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 99 of 106
Found at i:37670199 original size:2 final size:2
Alignment explanation
Indices: 37670192--37670216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37670182 CAATACATAC
37670192 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
37670217 GATGGATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37683617 original size:189 final size:189
Alignment explanation
Indices: 37683253--37683633 Score: 620
Period size: 190 Copynumber: 2.0 Consensus size: 189
37683243 TTCAGAGCAG
* * *
37683253 GAGATATCAACCCATAAAGTAAATAATATACAAAATAAAAAAATAATTATGAGAAGAGTAACACT
1 GAGATATCAACCCATAAAGTAAATAATAAACAAAATAAAAAAATAATCATGAGAAAAGTAACACT
37683318 AAGAAACAAGCTTCATTTATCACTGCTAAGTGCCACTCAACTGCAGTAAAGATCTACAAACTTCA
66 AAGAAACAAGCTTCATTTATCACTGCTAAGTGCCACTCAACTGCAGTAAAGATCTACAAACTTCA
* * * * *
37683383 CAGGACAGCAGGTGATTTAAGATTTCAAATTGTCCAAGAAAAAAAAAATCTAAAA-CAA
131 CAAGAAAGCAGGTGACTTAAGATGTCAAATTGCCCAAGAAAAAAAAAATCTAAAACCAA
* * *
37683441 GAGATATCAATCCATAAAGTAAATAATAAACAAAATAAAAAAAATAATCATTAGAAAAGTCACAC
1 GAGATATCAACCCATAAAGTAAATAATAAACAAAAT-AAAAAAATAATCATGAGAAAAGTAACAC
*
37683506 TAAGAAACAAGCTTCATTTATCACTGCTAAGTGCCCACTCAACTGCATTAAAGATCTACAAACTT
65 TAAGAAACAAGCTTCATTTATCACTGCTAAGTG-CCACTCAACTGCAGTAAAGATCTACAAACTT
*
37683571 CACAAGAAAGTAGGTGACTTAAGATGTCAAATTGCCCAAGAAAAAAAAAATCTAAAACCAA
129 CACAAGAAAGCAGGTGACTTAAGATGTCAAATTGCCCAAGAAAAAAAAAATCTAAAACCAA
37683632 GA
1 GA
37683634 AAAGTTCTCT
Statistics
Matches: 177, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
188 34 0.19
189 57 0.32
190 81 0.46
191 5 0.03
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (189 bp):
GAGATATCAACCCATAAAGTAAATAATAAACAAAATAAAAAAATAATCATGAGAAAAGTAACACT
AAGAAACAAGCTTCATTTATCACTGCTAAGTGCCACTCAACTGCAGTAAAGATCTACAAACTTCA
CAAGAAAGCAGGTGACTTAAGATGTCAAATTGCCCAAGAAAAAAAAAATCTAAAACCAA
Found at i:37684380 original size:28 final size:28
Alignment explanation
Indices: 37684349--37684420 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
37684339 TATATATATA
37684349 TGCATACATACATATGTGTGTGTGTGTG
1 TGCATACATACATATGTGTGTGTGTGTG
*
37684377 TGCATACATACATGTGTGTGTGTGTGTG
1 TGCATACATACATATGTGTGTGTGTGTG
37684405 TGTACATACATACATA
1 TG--CATACATACATA
37684421 CGTGCTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 29 0.73
30 11 0.28
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (28 bp):
TGCATACATACATATGTGTGTGTGTGTG
Found at i:37684382 original size:24 final size:25
Alignment explanation
Indices: 37684355--37684404 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
37684345 TATATGCATA
37684355 CATACAT-ATGTGTGTGTGTGTGTG
1 CATACATAATGTGTGTGTGTGTGTG
37684379 CATACATACATGTGTGTGTGTGTGTG
1 CATACATA-ATGTGTGTGTGTGTGTG
37684405 TGTACATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.29
26 17 0.71
ACGTcount: A:0.18, C:0.10, G:0.32, T:0.40
Consensus pattern (25 bp):
CATACATAATGTGTGTGTGTGTGTG
Found at i:37690015 original size:6 final size:6
Alignment explanation
Indices: 37690006--37690033 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
37689996 TGGTGGTGGT
37690006 CATGCC CATGCC CATGCC CATGCC CATG
1 CATGCC CATGCC CATGCC CATGCC CATG
37690034 ATCACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.18, T:0.18
Consensus pattern (6 bp):
CATGCC
Found at i:37697217 original size:27 final size:27
Alignment explanation
Indices: 37697187--37697240 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
37697177 GTGCTTGTAC
37697187 GAACACTGGTGGCTAAAGGACTCCCAA
1 GAACACTGGTGGCTAAAGGACTCCCAA
37697214 GAACACTGGTGGCTAAAGGACTCCCAA
1 GAACACTGGTGGCTAAAGGACTCCCAA
37697241 TGGCCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (27 bp):
GAACACTGGTGGCTAAAGGACTCCCAA
Found at i:37697823 original size:3 final size:3
Alignment explanation
Indices: 37697815--37697848 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
37697805 TTATCACAGC
* *
37697815 AGA AGA AGA AGA AGA AGA AGA GGA CGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
37697849 TAAAAAGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:37698612 original size:17 final size:15
Alignment explanation
Indices: 37698590--37698623 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
37698580 CTTTCTCAGC
37698590 TTTTCTTTTCTTTTCTT
1 TTTTCTTTT-TTTT-TT
37698607 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
37698622 TT
1 TT
37698624 ACCTTGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:37700854 original size:2 final size:2
Alignment explanation
Indices: 37700847--37700928 Score: 128
Period size: 2 Copynumber: 41.0 Consensus size: 2
37700837 TAGAGGGTTA
37700847 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
* * * *
37700889 AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37700929 GTTTCCATTG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37709096 original size:17 final size:17
Alignment explanation
Indices: 37709068--37709110 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
37709058 AAATCAAATA
* *
37709068 AAATAAAATAAAATCCT
1 AAATAAATTAAAATACT
*
37709085 AAATTAATTAAAATACT
1 AAATAAATTAAAATACT
37709102 AAATAAATT
1 AAATAAATT
37709111 TTCATATGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAATTAAAATACT
Found at i:37718653 original size:24 final size:24
Alignment explanation
Indices: 37718626--37718678 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
37718616 TTATACTAGA
37718626 ATAACAATTCC-TAATTATATTAAG
1 ATAA-AATTCCTTAATTATATTAAG
* * *
37718650 ATAAGATTCCTTAATTTTATTAGG
1 ATAAAATTCCTTAATTATATTAAG
37718674 ATAAA
1 ATAAA
37718679 GTTATTGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (24 bp):
ATAAAATTCCTTAATTATATTAAG
Found at i:37730123 original size:22 final size:23
Alignment explanation
Indices: 37730098--37730148 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
37730088 GAATGTAAAT
37730098 CATTGCATG-CT-TCTTGATTGGG
1 CATTGCATGACTGT-TTGATTGGG
37730120 CATTGCATGACTGTTTGATTGGG
1 CATTGCATGACTGTTTGATTGGG
37730143 CATTGC
1 CATTGC
37730149 GTGATTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.33
23 17 0.63
24 1 0.04
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (23 bp):
CATTGCATGACTGTTTGATTGGG
Found at i:37730214 original size:25 final size:25
Alignment explanation
Indices: 37730186--37730259 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
37730176 GATCAATTTA
*
37730186 TGAAAGGCATTACGTGACTGTTATC
1 TGAAAGGCATTACGTGACTATTATC
**
37730211 TGAAAGGCATTTTGTGACTATTATC
1 TGAAAGGCATTACGTGACTATTATC
* * *
37730236 T-ATAGGGCATTGCGTAACTATTAT
1 TGA-AAGGCATTACGTGACTATTAT
37730260 TTGTATCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (25 bp):
TGAAAGGCATTACGTGACTATTATC
Found at i:37730537 original size:22 final size:22
Alignment explanation
Indices: 37730512--37730571 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
37730502 CATAACAACT
37730512 AGTCATGTAATGCCTAATATCC
1 AGTCATGTAATGCCTAATATCC
** * * *
37730534 AGTCACATAGTACTTAATATCC
1 AGTCATGTAATGCCTAATATCC
* *
37730556 AGTGATGCAATGCCTA
1 AGTCATGTAATGCCTA
37730572 CAAATATTCA
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (22 bp):
AGTCATGTAATGCCTAATATCC
Found at i:37733942 original size:23 final size:23
Alignment explanation
Indices: 37733912--37733960 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
37733902 AGCACTATCG
*
37733912 TTATTGCACATCATGTTTTGGCT
1 TTATTGCACATCATGTTTTAGCT
37733935 TTATTGCACATCATGTTTTAGCT
1 TTATTGCACATCATGTTTTAGCT
37733958 TTA
1 TTA
37733961 CAGAATACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.49
Consensus pattern (23 bp):
TTATTGCACATCATGTTTTAGCT
Found at i:37743080 original size:16 final size:18
Alignment explanation
Indices: 37743054--37743086 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37743044 TTTAATACCA
37743054 AATCAAAGAAAA-CAAAT
1 AATCAAAGAAAAGCAAAT
37743071 AATC-AAGAAAAGCAAA
1 AATCAAAGAAAAGCAAA
37743087 AAAAATAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.12, G:0.09, T:0.09
Consensus pattern (18 bp):
AATCAAAGAAAAGCAAAT
Found at i:37755490 original size:162 final size:162
Alignment explanation
Indices: 37755218--37755702 Score: 747
Period size: 162 Copynumber: 3.0 Consensus size: 162
37755208 ATATCCCGTA
*
37755218 ATAAAGATTGTATCGACAAATCATTCTCATAATCATTACTAATTATTAT-CTCGTTAGTAGGGTT
1 ATAAAGATTGTATCGACAAATCATTCTCATAATCATTACTAAATATTATCCT-GTTAGTAGGGTT
* *
37755282 ATATACTAACTATTATATCCCATTAGTAGGACCGTGTGCTAACTTTTTCTTGAAAATTGATAATA
65 ATATGCTAACTATTATATCCCATTAGTAGGACCATGTGCTAACTTTTTCTTGAAAATTGATAATA
* * *
37755347 TGCCTTTGTTAAGTTAAAAGGAATATAAATATG
130 TGCTTTTATTAAGCTAAAAGGAATATAAATATG
* * * *
37755380 ATAAGGATTGTATCGACAAATCATTTTCATAATCATTATTAAATATTATCCTGTTAGTAGGGCTA
1 ATAAAGATTGTATCGACAAATCATTCTCATAATCATTACTAAATATTATCCTGTTAGTAGGGTTA
*
37755445 TATGCTAGCTATTATATCCCATTAGTAGGACCATGTGCTAACTTTTTCTTGAAAATTGATAATAT
66 TATGCTAACTATTATATCCCATTAGTAGGACCATGTGCTAACTTTTTCTTGAAAATTGATAATAT
37755510 GCTTTTATTAAGCTAAAAGGAATATAAATATG
131 GCTTTTATTAAGCTAAAAGGAATATAAATATG
* * * * * **
37755542 ACAAAGATTATATCGACAAATCATTCTCTTGATCATTACTAAATATTATCCCGTTAGTAAAGTTA
1 ATAAAGATTGTATCGACAAATCATTCTCATAATCATTACTAAATATTATCCTGTTAGTAGGGTTA
* * * *
37755607 TATGCTAACTATTATATCCCATTAGCAGGATCATGTGCTAATTTTTTCTTGAAAAATGATAATAT
66 TATGCTAACTATTATATCCCATTAGTAGGACCATGTGCTAACTTTTTCTTGAAAATTGATAATAT
*
37755672 GCTTTTATTAAGCTAAAAGGAGTATAAATAT
131 GCTTTTATTAAGCTAAAAGGAATATAAATAT
37755703 TCCACCATCA
Statistics
Matches: 294, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
162 292 0.99
163 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (162 bp):
ATAAAGATTGTATCGACAAATCATTCTCATAATCATTACTAAATATTATCCTGTTAGTAGGGTTA
TATGCTAACTATTATATCCCATTAGTAGGACCATGTGCTAACTTTTTCTTGAAAATTGATAATAT
GCTTTTATTAAGCTAAAAGGAATATAAATATG
Found at i:37760340 original size:19 final size:19
Alignment explanation
Indices: 37760318--37760367 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
37760308 TTTTAATGAG
37760318 AAATGAGATAAATAAT-TAA
1 AAATGAGATAAA-AATGTAA
* *
37760337 AAATTA-ATAAAAATGTGA
1 AAATGAGATAAAAATGTAA
*
37760355 AAGTGAGATAAAA
1 AAATGAGATAAAA
37760368 TAAATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 11 0.44
19 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATGAGATAAAAATGTAA
Found at i:37763274 original size:8 final size:7
Alignment explanation
Indices: 37763259--37763319 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
37763249 TTAAAATAAG
37763259 AAAATTT
1 AAAATTT
37763266 AAAATTT
1 AAAATTT
*
37763273 -TAA-TT
1 AAAATTT
37763278 ACAAATTAT
1 A-AAATT-T
*
37763287 AAAAATT
1 AAAATTT
*
37763294 AATATTT
1 AAAATTT
37763301 AAAATTT
1 AAAATTT
37763308 AAAATTTT
1 AAAA-TTT
37763316 AAAA
1 AAAA
37763320 ATTATTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
5 2 0.05
6 2 0.05
7 25 0.58
8 12 0.28
9 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:37763277 original size:13 final size:14
Alignment explanation
Indices: 37763259--37763319 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
37763249 TTAAAATAAG
37763259 AAAATTTAAAATTT
1 AAAATTTAAAATTT
*
37763273 -TAA-TTACAAATTAT
1 AAAATTTA-AAATT-T
* *
37763287 AAAAATTAATATTT
1 AAAATTTAAAATTT
37763301 AAAATTTAAAATTTT
1 AAAATTTAAAA-TTT
37763316 AAAA
1 AAAA
37763320 ATTATTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
12 3 0.08
13 7 0.19
14 11 0.30
15 13 0.35
16 3 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTTAAAATTT
Found at i:37763291 original size:22 final size:19
Alignment explanation
Indices: 37763259--37763317 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
37763249 TTAAAATAAG
37763259 AAAATTTAAAATTTTAATT
1 AAAATTTAAAATTTTAATT
* *
37763278 ACAAATTATAAAAATTAATATTT
1 A-AAATT-T-AAAATT-TTAATT
37763301 AAAATTTAAAATTTTAA
1 AAAATTTAAAATTTTAA
37763318 AAATTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 2 0.06
22 11 0.34
23 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTTAAAATTTTAATT
Found at i:37763460 original size:24 final size:24
Alignment explanation
Indices: 37763433--37763483 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
37763423 CTAAATTTTT
*
37763433 AATGAAAATAAAGTAAAAATGAAA
1 AATGAAAATAAAGAAAAAATGAAA
* * *
37763457 AATGCAAATAGAGAAAAAATTAAA
1 AATGAAAATAAAGAAAAAATGAAA
37763481 AAT
1 AAT
37763484 TATACTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.18
Consensus pattern (24 bp):
AATGAAAATAAAGAAAAAATGAAA
Found at i:37763766 original size:26 final size:26
Alignment explanation
Indices: 37763733--37763805 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
37763723 TATTTTTATC
**
37763733 ATAA-TAATATTTAAATTATAAATAAA
1 ATAATTAATATTTAAAAAATAAA-AAA
37763759 AT-ATTAATATTTAAAAAATAAAAAA
1 ATAATTAATATTTAAAAAATAAAAAA
37763784 ATAATTATATATTATAATAAAA
1 ATAATTA-ATATT-TAA-AAAA
37763806 GATATATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.15
26 22 0.55
27 5 0.12
28 3 0.08
29 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAATTAATATTTAAAAAATAAAAAA
Found at i:37765260 original size:20 final size:20
Alignment explanation
Indices: 37765235--37765272 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37765225 TTATATTTGA
*
37765235 TGTTATTATTATTTTTATTT
1 TGTTATAATTATTTTTATTT
37765255 TGTTATAATTATTTTTAT
1 TGTTATAATTATTTTTAT
37765273 AATTATAGAT
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:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TGTTATAATTATTTTTATTT
Found at i:37786761 original size:2 final size:2
Alignment explanation
Indices: 37786754--37786782 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37786744 CCTCCTTTCC
37786754 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
37786783 AAGTGCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:37786821 original size:2 final size:2
Alignment explanation
Indices: 37786814--37786839 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37786804 TCCTTCCTTC
37786814 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
37786840 AAAGTGCACT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:37794945 original size:6 final size:7
Alignment explanation
Indices: 37794928--37794952 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37794918 TGTGCATCTG
37794928 TTTTTGA
1 TTTTTGA
37794935 TTTTTGA
1 TTTTTGA
37794942 TTTTTGA
1 TTTTTGA
37794949 TTTT
1 TTTT
37794953 ATAATTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTTGA
Found at i:37796579 original size:17 final size:18
Alignment explanation
Indices: 37796557--37796590 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37796547 TTTTTTTATA
37796557 ATATTT-TAAAAAAATTT
1 ATATTTGTAAAAAAATTT
*
37796574 ATATTTGTTAAAAAATT
1 ATATTTGTAAAAAAATT
37796591 GACATGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTTGTAAAAAAATTT
Found at i:37796885 original size:33 final size:34
Alignment explanation
Indices: 37796837--37796906 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
37796827 ATCATATTAT
*
37796837 TATATCAAACATATCACATCATCATCAATTATGA
1 TATATCAAACATATCACATCACCATCAATTATGA
* * * *
37796871 TATATC-AGCATATCACGTTACCGTCAATTATGA
1 TATATCAAACATATCACATCACCATCAATTATGA
37796904 TAT
1 TAT
37796907 GCTAGCATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (34 bp):
TATATCAAACATATCACATCACCATCAATTATGA
Found at i:37806927 original size:15 final size:15
Alignment explanation
Indices: 37806904--37806938 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
37806894 AACTTATGCA
* *
37806904 ACATTGCATTTGCTG
1 ACATGGCATTTACTG
37806919 ACATGGCATTTACTG
1 ACATGGCATTTACTG
37806934 ACATG
1 ACATG
37806939 ACTACCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (15 bp):
ACATGGCATTTACTG
Found at i:37810599 original size:69 final size:74
Alignment explanation
Indices: 37810426--37810626 Score: 243
Period size: 75 Copynumber: 2.8 Consensus size: 74
37810416 CCATAAAAAA
* *
37810426 AAAAAAGGAAATTGTTTCCTACTTTAAAAG-TAATTCCTAAAATTAAGGATAGAATTTTAATTTT
1 AAAATAGGAAATTGTTTCCTACTTTAAAAGAT-ATTCCTAAAATTAAGGATAGTATTTTAATTTT
*
37810490 GAGTGATTCAT
65 GAGTGA-TAAT
37810501 AAAATAGGAAATTGTTTCCTACTTTAAAAGATATTCCTAAAATTAAGGATAGTATTTTAA-TTTG
1 AAAATAGGAAATTGTTTCCTACTTTAAAAGATATTCCTAAAATTAAGGATAGTATTTTAATTTTG
37810565 -G-GA-AAT
66 AGTGATAAT
** * * * * *
37810571 -TCATAGGAAATAGTTTCCTACTTCAAAAGAAATTTCTAAAATTATGTGATAGTATT
1 AAAATAGGAAATTGTTTCCTACTTTAAAAGATATTCCTAAAATTAAG-GATAGTATT
37810627 GAACTTTCCT
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
69 39 0.34
70 11 0.10
72 2 0.02
73 1 0.01
74 4 0.04
75 56 0.49
76 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.37
Consensus pattern (74 bp):
AAAATAGGAAATTGTTTCCTACTTTAAAAGATATTCCTAAAATTAAGGATAGTATTTTAATTTTG
AGTGATAAT
Found at i:37818305 original size:19 final size:19
Alignment explanation
Indices: 37818269--37818307 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
37818259 GACTATTGTT
**
37818269 TATGAATGATTCTCATAAA
1 TATGAATGATAATCATAAA
*
37818288 TATGAATGATAATGATAAA
1 TATGAATGATAATCATAAA
37818307 T
1 T
37818308 GTGTTACAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (19 bp):
TATGAATGATAATCATAAA
Found at i:37818972 original size:16 final size:16
Alignment explanation
Indices: 37818948--37818981 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37818938 TATTAAGAAG
*
37818948 AATTGATAATAAACTT
1 AATTAATAATAAACTT
*
37818964 AATTAATAATATACTT
1 AATTAATAATAAACTT
37818980 AA
1 AA
37818982 AATATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTAATAATAAACTT
Found at i:37823797 original size:71 final size:68
Alignment explanation
Indices: 37823665--37823797 Score: 239
Period size: 68 Copynumber: 1.9 Consensus size: 68
37823655 AGTTCTGTTG
37823665 ACATGATTCTCCTTTTAAAATTCTTAAAGTGTGCTTAAATTCTTGTTTCTGTAGTCCAATTAGTT
1 ACATGATTCTCCTTTTAAAATTCTTAAAGTGTGCTTAAATTCTTGTTTCTGTAGTCCAATTAGTT
37823730 TTA
66 TTA
37823733 ACATGATTCTCCTTTTAAAATTCTTAAAAGTGTGCTTAAATTACTTGCTTTCTGTAGTCCAATTA
1 ACATGATTCTCCTTTTAAAATTCTT-AAAGTGTGCTTAAATT-CTTG-TTTCTGTAGTCCAATTA
37823798 CCAATTCATT
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
68 25 0.40
69 16 0.26
70 4 0.06
71 17 0.27
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (68 bp):
ACATGATTCTCCTTTTAAAATTCTTAAAGTGTGCTTAAATTCTTGTTTCTGTAGTCCAATTAGTT
TTA
Found at i:37828642 original size:42 final size:42
Alignment explanation
Indices: 37828595--37828704 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
37828585 AAAGGGAAGG
* **
37828595 AAAGAGAGAGATAATTTGTTTTTCTTATCCT-ATCCCTATAGA
1 AAAGAGAAAGATAATTTGTTTTTCTTA-CCTAAAACCTATAGA
* * * *
37828637 AAAGAGAAAGATAATTTGTTTATCTTACCTAAAACTTGTAGT
1 AAAGAGAAAGATAATTTGTTTTTCTTACCTAAAACCTATAGA
*
37828679 AAAGAGAAAAATAATTTGTTTTTCTT
1 AAAGAGAAAGATAATTTGTTTTTCTT
37828705 TATGATTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 3 0.05
42 55 0.95
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (42 bp):
AAAGAGAAAGATAATTTGTTTTTCTTACCTAAAACCTATAGA
Found at i:37834878 original size:2 final size:2
Alignment explanation
Indices: 37834871--37834909 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37834861 AGTATAACAC
37834871 AT AT AT AT 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 AT AT AT AT A
37834910 AACAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37836523 original size:14 final size:15
Alignment explanation
Indices: 37836504--37836534 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
37836494 TTTTTGCGTG
37836504 TTGACTAGAAAG-GC
1 TTGACTAGAAAGAGC
37836518 TTGACTAGAAAGAGC
1 TTGACTAGAAAGAGC
37836533 TT
1 TT
37836535 CACTTCAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
TTGACTAGAAAGAGC
Found at i:37837627 original size:23 final size:23
Alignment explanation
Indices: 37837592--37837638 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
37837582 AAATTTATTA
* *
37837592 TTTAATAAATAATATTATTGCTC
1 TTTAATAAATAATAATAGTGCTC
37837615 TTTAA-AAATTAATAATAGTGCTC
1 TTTAATAAA-TAATAATAGTGCTC
37837638 T
1 T
37837639 ATTTACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (23 bp):
TTTAATAAATAATAATAGTGCTC
Found at i:37842407 original size:2 final size:2
Alignment explanation
Indices: 37842400--37842449 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
37842390 AACTGTAAAC
37842400 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
37842442 AT AT AT AT
1 AT AT AT AT
37842450 CTCTATCATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37866197 original size:25 final size:25
Alignment explanation
Indices: 37866169--37866219 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
37866159 TAATTACATG
*
37866169 TCTTTTACTTT-GTGGTAATTTAGTT
1 TCTTTTA-TTTAGTAGTAATTTAGTT
*
37866194 TCTTTTATTTAGTAGTTATTTAGTT
1 TCTTTTATTTAGTAGTAATTTAGTT
37866219 T
1 T
37866220 TACATGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.18, C:0.06, G:0.14, T:0.63
Consensus pattern (25 bp):
TCTTTTATTTAGTAGTAATTTAGTT
Found at i:37874421 original size:3 final size:3
Alignment explanation
Indices: 37874413--37874439 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
37874403 ATTGTAACTT
37874413 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
37874440 TATTAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:37876409 original size:15 final size:15
Alignment explanation
Indices: 37876389--37876417 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37876379 AAATTTGAGT
37876389 TTAAATTTTTTAGAA
1 TTAAATTTTTTAGAA
37876404 TTAAATTTTTTAGA
1 TTAAATTTTTTAGA
37876418 GTTACGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TTAAATTTTTTAGAA
Found at i:37876880 original size:27 final size:28
Alignment explanation
Indices: 37876849--37876918 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 28
37876839 CTTAAATATA
37876849 TTTTTAATATTATATATTTTATTTTTATT
1 TTTTTAATATTATATATTTTATTTTTA-T
*
37876878 TTTATGATAATATTATATATTTTGTTTTTAT
1 TTT-T--TAATATTATATATTTTATTTTTAT
37876909 TTTTTAATAT
1 TTTTTAATAT
37876919 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 6 0.16
29 3 0.08
30 2 0.05
31 4 0.11
32 22 0.59
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTAATATTATATATTTTATTTTTAT
Found at i:37876891 original size:32 final size:31
Alignment explanation
Indices: 37876853--37876956 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 31
37876843 AATATATTTT
37876853 TAATATTATATATTTTATTTTTATTTTTATGA
1 TAATATTATATATTTTATTTTTATTTTTAT-A
*
37876885 TAATATTATATATTTTGTTTTTATTTTTTAATA
1 TAATATTATATATTTTATTTTTA-TTTTT-ATA
* * * *
37876918 TAATTTTTTATATTATATATTTTATTTTAATTA
1 TAATATTATATATTTTAT-TTTTATTTTTA-TA
37876951 TAATAT
1 TAATAT
37876957 CATAAAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
32 23 0.38
33 31 0.51
34 7 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (31 bp):
TAATATTATATATTTTATTTTTATTTTTATA
Found at i:37877806 original size:3 final size:3
Alignment explanation
Indices: 37877798--37877827 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
37877788 TATAACATAC
37877798 AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
37877828 AAGTCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37882285 original size:5 final size:5
Alignment explanation
Indices: 37882268--37882300 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
37882258 TTGGTTGTTG
*
37882268 CTTTC CTTCC CTTTC CTTTC CTTTC CTTTC CTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTT
37882301 CTTAGTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
CTTTC
Found at i:37884503 original size:108 final size:109
Alignment explanation
Indices: 37884314--37884521 Score: 301
Period size: 108 Copynumber: 1.9 Consensus size: 109
37884304 AATGACTAAA
* * * *
37884314 TATATTTATTTAATTACAACTTTCATAATTTACAAATACACATTCTTTTAAAATTATTAAACTCT
1 TATATTAATTTAATTACAACTTTCACAATTTACAAATACAAATTCTTTTAAAATCATTAAACTCT
* *
37884379 TACCCAATTT-ACCTTTTATTTTAATTTACGCAAATTAGCAAAC
66 TACCCAATTTAACTTTTTATTTAAATTTACGCAAATTAGCAAAC
* ** *
37884422 TATATTAATTTAGTTACAACTTTCACAATTTACAAATACAAATTCTTTTGCAATCATTCAACTCT
1 TATATTAATTTAATTACAACTTTCACAATTTACAAATACAAATTCTTTTAAAATCATTAAACTCT
* *
37884487 TATCCAATTTAACTTTTTATTTAAATTTACTCAAA
66 TACCCAATTTAACTTTTTATTTAAATTTACGCAAA
37884522 ATTTCTTACA
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
108 66 0.76
109 21 0.24
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.44
Consensus pattern (109 bp):
TATATTAATTTAATTACAACTTTCACAATTTACAAATACAAATTCTTTTAAAATCATTAAACTCT
TACCCAATTTAACTTTTTATTTAAATTTACGCAAATTAGCAAAC
Found at i:37884754 original size:19 final size:18
Alignment explanation
Indices: 37884722--37884761 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
37884712 TTGAAATGTT
37884722 AAATAAAATAAAAATATAA
1 AAATAAAATAAAAAT-TAA
37884741 AAAT-AAATAAAAAATTAA
1 AAATAAAAT-AAAAATTAA
37884759 AAA
1 AAA
37884762 AGTGGAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAAAATTAA
Found at i:37886640 original size:18 final size:17
Alignment explanation
Indices: 37886598--37886647 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
37886588 TTTCATAATA
37886598 TAAAAGAAATATAATATTTT
1 TAAAA-AAAT-TAA-ATTTT
37886618 T-AAAAAATTAAATTATT
1 TAAAAAAATTAAATT-TT
37886635 TAAAAAAA-TAAAT
1 TAAAAAAATTAAAT
37886648 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 10 0.36
19 3 0.11
20 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAAAAATTAAATTTT
Found at i:37901379 original size:34 final size:33
Alignment explanation
Indices: 37901326--37901415 Score: 117
Period size: 34 Copynumber: 2.7 Consensus size: 33
37901316 TGGTGTCAGA
* *
37901326 TTACATTATCATGTCTAAAAAAAATCAATTAGTT
1 TTACCTTATCATGTTTAAAAAAAATCAATTAG-T
*
37901360 TTACCTTATCATATTTAAAAAAAAATCAATTAGT
1 TTACCTTATCATGTTT-AAAAAAAATCAATTAGT
* *
37901394 TTATCTTATCATGTTTTAAAAA
1 TTACCTTATCATGTTTAAAAAA
37901416 GAAAAGCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
33 5 0.10
34 28 0.57
35 16 0.33
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (33 bp):
TTACCTTATCATGTTTAAAAAAAATCAATTAGT
Found at i:37904148 original size:36 final size:37
Alignment explanation
Indices: 37904076--37904152 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
37904066 ACGTTTAAAT
37904076 GAAAATCAATCAGTTTTACCTTATCATATTGTAAAAA
1 GAAAATCAATCAGTTTTACCTTATCATATTGTAAAAA
* *
37904113 GAAAATCAATCAG-TTTATCTTATCATGTT-TAAAAA
1 GAAAATCAATCAGTTTTACCTTATCATATTGTAAAAA
*
37904148 AAAAA
1 GAAAA
37904153 AAAGCAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 10 0.27
36 14 0.38
37 13 0.35
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.34
Consensus pattern (37 bp):
GAAAATCAATCAGTTTTACCTTATCATATTGTAAAAA
Found at i:37905999 original size:42 final size:42
Alignment explanation
Indices: 37905948--37906066 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
37905938 TTTGATATAC
* *
37905948 TTATAACCCATGCCACTAGGGTTAATTGTGGTTTTGATACGA
1 TTATGACCCATGCCACTAGGGTTAATTGTGGTTTCGATACGA
* *
37905990 TTATGACCCATGCCACTAAGGTTAATTGTTGTTTCGATACGA
1 TTATGACCCATGCCACTAGGGTTAATTGTGGTTTCGATACGA
* * *
37906032 TTATGATCCATGCCATTGGGGTTAATTGTGGTTTC
1 TTATGACCCATGCCACTAGGGTTAATTGTGGTTTC
37906067 TGTTATAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
TTATGACCCATGCCACTAGGGTTAATTGTGGTTTCGATACGA
Found at i:37910606 original size:22 final size:22
Alignment explanation
Indices: 37910581--37910644 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
37910571 GATCTATTGC
* *
37910581 TGATTTGCTACTGGTTTGTGAG
1 TGATTTGCTGCTGATTTGTGAG
* * *
37910603 TGATTTGGTGCTGTTTTGTGAT
1 TGATTTGCTGCTGATTTGTGAG
*
37910625 TGATTTACTGCTGATTTGTG
1 TGATTTGCTGCTGATTTGTG
37910645 GGAGATGATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.12, C:0.08, G:0.30, T:0.50
Consensus pattern (22 bp):
TGATTTGCTGCTGATTTGTGAG
Found at i:37915384 original size:27 final size:27
Alignment explanation
Indices: 37915351--37915403 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
37915341 TTATTTTATT
37915351 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
37915378 TTTAAAATATTAATAATTGATAATTT
1 TTTAAAATATTAATAATTGATAATTT
37915404 TAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:37915784 original size:25 final size:26
Alignment explanation
Indices: 37915750--37915799 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
37915740 AATACTTGAG
37915750 AATTTAAATA-TT-AATATTTTATTAT
1 AATTTAAATATTTAAATA-TTTATTAT
37915775 AATTTAAATATTTAAATATTTATTA
1 AATTTAAATATTTAAATATTTATTA
37915800 AAAATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.43
26 9 0.39
27 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AATTTAAATATTTAAATATTTATTAT
Found at i:37925190 original size:4 final size:4
Alignment explanation
Indices: 37925183--37925212 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
37925173 TTTAATTAAT
37925183 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
37925213 TTCCATCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:37943608 original size:22 final size:21
Alignment explanation
Indices: 37943580--37943704 Score: 80
Period size: 22 Copynumber: 6.0 Consensus size: 21
37943570 TACGTCTTTG
** *
37943580 GTTTTTAGGCATTGTGTGATT
1 GTTTTTAGGCATTACGTGACT
37943601 AGTTTTTAGGCATTACGTGACT
1 -GTTTTTAGGCATTACGTGACT
*
37943623 GTGTTTTAGGCATTACATGACT
1 GT-TTTTAGGCATTACGTGACT
* * *
37943645 G-----AAGCATTGCGTAACT
1 GTTTTTAGGCATTACGTGACT
* *
37943661 GGGTTGTAGGCATTACGTGACT
1 -GTTTTTAGGCATTACGTGACT
* *
37943683 AGATTTTAGACATTACGTGACT
1 -GTTTTTAGGCATTACGTGACT
37943705 TAAGCGTTAC
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
16 11 0.14
17 1 0.01
21 2 0.02
22 67 0.83
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (21 bp):
GTTTTTAGGCATTACGTGACT
Found at i:37943671 original size:38 final size:38
Alignment explanation
Indices: 37943610--37943682 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
37943600 TAGTTTTTAG
* * *
37943610 GCATTACGTGACTGTGTTTTAGGCATTACATGACTGAA
1 GCATTACGTAACTGGGTTGTAGGCATTACATGACTGAA
* *
37943648 GCATTGCGTAACTGGGTTGTAGGCATTACGTGACT
1 GCATTACGTAACTGGGTTGTAGGCATTACATGACT
37943683 AGATTTTAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (38 bp):
GCATTACGTAACTGGGTTGTAGGCATTACATGACTGAA
Found at i:37950454 original size:22 final size:22
Alignment explanation
Indices: 37950378--37950457 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
37950368 CGGATTTGGG
* * *
37950378 GTCAGGTAATGCCTAATAACCA
1 GTCACGTAATACCTAATAATCA
** * * *
37950400 GTCACAAAATACTTAAAAATTA
1 GTCACGTAATACCTAATAATCA
*
37950422 GTCA-TTCAATACCTAATAATCA
1 GTCACGT-AATACCTAATAATCA
37950444 GTCACGTAATACCT
1 GTCACGTAATACCT
37950458 TAAATCTGTC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
22 41 0.98
23 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (22 bp):
GTCACGTAATACCTAATAATCA
Found at i:37950559 original size:22 final size:21
Alignment explanation
Indices: 37950531--37950603 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
37950521 TATGCCTAAT
37950531 AATGCCTTAAAACCAGTCACGC
1 AATGCC-TAAAACCAGTCACGC
* *
37950553 AATGCCTAATATCTAGTCACGC
1 AATGCCTAA-AACCAGTCACGC
* *
37950575 AATGCCCTATCAACCAATCACGC
1 AATG-CCTA-AAACCAGTCACGC
37950598 AATGCC
1 AATGCC
37950604 CATATGCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.07
22 22 0.52
23 17 0.40
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (21 bp):
AATGCCTAAAACCAGTCACGC
Found at i:37954054 original size:22 final size:21
Alignment explanation
Indices: 37954026--37954211 Score: 120
Period size: 22 Copynumber: 8.4 Consensus size: 21
37954016 TAATATCCAA
*
37954026 GCAATGCCTAGAACATAGTCAT
1 GCAATGCCTA-AAAATAGTCAT
*
37954048 GCAATGCCTTAAAAATCAGTCAC
1 GCAATGCC-TAAAAAT-AGTCAT
*
37954071 GCAATGCCTAAAAACTGGTCAT
1 GCAATGCCTAAAAA-TAGTCAT
* *
37954093 GCAATGCCTACATACTAGTCAT
1 GCAATGCCTA-AAAATAGTCAT
* * *
37954115 GCAATGCCCTAAAAACCAATCAC
1 GCAATG-CCTAAAAA-TAGTCAT
* **
37954138 GCAATGCACTATCAAGCAGTCAT
1 GCAATGC-CTA-AAAATAGTCAT
* * * *
37954161 GCAATGCTTATCAAACAGTCAC
1 GCAATGCCTA-AAAATAGTCAT
* * *
37954183 GTAATTCCTAAAAACAGTCAT
1 GCAATGCCTAAAAATAGTCAT
37954204 GCAATGCC
1 GCAATGCC
37954212 CTATCAACCT
Statistics
Matches: 130, Mismatches: 26, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
21 15 0.12
22 66 0.51
23 47 0.36
24 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (21 bp):
GCAATGCCTAAAAATAGTCAT
Found at i:37954142 original size:45 final size:42
Alignment explanation
Indices: 37954064--37954211 Score: 127
Period size: 45 Copynumber: 3.4 Consensus size: 42
37954054 CCTTAAAAAT
* ** *
37954064 CAGTCACGCAATGCCTAAAAACTGGTCATGCAATGCCTACATA
1 CAGTCATGCAATGCCTAAAAACCAGTCACGCAATGCCTACA-A
*
37954107 CTAGTCATGCAATGCCCTAAAAACCAATCACGCAATGCACTATCAA
1 C-AGTCATGCAATG-CCTAAAAACCAGTCACGCAATGC-CTA-CAA
* * * * *
37954153 GCAGTCATGCAATGCTTATCAAA-CAGTCACGTAATTCCTAAAAA
1 -CAGTCATGCAATGCCTA-AAAACCAGTCACGCAATGCCT-ACAA
37954197 CAGTCATGCAATGCC
1 CAGTCATGCAATGCC
37954212 CTATCAACCT
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
43 15 0.17
44 15 0.17
45 34 0.40
46 19 0.22
47 3 0.03
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (42 bp):
CAGTCATGCAATGCCTAAAAACCAGTCACGCAATGCCTACAA
Found at i:37954378 original size:22 final size:22
Alignment explanation
Indices: 37954292--37954412 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
37954282 AATCACGCAT
* * *
37954292 TGCCTAAAAACCAATCACGCAG
1 TGCCTAAAAACCAGTCATGCAA
* *
37954314 TGACTAAAAATCAGTCATGCAA
1 TGCCTAAAAACCAGTCATGCAA
* ** * *
37954336 TACCATATCAATCAGTGATGCAA
1 TGCC-TAAAAACCAGTCATGCAA
*
37954359 TGCCTAAAAACCAGTAATGCAA
1 TGCCTAAAAACCAGTCATGCAA
* **
37954381 TGCCTAAAAATCAAG-CACACAA
1 TGCCTAAAAA-CCAGTCATGCAA
37954403 TGCCTAAAAA
1 TGCCTAAAAA
37954413 TCGCTCACGC
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
22 57 0.73
23 21 0.27
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (22 bp):
TGCCTAAAAACCAGTCATGCAA
Found at i:37954425 original size:22 final size:21
Alignment explanation
Indices: 37954026--37954427 Score: 82
Period size: 22 Copynumber: 18.3 Consensus size: 21
37954016 TAATATCCAA
* * *
37954026 GCAATGCCTAGAACATAGTCAT
1 GCAATGCCTA-AAAATCGTCAC
37954048 GCAATGCCTTAAAAATCAGTCAC
1 GCAATGCC-TAAAAATC-GTCAC
* *
37954071 GCAATGCCTAAAAACTGGTCAT
1 GCAATGCCTAAAAA-TCGTCAC
* * * *
37954093 GCAATGCCTACATACTAGTCAT
1 GCAATGCCTA-AAAATCGTCAC
* *
37954115 GCAATGCCCTAAAAACCAATCAC
1 GCAATG-CCTAAAAATC-GTCAC
** * *
37954138 GCAATGCACTATCAAGCAGTCAT
1 GCAATGC-CTAAAAATC-GTCAC
* *
37954161 GCAATGCTTATCAAA-CAGTCAC
1 GCAATGCCTA-AAAATC-GTCAC
* * *
37954183 GTAATTCCTAAAAA-CAGTCAT
1 GCAATGCCTAAAAATC-GTCAC
** * ***
37954204 GCAATGCCCTATCAACCTGTGGT
1 GCAATG-CCTAAAAATC-GTCAC
* *
37954227 GTAATGACTAAAAATCAGTCAC
1 GCAATGCCTAAAAATC-GTCAC
* * * * *
37954249 ACAATACCTTATCAAGTAGTCAC
1 GCAATGCC-TA-AAAATCGTCAC
*
37954272 GTAATGCCT--AAA---TCAC
1 GCAATGCCTAAAAATCGTCAC
* * *
37954288 GCATTGCCTAAAAACCAATCAC
1 GCAATGCCTAAAAATC-GTCAC
* * *
37954310 GCAGTGACTAAAAATCAGTCAT
1 GCAATGCCTAAAAATC-GTCAC
* ** * *
37954332 GCAATACCATATCAATCAGTGAT
1 GCAATGCC-TAAAAATC-GTCAC
* * *
37954355 GCAATGCCTAAAAACCAGTAAT
1 GCAATGCCTAAAAATC-GTCAC
37954377 GCAATGCCTAAAAATCAAG-CAC
1 GCAATGCCTAAAAATC--GTCAC
*
37954399 ACAATGCCTAAAAATCGCTCAC
1 GCAATGCCTAAAAATCG-TCAC
37954421 GCAATGC
1 GCAATGC
37954428 TTTATCAACT
Statistics
Matches: 280, Mismatches: 78, Indels: 44
0.70 0.19 0.11
Matches are distributed among these distances:
16 11 0.04
18 3 0.01
19 2 0.01
20 1 0.00
21 13 0.05
22 157 0.56
23 90 0.32
24 3 0.01
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.22
Consensus pattern (21 bp):
GCAATGCCTAAAAATCGTCAC
Found at i:37957830 original size:21 final size:22
Alignment explanation
Indices: 37957804--37957845 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
37957794 ATTTTCTTTA
37957804 ATTATTATT-TTTTA-TATTTTG
1 ATTATT-TTATTTTATTATTTTG
37957825 ATTATTTTATTTTATTATTTT
1 ATTATTTTATTTTATTATTTT
37957846 AACATAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 11 0.58
22 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTATTTTATTTTATTATTTTG
Found at i:37957843 original size:13 final size:13
Alignment explanation
Indices: 37957808--37957846 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
37957798 TCTTTAATTA
*
37957808 TTATTTTTTATATT
1 TTATTATTT-TATT
37957822 TTGATTATTTTATT
1 TT-ATTATTTTATT
37957836 TTATTATTTTA
1 TTATTATTTTA
37957847 ACATAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 8 0.35
15 6 0.26
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTATTATTTTATT
Found at i:37959372 original size:8 final size:8
Alignment explanation
Indices: 37959359--37959397 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
37959349 TTTATTTCAA
*
37959359 ATTTTTTT
1 ATTTTATT
37959367 ATTTT-TT
1 ATTTTATT
37959374 ATTTTATT
1 ATTTTATT
37959382 ATTTTATT
1 ATTTTATT
37959390 ATTTTATT
1 ATTTTATT
37959398 GATTGATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
ATTTTATT
Found at i:37959377 original size:15 final size:15
Alignment explanation
Indices: 37959345--37959394 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
37959335 GTCTTTTCCC
***
37959345 TTTTTTTATTTCAAA
1 TTTTTTTATTTTTTA
37959360 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
*
37959375 TTTTATTATTTTATTA
1 TTTTTTTATTTT-TTA
37959391 TTTT
1 TTTT
37959395 ATTGATTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 23 0.77
16 7 0.23
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:37959385 original size:23 final size:22
Alignment explanation
Indices: 37959346--37959394 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
37959336 TCTTTTCCCT
*
37959346 TTTTTTATTTCAAATTTTTTTA
1 TTTTTTATTTCAAATTTTATTA
* *
37959368 TTTTTTATTTTATTATTTTATTA
1 TTTTTTATTTCA-AATTTTATTA
37959391 TTTT
1 TTTT
37959395 ATTGATTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTATTTCAAATTTTATTA
Found at i:37959393 original size:16 final size:15
Alignment explanation
Indices: 37959359--37959397 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
37959349 TTTATTTCAA
*
37959359 ATTTTTTTATTTTTT
1 ATTTTATTATTTTTT
37959374 ATTTTATTATTTTATT
1 ATTTTATTATTTT-TT
37959390 ATTTTATT
1 ATTTTATT
37959398 GATTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTATTATTTTTT
Found at i:37959597 original size:47 final size:46
Alignment explanation
Indices: 37959522--37959842 Score: 267
Period size: 47 Copynumber: 7.0 Consensus size: 46
37959512 GAATCAAGAC
* * * *
37959522 AAAAGCTCATCATCTTTAAATGAAGCTACGCAACTTTCAATGATTA
1 AAAAGCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATTA
* *
37959568 GAAAAGCTCCTCATCTCTAAGTGAGGCTACACAACTTTAAATGATTA
1 -AAAAGCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATTA
* *
37959615 AAAAGGCTCCTCATCTCTAAATGAGGCTTCACAACTTTAAATGATTGA
1 AAAA-GCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATT-A
* * * * * *
37959663 AAATGCTCTTCATCTC-AAAGCGAGGCTATGCAA--AT-AAT--TGA
1 AAAAGCTCCTCATCTCTAAA-TGAGGCTACGCAACTTTAAATGATTA
* *
37959704 AAAAGCTCTTCATCTCTAAATGAGGCTATGCAACTTTAAATGATTA
1 AAAAGCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATTA
* ** * ** * *
37959750 CAAATGCTTTTCATCTTTAAACAAGGCTACGTAACTTTAAATTATTGA
1 -AAAAGCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATT-A
* * * ** * *
37959798 AAAAGCTCTTTATTTCTAAACAAGGCTACACAAATTTAAATGATT
1 AAAAGCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATT
37959843 GGAAATTTTT
Statistics
Matches: 226, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
41 28 0.12
42 4 0.02
43 1 0.00
44 6 0.03
45 1 0.00
46 9 0.04
47 172 0.76
48 5 0.02
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (46 bp):
AAAAGCTCCTCATCTCTAAATGAGGCTACGCAACTTTAAATGATTA
Found at i:37959715 original size:41 final size:41
Alignment explanation
Indices: 37959653--37959736 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
37959643 TCACAACTTT
* *
37959653 AAATGATTGAAAATGCTCTTCATCTC-AAAGCGAGGCTATGC
1 AAATAATTGAAAAAGCTCTTCATCTCTAAA-CGAGGCTATGC
*
37959694 AAATAATTGAAAAAGCTCTTCATCTCTAAATGAGGCTATGC
1 AAATAATTGAAAAAGCTCTTCATCTCTAAACGAGGCTATGC
37959735 AA
1 AA
37959737 CTTTAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 36 0.92
42 3 0.08
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
AAATAATTGAAAAAGCTCTTCATCTCTAAACGAGGCTATGC
Found at i:37959777 original size:88 final size:88
Alignment explanation
Indices: 37959606--37959778 Score: 228
Period size: 88 Copynumber: 2.0 Consensus size: 88
37959596 ACACAACTTT
*
37959606 AAATGATTAAAAAGGCTCCTCATCTCTAAATGAGGCTTCACAACTTTAAATGATTGAAAATGCTC
1 AAATAATTAAAAAGGCTCCTCATCTCTAAATGAGGCTTCACAACTTTAAATGATTGAAAATGCTC
*
37959671 TTCATCTCAAAGCGAGGCTATGC
66 TTCATCTCAAAGCAAGGCTATGC
* *
37959694 AAATAATTGAAAAA-GCTCTTCATCTCTAAATGAGGCTAT-GCAACTTTAAATGATT-ACAAATG
1 AAATAATT-AAAAAGGCTCCTCATCTCTAAATGAGGCT-TCACAACTTTAAATGATTGA-AAATG
* *
37959756 CTTTTCATCTTTAAA-CAAGGCTA
63 CTCTTCATC-TCAAAGCAAGGCTA
37959779 CGTAACTTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
87 1 0.01
88 64 0.85
89 10 0.13
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (88 bp):
AAATAATTAAAAAGGCTCCTCATCTCTAAATGAGGCTTCACAACTTTAAATGATTGAAAATGCTC
TTCATCTCAAAGCAAGGCTATGC
Found at i:37959824 original size:135 final size:135
Alignment explanation
Indices: 37959569--37959825 Score: 327
Period size: 135 Copynumber: 1.9 Consensus size: 135
37959559 CAATGATTAG
*
37959569 AAAAGCTCCTCATCTCTAAGTGAGGCTACACAACTTTAAATGATTAAAAAGGCTCCTCATCTCTA
1 AAAAGCTCCTCATCTCTAAATGAGGCTACACAACTTTAAATGATTAAAAAGGCTCCTCATCTCTA
** * * *
37959634 AATGAGGCTTCACAACTTTAAATGATTGAAAATGCTCTTCATCTCAAAGCGAGGCTATGCAAATA
66 AACAAGGCTACACAACTTTAAATGATTGAAAAAGCTCTTCATCTCAAAGCAAGGCTATGCAAATA
37959699 ATTGA
131 ATTGA
* ** * * ** *
37959704 AAAAGCTCTTCATCTCTAAATGAGGCTATGCAACTTTAAATGATTACAAATGCTTTTCATCTTTA
1 AAAAGCTCCTCATCTCTAAATGAGGCTACACAACTTTAAATGATTAAAAAGGCTCCTCATCTCTA
** * * *
37959769 AACAAGGCTACGTAACTTTAAATTATTGAAAAAGCTCTTTATTTCTAAA-CAAGGCTA
66 AACAAGGCTACACAACTTTAAATGATTGAAAAAGCTCTTCATCTC-AAAGCAAGGCTA
37959826 CACAAATTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
135 99 0.97
136 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (135 bp):
AAAAGCTCCTCATCTCTAAATGAGGCTACACAACTTTAAATGATTAAAAAGGCTCCTCATCTCTA
AACAAGGCTACACAACTTTAAATGATTGAAAAAGCTCTTCATCTCAAAGCAAGGCTATGCAAATA
ATTGA
Found at i:37967443 original size:21 final size:21
Alignment explanation
Indices: 37967405--37967444 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37967395 CACAAAATAG
* *
37967405 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
37967426 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
37967445 ATACACACAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:37967716 original size:15 final size:14
Alignment explanation
Indices: 37967696--37967732 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
37967686 GTTATATATA
37967696 TTATAATTAATAATT
1 TTATAATT-ATAATT
37967711 TTATAAGTTATAATT
1 TTATAA-TTATAATT
37967726 TTATAAT
1 TTATAAT
37967733 GTTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TTATAATTATAATT
Found at i:37967786 original size:21 final size:21
Alignment explanation
Indices: 37967748--37967787 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37967738 CACAAAATAG
* *
37967748 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
37967769 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
37967788 ATACACACAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:37967952 original size:343 final size:346
Alignment explanation
Indices: 37967282--37968007 Score: 1332
Period size: 343 Copynumber: 2.1 Consensus size: 346
37967272 TTATCCAATT
* * * * *
37967282 AACTATTCTAATCTCATAACTTCCCTTCAGATTTATATGTTATAAGTTTATATAAATAATGGTAT
1 AACTATTCTAATCTCACAACTTCTCTTTAGATTTATA---TATAAGTTTATATAAACAAAGGTAT
* *
37967347 ATATATTGTAATTAATAATTTTATGAGTTATAATTTTTATAATGTTAACACAAAATAGAAAGTAA
63 ATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAGTAA
37967412 ATATGTTTATATTTAAAGTACATATATATATATATACACACACGCATACATAAAAGATATTTTAA
128 ATATGTTTATATTTAAAGTACATATATATATATATACACACACGCATACATAAAAGATATTTTAA
37967477 TATATATAAAATAGTAATTATATTCTTTATAAATGAATCTAATATTAAAAGACATTACAAGTTAA
193 TATATATAAAATAGTAATTATATTCTTTATAAATGAATCTAATATTAAAAGACATTACAAGTTAA
37967542 TTAATAATTATAGTTTCATGAATTAATTTAATTAACTATACTAGTTTGTCCTTAATTACATAAAA
258 TTAATAATTATAGTTTCATGAATTAATTTAATTAACTATACTAGTTTGTCCTTAATTACATAAAA
37967607 TTAAAAAAAATAATTAGATTTTAG
323 TTAAAAAAAATAATTAGATTTTAG
*
37967631 AACTATTCTAATCTCACAACTTCTCTTTAGATTTATA-A-AAGTTTATATAAACAAAGTTATATA
1 AACTATTCTAATCTCACAACTTCTCTTTAGATTTATATATAAGTTTATATAAACAAAGGTATATA
37967694 TATTATAATTAATAATTTTATAAGTTATAA-TTTTATAATGTTAACACAAAATAGAAAGTAAATA
66 TATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAGTAAATA
37967758 TGTTTATATTTAAAGTACATATATATATATATACACACACGCATACATAAAAGATATTTTAATAT
131 TGTTTATATTTAAAGTACATATATATATATATACACACACGCATACATAAAAGATATTTTAATAT
37967823 ATATAAAATAGTAATTATATTCTTTATAAATGAATCTAATATTAAAAGACATTACAAGTTAATTA
196 ATATAAAATAGTAATTATATTCTTTATAAATGAATCTAATATTAAAAGACATTACAAGTTAATTA
37967888 ATAATTATAGTTTCATGAATTAATTTAATTAACTATACTAGTTTGTCCTTAATTACATAAAATTA
261 ATAATTATAGTTTCATGAATTAATTTAATTAACTATACTAGTTTGTCCTTAATTACATAAAATTA
37967953 AAAAAAATAATTAGATTTTAG
326 AAAAAAATAATTAGATTTTAG
37967974 AACTATTCTAATCTCACAACTTCTCTTTAGATTT
1 AACTATTCTAATCTCACAACTTCTCTTTAGATTT
37968008 NGCTTCCAAA
Statistics
Matches: 369, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
343 284 0.77
344 50 0.14
345 1 0.00
349 34 0.09
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.40
Consensus pattern (346 bp):
AACTATTCTAATCTCACAACTTCTCTTTAGATTTATATATAAGTTTATATAAACAAAGGTATATA
TATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATAGAAAGTAAATA
TGTTTATATTTAAAGTACATATATATATATATACACACACGCATACATAAAAGATATTTTAATAT
ATATAAAATAGTAATTATATTCTTTATAAATGAATCTAATATTAAAAGACATTACAAGTTAATTA
ATAATTATAGTTTCATGAATTAATTTAATTAACTATACTAGTTTGTCCTTAATTACATAAAATTA
AAAAAAATAATTAGATTTTAG
Found at i:37988294 original size:24 final size:24
Alignment explanation
Indices: 37988248--37988300 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
37988238 GCACACGGGC
* * * *
37988248 CTCTTTCTATCTGTTTTTTTCTTT
1 CTCTTTCTACCTCTCTTTCTCTTT
37988272 CTCTTTCTACCTCTCTTTCTCTTT
1 CTCTTTCTACCTCTCTTTCTCTTT
37988296 C-CTTT
1 CTCTTT
37988301 TTCTCTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (24 bp):
CTCTTTCTACCTCTCTTTCTCTTT
Found at i:37990725 original size:11 final size:12
Alignment explanation
Indices: 37990711--37990752 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
37990701 GAGAATAAAA
*
37990711 AGAGAA-TAGGT
1 AGAGAATTAGAT
37990722 AGAGAATTAGAT
1 AGAGAATTAGAT
*
37990734 AGAGAAGTTAGAA
1 AGAGAA-TTAGAT
37990747 AGAGAA
1 AGAGAA
37990753 GCTCTAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 6 0.22
12 10 0.37
13 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (12 bp):
AGAGAATTAGAT
Found at i:37991031 original size:22 final size:22
Alignment explanation
Indices: 37991006--37991048 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
37990996 TAGAATAGCT
37991006 ATTCCAAGAGAATAAAATAAAC
1 ATTCCAAGAGAATAAAATAAAC
*
37991028 ATTCCAAGAGAATAGAATAAA
1 ATTCCAAGAGAATAAAATAAA
37991049 GGAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATTCCAAGAGAATAAAATAAAC
Found at i:37991393 original size:23 final size:22
Alignment explanation
Indices: 37991350--37991393 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
37991340 AAATACAAAC
**
37991350 ATATTTTTACTATAATTTAATA
1 ATATTTTTACTATAAGATAATA
*
37991372 ATATTTTGTATTATAAGATAAT
1 ATATTTT-TACTATAAGATAAT
37991394 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTTACTATAAGATAATA
Found at i:37992014 original size:17 final size:17
Alignment explanation
Indices: 37991992--37992047 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
37991982 TTATCCTAAT
*
37991992 TGTTCCGCATGAAGTAG
1 TGTTCCACATGAAGTAG
* ***
37992009 TGTTCCACTTGTCCTAG
1 TGTTCCACATGAAGTAG
37992026 TTGTTCCACATGAAGTAG
1 -TGTTCCACATGAAGTAG
37992044 TGTT
1 TGTT
37992048 TCACTTGTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (17 bp):
TGTTCCACATGAAGTAG
Found at i:37992014 original size:35 final size:34
Alignment explanation
Indices: 37991965--37992175 Score: 163
Period size: 35 Copynumber: 6.0 Consensus size: 34
37991955 GCTATTCGTG
* *
37991965 TGAAGTGGTTGTTCCACTTATCCTAATTGTTCCGCA
1 TGAAGTAG-TGTT-CACTTATTCTAATTGTTCCGCA
* * * *
37992001 TGAAGTAGTGTTCCACTTGTCCTAGTTGTTCCACA
1 TGAAGTAGTGTT-CACTTATTCTAATTGTTCCGCA
* * * **
37992036 TGAAGTAGTGTTTCACTTGTTTTAGTTGTTATGCA
1 TGAAGTAGTG-TTCACTTATTCTAATTGTTCCGCA
* * **
37992071 TGAAGTAGTGTTTCATTTATTCTAGTTGTTTTGCA
1 TGAAGTAGTG-TTCACTTATTCTAATTGTTCCGCA
* * **
37992106 TGAAATAGTGCTTCACTTGTTCTAATTGTTTTGCA
1 TGAAGTAGTG-TTCACTTATTCTAATTGTTCCGCA
* *
37992141 TGAAATAGTGCTTCACTCATTCTAATTGTT-CGCA
1 TGAAGTAGTG-TTCACTTATTCTAATTGTTCCGCA
37992175 T
1 T
37992176 CATTCTTTGT
Statistics
Matches: 153, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
34 4 0.03
35 140 0.92
36 9 0.06
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (34 bp):
TGAAGTAGTGTTCACTTATTCTAATTGTTCCGCA
Found at i:37992032 original size:18 final size:18
Alignment explanation
Indices: 37991972--37992034 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
37991962 GTGTGAAGTG
*
37991972 GTTGTTCCACTTATCCTA
1 GTTGTTCCACTTGTCCTA
* * * ***
37991990 ATTGTTCCGCATGAAGTA
1 GTTGTTCCACTTGTCCTA
37992008 G-TGTTCCACTTGTCCTA
1 GTTGTTCCACTTGTCCTA
37992025 GTTGTTCCAC
1 GTTGTTCCAC
37992035 ATGAAGTAGT
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (18 bp):
GTTGTTCCACTTGTCCTA
Found at i:37992044 original size:18 final size:18
Alignment explanation
Indices: 37991991--37992044 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
37991981 CTTATCCTAA
*
37991991 TTGTTCCGCATGAAGTAG
1 TTGTTCCACATGAAGTAG
* ***
37992009 -TGTTCCACTTGTCCTAG
1 TTGTTCCACATGAAGTAG
37992026 TTGTTCCACATGAAGTAG
1 TTGTTCCACATGAAGTAG
37992044 T
1 T
37992045 GTTTCACTTG
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (18 bp):
TTGTTCCACATGAAGTAG
Found at i:37992096 original size:70 final size:70
Alignment explanation
Indices: 37991987--37992171 Score: 208
Period size: 70 Copynumber: 2.6 Consensus size: 70
37991977 TCCACTTATC
** * * * * *
37991987 CTAATTGTTCCGCATGAAGTAGTGTTCCACTTGTCCTAGTTGTTCCACATGAAGTAGTGTTTCAC
1 CTAATTGTTATGCATGAAGTAGTGTTTCACTTATTCTAGTTGTTCCACATGAAATAGTGCTTCAC
37992052 TTGTT
66 TTGTT
* * * ***
37992057 TTAGTTGTTATGCATGAAGTAGTGTTTCATTTATTCTAGTTGTTTTGCATGAAATAGTGCTTCAC
1 CTAATTGTTATGCATGAAGTAGTGTTTCACTTATTCTAGTTGTTCCACATGAAATAGTGCTTCAC
37992122 TTGTT
66 TTGTT
* * * * *
37992127 CTAATTGTTTTGCATGAAATAGTGCTTCACTCATTCTAATTGTTC
1 CTAATTGTTATGCATGAAGTAGTGTTTCACTTATTCTAGTTGTTC
37992172 GCATCATTCT
Statistics
Matches: 93, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
70 93 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (70 bp):
CTAATTGTTATGCATGAAGTAGTGTTTCACTTATTCTAGTTGTTCCACATGAAATAGTGCTTCAC
TTGTT
Found at i:37998547 original size:3 final size:3
Alignment explanation
Indices: 37998539--37998602 Score: 96
Period size: 3 Copynumber: 21.3 Consensus size: 3
37998529 CTGCTCTATC
37998539 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA
37998584 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
37998603 CACTCCATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.04
3 53 0.93
4 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38039531 original size:21 final size:22
Alignment explanation
Indices: 38039489--38039533 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38039479 AAGCCTTAAT
*
38039489 AATTTTTTTTACATAATCTCAA
1 AATTTTTTTTAAATAATCTCAA
38039511 AATTTTTTTTGAAAT-AT-TCAA
1 AATTTTTTTT-AAATAATCTCAA
38039532 AA
1 AA
38039534 AAAAATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 12 0.57
23 3 0.14
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTTTTTTTAAATAATCTCAA
Found at i:38039878 original size:29 final size:29
Alignment explanation
Indices: 38039818--38039900 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
38039808 GTATTTTAAT
* *
38039818 TAAAAATATAAAAACTTATTTAATTCAAAA
1 TAAAAATATAAAAATTTATTTAA-ACAAAA
* *
38039848 TAAAAATATAAAAATTTAATTAAACATAA
1 TAAAAATATAAAAATTTATTTAAACAAAA
*
38039877 TAAAATTATAAAAATTTATTTAAA
1 TAAAAATATAAAAATTTATTTAAA
38039901 TTTTTTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 26 0.55
30 21 0.45
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAAAATATAAAAATTTATTTAAACAAAA
Found at i:38040129 original size:18 final size:18
Alignment explanation
Indices: 38040106--38040161 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
38040096 TTTTTGAAAT
38040106 TTTTTATATATTATATAA
1 TTTTTATATATTATATAA
*
38040124 TTTTTA-ATATTTTTATAA
1 TTTTTATATA-TTATATAA
* *
38040142 TATTTT-TTTATTAAATAA
1 T-TTTTATATATTATATAA
38040160 TT
1 TT
38040162 AATATAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 4 0.13
18 21 0.68
19 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTATATATTATATAA
Found at i:38040317 original size:18 final size:18
Alignment explanation
Indices: 38040296--38040367 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 18
38040286 AAGAGATAAA
38040296 ATTTTATTTTATTTTTTT
1 ATTTTATTTTATTTTTTT
38040314 ATTTATATTTTTATTATTATTT
1 ATTT-TA-TTTTATT-TT-TTT
*
38040336 ATATTA-TTTATTTTTTT
1 ATTTTATTTTATTTTTTT
* *
38040353 AATTATATTCTATTT
1 -ATTTTATTTTATTT
38040368 GTTCATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
17 3 0.07
18 10 0.23
19 14 0.32
20 7 0.16
21 4 0.09
22 6 0.14
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTATTTTATTTTTTT
Found at i:38040318 original size:12 final size:12
Alignment explanation
Indices: 38040297--38040358 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 12
38040287 AGAGATAAAA
38040297 TTTTATTTTATTT
1 TTTTA-TTTATTT
*
38040310 TTTTATTTATAT
1 TTTTATTTATTT
38040322 TTTTATTATTATTT
1 TTTTA-T-TTATTT
*
38040336 ATATTATTTATTT
1 -TTTTATTTATTT
*
38040349 TTTTAATTAT
1 TTTTATTTAT
38040359 ATTCTATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
12 19 0.46
13 12 0.29
14 6 0.15
15 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:38040340 original size:9 final size:9
Alignment explanation
Indices: 38040298--38040358 Score: 58
Period size: 8 Copynumber: 7.1 Consensus size: 9
38040288 GAGATAAAAT
*
38040298 TTTATTTTA
1 TTTATATTA
*
38040307 TTT-TTTTA
1 TTTATATTA
38040315 TTTATATT-
1 TTTATATTA
38040323 TTTATTATTA
1 TTTA-TATTA
38040333 TTTATATTA
1 TTTATATTA
*
38040342 TTTAT-TTT
1 TTTATATTA
38040350 TTTA-ATTA
1 TTTATATTA
38040358 T
1 T
38040359 ATTCTATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 21 0.47
9 20 0.44
10 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATATTA
Found at i:38040509 original size:15 final size:16
Alignment explanation
Indices: 38040491--38040520 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38040481 TTATTATGTG
38040491 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
38040506 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
38040521 AATTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:38046578 original size:2 final size:2
Alignment explanation
Indices: 38046565--38046595 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38046555 AAGTTAGTGA
*
38046565 AT AT AC 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
38046596 CACACACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38056393 original size:22 final size:23
Alignment explanation
Indices: 38056361--38056407 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
38056351 TTTTTAAAAC
* *
38056361 AAATTATATAATAATAATACTTT
1 AAATTATATAAAAAAAATACTTT
*
38056384 AAATT-TATAAAAAAAATATTTT
1 AAATTATATAAAAAAAATACTTT
38056406 AA
1 AA
38056408 TTTTTTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTATATAAAAAAAATACTTT
Found at i:38060098 original size:15 final size:16
Alignment explanation
Indices: 38060078--38060124 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
38060068 AAAACTTTTG
38060078 TAAATTAATATTTAA-
1 TAAATTAATATTTAAT
*
38060093 TAAATTAATAACTTCAAT
1 TAAATTAAT-A-TTTAAT
38060111 TAAA-TAATATTTAA
1 TAAATTAATATTTAA
38060125 CCGGTTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 8 0.30
18 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTAATATTTAAT
Found at i:38061799 original size:2 final size:2
Alignment explanation
Indices: 38061792--38061824 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38061782 TATTCTTCAC
38061792 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38061825 AGGCATTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38062280 original size:29 final size:29
Alignment explanation
Indices: 38062248--38062307 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
38062238 GTCATGTCAA
*
38062248 AATTTTAAAA-ATAATAAATAAAATATTTT
1 AATTTTAAAATA-AATAAATAAAAAATTTT
* *
38062277 AATTTTATATTAAATAAATAAAAAATTTT
1 AATTTTAAAATAAATAAATAAAAAATTTT
38062306 AA
1 AA
38062308 AAATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTTTAAAATAAATAAATAAAAAATTTT
Found at i:38062552 original size:33 final size:29
Alignment explanation
Indices: 38062495--38062554 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 29
38062485 GATTAGAATA
38062495 AATAAATAAAATATTTTAATTTTATATCG
1 AATAAATAAAATATTTTAATTTTATATCG
38062524 AATAAATAAAATAATCTTTAATAATTTATAT
1 AATAAATAAAAT-AT-TTTAAT--TTTATAT
38062555 GGACAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 12 0.44
30 2 0.07
31 6 0.22
33 7 0.26
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (29 bp):
AATAAATAAAATATTTTAATTTTATATCG
Found at i:38077253 original size:144 final size:143
Alignment explanation
Indices: 38077022--38077296 Score: 424
Period size: 144 Copynumber: 1.9 Consensus size: 143
38077012 TTTTTATATT
* * * * ** *
38077022 AATTGATTACATATTCTGCATATTTACAACTATAATTAGTGATTAATAATCGAAAGAAGTGGTTA
1 AATTAATTACATATTCTGAACACTTACAACTATAATTAACGATTAATAATCGAAAGAAGTGGCTA
*
38077087 GTTAGCAAAATACACTCAATGTAACTAAAATAATGTCGCCACGTCAATAAATTTAATGATTCAAT
66 GTTAGCAAAATACACTCAATGTAACTAAAATAA-GTCACCACGTCAATAAATTTAATGATTCAAT
38077152 ATTCAAGTCAACGA
130 ATTCAAGTCAACGA
* *
38077166 AATTAATTACATATTCTGAACACTTACAACTATAATTAACGATTAATAATTGAAAGAAGTGGCTC
1 AATTAATTACATATTCTGAACACTTACAACTATAATTAACGATTAATAATCGAAAGAAGTGGCTA
* * *
38077231 GTTAGCAAAATTCACTCCATGTAAGTAAAATAAGTCACCACGTCAATAAATTTAATGATTCAATA
66 GTTAGCAAAATACACTCAATGTAACTAAAATAAGTCACCACGTCAATAAATTTAATGATTCAATA
38077296 T
131 T
38077297 CCAGGTTGAT
Statistics
Matches: 118, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
143 32 0.27
144 86 0.73
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (143 bp):
AATTAATTACATATTCTGAACACTTACAACTATAATTAACGATTAATAATCGAAAGAAGTGGCTA
GTTAGCAAAATACACTCAATGTAACTAAAATAAGTCACCACGTCAATAAATTTAATGATTCAATA
TTCAAGTCAACGA
Found at i:38102597 original size:20 final size:21
Alignment explanation
Indices: 38102554--38102612 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
38102544 ATATTAATAA
* *
38102554 ATAATTTTTACTATTTTGAAT
1 ATAATTATTAATATTTTGAAT
*
38102575 ATAATTATTAATATTTTAATAT
1 ATAATTATTAATATTTTGA-AT
* *
38102597 ATAAATATTACTATTT
1 ATAATTATTAATATTT
38102613 ATTTTTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTATTAATATTTTGAAT
Found at i:38102605 original size:22 final size:22
Alignment explanation
Indices: 38102547--38102612 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
38102537 TGTTAAAATA
* *
38102547 TTAATAAATAATTTTTACTATT
1 TTAATATATAATTATTACTATT
* *
38102569 TTGA-ATATAATTATTAATATT
1 TTAATATATAATTATTACTATT
*
38102590 TTAATATATAAATATTACTATT
1 TTAATATATAATTATTACTATT
38102612 T
1 T
38102613 ATTTTTAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATATATAATTATTACTATT
Found at i:38102984 original size:30 final size:28
Alignment explanation
Indices: 38102950--38103014 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
38102940 TCCCAGGGAA
38102950 AGAAGGAAGAGACAGAAAAGAGGAAGAG-GG
1 AGAAGGAAGAG-CAG-AAA-AGGAAGAGTGG
* *
38102980 AGAAGAGATGAGCAGAAATGGAAGAGTGG
1 AGAAG-GAAGAGCAGAAAAGGAAGAGTGG
38103009 AGAAGG
1 AGAAGG
38103015 CTCTTAGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 8 0.26
29 10 0.32
30 8 0.26
31 5 0.16
ACGTcount: A:0.49, C:0.03, G:0.43, T:0.05
Consensus pattern (28 bp):
AGAAGGAAGAGCAGAAAAGGAAGAGTGG
Found at i:38105569 original size:2 final size:2
Alignment explanation
Indices: 38105562--38105588 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38105552 CTGGCTTATC
38105562 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
38105589 TATAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38109379 original size:2 final size:2
Alignment explanation
Indices: 38109372--38109412 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
38109362 CAAAGAGCAA
38109372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38109413 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:38118317 original size:13 final size:12
Alignment explanation
Indices: 38118291--38118320 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
38118281 AAAAAATATA
38118291 TTTTAAAATTTT
1 TTTTAAAATTTT
38118303 TTTTAAAATTATT
1 TTTTAAAATT-TT
38118316 TTTTA
1 TTTTA
38118321 TTAAGTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:38118414 original size:21 final size:20
Alignment explanation
Indices: 38118382--38118422 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
38118372 ATTGATGTAT
*
38118382 CATAATAAATAATTATGTGA
1 CATAATAAATAATCATGTGA
*
38118402 CATATTAACATAATCATGTGA
1 CATAATAA-ATAATCATGTGA
38118423 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
CATAATAAATAATCATGTGA
Found at i:38119356 original size:6 final size:6
Alignment explanation
Indices: 38119348--38119377 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
38119338 TAAAGAAATA
*
38119348 GGAAAA GGAAAG GGAAAG GGAAAG GGAAAG
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG
38119378 ATTATTCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:38121273 original size:19 final size:19
Alignment explanation
Indices: 38121249--38121316 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
38121239 ATTCATTTGT
38121249 CACGTGATAATACATCTAC
1 CACGTGATAATACATCTAC
* * **
38121268 CACGTGCATTATCAACTCATTTGT
1 CACGTG-ATAAT--A--CATCTAC
38121292 CACGTGATAATACATCTAC
1 CACGTGATAATACATCTAC
38121311 CACGTG
1 CACGTG
38121317 CATTATCCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
19 16 0.44
20 4 0.11
21 1 0.03
22 1 0.03
23 4 0.11
24 10 0.28
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (19 bp):
CACGTGATAATACATCTAC
Found at i:38121295 original size:43 final size:43
Alignment explanation
Indices: 38121234--38121323 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
38121224 GATATATCCA
*
38121234 TATCAATTCATTTGTCACGTGATAATACATCTACCACGTGCAT
1 TATCAACTCATTTGTCACGTGATAATACATCTACCACGTGCAT
38121277 TATCAACTCATTTGTCACGTGATAATACATCTACCACGTGCAT
1 TATCAACTCATTTGTCACGTGATAATACATCTACCACGTGCAT
38121320 TATC
1 TATC
38121324 CTTGGGTAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (43 bp):
TATCAACTCATTTGTCACGTGATAATACATCTACCACGTGCAT
Found at i:38137571 original size:4 final size:4
Alignment explanation
Indices: 38137562--38137632 Score: 65
Period size: 4 Copynumber: 17.8 Consensus size: 4
38137552 ATCATATGTT
* * * *
38137562 CATA CATA CATA CATA CATA CATT CAT- -ATA CATG CATA TATT CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
38137608 CATA CATA TATA CATTCA CATA CAT
1 CATA CATA CATA CA-T-A CATA CAT
38137633 TTTCTAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
2 2 0.04
4 47 0.87
5 2 0.04
6 3 0.06
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.32
Consensus pattern (4 bp):
CATA
Found at i:38137594 original size:18 final size:18
Alignment explanation
Indices: 38137571--38137632 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
38137561 TCATACATAC
38137571 ATACATACATACATTCAT
1 ATACATACATACATTCAT
* *
38137589 ATACATGCATATATTCAT
1 ATACATACATACATTCAT
* *
38137607 ACATACATATATACATTCAC
1 --ATACATACATACATTCAT
38137627 ATACAT
1 ATACAT
38137633 TTTCTAATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 22 0.61
20 14 0.39
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.34
Consensus pattern (18 bp):
ATACATACATACATTCAT
Found at i:38137599 original size:26 final size:26
Alignment explanation
Indices: 38137563--38137617 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
38137553 TCATATGTTC
*
38137563 ATACATACATACATACATACATTCAT
1 ATACATACATACATACATACATACAT
* * *
38137589 ATACATGCATATATTCATACATACAT
1 ATACATACATACATACATACATACAT
38137615 ATA
1 ATA
38137618 TACATTCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (26 bp):
ATACATACATACATACATACATACAT
Found at i:38141482 original size:53 final size:54
Alignment explanation
Indices: 38141411--38141512 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 54
38141401 TTCTTTCTCG
* * * *
38141411 AACATCACCGCTGGGTATTTACATTAGATAGCATTCAGTC-GCTACCAACACCA
1 AACATCAACACTGCGTATTTACATTAGATAGCATACAGTCAGCTACCAACACCA
38141464 AACATCAACACTGCGTATTTACATTAGATAGCATACAGTCAGCTACCAA
1 AACATCAACACTGCGTATTTACATTAGATAGCATACAGTCAGCTACCAA
38141513 TACAATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 36 0.82
54 8 0.18
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (54 bp):
AACATCAACACTGCGTATTTACATTAGATAGCATACAGTCAGCTACCAACACCA
Found at i:38143119 original size:67 final size:66
Alignment explanation
Indices: 38143011--38143158 Score: 215
Period size: 67 Copynumber: 2.2 Consensus size: 66
38143001 CCCTATACCA
* * * *
38143011 CCCCTCCCTCCCCTCTTTTCTTTTCTCAGGAAAGAAAAGGTGGATGATATAGAAGTGACCTTTAG
1 CCCCTCCCTCCCCTCTTTTCTTTTCTCAGGAAAAAAAAGGTGGATAATATAGAAATGACCTTCAG
38143076 T
66 T
*
38143077 CCCCTCCACTCCCCTCTTTTCTTTTCTTAGGAAAAAAAAGGTGGATAATATAGAAATGACCTTCA
1 CCCCTCC-CTCCCCTCTTTTCTTTTCTCAGGAAAAAAAAGGTGGATAATATAGAAATGACCTTCA
38143142 GT
65 GT
*
38143144 CACCCCTCCCCCCCC
1 --CCCCTCCCTCCCC
38143159 CTCCCCCCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
66 7 0.10
67 54 0.74
68 5 0.07
69 7 0.10
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (66 bp):
CCCCTCCCTCCCCTCTTTTCTTTTCTCAGGAAAAAAAAGGTGGATAATATAGAAATGACCTTCAG
T
Found at i:38154945 original size:2 final size:2
Alignment explanation
Indices: 38154938--38154968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38154928 GGTAAAATAC
38154938 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
38154969 GACACACGCA
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:38161981 original size:22 final size:21
Alignment explanation
Indices: 38161956--38162005 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
38161946 AAAACTACCC
38161956 ATTTTTTCTTTTTACATAAC-CT
1 ATTTTTTCTTTTTA-A-AACACT
* *
38161978 ATTTTCTGTTTTTAAAACACT
1 ATTTTTTCTTTTTAAAACACT
38161999 ATTTTTT
1 ATTTTTT
38162006 TACCTCTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
22 12 0.50
ACGTcount: A:0.24, C:0.14, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTTTCTTTTTAAAACACT
Found at i:38161982 original size:21 final size:20
Alignment explanation
Indices: 38161958--38162004 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
38161948 AACTACCCAT
38161958 TTTTTCTTTTTACATAAC-CTA
1 TTTTTCTTTTTA-A-AACACTA
*
38161979 TTTTCTGTTTTTAAAACACTA
1 TTTT-TCTTTTTAAAACACTA
38162000 TTTTT
1 TTTTT
38162005 TTACCTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTCTTTTTAAAACACTA
Done.