Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold174
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: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 11 of 15
Found at i:1250606 original size:22 final size:22
Alignment explanation
Indices: 1250555--1250606 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
1250545 TAATGGGTAA
* *
1250555 AAATATTTAACCTATTTATTAT
1 AAATTTTTAACCTATTTATGAT
*
1250577 AATATTTTAAACCTATTT-TGAT
1 AA-ATTTTTAACCTATTTATGAT
1250599 AAATTTTT
1 AAATTTTT
1250607 TAAATTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 5 0.20
22 7 0.28
23 13 0.52
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATTTTTAACCTATTTATGAT
Found at i:1250610 original size:23 final size:23
Alignment explanation
Indices: 1250556--1250605 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1250546 AATGGGTAAA
*
1250556 AATA-TTT-AACCTATTTATTAT
1 AATATTTTAAACCTATTTATGAT
1250577 AATATTTTAAACCTATTT-TGAT
1 AATATTTTAAACCTATTTATGAT
1250599 AA-ATTTT
1 AATATTTT
1250606 TTAAATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (23 bp):
AATATTTTAAACCTATTTATGAT
Found at i:1250660 original size:3 final size:3
Alignment explanation
Indices: 1250652--1250684 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1250642 AATAGTGAAC
1250652 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1250685 TTCAAAAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1251514 original size:27 final size:29
Alignment explanation
Indices: 1251452--1251524 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1251442 GAGTAGATAT
*
1251452 AAAATTTTATAAAAATTATATTTATTTTT
1 AAAATTTTATAAAAATTATATTTATTTTA
*
1251481 AATATTTTA-AAAATATT-TATTT-TTTTA
1 AAAATTTTATAAAA-ATTATATTTATTTTA
*
1251508 AAAATTTGATTAAAAAT
1 AAAATTTTA-TAAAAAT
1251525 ATACTTAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 11 0.30
28 11 0.30
29 15 0.41
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
AAAATTTTATAAAAATTATATTTATTTTA
Found at i:1252026 original size:26 final size:25
Alignment explanation
Indices: 1251979--1252031 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1251969 TCTTTAAATT
* * * *
1251979 TTTTTAAATAATACTAATTAATTTA
1 TTTTTAAATAAAAATAAATAATATA
1252004 TTTTTAAATAAAAATAACATAATATA
1 TTTTTAAATAAAAATAA-ATAATATA
1252030 TT
1 TT
1252032 AATATCAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTTAAATAAAAATAAATAATATA
Found at i:1252286 original size:17 final size:18
Alignment explanation
Indices: 1252266--1252299 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1252256 TTTTATAATT
*
1252266 AAAAATATTTAA-AAATA
1 AAAAATAATTAATAAATA
1252283 AAAAATAATTAATAAAT
1 AAAAATAATTAATAAAT
1252300 GGCATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAATTAATAAATA
Found at i:1263474 original size:13 final size:13
Alignment explanation
Indices: 1263456--1263536 Score: 52
Period size: 13 Copynumber: 6.6 Consensus size: 13
1263446 ACAGTCAATT
1263456 ATAATAAATATTA
1 ATAATAAATATTA
1263469 ATAATAAA-A-TA
1 ATAATAAATATTA
*
1263480 AT--TAAAAATTA
1 ATAATAAATATTA
1263491 A-AATAAATA--A
1 ATAATAAATATTA
*
1263501 ATATTATAATTAATT-
1 ATA--ATAAAT-ATTA
*
1263516 ATAGTAAATATTA
1 ATAATAAATATTA
1263529 ATAATAAA
1 ATAATAAA
1263537 ATAATTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 22
0.66 0.06 0.28
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 8 0.15
12 9 0.17
13 24 0.46
14 1 0.02
15 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:1263492 original size:16 final size:16
Alignment explanation
Indices: 1263461--1263516 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1263451 CAATTATAAT
*
1263461 AAAT-ATTAATAA-TA
1 AAATAATTAAAAATTA
1263475 AAATAATTAAAAATTA
1 AAATAATTAAAAATTA
* *
1263491 AAATAAATAAATATTA
1 AAATAATTAAAAATTA
*
1263507 TAATTAATTA
1 -AAATAATTA
1263517 TAGTAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 16 0.47
17 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATTAAAAATTA
Found at i:1263495 original size:21 final size:21
Alignment explanation
Indices: 1263456--1263497 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1263446 ACAGTCAATT
*
1263456 ATAATAAATATTAATAATAAA
1 ATAATAAAAATTAATAATAAA
1263477 ATAATTAAAAATTAA-AATAAA
1 ATAA-TAAAAATTAATAATAAA
1263498 TAAATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATAAAAATTAATAATAAA
Found at i:1263511 original size:22 final size:22
Alignment explanation
Indices: 1263486--1263552 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1263476 AATAATTAAA
1263486 AATTAAAATAAATAAATATTAT
1 AATTAAAATAAATAAATATTAT
* *
1263508 AATT-AATTATAGTAAATATTAAT
1 AATTAAAATA-AATAAATATT-AT
*
1263531 AA-TAAAATAATTAAA-ATTAT
1 AATTAAAATAAATAAATATTAT
1263551 AA
1 AA
1263553 AATTACGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.11
21 7 0.18
22 19 0.50
23 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (22 bp):
AATTAAAATAAATAAATATTAT
Found at i:1263514 original size:44 final size:42
Alignment explanation
Indices: 1263465--1263552 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 42
1263455 TATAATAAAT
1263465 ATTAATAATA-AAATAATTAAAAATTAAAATAAATAAATATTATA
1 ATTAATAATAGAAAT-ATTAAAAA-TAAAATAAATAAA-ATTATA
* * *
1263509 ATTAATTATAGTAAATATTAATAATAAAATAATTAAAATTATA
1 ATTAATAATAG-AAATATTAAAAATAAAATAAATAAAATTATA
1263552 A
1 A
1263553 AATTACGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
43 7 0.18
44 21 0.54
45 7 0.18
46 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (42 bp):
ATTAATAATAGAAATATTAAAAATAAAATAAATAAAATTATA
Found at i:1263524 original size:60 final size:61
Alignment explanation
Indices: 1263434--1263555 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 61
1263424 TAAGTAGGAG
*
1263434 TAAATAAATATTACAGTCAATTATAATAAATATTAATAATAAAATAATTAAAAAT-TAAAA
1 TAAATAAATATTACAATCAATTATAATAAATATTAATAATAAAATAATTAAAAATATAAAA
* * * *
1263494 TAAATAAATATTATAATTAATTATAGTAAATATTAATAATAAAATAATTAAAATTATAAAA
1 TAAATAAATATTACAATCAATTATAATAAATATTAATAATAAAATAATTAAAAATATAAAA
1263555 T
1 T
1263556 TACGATGTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 50 0.89
61 6 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (61 bp):
TAAATAAATATTACAATCAATTATAATAAATATTAATAATAAAATAATTAAAAATATAAAA
Found at i:1263529 original size:38 final size:39
Alignment explanation
Indices: 1263458--1263536 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
1263448 AGTCAATTAT
*
1263458 AATAAATATTAATAATAAAATAATTAAAAATTAA-AATA
1 AATAAATATTAATAATAAAATAAGTAAAAATTAATAATA
* * *
1263496 AATAAATATT-ATAATTAATTATAGTAAATATTAATAATA
1 AATAAATATTAATAATAAAATA-AGTAAAAATTAATAATA
1263535 AA
1 AA
1263537 ATAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 9 0.26
38 20 0.57
39 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (39 bp):
AATAAATATTAATAATAAAATAAGTAAAAATTAATAATA
Found at i:1264867 original size:24 final size:24
Alignment explanation
Indices: 1264800--1264872 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 24
1264790 AAAATATTTG
*
1264800 AAAA-AATAATTTTTAATTTAATA
1 AAAATAATAATATTTAATTTAATA
* **
1264823 AAAATAATAAATTAATATAATTTTTTA
1 AAAATAAT-AA-T-ATTTAATTTAATA
1264850 AAAATAATAATATTTAA-TTAATA
1 AAAATAATAATATTTAATTTAATA
1264873 TCGATATGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
23 8 0.21
24 8 0.21
25 3 0.08
26 3 0.08
27 17 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAATAATAATATTTAATTTAATA
Found at i:1264872 original size:17 final size:17
Alignment explanation
Indices: 1264804--1264872 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
1264794 TATTTGAAAA
*
1264804 AATAATTTTTAATTTAAT
1 AATAATATTTAA-TTAAT
* * *
1264822 AAAAATAATAAATTAAT
1 AATAATATTTAATTAAT
* *
1264839 -ATAATTTTTTAA-AAAT
1 AATAA-TATTTAATTAAT
1264855 AATAATATTTAATTAAT
1 AATAATATTTAATTAAT
1264872 A
1 A
1264873 TCGATATGCA
Statistics
Matches: 37, Mismatches: 11, Indels: 7
0.67 0.20 0.13
Matches are distributed among these distances:
16 12 0.32
17 17 0.46
18 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATATTTAATTAAT
Found at i:1265150 original size:24 final size:24
Alignment explanation
Indices: 1265126--1265173 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1265116 ATATTTTAAA
1265126 TAATTATTTATATTTTATAAAAAAT
1 TAATTATTT-TATTTTATAAAAAAT
*
1265151 TATTTATTTTATTTTATAAAAAA
1 TAATTATTTTATTTTATAAAAAA
1265174 ACCCACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTATTTTATTTTATAAAAAAT
Found at i:1265240 original size:17 final size:16
Alignment explanation
Indices: 1265208--1265243 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1265198 TAATATATAA
*
1265208 TAATTTTTACATTTAT
1 TAATTTTTAAATTTAT
1265224 TAATTTTATAAATTTAT
1 TAATTTT-TAAATTTAT
1265241 TAA
1 TAA
1265244 AAAACTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTTTAAATTTAT
Found at i:1271322 original size:20 final size:20
Alignment explanation
Indices: 1271276--1271321 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
1271266 ATTAAAGATA
1271276 TTATATATTTATATAAATTT
1 TTATATATTTATATAAATTT
*
1271296 TGATATA-TTA-ATAAATTAT
1 TTATATATTTATATAAATT-T
1271315 TT-TATAT
1 TTATATAT
1271322 AAATTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATATATTTATATAAATTT
Found at i:1271324 original size:32 final size:32
Alignment explanation
Indices: 1271283--1271358 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
1271273 ATATTATATA
* *
1271283 TTTATATAAATTTTGATATATTAATAAATTAT
1 TTTATATAAATTTTAACATATTAATAAATTAT
* *
1271315 TTTATATAAATTTTAACATATTTATATATTAT
1 TTTATATAAATTTTAACATATTAATAAATTAT
*
1271347 TATCATATAAAT
1 T-TTATATAAAT
1271359 ATTATTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
32 29 0.76
33 9 0.24
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTATATAAATTTTAACATATTAATAAATTAT
Found at i:1272253 original size:2 final size:2
Alignment explanation
Indices: 1272246--1272276 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1272236 TACAGAGAAA
1272246 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 A
1272277 TAAAAGGGAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1279955 original size:39 final size:41
Alignment explanation
Indices: 1279911--1280004 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 41
1279901 TTTATATTTT
* **
1279911 TATAATTAAATTTAAATAAAAATATTTTATTTTAT-AAATA
1 TATAATTAAATTTAAATAAAAATAATTTAAATTATAAAATA
* *
1279951 -ATAATCTAAA-TTAAATTAAATTAATTTAAATTATAAAATA
1 TATAAT-TAAATTTAAATAAAAATAATTTAAATTATAAAATA
1279991 TTATAATTAAATTT
1 -TATAATTAAATTT
1280005 GGTTTAATCT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
39 24 0.55
40 9 0.20
41 4 0.09
42 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (41 bp):
TATAATTAAATTTAAATAAAAATAATTTAAATTATAAAATA
Found at i:1282111 original size:19 final size:20
Alignment explanation
Indices: 1282087--1282124 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1282077 TGCACAATCA
*
1282087 TGTATATATGTAT-TGTGTG
1 TGTATATATATATATGTGTG
1282106 TGTATATATATATATGTGT
1 TGTATATATATATATGTGT
1282125 ATGTCTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (20 bp):
TGTATATATATATATGTGTG
Found at i:1282430 original size:2 final size:2
Alignment explanation
Indices: 1282425--1282452 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1282415 AGAGATTTAG
1282425 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
1282453 GTATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1282710 original size:327 final size:326
Alignment explanation
Indices: 1282108--1282742 Score: 968
Period size: 327 Copynumber: 1.9 Consensus size: 326
1282098 ATTGTGTGTG
1282108 TATATATATATATGTGTATGTCTTGGAGAAAAATGTGCCATATATACCTACATATATTCATATAA
1 TATATATATATATGTGTATGTCTTGGAGAAAAATGTGCCATATATACCTACATATATTCATATAA
* * * * * *
1282173 ACATACATTATGCGTAGTTGTATCCATATAGTGCATATATGGGTTATTTGTATATTATACTTATT
66 ACATACATTATGCATAGTTATATCCATACAATACATACATGGGTTATTTGTATATTATAC-----
** * * **
1282238 TGTTATTTGTTTGATTGTGAGAATTTTAATCTTTTTTACTGACATGCATCAATAAATAAAAATTA
126 T-TTATTTGTTTGATTGCAAGAATTTCAATCTTTTTAACTGACACACATCAATAAATAAAAATTA
* * *
1282303 TTACGTCAAATTTCTATTGTTATATCTTTATAGACATAAATTTTTTAAAGAATTTAAAATTTTAC
190 TGACATCAAATTTCTATTATTATATCTTTATAGACATAAATTTTTTAAAGAATTTAAAATTTTAC
1282368 TATATTAATCATTTGTTGTTATATGCATGAC-AGCACATTTCATGTAGAGAGATTTAGATATATA
255 TATATTAATCATTTGTTGTTATATGCATGACTA-CACATTTCATGTAGAGAGATTTAGATATATA
1282432 TATATATA
319 TATATATA
1282440 TATATATATATATGTATGTATGTCTTGGAGAAAAATGTGCCATATATACCTACATATATTCATAT
1 TATATATATATATG--TGTATGTCTTGGAGAAAAATGTGCCATATATACCTACATATATTCATAT
* * **
1282505 AAACATACATTATGTATATTTATATCCATACAATATGTACATGGGTTATTTGTATATTATAC-TT
64 AAACATACATTATGCATAGTTATATCCATACAATACATACATGGGTTATTTGTATATTATACTTT
* * *
1282569 ATTTGTTTGATTGCAAGAATTTCAATCTTTTTAATTGACACACATCGATAAATGAAAATTATGAC
129 ATTTGTTTGATTGCAAGAATTTCAATCTTTTTAACTGACACACATCAATAAATAAAAATTATGAC
*
1282634 ATCAAATTTCTATTATTATATCTTTATAGACATAAATTTTTTAAAGAATTTAAAATTTTACTATG
194 ATCAAATTTCTATTATTATATCTTTATAGACATAAATTTTTTAAAGAATTTAAAATTTTACTATA
1282699 TTAATCATTTGTTGTTATATGCATGACTACACATTTCATGTAGA
259 TTAATCATTTGTTGTTATATGCATGACTACACATTTCATGTAGA
1282743 TAGACTTGTG
Statistics
Matches: 277, Mismatches: 23, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
327 161 0.58
328 1 0.00
332 14 0.05
334 101 0.36
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (326 bp):
TATATATATATATGTGTATGTCTTGGAGAAAAATGTGCCATATATACCTACATATATTCATATAA
ACATACATTATGCATAGTTATATCCATACAATACATACATGGGTTATTTGTATATTATACTTTAT
TTGTTTGATTGCAAGAATTTCAATCTTTTTAACTGACACACATCAATAAATAAAAATTATGACAT
CAAATTTCTATTATTATATCTTTATAGACATAAATTTTTTAAAGAATTTAAAATTTTACTATATT
AATCATTTGTTGTTATATGCATGACTACACATTTCATGTAGAGAGATTTAGATATATATATATAT
A
Found at i:1288228 original size:2 final size:2
Alignment explanation
Indices: 1288211--1288263 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
1288201 TGCAAAAGAA
*
1288211 AT AT AT -T AT A- AG 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
1288251 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1288264 CTCCGAAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1288452 original size:20 final size:18
Alignment explanation
Indices: 1288427--1288467 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
1288417 AAAATATTTA
*
1288427 TAAATTTAGATTAATTTAAT
1 TAAATTTAAATT-A-TTAAT
1288447 TAAATTTAAATTATTAAT
1 TAAATTTAAATTATTAAT
1288465 TAA
1 TAA
1288468 TAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAATTTAAATTATTAAT
Found at i:1293548 original size:25 final size:24
Alignment explanation
Indices: 1293494--1293561 Score: 61
Period size: 27 Copynumber: 2.8 Consensus size: 24
1293484 ATTAAATTTA
1293494 AAAAATTTAATTAATTTATTAAAAT
1 AAAAATTTAATTAATTTATT-AAAT
*
1293519 TAAAATTTAATTTAATTTTATTGATAA-
1 AAAAATTTAA-TTAA-TTTATT-A-AAT
1293546 AAAAA-TTAA-TAATTTA
1 AAAAATTTAATTAATTTA
1293562 AATTTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 4 0.11
24 3 0.08
25 9 0.24
26 8 0.22
27 11 0.30
28 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
AAAAATTTAATTAATTTATTAAAT
Found at i:1293549 original size:26 final size:24
Alignment explanation
Indices: 1293492--1293555 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
1293482 AAATTAAATT
1293492 TAAAAAATTTAA-TTAATTTATTA
1 TAAAAAATTTAATTTAATTTATTA
*
1293515 AAATTAAAATTTAATTTAATTTTATTGA
1 TAA--AAAATTTAATTTAA-TTTATT-A
*
1293543 TAAAAAAATTAAT
1 TAAAAAATTTAAT
1293556 AATTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 2 0.06
25 9 0.27
26 13 0.39
27 6 0.18
28 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAAAAATTTAATTTAATTTATTA
Found at i:1293587 original size:17 final size:17
Alignment explanation
Indices: 1293553--1293603 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1293543 TAAAAAAATT
*
1293553 AATAATTTAAATTTAAA
1 AATAATTTAAATTCAAA
*
1293570 AATAATTTATATTC-AA
1 AATAATTTAAATTCAAA
* *
1293586 AATGATTTGAATTCAAA
1 AATAATTTAAATTCAAA
1293603 A
1 A
1293604 TAACTCGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
AATAATTTAAATTCAAA
Found at i:1293593 original size:16 final size:16
Alignment explanation
Indices: 1293553--1293606 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1293543 TAAAAAAATT
* *
1293553 AATAATTTAAATTTAAA
1 AATAATTTGAA-TTCAA
1293570 AATAATTT-ATATTCAA
1 AATAATTTGA-ATTCAA
*
1293586 AATGATTTGAATTCAA
1 AATAATTTGAATTCAA
1293602 AATAA
1 AATAA
1293607 CTCGAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 22 0.69
17 10 0.31
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (16 bp):
AATAATTTGAATTCAA
Found at i:1293751 original size:37 final size:36
Alignment explanation
Indices: 1293665--1293780 Score: 110
Period size: 37 Copynumber: 3.1 Consensus size: 36
1293655 CACAAATCTA
1293665 AATTTACTTAAA-TAATTAATTCAAAATGACTTAAATTT
1 AATTTACTTAAATTAATTAATTC-AAATG--TTAAATTT
* *
1293703 AAAATTA-TTAAATTTAATTAATTCGAATGTTAAATTT
1 -AATTTACTTAAA-TTAATTAATTCAAATGTTAAATTT
* * * *
1293740 AATTTACTTAAAATCAATTAATTTAAATATTAAATCT
1 AATTTACTT-AAATTAATTAATTCAAATGTTAAATTT
1293777 AATT
1 AATT
1293781 AATTCAAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
36 5 0.08
37 33 0.51
38 8 0.12
39 9 0.14
40 10 0.15
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (36 bp):
AATTTACTTAAATTAATTAATTCAAATGTTAAATTT
Found at i:1293794 original size:21 final size:21
Alignment explanation
Indices: 1293750--1293794 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1293740 AATTTACTTA
* *
1293750 AAATCAATTAATTTAAATATT
1 AAATCAATTAATTCAAATAGT
1293771 AAATCTAATTAATTCAAA-AGT
1 AAATC-AATTAATTCAAATAGT
1293792 AAA
1 AAA
1293795 ATGATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATCAATTAATTCAAATAGT
Found at i:1293822 original size:11 final size:11
Alignment explanation
Indices: 1293806--1293834 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1293796 TGATAAAAAA
1293806 TTAAAATTATT
1 TTAAAATTATT
1293817 TTAAAA-TATT
1 TTAAAATTATT
1293827 TTAAAATT
1 TTAAAATT
1293835 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:1294377 original size:19 final size:18
Alignment explanation
Indices: 1294353--1294392 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1294343 ATAAAATATT
1294353 TTAAAATATAAT-TATAATA
1 TTAAAATA-AATATATAA-A
1294372 TTAAAATAAATATATAAA
1 TTAAAATAAATATATAAA
1294390 TTA
1 TTA
1294393 TCATATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAATAAATATATAAA
Found at i:1294389 original size:48 final size:49
Alignment explanation
Indices: 1294259--1294390 Score: 132
Period size: 48 Copynumber: 2.8 Consensus size: 49
1294249 AATACGATTA
* * * *
1294259 TATAAATATAATAAAAAATAAAAATATA-ATATAAATATATAAATTTTT
1 TATAAATATAATTAAATATTAAAATATATATATAAATATATAAATATTT
* *
1294307 TATAAAT-T-ATTAATATAATTAAAAT-TTTACATAAATATA-AAATATTT
1 TATAAATATAATTAA-AT-ATTAAAATATATATATAAATATATAAATATTT
*
1294354 TA-AAATATAATTATAATATTAAAATAAATATATAAAT
1 TATAAATATAATTA-AATATTAAAATATATATATAAAT
1294391 TATCATATCT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
46 8 0.12
47 21 0.31
48 38 0.56
49 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (49 bp):
TATAAATATAATTAAATATTAAAATATATATATAAATATATAAATATTT
Found at i:1295331 original size:10 final size:11
Alignment explanation
Indices: 1295308--1295336 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1295298 TATTAAGTAA
1295308 ATATAAAAATT
1 ATATAAAAATT
1295319 ATATAAAAA-T
1 ATATAAAAATT
1295329 ATATAAAA
1 ATATAAAA
1295337 CTAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:1297482 original size:21 final size:21
Alignment explanation
Indices: 1297458--1297559 Score: 81
Period size: 21 Copynumber: 4.9 Consensus size: 21
1297448 GTTAAATTAT
1297458 TTTAAATTTATATTAATTAAA
1 TTTAAATTTATATTAATTAAA
1297479 TTTAAAATTT-TAATTAA-TAAA
1 TTT-AAATTTAT-ATTAATTAAA
*
1297500 TTTAAAATTTA-AATAATTTAAA
1 TTT-AAATTTATATTAA-TTAAA
1297522 TTT-AA-TT-TATTAATTTAAA
1 TTTAAATTTATATTAA-TTAAA
* * *
1297541 ATTAAATTTAAATAAATTA
1 TTTAAATTTATATTAATTA
1297560 TTTAATCAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
19 14 0.21
20 8 0.12
21 23 0.34
22 22 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAATTTATATTAATTAAA
Found at i:1297483 original size:6 final size:6
Alignment explanation
Indices: 1297458--1297553 Score: 62
Period size: 6 Copynumber: 16.2 Consensus size: 6
1297448 GTTAAATTAT
* *
1297458 TTTAAA TTTATA -TT-AA -TTAAA TTTAAAA TTTTAA TTAATAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TT--TAAA TTT-AAA
*
1297507 TTTAAA --T-AA TTTAAA TTT-AA TTTATTAA TTTAAA ATTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
1297553 T
1 T
1297554 AAATTATTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
3 2 0.03
4 4 0.06
5 10 0.14
6 33 0.46
7 12 0.17
8 11 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:1297486 original size:22 final size:22
Alignment explanation
Indices: 1297456--1297526 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
1297446 GAGTTAAATT
*
1297456 ATTTTAAATTTATATTAATTAA
1 ATTTAAAATTTATATTAATTAA
1297478 ATTTAAAATTT-TAATTAA-TAA
1 ATTTAAAATTTAT-ATTAATTAA
*
1297499 ATTTAAAATTTA-AATAATTTAA
1 ATTTAAAATTTATATTAA-TTAA
1297521 ATTTAA
1 ATTTAA
1297527 TTTATTAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 4 0.09
21 15 0.35
22 24 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAAATTTATATTAATTAA
Found at i:1297493 original size:28 final size:27
Alignment explanation
Indices: 1297456--1297551 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 27
1297446 GAGTTAAATT
1297456 ATTTTAAATTTATATTAATTAAATTTAAA
1 ATTTT-AATTTA-ATTAATTAAATTTAAA
*
1297485 ATTTTAA-TTAATAAATTTAAAATTTAAATA
1 ATTTTAATTTAATTAA-TT-AAATTT-AA-A
* *
1297515 ATTTAAATTTAATTTATT-AATTTAAA
1 ATTTTAATTTAATTAATTAAATTTAAA
*
1297541 A-TTAAATTTAA
1 ATTTTAATTTAA
1297552 ATAAATTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
25 10 0.17
26 6 0.10
27 7 0.12
28 13 0.22
29 7 0.12
30 9 0.16
31 6 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTTAATTTAATTAATTAAATTTAAA
Found at i:1297508 original size:15 final size:16
Alignment explanation
Indices: 1297490--1297545 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 16
1297480 TTAAAATTTT
1297490 AATTAATA-AATTTAA
1 AATTAATATAATTTAA
1297505 AATTTAA-ATAATTTAA
1 AA-TTAATATAATTTAA
*
1297521 ATTTAATTTATTAATTTAA
1 AATTAA--TA-TAATTTAA
1297540 AATTAA
1 AATTAA
1297546 ATTTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.21
16 12 0.36
18 1 0.03
19 13 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAATATAATTTAA
Found at i:1297521 original size:43 final size:39
Alignment explanation
Indices: 1297458--1297555 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 39
1297448 GTTAAATTAT
*
1297458 TTTAAATTTATATTAATTAAATTTAAAATT-TTAATTAATAAA
1 TTTAAATTTA-AATAATTAAATTT-AAATTATTAATT--TAAA
*
1297500 TTTAAAATTTAAATAATTTAAATTTAATTTATTAATTTAAA
1 TTT-AAATTTAAATAA-TTAAATTTAAATTATTAATTTAAA
*
1297541 ATTAAATTTAAATAA
1 TTTAAATTTAAATAA
1297556 ATTATTTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
40 12 0.24
41 6 0.12
42 11 0.22
43 21 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
TTTAAATTTAAATAATTAAATTTAAATTATTAATTTAAA
Found at i:1297528 original size:20 final size:21
Alignment explanation
Indices: 1297504--1297555 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1297494 AATAAATTTA
1297504 AAATTTAAATAATTT-AAATT
1 AAATTTAAATAATTTAAAATT
* *
1297524 TAATTT-ATTAATTTAAAATT
1 AAATTTAAATAATTTAAAATT
1297544 AAATTTAAATAA
1 AAATTTAAATAA
1297556 ATTATTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 15 0.58
21 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTTAAATAATTTAAAATT
Found at i:1297537 original size:35 final size:36
Alignment explanation
Indices: 1297460--1297547 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 36
1297450 TAAATTATTT
* *
1297460 TAAATTT-ATATTAATTAAATTTAAAATTTTAATTAA
1 TAAATTTAAAATTAAAT-AATTTAAAATTTTAATTAA
*
1297496 TAAATTTAAAATTTAAATAATTT-AAA-TTTAATTTA
1 TAAATTTAAAA-TTAAATAATTTAAAATTTTAATTAA
*
1297531 TTAATTTAAAATTAAAT
1 TAAATTTAAAATTAAAT
1297548 TTAAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 6 0.13
35 18 0.39
36 10 0.22
37 7 0.15
38 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TAAATTTAAAATTAAATAATTTAAAATTTTAATTAA
Found at i:1297557 original size:15 final size:14
Alignment explanation
Indices: 1297459--1297559 Score: 68
Period size: 15 Copynumber: 7.2 Consensus size: 14
1297449 TTAAATTATT
*
1297459 TTAAATTTATATTAA
1 TTAAATTTA-ATAAA
*
1297474 TTAAATTTAA-AAT
1 TTAAATTTAATAAA
*
1297487 TTTAA-TTAATAAA
1 TTAAATTTAATAAA
*
1297500 TTTAAAATTTAAATAAT
1 -TT-AAATTT-AATAAA
**
1297517 TTAAATTTAATTTA
1 TTAAATTTAATAAA
1297531 TT-AATTT-A-AAA
1 TTAAATTTAATAAA
1297542 TTAAATTTAAATAAA
1 TTAAATTT-AATAAA
1297557 TTA
1 TTA
1297560 TTTAATCAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
11 3 0.05
12 10 0.15
13 12 0.18
14 9 0.14
15 23 0.35
16 4 0.06
17 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAATTTAATAAA
Found at i:1297557 original size:35 final size:35
Alignment explanation
Indices: 1297472--1297558 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
1297462 AATTTATATT
*
1297472 AATTAAATTT-AA-AATTTTAATTAATAAATTTAA
1 AATTAAATTTAAATAAATTTAATTAATAAATTTAA
* * *
1297505 AATTTAAA--TAATTTAAATTTAATTTATTAATTTAA
1 AA-TTAAATTTAA-ATAAATTTAATTAATAAATTTAA
1297540 AATTAAATTTAAATAAATT
1 AATTAAATTTAAATAAATT
1297559 ATTTAATCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
32 1 0.02
33 3 0.07
34 10 0.23
35 26 0.60
36 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (35 bp):
AATTAAATTTAAATAAATTTAATTAATAAATTTAA
Found at i:1297562 original size:25 final size:25
Alignment explanation
Indices: 1297517--1297564 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1297507 TTTAAATAAT
**
1297517 TTAAATTTAATTTATTAATTTAAAA
1 TTAAATTTAATAAATTAATTTAAAA
1297542 TTAAATTTAAATAAATT-ATTTAA
1 TTAAATTT-AATAAATTAATTTAA
1297565 TCAAATCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAAATTTAATAAATTAATTTAAAA
Found at i:1298243 original size:19 final size:18
Alignment explanation
Indices: 1298214--1298264 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1298204 AACATATATA
*
1298214 TAATTAAAATTTTTAAAT
1 TAATAAAAATTTTTAAAT
*
1298232 TAATAAAAAATTAATTAAAT
1 TAAT-AAAAATT-TTTAAAT
*
1298252 TGATAAAAATTTT
1 TAATAAAAATTTT
1298265 AAAAAACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 5 0.19
19 13 0.48
20 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATAAAAATTTTTAAAT
Found at i:1298456 original size:13 final size:13
Alignment explanation
Indices: 1298431--1298464 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1298421 TAATACAATC
1298431 AATAAATTTAATTA
1 AATAAA-TTAATTA
*
1298445 ATTAAATTAATTA
1 AATAAATTAATTA
1298458 AATAAAT
1 AATAAAT
1298465 AATAAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAAATTAATTA
Found at i:1298524 original size:22 final size:22
Alignment explanation
Indices: 1298499--1298541 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1298489 TTAATTTAAT
*
1298499 TTTTTTAAAATTAAAT-TAAAA
1 TTTTTTAAAAATAAATATAAAA
1298520 TTTTTTAAAAATAAATATAAAA
1 TTTTTTAAAAATAAATATAAAA
1298542 ACACAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTTTAAAAATAAATATAAAA
Found at i:1302343 original size:2 final size:2
Alignment explanation
Indices: 1302336--1302365 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1302326 TTTCGCTTCC
1302336 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
1302366 TGCAGGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1303233 original size:19 final size:19
Alignment explanation
Indices: 1303211--1303248 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1303201 TAAATACATT
1303211 TTTTTTTAT-TTTATAACTA
1 TTTTTTTATATTT-TAACTA
1303230 TTTTTTTATATTTTAACTA
1 TTTTTTTATATTTTAACTA
1303249 AGATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTTATATTTTAACTA
Found at i:1303325 original size:111 final size:112
Alignment explanation
Indices: 1303210--1303423 Score: 353
Period size: 111 Copynumber: 1.9 Consensus size: 112
1303200 GTAAATACAT
* * *
1303210 TTTTTTTTATTTTATAACTA-TTTT-TTTATATTTTAACTAAGATTTTTTAAGTTTTACTGCATT
1 TTTTTTTTATTTTATAACAATTTTTATTTATATTTTAACTAACATTTTTTAAGTTTTACTACATT
* *
1303273 TTATCACATTA-TTTCTTTAATAGGCAATTTAAAAAAAATTAATTTA
66 TCATCACATTATTTTCTTTAATAGGCAAATTAAAAAAAATTAATTTA
*
1303319 TTTTTTTTATTTTATAGCAATTTTTATTTATATTTTAACTAACATTTTTTAAGTTTTACTACATT
1 TTTTTTTTATTTTATAACAATTTTTATTTATATTTTAACTAACATTTTTTAAGTTTTACTACATT
1303384 TCATCACATTATTTTCTTTAATAGGCAAATTAAAAAAAAT
66 TCATCACATTATTTTCTTTAATAGGCAAATTAAAAAAAAT
1303424 GGAGACCAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 18 0.19
110 4 0.04
111 47 0.49
112 27 0.28
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (112 bp):
TTTTTTTTATTTTATAACAATTTTTATTTATATTTTAACTAACATTTTTTAAGTTTTACTACATT
TCATCACATTATTTTCTTTAATAGGCAAATTAAAAAAAATTAATTTA
Found at i:1306872 original size:183 final size:182
Alignment explanation
Indices: 1306564--1306923 Score: 711
Period size: 183 Copynumber: 2.0 Consensus size: 182
1306554 GAGTTTAGGG
1306564 CTCCTCTATAGTTCTTTTTGTATATAAAATATTCTTTCATACACTTAGCAATCCTACACCCATTT
1 CTCCTCTATAGTTCTTTTTGTATATAAAATATTCTTTCATACACTTAGCAATCCTACACCCATTT
1306629 GAGCATATTGAATTTGCATCCTAAAGCAAATAAAACACGAATTCATAATTTCATCAGTTCAACTT
66 GAGCATATTGAATTTGCATCCTAAAGCAAATAAAACACGAATTCATAATTTCATCAGTTCAACTT
1306694 TAAAGTAATTCTCCTAAAAAACCTTCGAAGATAAGTGAGGTAATTAAAATATT
131 TAAAGTAATTCTCCT-AAAAACCTTCGAAGATAAGTGAGGTAATTAAAATATT
1306747 CTCCTCTATAGTTCTTTTTGTATATAAAATATTCTTTCATACACTTAGCAATCCTACACCCATTT
1 CTCCTCTATAGTTCTTTTTGTATATAAAATATTCTTTCATACACTTAGCAATCCTACACCCATTT
1306812 GAGCATATTGAATTTGCATCCTAAAGCAAATAAAACACGAATTCATAATTTCATCAGTTCAACTT
66 GAGCATATTGAATTTGCATCCTAAAGCAAATAAAACACGAATTCATAATTTCATCAGTTCAACTT
1306877 TAAAGTAATTCTCCTAAAAACCTTCGAAGATAAGTGAGGTAATTAAA
131 TAAAGTAATTCTCCTAAAAACCTTCGAAGATAAGTGAGGTAATTAAA
1306924 CCTGGGTCAT
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 32 0.18
183 145 0.82
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (182 bp):
CTCCTCTATAGTTCTTTTTGTATATAAAATATTCTTTCATACACTTAGCAATCCTACACCCATTT
GAGCATATTGAATTTGCATCCTAAAGCAAATAAAACACGAATTCATAATTTCATCAGTTCAACTT
TAAAGTAATTCTCCTAAAAACCTTCGAAGATAAGTGAGGTAATTAAAATATT
Found at i:1315627 original size:25 final size:25
Alignment explanation
Indices: 1315589--1315643 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1315579 AAAATTTTAA
* *
1315589 TAATTTATTTAATAATATATAAAAT
1 TAATTTAATAAATAATATATAAAAT
* * *
1315614 TAATTTAATAAATAATTTTTATAAT
1 TAATTTAATAAATAATATATAAAAT
1315639 TAATT
1 TAATT
1315644 AAATTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATTTAATAAATAATATATAAAAT
Found at i:1315983 original size:29 final size:29
Alignment explanation
Indices: 1315951--1316007 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1315941 AATTTTTAAA
* * *
1315951 TAAATTTATTTTTTACTTAAATTTATTTT
1 TAAATTAATATTTTACTTAAATTCATTTT
*
1315980 TAAATTAATATTTTATTTAAATTCATTT
1 TAAATTAATATTTTACTTAAATTCATTT
1316008 AAATTTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
TAAATTAATATTTTACTTAAATTCATTTT
Found at i:1315987 original size:17 final size:17
Alignment explanation
Indices: 1315942--1316002 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1315932 TGACTTTAAA
1315942 ATTTTTAAA-TAAATTT
1 ATTTTTAAATTAAATTT
* *
1315958 ATTTTTTACTTAAATTT
1 ATTTTTAAATTAAATTT
1315975 ATTTTTAAATTAATATTT
1 ATTTTTAAATTAA-ATTT
*
1315993 -TATTTAAATT
1 ATTTTTAAATT
1316003 CATTTAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
16 7 0.18
17 27 0.71
18 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAAATTAAATTT
Found at i:1316276 original size:14 final size:14
Alignment explanation
Indices: 1316257--1316287 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1316247 TTTGCTTAAC
1316257 AAAATAAATAAATA
1 AAAATAAATAAATA
*
1316271 AAAATAATTAAATA
1 AAAATAAATAAATA
1316285 AAA
1 AAA
1316288 TGGGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:1316746 original size:13 final size:13
Alignment explanation
Indices: 1316730--1316762 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1316720 TAAGATAAAA
1316730 ATTAAATTT-TTT
1 ATTAAATTTATTT
1316742 GATTAAATTTATTT
1 -ATTAAATTTATTT
1316756 ATTAAAT
1 ATTAAAT
1316763 AAAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
ATTAAATTTATTT
Found at i:1318298 original size:29 final size:29
Alignment explanation
Indices: 1318222--1318300 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
1318212 ATTTATCTCG
1318222 TTTATAAAAAA-TAATATTAATAATAAATA
1 TTTATAAAAAATTAATATT-ATAATAAATA
** * ** *
1318251 TTTATAAAATTTTATTATTATAATTTATT
1 TTTATAAAAAATTAATATTATAATAAATA
*
1318280 TTTTTAAAAAATTAATATTAT
1 TTTATAAAAAATTAATATTAT
1318301 TTATACATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 33 0.85
30 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTATAAAAAATTAATATTATAATAAATA
Found at i:1319869 original size:19 final size:20
Alignment explanation
Indices: 1319842--1319880 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1319832 TAAATTTAAA
1319842 AAAAGTTATATTAATTAATT
1 AAAAGTTATATTAATTAATT
* *
1319862 AAAA-TTATTTTGATTAATT
1 AAAAGTTATATTAATTAATT
1319881 TAATTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AAAAGTTATATTAATTAATT
Found at i:1320058 original size:25 final size:25
Alignment explanation
Indices: 1320029--1320076 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1320019 AAATATAATA
*
1320029 TAAATAATTAAATA-TATTAAAATTT
1 TAAAT-ATTAAATATTAATAAAATTT
1320054 TAAATATTAAATATTAATAAAAT
1 TAAATATTAAATATTAATAAAAT
1320077 CATATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAATATTAAATATTAATAAAATTT
Found at i:1323117 original size:17 final size:16
Alignment explanation
Indices: 1323086--1323124 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1323076 TATGAATATA
*
1323086 TTTATTTTTAAAATTT
1 TTTATTTTAAAAATTT
1323102 TTTATATTTAAAAATTT
1 TTTAT-TTTAAAAATTT
*
1323119 TATATT
1 TTTATT
1323125 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATTTTAAAAATTT
Found at i:1323121 original size:15 final size:16
Alignment explanation
Indices: 1323080--1323124 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1323070 GTTTTATATG
*
1323080 AATATATTTATTTTTAA
1 AATAT-TTTATATTTAA
*
1323097 AATTTTTTATATTTAA
1 AATATTTTATATTTAA
1323113 AA-ATTTTATATT
1 AATATTTTATATT
1323125 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.36
16 12 0.48
17 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATATTTTATATTTAA
Found at i:1330190 original size:20 final size:20
Alignment explanation
Indices: 1330162--1330206 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1330152 GTGTGTAAAT
1330162 GATTGTATGTTACGTTTTAA
1 GATTGTATGTTACGTTTTAA
* * *
1330182 GATTTTATGTTGCTTTTTAA
1 GATTGTATGTTACGTTTTAA
1330202 GATTG
1 GATTG
1330207 CATGCTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.53
Consensus pattern (20 bp):
GATTGTATGTTACGTTTTAA
Found at i:1336670 original size:29 final size:31
Alignment explanation
Indices: 1336613--1336682 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
1336603 GAAAGTCTAT
* *
1336613 TTATCTAAATGTAAATTAAAAATTTAAAAAA
1 TTATTTAAATGTAAATTAAAAATATAAAAAA
* *
1336644 TTATTTAAATGT-AA-TAAAGATATAAAAAT
1 TTATTTAAATGTAAATTAAAAATATAAAAAA
1336673 TTATTTAAAT
1 TTATTTAAAT
1336683 AAAATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 22 0.63
30 2 0.06
31 11 0.31
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (31 bp):
TTATTTAAATGTAAATTAAAAATATAAAAAA
Found at i:1336700 original size:23 final size:24
Alignment explanation
Indices: 1336656--1336701 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1336646 ATTTAAATGT
* *
1336656 AATAAAGATATAAAAATTTATTTA
1 AATAAAGATAAAAAAATATATTTA
1336680 AATAAA-ATAAAAAAATATATTT
1 AATAAAGATAAAAAAATATATTT
1336702 TTTAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAAAGATAAAAAAATATATTTA
Found at i:1337036 original size:20 final size:21
Alignment explanation
Indices: 1337013--1337058 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1337003 TGAAAATATT
*
1337013 TTAAAATTTTTATTTTTAT-A
1 TTAAAATTTATATTTTTATAA
*
1337033 TTAATATTTATATTTTTATAA
1 TTAAAATTTATATTTTTATAA
1337054 TTAAA
1 TTAAA
1337059 TATATATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAAATTTATATTTTTATAA
Found at i:1337064 original size:20 final size:20
Alignment explanation
Indices: 1337023--1337065 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1337013 TTAAAATTTT
*
1337023 TATTTTTATATTAATATTTA
1 TATTTTTATATTAATATATA
1337043 TATTTTTATAATTAA-ATATA
1 TATTTTTAT-ATTAATATATA
1337063 TAT
1 TAT
1337066 ACAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTATATTAATATATA
Found at i:1337397 original size:18 final size:19
Alignment explanation
Indices: 1337374--1337434 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
1337364 TAATATTAAA
* *
1337374 AAATTTTAATGTAAAT-TT
1 AAATTTAAATATAAATATT
1337392 AAATTTAAATATAAATAATT
1 AAATTTAAATATAAAT-ATT
*
1337412 AAATTTAAA-ATAAATATA
1 AAATTTAAATATAAATATT
1337430 AAATT
1 AAATT
1337435 ATTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 21 0.55
19 6 0.16
20 11 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATTTAAATATAAATATT
Found at i:1337415 original size:20 final size:19
Alignment explanation
Indices: 1337390--1337427 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1337380 TAATGTAAAT
1337390 TTAAATTTAAATATAAATAA
1 TTAAATTTAAA-ATAAATAA
1337410 TTAAATTTAAAATAAATA
1 TTAAATTTAAAATAAATA
1337428 TAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATTTAAAATAAATAA
Found at i:1337433 original size:26 final size:27
Alignment explanation
Indices: 1337380--1337431 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
1337370 TAAAAAATTT
*
1337380 TAATGTAAATTTAAATTTAAATATAAA
1 TAATGTAAATTTAAATATAAATATAAA
1337407 TAAT-TAAATTTAAA-ATAAATATAAA
1 TAATGTAAATTTAAATATAAATATAAA
1337432 ATTATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.42
26 10 0.42
27 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TAATGTAAATTTAAATATAAATATAAA
Found at i:1337607 original size:30 final size:30
Alignment explanation
Indices: 1337571--1337628 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1337561 CCACGTAAAA
* *
1337571 ATTTGTGGCTGTTAATAGACGCGCATTTAC
1 ATTTGTGGATGTTAATAAACGCGCATTTAC
1337601 ATTTGTGGATGTTAATAAACGCGCATTT
1 ATTTGTGGATGTTAATAAACGCGCATTT
1337629 CTCGCGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (30 bp):
ATTTGTGGATGTTAATAAACGCGCATTTAC
Found at i:1339546 original size:13 final size:14
Alignment explanation
Indices: 1339516--1339548 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1339506 TAAAATTTAA
*
1339516 TAAAAATAATATAT
1 TAAATATAATATAT
1339530 TAAATATAATA-AT
1 TAAATATAATATAT
1339543 TAAATA
1 TAAATA
1339549 ATTTTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATATAATATAT
Found at i:1340660 original size:5 final size:5
Alignment explanation
Indices: 1340650--1340734 Score: 72
Period size: 5 Copynumber: 17.4 Consensus size: 5
1340640 GTATTATTTT
* * *
1340650 TTATA TTATA TATATA TTA-A -TATA TTTATA TAATT TTATA TTATT TTAATA
1 TTATA TTATA T-TATA TTATA TTATA -TTATA TTATA TTATA TTATA TT-ATA
*
1340701 TTATA TTATA TT-T- TTA-A TTATT TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
1340735 TACGTAATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
3 4 0.06
4 6 0.09
5 41 0.64
6 13 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1340687 original size:35 final size:39
Alignment explanation
Indices: 1340648--1340733 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 39
1340638 TCGTATTATT
1340648 TTTTATATTATATAT-ATATTA-A-TATATTTAT-ATAA
1 TTTTATATTATATATAATATTATATTATATTTATAATAA
* * *
1340683 TTTTATATTAT-TTTAATATTATATTATATTTTTAATTA
1 TTTTATATTATATATAATATTATATTATATTTATAATAA
1340721 TTTTATATTATAT
1 TTTTATATTATAT
1340734 TTACGTAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
34 2 0.05
35 17 0.40
36 1 0.02
37 8 0.19
38 14 0.33
39 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTATATTATATATAATATTATATTATATTTATAATAA
Found at i:1340701 original size:27 final size:25
Alignment explanation
Indices: 1340670--1340733 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 25
1340660 TATATATTAA
1340670 TATATTTATATAATTTTATATTATTT
1 TATATTTATATAATTTTA-ATTATTT
*
1340696 TAATATTATATTATATTTTTAATTATTT
1 T-ATATT-TA-TATAATTTTAATTATTT
1340724 TATA-TTATAT
1 TATATTTATAT
1340734 TTACGTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 3 0.09
25 2 0.06
26 2 0.06
27 8 0.24
28 10 0.29
29 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATATTTATATAATTTTAATTATTT
Found at i:1341212 original size:2 final size:2
Alignment explanation
Indices: 1341205--1341234 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1341195 ATTCAGTTGG
1341205 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
1341235 TAGATTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1345351 original size:22 final size:20
Alignment explanation
Indices: 1345317--1345358 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1345307 TTGAATTTAT
1345317 AATCTATTAATTATATATTAAA
1 AATCTATTAATTA-A-ATTAAA
1345339 AATCATATT-ATTAAATTAAA
1 AATC-TATTAATTAAATTAAA
1345359 TATAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 8 0.42
23 4 0.21
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
AATCTATTAATTAAATTAAA
Found at i:1345666 original size:18 final size:18
Alignment explanation
Indices: 1345643--1345678 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1345633 TGCTAAAAAG
1345643 CCTTTAATTCATCATTCT
1 CCTTTAATTCATCATTCT
*
1345661 CCTTTAGTTCATCATTCT
1 CCTTTAATTCATCATTCT
1345679 TAGGGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (18 bp):
CCTTTAATTCATCATTCT
Found at i:1346385 original size:3 final size:3
Alignment explanation
Indices: 1346377--1346422 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1346367 ATTTTTACAT
1346377 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1346423 GATGATGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1346427 original size:3 final size:3
Alignment explanation
Indices: 1346421--1346452 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1346411 AATAATAATA
1346421 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1346453 CATCATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1346457 original size:3 final size:3
Alignment explanation
Indices: 1346451--1346479 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1346441 GATGATGATG
1346451 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1346480 GATACTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:1348144 original size:18 final size:17
Alignment explanation
Indices: 1348092--1348145 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 17
1348082 ATAAAAGATT
1348092 TATATT-TAATAAATTA
1 TATATTATAATAAATTA
*
1348108 T-TAGTAT-ATAAATTTA
1 TATATTATAATAAA-TTA
1348124 TATATTATAAGTAAATTA
1 TATATTATAA-TAAATTA
1348142 TATA
1 TATA
1348146 ATATGCGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 8 0.26
16 6 0.19
17 5 0.16
18 8 0.26
19 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
TATATTATAATAAATTA
Found at i:1348592 original size:5 final size:4
Alignment explanation
Indices: 1348549--1348590 Score: 57
Period size: 4 Copynumber: 9.8 Consensus size: 4
1348539 ATTACTCTGG
1348549 AAAT AACAT AAAAT AAAT AAAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AA-AT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAA
1348591 ATCTTAGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 25 0.71
5 8 0.23
6 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1349458 original size:20 final size:22
Alignment explanation
Indices: 1349435--1349484 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
1349425 TATTAAAAAT
1349435 TATATAATAAAAATTAT-T-AA
1 TATATAATAAAAATTATATAAA
*
1349455 TATAT--TAAAATTTATATAAA
1 TATATAATAAAAATTATATAAA
1349475 TATATAATAA
1 TATATAATAA
1349485 TTTAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 12 0.48
22 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATAATAAAAATTATATAAA
Found at i:1349463 original size:18 final size:18
Alignment explanation
Indices: 1349425--1349479 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 18
1349415 TATATGTATT
1349425 TATTAAAAATTA-T-ATA
1 TATTAAAAATTATTAATA
1349441 -A-TAAAAATTATTAATA
1 TATTAAAAATTATTAATA
*
1349457 TATTAAAATTTATATAAATA
1 TATTAAAAATTAT-T-AATA
1349477 TAT
1 TAT
1349480 AATAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 9 0.28
15 2 0.06
16 3 0.09
17 1 0.03
18 9 0.28
19 1 0.03
20 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAAAAATTATTAATA
Found at i:1349495 original size:22 final size:20
Alignment explanation
Indices: 1349436--1349488 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
1349426 ATTAAAAATT
* *
1349436 ATATAATAAAAATTAT-T-A
1 ATATATTAAAATTTATATAA
1349454 ATATATTAAAATTTATATAA
1 ATATATTAAAATTTATATAA
1349474 ATATA-TAATAATTTA
1 ATATATTAA-AATTTA
1349489 AATATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.47
19 4 0.13
20 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATTAAAATTTATATAA
Found at i:1351236 original size:2 final size:2
Alignment explanation
Indices: 1351229--1351267 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1351219 TGTTCCACTT
1351229 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
1351268 GTATGTATGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1360699 original size:9 final size:9
Alignment explanation
Indices: 1360685--1360730 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
1360675 CTTCAGGTTG
1360685 AACATCAGC
1 AACATCAGC
* *
1360694 AACATCTGG
1 AACATCAGC
1360703 AACATCAGC
1 AACATCAGC
* *
1360712 AACATCTGA
1 AACATCAGC
1360721 AACATCAGC
1 AACATCAGC
1360730 A
1 A
1360731 TTCTTGCTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.15
Consensus pattern (9 bp):
AACATCAGC
Found at i:1360707 original size:18 final size:18
Alignment explanation
Indices: 1360684--1360730 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1360674 TCTTCAGGTT
1360684 GAACATCAGCAACATCTG
1 GAACATCAGCAACATCTG
1360702 GAACATCAGCAACATCTG
1 GAACATCAGCAACATCTG
*
1360720 AAACATCAGCA
1 GAACATCAGCA
1360731 TTCTTGCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.15
Consensus pattern (18 bp):
GAACATCAGCAACATCTG
Found at i:1362489 original size:3 final size:3
Alignment explanation
Indices: 1362481--1362513 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1362471 CTGAAGAATG
1362481 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1362514 TTTCCAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1364617 original size:24 final size:24
Alignment explanation
Indices: 1364585--1364643 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1364575 ATATATATCG
1364585 TATTT-ATAATTAAAATTT-TAATA
1 TATTTAATAATTAAAATTTAT-ATA
* *
1364608 TATTTAATAATTTAAATTTATTTA
1 TATTTAATAATTAAAATTTATATA
1364632 TATTTATATAAT
1 TATTTA-ATAAT
1364644 GAACATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 20 0.65
25 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTAATAATTAAAATTTATATA
Found at i:1364629 original size:18 final size:17
Alignment explanation
Indices: 1364589--1364631 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1364579 ATATCGTATT
* *
1364589 TATAATTAAAATTTTAA
1 TATATTTAAAATTTAAA
1364606 TATATTTAATAATTTAAA
1 TATATTTAA-AATTTAAA
*
1364624 TTTATTTA
1 TATATTTA
1364632 TATTTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTTAAAATTTAAA
Found at i:1365221 original size:13 final size:13
Alignment explanation
Indices: 1365191--1365243 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
1365181 ATCTTGATTA
*
1365191 TAAATATTAAAATT
1 TAAATATT-AATTT
1365205 TAAATATTAATTT
1 TAAATATTAATTT
* *
1365218 TAAATAATAATTA
1 TAAATATTAATTT
1365231 TATAA-ATTAATTT
1 TA-AATATTAATTT
1365244 AAGTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATATTAATTT
Found at i:1366392 original size:19 final size:18
Alignment explanation
Indices: 1366368--1366422 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
1366358 TGGTTTTTTT
1366368 TTTTTAAAGTAATATAAA
1 TTTTTAAAGTAATATAAA
*
1366386 GTTTTT-ATGTAA-ATATAA
1 -TTTTTAAAGTAATATA-AA
1366404 TTTTTAAA--AATATAAA
1 TTTTTAAAGTAATATAAA
1366420 TTT
1 TTT
1366423 AGGGTGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 7 0.23
17 11 0.35
18 8 0.26
19 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTTTAAAGTAATATAAA
Found at i:1366641 original size:37 final size:37
Alignment explanation
Indices: 1366566--1366653 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
1366556 TTAAAATTAT
*
1366566 TATTTATATAATAAAAATTATTTAAATTTAATTATAAA
1 TATTAATATAA-AAAAATTATTTAAATTTAATTATAAA
* * *
1366604 TATTAATATAAAAATATTTTTTAAATATT-ATTTTAAA
1 TATTAATATAAAAAAATTATTTAAAT-TTAATTATAAA
* *
1366641 TAATAAAATAAAA
1 TATTAATATAAAA
1366654 TTTTAAGTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
37 31 0.72
38 12 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (37 bp):
TATTAATATAAAAAAATTATTTAAATTTAATTATAAA
Found at i:1366945 original size:21 final size:21
Alignment explanation
Indices: 1366893--1366948 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1366883 ATTATTTTAT
*
1366893 TAAAATTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
1366915 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
1366935 TAATTTTTTAATAT
1 TAA-ATTTTAATAT
1366949 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 15 0.52
22 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1366987 original size:31 final size:31
Alignment explanation
Indices: 1366929--1366987 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1366919 TATTAATATA
* **
1366929 AAAATATAATTTTTTAATATTTTTAAATAAT
1 AAAATATAATTTTTTAAAATTGATAAATAAT
1366960 AAAAT-TAATTTTTTAAAATTCGATAAAT
1 AAAATATAATTTTTTAAAATT-GATAAAT
1366988 TAAATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
AAAATATAATTTTTTAAAATTGATAAATAAT
Found at i:1368371 original size:13 final size:14
Alignment explanation
Indices: 1368341--1368385 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1368331 ATAAATTGGA
*
1368341 TAAAATTAAATTTC
1 TAAATTTAAATTTC
1368355 TAAATTTAAATTT-
1 TAAATTTAAATTTC
* *
1368368 TAAATTTTAATATC
1 TAAATTTAAATTTC
1368382 TAAA
1 TAAA
1368386 AAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTAAATTTC
Found at i:1368385 original size:21 final size:21
Alignment explanation
Indices: 1368346--1368385 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1368336 TTGGATAAAA
*
1368346 TTAAATTTCTAAATTTAAATT
1 TTAAATTTCTAAATCTAAATT
1368367 TTAAATTT-TAATATCTAAA
1 TTAAATTTCTAA-ATCTAAA
1368386 AAAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATTTCTAAATCTAAATT
Found at i:1368841 original size:53 final size:50
Alignment explanation
Indices: 1368747--1368846 Score: 114
Period size: 53 Copynumber: 1.9 Consensus size: 50
1368737 AGTATTTAAA
**
1368747 ATATATTAAAATATTTTAAGTTAATATTTATATATTTTTATAATTAAATTT
1 ATATATTAAAATATTTTAAGTTAATATTTATATATACTTAT-ATTAAATTT
*
1368798 ATATATTAAAAAATATTTTATA-TTAATTATTTATCTA-ACTTATATTAAA
1 ATATATT--AAAATATTTTA-AGTTAA-TATTTATATATACTTATATTAAA
1368847 GAGATGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
51 7 0.17
52 6 0.14
53 19 0.45
54 10 0.24
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (50 bp):
ATATATTAAAATATTTTAAGTTAATATTTATATATACTTATATTAAATTT
Found at i:1369340 original size:25 final size:28
Alignment explanation
Indices: 1369305--1369361 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 28
1369295 CTTTTATCTC
1369305 TAATACATATTAAATGTAAT-TAAAAT-
1 TAATACATATTAAATGTAATATAAAATA
* *
1369331 TAATA-ATATTATATGTGATATAAAATA
1 TAATACATATTAAATGTAATATAAAATA
1369358 TAAT
1 TAAT
1369362 TTAAAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 12 0.44
26 11 0.41
27 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (28 bp):
TAATACATATTAAATGTAATATAAAATA
Found at i:1369454 original size:32 final size:33
Alignment explanation
Indices: 1369412--1369513 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 33
1369402 TGAATACATA
* * *
1369412 AATATTTTAAAATTTATAT-AATATAAATTATT
1 AATATATTAAAAATTATATAAATATAAAATATT
1369444 AATATATTAAAAATTATATAAATATAAAATATTTT
1 AATATATTAAAAATTATATAAATATAAAATA--TT
*
1369479 AAATATAATTAAAATATAATA-AAATATATAAATAT
1 -AATAT-ATTAAAA-ATTATATAAATATA-AAATAT
1369514 ACATATTACT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.29
33 10 0.17
35 2 0.03
36 6 0.10
37 14 0.24
38 10 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATATTAAAAATTATATAAATATAAAATATT
Found at i:1369457 original size:18 final size:18
Alignment explanation
Indices: 1369436--1369492 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
1369426 TATATAATAT
1369436 AAATTATTAATATATTAA
1 AAATTATTAATATATTAA
1369454 AAATTATATAA-ATA-TAA
1 AAATTAT-TAATATATTAA
1369471 AATATT-TTAAATATAATTAA
1 AA-ATTATT-AATAT-ATTAA
1369491 AA
1 AA
1369493 TATAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.03
17 8 0.24
18 15 0.45
19 4 0.12
20 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTATTAATATATTAA
Found at i:1369513 original size:18 final size:18
Alignment explanation
Indices: 1369348--1369514 Score: 54
Period size: 18 Copynumber: 8.7 Consensus size: 18
1369338 ATTATATGTG
1369348 ATATA-AAATATAATTTAAA
1 ATATATAAATATAA--TAAA
* *
1369367 ATATGATAAAAATATGATATA
1 ATAT-AT--AAATATAATAAA
* * *
1369388 ATATAAAAATATTAT-GA
1 ATATATAAATATAATAAA
* **
1369405 ATACATAAATATTTTAAA
1 ATATATAAATATAATAAA
* *
1369423 ATTTATATAATATAAATTATTA
1 ATATATA-AATAT-AA-TA-AA
* *
1369445 ATATATTAAAAATTATATAA
1 ATATA-TAAATATAATA-AA
* *
1369465 ATATA-AAATAT-TTTAA
1 ATATATAAATATAATAAA
1369481 ATATAATTAAAATATAATAAA
1 ATAT-A-T-AAATATAATAAA
1369502 ATATATAAATATA
1 ATATATAAATATA
1369515 CATATTACTT
Statistics
Matches: 110, Mismatches: 23, Indels: 31
0.67 0.14 0.19
Matches are distributed among these distances:
16 6 0.05
17 15 0.14
18 26 0.24
19 10 0.09
20 18 0.16
21 17 0.15
22 9 0.08
23 9 0.08
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATATAAATATAATAAA
Found at i:1369864 original size:20 final size:20
Alignment explanation
Indices: 1369839--1369882 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1369829 TCCTGCTCAA
*
1369839 ATTTAAATTTAATT-TTTATG
1 ATTTAAATTAAATTATTT-TG
1369859 ATTTAAATTAAATTATTTTG
1 ATTTAAATTAAATTATTTTG
1369879 ATTT
1 ATTT
1369883 TATTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTTAAATTAAATTATTTTG
Found at i:1369914 original size:31 final size:32
Alignment explanation
Indices: 1369873--1369937 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
1369863 AAATTAAATT
* *
1369873 ATTTTGATTTT-A-TTAATATTAATTGATTAAA
1 ATTTTAATTTTAATTTAATATTAATT-ATAAAA
*
1369904 ATTTTAATTTTAATTTAATTTTAATTATAAAA
1 ATTTTAATTTTAATTTAATATTAATTATAAAA
1369936 AT
1 AT
1369938 AAATAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
32 8 0.28
33 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
ATTTTAATTTTAATTTAATATTAATTATAAAA
Found at i:1371362 original size:16 final size:16
Alignment explanation
Indices: 1371333--1371366 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1371323 TAATATATAT
1371333 TAAACATAAAAAAATA
1 TAAACATAAAAAAATA
1371349 TAAA-ATAAATAAAATA
1 TAAACATAAA-AAAATA
1371365 TA
1 TA
1371367 CGACAACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAACATAAAAAAATA
Found at i:1371712 original size:51 final size:47
Alignment explanation
Indices: 1371651--1371767 Score: 117
Period size: 51 Copynumber: 2.4 Consensus size: 47
1371641 ATCACACGTG
* * * **
1371651 ATAATAATATTAAATTTGATATTATTAAATAATATAAAATATTTATAAATT
1 ATAAT-ATATTAAATTTAATATAAATAAA-AA-ATAAAATAAATAT-AATT
*
1371702 ATAAATATATTGAATTTAATATAAATAAAAAATAAAATAAATATAATT
1 AT-AATATATTAAATTTAATATAAATAAAAAATAAAATAAATATAATT
*
1371750 ATAATATAATAAAATTTA
1 ATAATAT-ATTAAATTTA
1371768 TAAATTCGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
47 5 0.09
48 14 0.25
49 11 0.20
50 2 0.04
51 21 0.38
52 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (47 bp):
ATAATATATTAAATTTAATATAAATAAAAAATAAAATAAATATAATT
Found at i:1375021 original size:33 final size:35
Alignment explanation
Indices: 1374961--1375027 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 35
1374951 TATGAGTATA
1374961 TTTTTACTTAAATTTAAATATAAATAATTAAATTAT
1 TTTTTACTTAAA-TTAAATATAAATAATTAAATTAT
*
1374997 TTTTTA-TTAAA-TAAATA-AATATAATTTAATT
1 TTTTTACTTAAATTAAATATAA-ATAATTAAATT
1375028 TTTATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 2 0.07
33 16 0.55
35 5 0.17
36 6 0.21
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTTTACTTAAATTAAATATAAATAATTAAATTAT
Found at i:1376561 original size:17 final size:18
Alignment explanation
Indices: 1376539--1376573 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1376529 TGAAGTGTTT
1376539 TAAAAC-TAAATTAATCC
1 TAAAACATAAATTAATCC
1376556 TAAAACTATAAATTAATC
1 TAAAAC-ATAAATTAATC
1376574 TTGAGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAACATAAATTAATCC
Found at i:1376998 original size:16 final size:16
Alignment explanation
Indices: 1376964--1377018 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1376954 TATTTTTAAT
* * *
1376964 TTTTGAGTTTATATCA
1 TTTTAAGTTTAAATTA
* *
1376980 TTTTAATTTTTAATTA
1 TTTTAAGTTTAAATTA
1376996 TTTTTAAGTTTAAATTA
1 -TTTTAAGTTTAAATTA
1377013 TTTTAA
1 TTTTAA
1377019 AATTAAATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTAAGTTTAAATTA
Found at i:1377000 original size:17 final size:17
Alignment explanation
Indices: 1376940--1377016 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
1376930 TAATTAAATT
1376940 AATTATTTTTAA-TTTA
1 AATTATTTTTAAGTTTA
** *
1376956 TTTTTAATTTTTGAGTTTA
1 -AATT-ATTTTTAAGTTTA
* * * *
1376975 TATCA-TTTTAATTTTT
1 AATTATTTTTAAGTTTA
1376991 AATTATTTTTAAGTTTA
1 AATTATTTTTAAGTTTA
1377008 AATTATTTT
1 AATTATTTT
1377017 AAAATTAAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 11 0.24
17 21 0.47
18 9 0.20
19 4 0.09
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (17 bp):
AATTATTTTTAAGTTTA
Found at i:1377086 original size:22 final size:22
Alignment explanation
Indices: 1377061--1377102 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1377051 TTATTTTCCG
* *
1377061 TTTAGATTAAATAAGTTTAATA
1 TTTAAATTAAATAAATTTAATA
*
1377083 TTTAAATTAATTAAATTTAA
1 TTTAAATTAAATAAATTTAA
1377103 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTAAATTAAATAAATTTAATA
Found at i:1377102 original size:15 final size:16
Alignment explanation
Indices: 1377077--1377116 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1377067 TTAAATAAGT
1377077 TTAATATTTAAATTA-A
1 TTAA-ATTTAAATTATA
*
1377093 TTAAATTTAAATTATT
1 TTAAATTTAAATTATA
1377109 TTAAATTT
1 TTAAATTT
1377117 GATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTATA
Found at i:1377664 original size:31 final size:31
Alignment explanation
Indices: 1377601--1377661 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1377591 TCGTTCGATT
* *
1377601 TAAATTTAAATAAAGTATATTTATTTATAAA
1 TAAATTTAATTAAAGTATATTTATTTAAAAA
1377632 TAAATTTAATTAAAGTAT-TGTT-TTTAAAAA
1 TAAATTTAATTAAAGTATAT-TTATTTAAAAA
1377662 ATATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (31 bp):
TAAATTTAATTAAAGTATATTTATTTAAAAA
Found at i:1378835 original size:3 final size:3
Alignment explanation
Indices: 1378827--1378858 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1378817 CCAATGTAAA
1378827 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1378859 ATAGTAGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1379839 original size:14 final size:15
Alignment explanation
Indices: 1379819--1379855 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1379809 ATTCGTATAT
1379819 TTATATTATTT-TTTA
1 TTATATT-TTTATTTA
1379834 -TATATTTTTATTTA
1 TTATATTTTTATTTA
1379848 TTATATTT
1 TTATATTT
1379856 ATGTTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 10 0.50
15 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATATTTTTATTTA
Found at i:1379862 original size:15 final size:14
Alignment explanation
Indices: 1379814--1379933 Score: 52
Period size: 15 Copynumber: 8.4 Consensus size: 14
1379804 ATTAAATTCG
1379814 TATATTTATAT-TAT
1 TATATTTATATAT-T
1379828 T-T-TTTATATATT
1 TATATTTATATATT
*
1379840 TTTATTTATTATATT
1 TATATTTA-TATATT
* *
1379855 TATGTTTAAGATATT
1 TATATTT-ATATATT
* *
1379870 AAATATTTATATAAT
1 -TATATTTATATATT
*
1379885 T-T-TTTATAAATT
1 TATATTTATATATT
* *
1379897 AATAATTTATATTATA
1 TAT-ATTTATA-TATT
*
1379913 TAAATTTTAATATATT
1 TATA-TTT-ATATATT
1379929 TATAT
1 TATAT
1379934 ATTCGTATTA
Statistics
Matches: 77, Mismatches: 17, Indels: 23
0.66 0.15 0.20
Matches are distributed among these distances:
12 17 0.22
13 5 0.06
14 5 0.06
15 29 0.38
16 18 0.23
17 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TATATTTATATATT
Done.