATTATTTACGGCGCTTTTAGAAA
AAACGCCACAACTAAAACTTATTCCCTAAGCCGAAACGACGCCGTATCGATAAATGCAATAAATA
TTTGTGGCTTTTTTTATCAAAACGCCGGTAATGTCTACCT
Found at i:57122625 original size:24 final size:23
Alignment explanation
Indices: 57122598--57122678 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 23
57122588 TGTATCATTC
57122598 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTAT-T
*
57122622 ATTTAAACAATTAATTACCTAAAAATT
1 ATTTAAATAATTAATTACCT----ATT
57122649 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTA-TT
57122674 ATTTA
1 ATTTA
57122679 TTTATTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
24 25 0.51
25 2 0.04
27 1 0.02
28 21 0.43
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAAATAATTAATTACCTATT
Found at i:57122681 original size:28 final size:26
Alignment explanation
Indices: 57122598--57122682 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 26
57122588 TGTATCATTC
*
57122598 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
57122622 ATTTAAACAATTAATTACCTAAAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
57122650 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
57122678 ATTTA
1 ATTTA
57122683 TTTTTTCTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 18 0.38
26 1 0.02
28 29 0.60
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:57123205 original size:15 final size:15
Alignment explanation
Indices: 57123185--57123214 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57123175 CTCTAACATG
57123185 ACCCTAAATCCCTAA
1 ACCCTAAATCCCTAA
57123200 ACCCTAAATCCCTAA
1 ACCCTAAATCCCTAA
57123215 CTATTAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (15 bp):
ACCCTAAATCCCTAA
Found at i:57123206 original size:7 final size:8
Alignment explanation
Indices: 57123186--57123214 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
57123176 TCTAACATGA
57123186 CCCTAAAT
1 CCCTAAAT
57123194 CCCTAAA-
1 CCCTAAAT
57123201 CCCTAAAT
1 CCCTAAAT
57123209 CCCTAA
1 CCCTAA
57123215 CTATTAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (8 bp):
CCCTAAAT
Found at i:57123237 original size:7 final size:7
Alignment explanation
Indices: 57123225--57123264 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
57123215 CTATTAGCAT
57123225 CTAACCC
1 CTAACCC
57123232 CTAA--C
1 CTAACCC
57123237 CTAACCC
1 CTAACCC
57123244 CTAACCC
1 CTAACCC
57123251 CTAACCC
1 CTAACCC
*
57123258 TTAACCC
1 CTAACCC
57123265 ATAAACCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.17
7 25 0.83
ACGTcount: A:0.30, C:0.53, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAACCC
Found at i:57123242 original size:12 final size:12
Alignment explanation
Indices: 57123225--57123263 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
57123215 CTATTAGCAT
57123225 CTAACCCCTAAC
1 CTAACCCCTAAC
57123237 CTAACCCCTAACCC
1 CTAACCCCTAA--C
*
57123251 CTAACCCTTAAC
1 CTAACCCCTAAC
57123263 C
1 C
57123264 CATAAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:57123321 original size:14 final size:14
Alignment explanation
Indices: 57123256--57123330 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
57123246 AACCCCTAAC
* *
57123256 CCTTAACCCATAAA
1 CCTTAATCCATAAT
*
57123270 CCTTAAATCACATTAAC
1 CCTT-AATC-CA-TAAT
* *
57123287 CCTTAAACCAGAAT
1 CCTTAATCCATAAT
*
57123301 CCCTAATCCATAAT
1 CCTTAATCCATAAT
57123315 CCTTAATTCCATAAT
1 CCTTAA-TCCATAAT
57123330 C
1 C
57123331 TATAAAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 22 0.46
15 14 0.29
16 5 0.10
17 7 0.15
ACGTcount: A:0.39, C:0.32, G:0.01, T:0.28
Consensus pattern (14 bp):
CCTTAATCCATAAT
Found at i:57123404 original size:20 final size:21
Alignment explanation
Indices: 57123379--57123422 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57123369 ATCCTAAATT
*
57123379 AACCATATATA-TATACCCTA
1 AACCATATATATTAAACCCTA
*
57123399 AACCATATTTATTAAACCCTA
1 AACCATATATATTAAACCCTA
57123420 AAC
1 AAC
57123423 TATAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (21 bp):
AACCATATATATTAAACCCTA
Found at i:57124088 original size:115 final size:115
Alignment explanation
Indices: 57123876--57124339 Score: 671
Period size: 115 Copynumber: 4.0 Consensus size: 115
57123866 TAAATTATTT
* * * *
57123876 TAAATCCCTAAGCATTAGCGGTGCTTACTTAAAAAA-AGCCGCTAAATCCCTGAAAGCTCAGAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAAACA-CCGCTAAATCCCCGAAAGCTCAGAAA
* *
57123940 ACAACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCAC
65 ACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
57123991 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAA
* *
57124056 CGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAGCAAAAACGCCGC
66 CGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
* * * * * *
57124106 TAAAGCGTCTGAGCATTAGCGGCACTTAATT-AAAAACGCCGCAAAATCCCTGAAAGCTCAGAAA
1 TAAAGC-CCTGAGCATTAGCGGCGCTTACTTAAAAAACACCGCTAAATCCCCGAAAGCTCAGAAA
* *
57124170 ATGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
65 ACGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
* * * * * ** *
57124221 TAAAGCCCTGGGTATTAGTGTCGCTTCCCGAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAA
*
57124286 CGACGTCGTTGGGATTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
66 CGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
57124336 TAAA
1 TAAA
57124340 TCCCCGAAAG
Statistics
Matches: 315, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
114 14 0.04
115 279 0.89
116 22 0.07
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.25
Consensus pattern (115 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAA
CGACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCGC
Found at i:57124334 original size:73 final size:73
Alignment explanation
Indices: 57124252--57124394 Score: 259
Period size: 73 Copynumber: 2.0 Consensus size: 73
57124242 CGCTTCCCGA
*
57124252 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
*
57124317 GCTTTATC
66 ACTTTATC
*
57124325 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
57124390 ACTTT
66 ACTTT
57124395 CGCAAAATCG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
ACTTTATC
Found at i:57124370 original size:188 final size:187
Alignment explanation
Indices: 57124137--57124508 Score: 541
Period size: 188 Copynumber: 2.0 Consensus size: 187
57124127 GCACTTAATT
* * * *
57124137 AAAAACGCCGCAAAATCCCTGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGTGGC
1 AAAAACGCCGCAAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
* * * * *
57124202 GCTTTATCAAAAACGCCGCTAAAGCCCTGGGTATTAGTGTCGCTTC-CCGAAAAAACGCCGCTAA
66 ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTCTCC-AAAAAA-GCCGCTAA
* *
57124266 ATCCCCGAAAGCTCAGAAAACGACGTCGTT-GGGATTAGGTTTTTTTGTGGCGCTTTATC
129 ATCCCCGAAAGCTCAGAAAACGACATCGTTAGGCATTAGG-TTTTTTGTGGCGCTTTATC
*
57124325 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCAAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
* * * *
57124390 ACTTTCGCAAAATCGCTGCTAATGCCCTGGGCATTAGCGGCGCTTCTCCAAAAAAGCCGCTAAAT
66 ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTCTCCAAAAAAGCCGCTAAAT
* *
57124455 CCCCGAAAGCTCAGAAAACGGCATCGTTAGGCTTTAGGTTTTTTGTGGCGCTTT
131 CCCCGAAAGCTCAGAAAACGACATCGTTAGGCATTAGGTTTTTTGTGGCGCTTT
57124509 CGCAAAAAGA
Statistics
Matches: 164, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
187 52 0.32
188 110 0.67
189 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (187 bp):
AAAAACGCCGCAAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
ACTTTAGCAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTCTCCAAAAAAGCCGCTAAAT
CCCCGAAAGCTCAGAAAACGACATCGTTAGGCATTAGGTTTTTTGTGGCGCTTTATC
Found at i:57124401 original size:73 final size:73
Alignment explanation
Indices: 57124252--57124411 Score: 257
Period size: 73 Copynumber: 2.2 Consensus size: 73
57124242 CGCTTCCCGA
*
57124252 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
* *
57124317 GCTTTATC
66 ACTTTAGC
*
57124325 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
*
57124390 ACTTTCGC
66 ACTTTAGC
* *
57124398 AAAATCGCTGCTAA
1 AAAAACGCCGCTAA
57124412 TGCCCTGGGC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGC
ACTTTAGC
Found at i:57124514 original size:114 final size:111
Alignment explanation
Indices: 57124314--57124642 Score: 408
Period size: 114 Copynumber: 2.9 Consensus size: 111
57124304 GTTTTTTTGT
** * *
57124314 GGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGT
1 GGCGCTTCCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTT-GGCTTAGG-
* * *
57124379 TTTTTTGTGGCACTTTCGCAAAATCGCTGCTAATGCCCTGGGCATTAGC
64 TTTTTTGTGGCGCTTTCGCAAAA-CGCCGCTAATGCCCTGAGCATTAGC
* *
57124428 GGCGCTT-CTCCAAAAAAGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTAGGCTTTAG
1 GGCGCTTCCT-CAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTT-GGC-TTAG
* * *
57124492 GTTTTTTGTGGCGCTTTCGCAAAAAGACCACTAAAGCCCTGAGCATTAGC
63 GTTTTTTGTGGCGCTTTCGCAAAACG-CCGCTAATGCCCTGAGCATTAGC
* *
57124542 GGCGCTTCCTTAAAAACGCCGCTAAATCCCCCGAAAGCTCAAAAAACGGCATCGTTGGGCTTAAG
1 GGCGCTTCCTCAAAAACGCCGCTAAAT-CCCCGAAAGCTCAAAAAACGGCATCGTT-GGCTTAGG
* * *
57124607 TATTTTGCGGCGCTTTCTGGAAAACGCCGCTAATGC
64 TTTTTTGTGGCGCTTTC-GCAAAACGCCGCTAATGC
57124643 TTATTTTCAG
Statistics
Matches: 186, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
113 2 0.01
114 141 0.76
115 43 0.23
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (111 bp):
GGCGCTTCCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTGGCTTAGGTT
TTTTGTGGCGCTTTCGCAAAACGCCGCTAATGCCCTGAGCATTAGC
Found at i:57124576 original size:302 final size:302
Alignment explanation
Indices: 57124022--57124639 Score: 814
Period size: 302 Copynumber: 2.0 Consensus size: 302
57124012 CGCTTACTTA
* * *
57124022 AAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
* * * *
57124087 GCTTTAGCAAAAACGCCGCTAAAGCGTCTGAGCATTAGCGGCACTTAATTAAAAACGCCGCAAAA
66 ACTTTAGCAAAAACGCCGCTAAAGCGCCTGAGCATTAGCGGCACTTAATCAAAAAAGCCGCAAAA
* * * * *
57124152 TCCCTGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACG
131 TCCCCGAAAGCTCAGAAAACGGCATCGTTAGGCTTAGGTTTTTTTGTGGCGCTTTAGCAAAAACG
* * * * * *
57124217 CCGCTAAAGCCCTGGGTATTAGTGTCGCTTCCCGAAAAAACGCCGCTAAATCCCCGAAAGCTCAG
196 CCACTAAAGCCCTGAGCATTAGCGGCGCTTCCCGAAAAAACGCCGCTAAATCCCCGAAAGCTCAA
* * * *
57124282 AAAACGACGTCGTTGGGATTAGGTTTTTTTGTGGCGCTTTATC
261 AAAACGACATCGTTGGGATTAAG-TATTTTGCGGCGCTTTATC
57124325 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
* * * * * * * *
57124390 ACTTTCGCAAAATCGCTGCTAATGC-CCTGGGCATTAGCGGCGCTT-CTCCAAAAAAGCCGCTAA
66 ACTTTAGCAAAAACGCCGCTAAAGCGCCTGAGCATTAGCGGCACTTAAT-CAAAAAAGCCGCAAA
*
57124453 ATCCCCGAAAGCTCAGAAAACGGCATCGTTAGGCTTTAGG-TTTTTTGTGGCGCTTTCGCAAAAA
130 ATCCCCGAAAGCTCAGAAAACGGCATCGTTAGGC-TTAGGTTTTTTTGTGGCGCTTTAGCAAAAA
**
57124517 -GACCACTAAAGCCCTGAGCATTAGCGGCGCTT-CCTTAAAAACGCCGCTAAATCCCCCGAAAGC
194 CG-CCACTAAAGCCCTGAGCATTAGCGGCGCTTCCCGAAAAAACGCCGCTAAAT-CCCCGAAAGC
* * * *
57124580 TCAAAAAACGGCATCGTTGGGCTTAAGTATTTTGCGGCGCTTTCTG
257 TCAAAAAACGACATCGTTGGGATTAAGTATTTTGCGGCGCTTTATC
*
57124626 GAAAACGCCGCTAA
1 AAAAACGCCGCTAA
57124640 TGCTTATTTT
Statistics
Matches: 273, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
301 48 0.18
302 138 0.51
303 87 0.32
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (302 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGATTAGGTTTTTTTGTGGC
ACTTTAGCAAAAACGCCGCTAAAGCGCCTGAGCATTAGCGGCACTTAATCAAAAAAGCCGCAAAA
TCCCCGAAAGCTCAGAAAACGGCATCGTTAGGCTTAGGTTTTTTTGTGGCGCTTTAGCAAAAACG
CCACTAAAGCCCTGAGCATTAGCGGCGCTTCCCGAAAAAACGCCGCTAAATCCCCGAAAGCTCAA
AAAACGACATCGTTGGGATTAAGTATTTTGCGGCGCTTTATC
Found at i:57128701 original size:88 final size:86
Alignment explanation
Indices: 57128549--57129334 Score: 893
Period size: 88 Copynumber: 9.0 Consensus size: 86
57128539 NNNNNNNNNN
* * *
57128549 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTGT-TTTCAACCAGCTCCACTATAACC-AAGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT-AACCAGCTCCACTACAACCGATG-
57128612 GAGGCAAGGTTTGTGTCTTCGATCT
64 GAGGCAAGGTTTGT-T-TTCGATCT
* * * * * * *
57128637 GCTTCACTGTCAAGGCAGGAAGACAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAG
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATG-G
*
57128701 AGGCAAGGTTTGTGTCTTCGATAT
65 AGGCAAGGTTTGT-T-TTCGATCT
* * * * * *
57128725 GCTTCGCTGTCAAGGCAGGAAGGAAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAG
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATG-G
57128789 AGGCAAGGTTTGTGTCTTCGATCT
65 AGGCAAGGTTTGT-T-TTCGATCT
* * * * * * * *
57128813 GCTTCGCTGTCAAGGCAGGAAGGCAAAATCTACTATCTTTAACTAACTCCACTGCAATCGATGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
**
57128878 GGCAATTCTTTGTTTTCGATCT
66 GGCAA-GGTTTGTTTTCGATCT
* * * *
57128900 ACTTCGCTGTTAATGCATGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
57128965 GGCAAGGCTTTGTTTTCGATCT
66 GGCAAGG-TTTGTTTTCGATCT
57128987 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
* *
57129052 GGCAAGACTTT-TTTTTGATCT
66 GGCAAG-GTTTGTTTTCGATCT
57129073 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
*
57129138 GGCAAGACTTTGTTTTCGATCT
66 GGCAAG-GTTTGTTTTCGATCT
57129160 GCTT---TG-T-----AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTACAACCGATGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
57129215 GGCAAGGCTTTGTTTTCGATCT
66 GGCAAGG-TTTGTTTTCGATCT
57129237 GCTTCGCTGTTAACTTTGCTGTTAACGTAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT
1 GCTTCGCTGTTAA-----C-G----C--AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
*
57129301 GCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
54 ACAACCGATGGAGGCAAGG-TTTGTTTTCGATCT
57129335 TCACTGATCT
Statistics
Matches: 625, Mismatches: 44, Indels: 48
0.87 0.06 0.07
Matches are distributed among these distances:
77 54 0.09
78 18 0.03
80 2 0.00
81 1 0.00
83 1 0.00
84 2 0.00
86 85 0.14
87 166 0.27
88 218 0.35
89 9 0.01
98 69 0.11
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (86 bp):
GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
GGCAAGGTTTGTTTTCGATCT
Found at i:57129217 original size:77 final size:78
Alignment explanation
Indices: 57129089--57129240 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 78
57129079 CTGTTAACGC
57129089 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGACTTTGTTTT
57129154 CGATCTGCTTTGT
66 CGATCTGCTTTGT
*
57129167 AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGACTTTGTTTT
57129231 CGATCTGCTT
66 CGATCTGCTT
57129241 CGCTGTTAAC
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 55 0.75
78 18 0.25
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (78 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGACTTTGTTTT
CGATCTGCTTTGT
Found at i:57130578 original size:20 final size:18
Alignment explanation
Indices: 57130555--57130604 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 18
57130545 TAGCCTCTCT
57130555 ATTTTACTTTTCATTTTTTC
1 ATTTT-CTTTTCA-TTTTTC
57130575 ATTTTCATTTTCATTTTTC
1 ATTTTC-TTTTCATTTTTC
57130594 ATCTTTCTTTT
1 AT-TTTCTTTT
57130605 TTTTGAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTCTTTTCATTTTTC
Found at i:57130605 original size:20 final size:20
Alignment explanation
Indices: 57130562--57130604 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
57130552 TCTATTTTAC
57130562 TTTTCATTTTTTCATTTTCA
1 TTTTCATTTTTTCATTTTCA
57130582 TTTTCA-TTTTTCATCTTTC-
1 TTTTCATTTTTTCAT-TTTCA
57130601 TTTT
1 TTTT
57130605 TTTTGAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCATTTTTTCATTTTCA
Found at i:57131016 original size:50 final size:49
Alignment explanation
Indices: 57130957--57131057 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 49
57130947 TTTTCTTTGC
* *
57130957 TTTTCATATTTTTATTTTGACTTTGATTGATTTCTCTTTTTCTTTTTGTT
1 TTTTCATATTTTGATTTTGACTTTGATT-ATTTCTCTTTTTCTTTTTCTT
* * * *
57131007 TTTTTATATTTTGATTTTGATTTTGATTTTTTTTCTTTTTCTTTTTCTT
1 TTTTCATATTTTGATTTTGACTTTGATTATTTCTCTTTTTCTTTTTCTT
57131056 TT
1 TT
57131058 CCTTTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
49 20 0.44
50 25 0.56
ACGTcount: A:0.11, C:0.08, G:0.07, T:0.74
Consensus pattern (49 bp):
TTTTCATATTTTGATTTTGACTTTGATTATTTCTCTTTTTCTTTTTCTT
Found at i:57131057 original size:27 final size:26
Alignment explanation
Indices: 57130991--57131068 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
57130981 GATTGATTTC
*
57130991 TCTTTTTCTTTTTGTTTTTTTATATTTT
1 TCTTTTTC-TTTTGTTTTTTT-TCTTTT
** **
57131019 GATTTTGATTTTGATTTTTTTTCTTTT
1 TCTTTTTCTTTTG-TTTTTTTTCTTTT
*
57131046 TCTTTTTCTTTTCCTTTTTTTTC
1 TCTTTTTCTTTT-GTTTTTTTTC
57131069 GAATCGGATC
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
27 27 0.71
28 11 0.29
ACGTcount: A:0.06, C:0.10, G:0.05, T:0.78
Consensus pattern (26 bp):
TCTTTTTCTTTTGTTTTTTTTCTTTT
Found at i:57132395 original size:22 final size:22
Alignment explanation
Indices: 57132367--57132496 Score: 188
Period size: 22 Copynumber: 5.9 Consensus size: 22
57132357 CCGGAATTGG
57132367 CGTACTAAGCTCTCATGTTTAA
1 CGTACTAAGCTCTCATGTTTAA
57132389 CGTACTAAGCTCTCATGTTTAA
1 CGTACTAAGCTCTCATGTTTAA
* * * **
57132411 CGAACTAAACCCTCATGGCTAA
1 CGTACTAAGCTCTCATGTTTAA
**
57132433 CGTACTAAGCTCTCATGGCTAA
1 CGTACTAAGCTCTCATGTTTAA
*
57132455 CGTACTAAGCTCTCATGTTTCA
1 CGTACTAAGCTCTCATGTTTAA
57132477 CGTACTAAGCTCTCATGTTT
1 CGTACTAAGCTCTCATGTTT
57132497 GAACAATAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 97 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (22 bp):
CGTACTAAGCTCTCATGTTTAA
Found at i:57135463 original size:12 final size:12
Alignment explanation
Indices: 57135446--57135471 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57135436 CTCTCCAGAA
57135446 TCCGGCCAGGGG
1 TCCGGCCAGGGG
57135458 TCCGGCCAGGGG
1 TCCGGCCAGGGG
57135470 TC
1 TC
57135472 ACCGCACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.46, T:0.12
Consensus pattern (12 bp):
TCCGGCCAGGGG
Found at i:57136170 original size:2 final size:2
Alignment explanation
Indices: 57136163--57136209 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
57136153 ATTCAAAGAC
57136163 TA TA TA TA TA TA TA TA TA TA 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
57136205 TA TA T
1 TA TA T
57136210 CATTAATGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57136573 original size:15 final size:15
Alignment explanation
Indices: 57136546--57136584 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
57136536 TTAAACTTTA
57136546 AAAATATTA-AATGT
1 AAAATATTATAATGT
57136560 AAAATATTATAATGT
1 AAAATATTATAATGT
**
57136575 TTAATATTAT
1 AAAATATTAT
57136585 TAAACATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
AAAATATTATAATGT
Found at i:57137657 original size:110 final size:112
Alignment explanation
Indices: 57137404--57137722 Score: 527
Period size: 110 Copynumber: 2.9 Consensus size: 112
57137394 GAAATTCGAG
* * *
57137404 AGGATATTT-GACTATTTGGTTAAACGAGAAAAATCGACACCCATCACCTTAGGGCACGTTTTCT
1 AGGATATTTAG-CCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCT
*
57137468 CGAATTTCCCAAATGCAAAACATTGCCTTATTTCGAAAATTTTTTAAA
65 CGAATTTCCCAAACGCAAAACATTGCCTTATTTCGAAAATTTTTTAAA
*
57137516 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
57137581 GAATTTCCCAAACGCAAAACATTGCCTTATTT-GAAAA-TTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTCGAAAATTTTTTAAA
*
57137626 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* * *
57137691 GAATTTCCCAAACGCGAAATATTGTCTTATTT
66 GAATTTCCCAAACGCAAAACATTGCCTTATTT
57137723 AGGAAAAGTT
Statistics
Matches: 196, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
110 100 0.51
111 5 0.03
112 90 0.46
113 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (112 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCCAAACGCAAAACATTGCCTTATTTCGAAAATTTTTTAAA
Found at i:57140829 original size:18 final size:16
Alignment explanation
Indices: 57140793--57140836 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
57140783 GATCTCTCTC
57140793 AATAAAAAATTTCAAA
1 AATAAAAAATTTCAAA
*
57140809 AATAAAAATATTTATAAA
1 AATAAAAA-ATTT-CAAA
57140827 AATTAAAAAA
1 AA-TAAAAAA
57140837 AACTAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 4 0.17
18 6 0.25
19 6 0.25
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAAATTTCAAA
Found at i:57140837 original size:28 final size:31
Alignment explanation
Indices: 57140806--57140866 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
57140796 AAAAAATTTC
*
57140806 AAAAA-TAAA-AATATTTATAA-AAA-TTAAA
1 AAAAACTAAAGAATATATA-AAGAAACTTAAA
57140834 AAAAACTAAAGAATATATAAAGAAACTTAAA
1 AAAAACTAAAGAATATATAAAGAAACTTAAA
57140865 AA
1 AA
57140867 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 5 0.18
29 6 0.21
30 10 0.36
31 7 0.25
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (31 bp):
AAAAACTAAAGAATATATAAAGAAACTTAAA
Found at i:57161276 original size:29 final size:27
Alignment explanation
Indices: 57161235--57161291 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
57161225 AGAGAAATGA
*
57161235 AGAAGAGAGGAAAACAAAAGGAAAAAT
1 AGAAGAGAGGAAAACAAAAAGAAAAAT
* *
57161262 AGAAGAGGATGGAAAATAAAAATAAAAAT
1 AGAAGA-GA-GGAAAACAAAAAGAAAAAT
57161291 A
1 A
57161292 AAAAGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.24
28 2 0.08
29 17 0.68
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.09
Consensus pattern (27 bp):
AGAAGAGAGGAAAACAAAAAGAAAAAT
Found at i:57169417 original size:2 final size:2
Alignment explanation
Indices: 57169406--57169438 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
57169396 TTCATGTGCT
57169406 TA TA -A TA TA TA 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
57169439 AGATATCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:57170809 original size:40 final size:42
Alignment explanation
Indices: 57170765--57170861 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
57170755 CATAAGGTGT
*
57170765 ATATTATTATAAAAAAT-TTAA-AGTTAAA-ATATATATTATA
1 ATATTATAATAAAAAATCTTAATA-TTAAATATATATATTATA
**
57170805 ATATTATAATATTAAATCTTAATTATTAAATATATATATTATA
1 ATATTATAATAAAAAATCTTAA-TATTAAATATATATATTATA
* *
57170848 TTATAATAATAAAA
1 ATATTATAATAAAA
57170862 TAAGTAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 14 0.30
41 4 0.09
42 5 0.11
43 23 0.50
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (42 bp):
ATATTATAATAAAAAATCTTAATATTAAATATATATATTATA
Found at i:57170810 original size:8 final size:8
Alignment explanation
Indices: 57170797--57170858 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
57170787 GTTAAAATAT
57170797 ATATTATA
1 ATATTATA
57170805 ATATTATA
1 ATATTATA
57170813 ATATTA-A
1 ATATTATA
*
57170820 ATCTTA-A
1 ATATTATA
*
57170827 TTATTA-A
1 ATATTATA
57170834 ATA-TAT-
1 ATATTATA
57170840 ATATTATA
1 ATATTATA
* *
57170848 TTATAATA
1 ATATTATA
57170856 ATA
1 ATA
57170859 AAATAAGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 5 0.11
7 17 0.39
8 22 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATTATA
Found at i:57170885 original size:4 final size:4
Alignment explanation
Indices: 57170876--57170935 Score: 70
Period size: 4 Copynumber: 15.0 Consensus size: 4
57170866 TAATAAAAAT
* *
57170876 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA- AAGAA AAAG AAA- AAGGG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG AAAG AAAG AA-AG
57170924 AAAG AAAG AAAG
1 AAAG AAAG AAAG
57170936 GAGAAAGACA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 4 0.08
4 41 0.84
5 4 0.08
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:57172365 original size:41 final size:41
Alignment explanation
Indices: 57172306--57172428 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 41
57172296 CGACTTTGAG
57172306 TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTAAT
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTAAT
* * * * *
57172347 TCGATGAGGCACTAGGTGTC--TAT-TTACTTCAGTTTAAC
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTAAT
* *
57172385 T-GATGAGACACTGGGTATCAATTTATTAATTC-GAATT-AT
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCAG-ATTAAT
57172424 TCGAT
1 TCGAT
57172429 AAGGCTCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
37 15 0.23
38 14 0.22
39 7 0.11
40 11 0.17
41 18 0.28
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (41 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTAAT
Found at i:57172409 original size:37 final size:38
Alignment explanation
Indices: 57172306--57172409 Score: 120
Period size: 37 Copynumber: 2.7 Consensus size: 38
57172296 CGACTTTGAG
*
57172306 TCGATGAGACACTGGGTGTCAATTTATTACTTCAGATTAAT
1 TCGATGAGACACTGGGTGTCAA--T-TTACTTCAGATTAAC
* * * *
57172347 TCGATGAGGCACTAGGTGTCTATTTACTTCAGTTTAAC
1 TCGATGAGACACTGGGTGTCAATTTACTTCAGATTAAC
*
57172385 T-GATGAGACACTGGGTATCAATTTA
1 TCGATGAGACACTGGGTGTCAATTTA
57172410 TTAATTCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 20 0.37
38 14 0.26
39 1 0.02
41 19 0.35
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (38 bp):
TCGATGAGACACTGGGTGTCAATTTACTTCAGATTAAC
Found at i:57176952 original size:46 final size:46
Alignment explanation
Indices: 57176880--57177019 Score: 235
Period size: 46 Copynumber: 3.0 Consensus size: 46
57176870 ACAATGCTAT
* * *
57176880 AACTCGGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
57176926 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
57176972 AACCCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
57177018 AA
1 AA
57177020 TTTTCCATGG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:57184201 original size:34 final size:34
Alignment explanation
Indices: 57184158--57184228 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
57184148 AGCTTCCTCA
57184158 AAAATTGAGTGGACATCATCAATATGAGTCAATT
1 AAAATTGAGTGGACATCATCAATATGAGTCAATT
57184192 AAAATTGAGTGGACATCATCAATATGAGTCAATT
1 AAAATTGAGTGGACATCATCAATATGAGTCAATT
57184226 AAA
1 AAA
57184229 TTGGCACTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (34 bp):
AAAATTGAGTGGACATCATCAATATGAGTCAATT
Found at i:57187325 original size:21 final size:20
Alignment explanation
Indices: 57187265--57187325 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
57187255 ATTTATTAAA
* *
57187265 ATAAATAAATAAAAAATATT
1 ATAAATTAATAAAAAAAATT
* *
57187285 ATCAAATTAATATAAGAAATT
1 AT-AAATTAATAAAAAAAATT
57187306 ATAAATTATATAAAAAAAAT
1 ATAAATTA-ATAAAAAAAAT
57187326 CAAGCTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.24
21 25 0.76
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAAATTAATAAAAAAAATT
Found at i:57190320 original size:18 final size:17
Alignment explanation
Indices: 57190292--57190325 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
57190282 TGTTTATTGC
57190292 ATTTTATTTTTGTTTTT
1 ATTTTATTTTTGTTTTT
57190309 ATTTTAATTTTTGTTTT
1 ATTTT-ATTTTTGTTTT
57190326 CTAATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
ATTTTATTTTTGTTTTT
Found at i:57192286 original size:43 final size:43
Alignment explanation
Indices: 57192235--57192353 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 43
57192225 GTAAAATACC
* * *
57192235 AACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGC-
1 AACGTCCCAGACGTGGTCTTACACGTAAACACAAATCGATGCT
* *
57192277 CACTGTCCCAGACAG-GGTCTTACACGTAAACACAAATTGATGCT
1 AAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAATCGATGCT
*
57192321 AACGTCCCAGACGTGGTCTTACACGAAAACACA
1 AACGTCCCAGACGTGGTCTTACACGTAAACACA
57192354 TATAAAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.05
43 60 0.91
44 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
AACGTCCCAGACGTGGTCTTACACGTAAACACAAATCGATGCT
Found at i:57197152 original size:7 final size:7
Alignment explanation
Indices: 57197152--57197185 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
57197142 TTTTATTTTT
57197152 TTTATTG
1 TTTATTG
57197159 TTTATTG
1 TTTATTG
57197166 TTTATTG
1 TTTATTG
57197173 TTTATTG
1 TTTATTG
57197180 TTTATT
1 TTTATT
57197186 ATCTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (7 bp):
TTTATTG
Found at i:57197192 original size:21 final size:21
Alignment explanation
Indices: 57197152--57197192 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57197142 TTTTATTTTT
* *
57197152 TTTATTGTTTATTGTTTATTG
1 TTTATTGTTTATTATCTATTG
57197173 TTTATTGTTTATTATCTATT
1 TTTATTGTTTATTATCTATT
57197193 ATTTTTATTA
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:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (21 bp):
TTTATTGTTTATTATCTATTG
Found at i:57198973 original size:25 final size:25
Alignment explanation
Indices: 57198910--57198973 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
57198900 TTTCTTTATT
*
57198910 TTATTTTTATTGTTATTTTCTTAGAC
1 TTATTTTTATT-TTATTTTCTGAGAC
57198936 TTATTTTGT-TTTTATCTTT-TGA-AC
1 TTATTTT-TATTTTAT-TTTCTGAGAC
57198960 TATATTTTTATTTT
1 T-TATTTTTATTTT
57198974 TTATGATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 4 0.12
25 16 0.48
26 12 0.36
27 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTTTATTTTATTTTCTGAGAC
Found at i:57199943 original size:18 final size:17
Alignment explanation
Indices: 57199912--57199945 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
57199902 TATAAAAAAG
57199912 AAACGAAAAAAACAAAC
1 AAACGAAAAAAACAAAC
*
57199929 AAACAGAAAATAACAAA
1 AAAC-GAAAAAAACAAA
57199946 AAAAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (17 bp):
AAACGAAAAAAACAAAC
Found at i:57208847 original size:17 final size:17
Alignment explanation
Indices: 57208822--57208864 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
57208812 AGGAAGTATT
*
57208822 AGCGGCGCATTGCAGAA
1 AGCGCCGCATTGCAGAA
*
57208839 AGCGCCGCATTGTAGAA
1 AGCGCCGCATTGCAGAA
*
57208856 AGCACCGCA
1 AGCGCCGCA
57208865 AAAATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (17 bp):
AGCGCCGCATTGCAGAA
Found at i:57209502 original size:114 final size:113
Alignment explanation
Indices: 57209117--57209655 Score: 425
Period size: 114 Copynumber: 4.7 Consensus size: 113
57209107 GTTTAAGGGA
* *
57209117 AAACGCCGCTAATGCATAATATTAGCGGCG-TTT-TGAGAAAAGCGCCGCAAAATATCTTAACCA
1 AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGAG--AAGCGCCGCAAAATATC-TAACCA
* ** *
57209180 AAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGC--AAAGGG
63 AAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTTATCGAG
* * * * * * * * *
57209229 TACACGCCGCTAAGGCATACTATTAGCGGTGTTTTCAGAGAAGCGCCGCAACATTTGGTAACCAA
1 -AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGAGAAGCGCCGCAAAATAT-CTAACCAA
* * * * * *
57209294 AACGCA-ACGTTTTTGTCTTGATGTATAC-AGTTATTAGTGGCACATATCAAA
64 AACGCAGA-G-TTTTGTCTTGAGGTATACTAG-AATTAGTGGCGCTTATCGAG
* * ** * * *
57209345 AAACGCCACTAAATCATAGTATTAGCGGCGCTGGGC-AAAAAGCGCCGCAAAATATGCTCACCAA
1 AAACGCCGCTAAAGCATAGTATTAGCGGCGCT-TTCTGAGAAGCGCCGCAAAATAT-CTAACCAA
* * * * * *
57209409 AACGCAGAGTTTTTTCATGAGGTATATTAGACTTAGTGGCGCTTATGGGG
64 AACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTTATCGAG
* * * * * *
57209459 GAATGCCGCTAAAGCATATTATTTGCGGCGCTTTCTGAGAAGCGCCGCAAAATATATTAACAAAA
1 AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGAGAAGCGCCGCAAAATAT-CTAACCAAA
* * * *
57209524 ACGCAGCA-TTTAAGTCTTGATGTATACTGGAATTAGTGGCG-TCCA-CGAG
65 ACGCAG-AGTTT-TGTCTTGAGGTATACTAGAATTAGTGGCGCT-TATCGAG
* * *
57209573 AAATCGCCGCTAAAGCATCGTATTAGCGGCGC-TTCTCAGAAGCGCCGGAAAATATCTTAACCAA
1 AAA-CGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGAGAAGCGCCGCAAAATATC-TAACCAA
57209637 AACGCAGAGTTTTGGTCTT
64 AACGCAGAGTTTT-GTCTT
57209656 AACCATGCAT
Statistics
Matches: 329, Mismatches: 78, Indels: 37
0.74 0.18 0.08
Matches are distributed among these distances:
112 1 0.00
113 58 0.18
114 160 0.49
115 107 0.33
116 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (113 bp):
AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGAGAAGCGCCGCAAAATATCTAACCAAAA
CGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTTATCGAG
Found at i:57209647 original size:228 final size:227
Alignment explanation
Indices: 57209115--57209650 Score: 569
Period size: 228 Copynumber: 2.3 Consensus size: 227
57209105 GCGTTTAAGG
* * * *
57209115 GAAAACGCCGCTAATGCATAATATTAGCGGCG-TTTTGAGAAAAGCGCCGCAAAATATCTTAACC
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTCTCAG--AAGCGCCGCAAAATATCTTAACC
* * * *
57209179 AAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCAAAGGGTACACGCCGCTAAGG
64 AAAACGCAGAGTTTTGTCATGAGGTATACTAGAATTAGTGGCGCAAAGGGGACACGCCGCTAAAG
* * * * * * * **
57209244 CATACTATTAGCGGTGTTTTCAGAGAAGCGCCGCAACATTTGGTAACCAAAACGCAACGTTTTTG
129 CATACTATTAGCGGCGCTTTCAGAGAAGCGCCGCAAAATATAGTAACAAAAACGCAACATTTAAG
** *
57209309 TCTTGATGTATACAGTTATTAGTGGCACATATCA
194 TCTTGATGTATACAGGAATTAGTGGCACACATCA
* * * *** * *
57209343 AAAAACGCCACTAAATCATAGTATTAGCGGCGCTGGGCAAAAAGCGCCGCAAAATATGC-TCACC
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTCTC-AGAAGCGCCGCAAAATAT-CTTAACC
* * * ** *
57209407 AAAACGCAGAGTTTTTTCATGAGGTATATTAGACTTAGTGGCGCTTATGGGGGA-ATGCCGCTAA
64 AAAACGCAGAGTTTTGTCATGAGGTATACTAGAATTAGTGGCGC--AAAGGGGACACGCCGCTAA
* * * * *
57209471 AGCATATTATTTGCGGCGCTTTCTGAGAAGCGCCGCAAAATATATTAACAAAAACGCAGCATTTA
127 AGCATACTATTAGCGGCGCTTTCAGAGAAGCGCCGCAAAATATAGTAACAAAAACGCAACATTTA
* *
57209536 AGTCTTGATGTATACTGGAATTAGTGGCGTC-CA-CGA
192 AGTCTTGATGTATACAGGAATTAGTGGC-ACACATC-A
* * *
57209572 GAAATCGCCGCTAAAGCATCGTATTAGCGGCGCTTCTCAGAAGCGCCGGAAAATATCTTAACCAA
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTCTCAGAAGCGCCGCAAAATATCTTAACCAA
57209637 AACGCAGAGTTTTG
66 AACGCAGAGTTTTG
57209651 GTCTTAACCA
Statistics
Matches: 248, Mismatches: 52, Indels: 16
0.78 0.16 0.05
Matches are distributed among these distances:
227 1 0.00
228 122 0.49
229 118 0.48
230 7 0.03
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (227 bp):
GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTCTCAGAAGCGCCGCAAAATATCTTAACCAA
AACGCAGAGTTTTGTCATGAGGTATACTAGAATTAGTGGCGCAAAGGGGACACGCCGCTAAAGCA
TACTATTAGCGGCGCTTTCAGAGAAGCGCCGCAAAATATAGTAACAAAAACGCAACATTTAAGTC
TTGATGTATACAGGAATTAGTGGCACACATCA
Found at i:57209739 original size:21 final size:20
Alignment explanation
Indices: 57209715--57209753 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
57209705 TTTGGTCTAT
*
57209715 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTT-AAGGTTGG
57209736 GGTTTAAGGTTTAAGGTT
1 GGTTTAAGGTTTAAGGTT
57209754 ATGTGTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTTAAGGTTTAAGGTTGG
Found at i:57214654 original size:36 final size:36
Alignment explanation
Indices: 57214608--57214716 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
57214598 GGTAGCTTTA
*
57214608 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
57214644 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
57214680 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
57214716 G
1 G
57214717 TTAGCCTTAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:57214664 original size:21 final size:20
Alignment explanation
Indices: 57214636--57214701 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
57214626 AGTGAAAAAG
57214636 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
*
57214656 TGATCAAGTGAC-A-A---A-G
1 TGAT-AAGTG-CTATACTTATC
57214672 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
57214692 TGATCAAGTG
1 TGAT-AAGTG
57214702 AAAAAGTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 17
0.65 0.04 0.31
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 5 0.14
17 1 0.03
19 1 0.03
20 9 0.26
21 11 0.31
22 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:57214788 original size:45 final size:46
Alignment explanation
Indices: 57214680--57214788 Score: 184
Period size: 46 Copynumber: 2.4 Consensus size: 46
57214670 AGTGATAAGT
* *
57214680 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAGCCTTA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTA
*
57214726 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTA
57214771 GCTACACTTATCTGATCA
1 GCTACACTTATCTGATCA
57214789 GGGATGAGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
45 20 0.33
46 40 0.67
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTA
Found at i:57215513 original size:21 final size:21
Alignment explanation
Indices: 57215487--57215543 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
57215477 GTAGACGCGG
* *
57215487 CAGCGAGGGAAGCAGAGGCTA
1 CAGCGAGAGAAGCAGAGGCCA
*
57215508 CAGCGAGAGAAGCAGAGGCCG
1 CAGCGAGAGAAGCAGAGGCCA
57215529 CAGCGAGAGAAGCAG
1 CAGCGAGAGAAGCAG
57215544 CGAGAGAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.21, G:0.42, T:0.02
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCCA
Found at i:57215545 original size:12 final size:12
Alignment explanation
Indices: 57215508--57215567 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
57215498 GCAGAGGCTA
57215508 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
57215520 CA--GAG-GCCG
1 CAGCGAGAGAAG
57215529 CAGCGAGAGAAG
1 CAGCGAGAGAAG
57215541 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
57215553 CAGCGATAGAAG
1 CAGCGAGAGAAG
57215565 CAG
1 CAG
57215568 AGGTTCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 30 0.75
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.02
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:57216137 original size:85 final size:85
Alignment explanation
Indices: 57216001--57216179 Score: 240
Period size: 85 Copynumber: 2.1 Consensus size: 85
57215991 GTTTGTGAAA
* *
57216001 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTTCCCAAGCGCCGCTATAGAACATTA-
1 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGAT
*
57216065 CTTTTAGCGGCGTTTTTTTC-
66 C-TTTAGCGGCATTTTTTTCG
**
57216085 TAAGCGCCGCTAAAGAACA-TGA-TCTTTAGCGGCGTTTATTTCCTTAGCGCCGCTAAAGAACAT
1 TAAGCGCCGCTAAAGAACACT-ACT-TTTAGCGGCGTTT-TTTCCCAAGCGCCGCTAAAGAACAT
57216148 GATCTTTAGCGGCATTTTTTTCTG
63 GATCTTTAGCGGCATTTTTTTC-G
57216172 TAAGCGCC
1 TAAGCGCC
57216180 ACAAAAGTTA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
83 2 0.02
84 33 0.39
85 40 0.48
86 1 0.01
87 8 0.10
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (85 bp):
TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGAT
CTTTAGCGGCATTTTTTTCG
Found at i:57216146 original size:43 final size:42
Alignment explanation
Indices: 57216001--57216167 Score: 223
Period size: 42 Copynumber: 4.0 Consensus size: 42
57215991 GTTTGTGAAA
57216001 TAAGCGCCGCTAAAGAACACT-ACTTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTTTCC
* * * *
57216043 CAAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
57216085 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTT-TTTCC
* *
57216128 TTAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCATTTTTT
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTT
57216168 TCTGTAAGCG
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.02
42 72 0.64
43 39 0.35
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
Found at i:57219295 original size:18 final size:17
Alignment explanation
Indices: 57219272--57219317 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
57219262 TAAATTTTTT
*
57219272 TTTTCTCTTTTTCTCTTC
1 TTTTCTCTTCTTC-CTTC
57219290 TTTTCTCTCTCTTCCTTC
1 TTTTCTCT-TCTTCCTTC
57219308 TTTT-TCTTCT
1 TTTTCTCTTCT
57219318 GTAGTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 16 0.62
19 4 0.15
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTCTCTTCTTCCTTC
Found at i:57221373 original size:44 final size:42
Alignment explanation
Indices: 57221322--57221440 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 42
57221312 CCCATATTTG
57221322 ATTAAAAATAAAATATATATTTAATATATAATTCAGATTAAA
1 ATTAAAAATAAAATATATATTTAATATATAATTCAGATTAAA
* *
57221364 AGTTTAAAAAT---ATATATATTTAATAAAAAGTATATT-TGATTAAA
1 A--TTAAAAATAAAATATATATTTAAT--ATA-TA-ATTCAGATTAAA
*
57221408 AATAAAAATAAAA-ATATATTTAATATATAATTC
1 ATTAAAAATAAAATATATATTTAATATATAATTC
57221441 GGGCCGAGCC
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
40 3 0.05
41 15 0.24
42 10 0.16
43 2 0.03
44 29 0.46
45 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (42 bp):
ATTAAAAATAAAATATATATTTAATATATAATTCAGATTAAA
Found at i:57221721 original size:14 final size:14
Alignment explanation
Indices: 57221702--57221741 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
57221692 TTGATTGCCA
57221702 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
57221716 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
57221730 GGAAAATGTTTT
1 GTAAAATGTTTT
57221742 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:57221750 original size:20 final size:20
Alignment explanation
Indices: 57221725--57221764 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57221715 CGTAAAATGA
*
57221725 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
57221745 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
57221765 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:57221754 original size:34 final size:35
Alignment explanation
Indices: 57221710--57221776 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
57221700 CAGTAAAATG
* *
57221710 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
57221744 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
57221777 CTGCTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:57222744 original size:18 final size:17
Alignment explanation
Indices: 57222704--57222815 Score: 57
Period size: 19 Copynumber: 6.0 Consensus size: 17
57222694 TTAAAAATTC
57222704 ATATTAAAATTATAAAA
1 ATATTAAAATTATAAAA
57222721 ATTATTAGAAATTA-AAACA
1 A-TATTA-AAATTATAAA-A
*
57222740 ATATTAAAGAGATATTAAAA
1 ATATTAAA-A-TTA-TAAAA
* *
57222760 TTTATATAAACTTATAAAAA
1 -ATAT-TAAAATTAT-AAAA
*
57222780 ATCATAAAAACTTATAAAA
1 AT-ATTAAAA-TTATAAAA
*
57222799 TTTATTAAAA-TATAAAA
1 -ATATTAAAATTATAAAA
57222816 TAGAAATTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
17 10 0.14
18 14 0.19
19 25 0.34
20 14 0.19
21 6 0.08
22 4 0.05
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (17 bp):
ATATTAAAATTATAAAA
Found at i:57222807 original size:20 final size:19
Alignment explanation
Indices: 57222755--57222816 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
57222745 AAAGAGATAT
*
57222755 TAAAATTTATATAAACTTA
1 TAAAATTTATAAAAACTTA
* *
57222774 TAAAAAATCATAAAAACTTA
1 T-AAAATTTATAAAAACTTA
*
57222794 TAAAATTTATTAAAA--TA
1 TAAAATTTATAAAAACTTA
57222811 TAAAAT
1 TAAAAT
57222817 AGAAATTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 8 0.22
19 12 0.33
20 16 0.44
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATTTATAAAAACTTA
Found at i:57223017 original size:20 final size:19
Alignment explanation
Indices: 57222984--57223023 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
57222974 GATATTCTCC
57222984 TTTTTATTGATAAATTATTT
1 TTTTTATTGATAAATT-TTT
**
57223004 TTTTTATTTTTAAATTTTT
1 TTTTTATTGATAAATTTTT
57223023 T
1 T
57223024 ATCTCCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTATTGATAAATTTTT
Found at i:57223976 original size:60 final size:61
Alignment explanation
Indices: 57223912--57224028 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 61
57223902 TTTTGTGAGA
* *
57223912 TTTAAAAATATCACGAAAATATGT-GAA-AAAAACATCACAAAAATAT-CCAATTTGGTAAGG
1 TTTAAAAATATCACGAAAAGAT-TAAAAGAAAAACATCACAAAAA-ATCCCAATTTGGTAAGG
*
57223972 TTTAAAAATGTCACGAAAAGATTAAAAGAAAAACATCACAAAAAATCCCAATTTGGT
1 TTTAAAAATATCACGAAAAGATTAAAAGAAAAACATCACAAAAAATCCCAATTTGGT
57224029 GTGGTCTCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
59 1 0.02
60 24 0.47
61 26 0.51
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (61 bp):
TTTAAAAATATCACGAAAAGATTAAAAGAAAAACATCACAAAAAATCCCAATTTGGTAAGG
Found at i:57224064 original size:61 final size:59
Alignment explanation
Indices: 57223915--57224056 Score: 144
Period size: 61 Copynumber: 2.3 Consensus size: 59
57223905 TGTGAGATTT
* * *
57223915 AAAAATATCACGAAAATATGTGAA-AAAAACATCACAAAAATATCCAATTTGGTAAGGTTT
1 AAAAATGTCACGAAAAGAT-T-AAGAAAAACATCACAAAAATATCCAATTTGGTAAGGTTC
**
57223975 AAAAATGTCACGAAAAGATTAAAAGAAAAACATCACAAAAA-ATCCCAATTTGGTGTGGTCTC
1 AAAAATGTCACGAAAAGATT--AAGAAAAACATCACAAAAATAT-CCAATTTGGTAAGGT-TC
* *
57224037 ACAAATTGTCATGAAAAGAT
1 A-AAAATGTCACGAAAAGAT
57224057 CTTGAAAAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.01
60 21 0.30
61 29 0.42
62 2 0.03
63 16 0.23
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (59 bp):
AAAAATGTCACGAAAAGATTAAGAAAAACATCACAAAAATATCCAATTTGGTAAGGTTC
Done.