Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold500
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: 2046043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1713324 original size:23 final size:22
Alignment explanation
Indices: 1713259--1713324 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
1713249 ATTTATTTTT
* *
1713259 ATTTAAAATTAATTAATAATTAAT
1 ATTTAAAA-TAAATAA-AATTAAA
**
1713283 ATTTAAAA-AAATATTATTAAA
1 ATTTAAAATAAATAAAATTAAA
1713304 ATTTTAAAATAAATAAAATTA
1 A-TTTAAAATAAATAAAATTA
1713325 TTTTTAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 6 0.18
22 11 0.32
23 9 0.26
24 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTAAAATAAATAAAATTAAA
Found at i:1713327 original size:20 final size:19
Alignment explanation
Indices: 1713304--1713341 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1713294 TATTATTAAA
1713304 ATTTTAAAATAAATAAAATT
1 ATTTTAAAATAAA-AAAATT
*
1713324 ATTTTTAAATAAAAAAAT
1 ATTTTAAAATAAAAAAAT
1713342 GATAATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTTAAAATAAAAAAATT
Found at i:1717553 original size:3 final size:3
Alignment explanation
Indices: 1717541--1717576 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
1717531 TTGAACAATT
1717541 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1717577 GCAATATCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1720121 original size:3 final size:3
Alignment explanation
Indices: 1720113--1720162 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1720103 CATACAAAGA
*
1720113 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1720161 AA
1 AA
1720163 CAAAAGGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1725824 original size:2 final size:2
Alignment explanation
Indices: 1725819--1725847 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1725809 CATCAAAAAA
1725819 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1725848 TTTACTTAGC
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1729095 original size:5 final size:5
Alignment explanation
Indices: 1729085--1729114 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1729075 GTAGTGGTAA
1729085 AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
1729115 TAGTGTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:1734691 original size:2 final size:2
Alignment explanation
Indices: 1734684--1734732 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1734674 TCGGGGACAA
*
1734684 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT -T 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
1734725 AT AT AT AT
1 AT AT AT AT
1734733 CTTGTTACGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1739073 original size:2 final size:2
Alignment explanation
Indices: 1739061--1739095 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1739051 TGGTGTTGTA
1739061 AT AT AT A- AT AT AT A- 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 A
1739096 GGGATAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1739352 original size:12 final size:12
Alignment explanation
Indices: 1739335--1739359 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1739325 CTACTCTCCC
1739335 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1739347 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1739359 T
1 T
1739360 TAAATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:1743298 original size:57 final size:57
Alignment explanation
Indices: 1743228--1743342 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
1743218 GTTTCGTTGA
* * * *
1743228 TTCTAAATCTCTATTGTCATCAATGAACAATCCTGTCATCCATGGATATCAAACGAC
1 TTCTAAACCTCTATGGTCATCAATGAACAAACCTGTCATCCATAGATATCAAACGAC
*
1743285 TTCTAAACCTCTATGGTCATCAATGAACAAACCTGTCATCCATAGATATCAAATGAC
1 TTCTAAACCTCTATGGTCATCAATGAACAAACCTGTCATCCATAGATATCAAACGAC
1743342 T
1 T
1743343 CCATTTACCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.30
Consensus pattern (57 bp):
TTCTAAACCTCTATGGTCATCAATGAACAAACCTGTCATCCATAGATATCAAACGAC
Found at i:1746158 original size:102 final size:102
Alignment explanation
Indices: 1745982--1746180 Score: 290
Period size: 102 Copynumber: 2.0 Consensus size: 102
1745972 CACAGATAGG
* * * * * * *
1745982 TCTTTGTTCTGTAACAACCGCATCGACGCACAGTATACAACTCTTTTTTTGTCGTTCTTAATCTG
1 TCTTTGTCCTGTAACAACCGCATCAACGCACAGCACACAACTCTTTTTGTCTCATTCTTAATCTG
*
1746047 CAGGAATGCAAACATCAGAAAATAACCATTTAGCCAA
66 CAGGAATGCAAACATCAGAAAAGAACCATTTAGCCAA
* * * *
1746084 TCTTTGTCCTGTAACAACCGCATTAAGGCACAGCACACAATTGTTTTTGTCTCATTCTTAATCTG
1 TCTTTGTCCTGTAACAACCGCATCAACGCACAGCACACAACTCTTTTTGTCTCATTCTTAATCTG
1746149 CAGGAATGCAAACATCAGAAAAGAACCATTTA
66 CAGGAATGCAAACATCAGAAAAGAACCATTTA
1746181 TGACAAATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (102 bp):
TCTTTGTCCTGTAACAACCGCATCAACGCACAGCACACAACTCTTTTTGTCTCATTCTTAATCTG
CAGGAATGCAAACATCAGAAAAGAACCATTTAGCCAA
Found at i:1752190 original size:24 final size:24
Alignment explanation
Indices: 1752162--1752211 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1752152 TGAACATTAA
1752162 TTAAAATTTATTTAATT-AT-TATTT
1 TTAAAATTT-TTT-ATTAATATATTT
1752186 TTAAAATTTTTTATTAATATATTT
1 TTAAAATTTTTTATTAATATATTT
1752210 TT
1 TT
1752212 TATTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 3 0.12
23 5 0.21
24 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTAAAATTTTTTATTAATATATTT
Found at i:1764567 original size:2 final size:2
Alignment explanation
Indices: 1764560--1764595 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1764550 CATAAACATA
1764560 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1764596 TGAATTTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1765502 original size:7 final size:7
Alignment explanation
Indices: 1765490--1765518 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1765480 ATATATATAT
1765490 ATATAAA
1 ATATAAA
1765497 ATATAAA
1 ATATAAA
1765504 ATATAAA
1 ATATAAA
1765511 ATATAAA
1 ATATAAA
1765518 A
1 A
1765519 AACACGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATATAAA
Found at i:1765651 original size:45 final size:45
Alignment explanation
Indices: 1765600--1765693 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
1765590 TAAACCAAGT
1765600 GTGAATGAGGTTTGGTTGGTCTAATTACATCAATTTAATTTAAGG
1 GTGAATGAGGTTTGGTTGGTCTAATTACATCAATTTAATTTAAGG
1765645 GTGAATGAGGTTTGGTTGGTCTAATTACATCAATTTAATTTAAGG
1 GTGAATGAGGTTTGGTTGGTCTAATTACATCAATTTAATTTAAGG
1765690 GTGA
1 GTGA
1765694 CCCTGCAGCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (45 bp):
GTGAATGAGGTTTGGTTGGTCTAATTACATCAATTTAATTTAAGG
Found at i:1771008 original size:2 final size:2
Alignment explanation
Indices: 1771001--1771035 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1770991 ATTTTACCTC
*
1771001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1771036 ACTAACAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1771236 original size:21 final size:19
Alignment explanation
Indices: 1771202--1771275 Score: 94
Period size: 21 Copynumber: 3.6 Consensus size: 19
1771192 TTTAAAATAT
*
1771202 ATATTTATATATAAAATTAT
1 ATATTTA-ATATAAAATTAC
1771222 ATATTATCAATATAAAATTAC
1 ATATT-T-AATATAAAATTAC
1771243 ATATTATCAATATAAAATTAC
1 ATATT-T-AATATAAAATTAC
1771264 ATATTTAATATA
1 ATATTTAATATA
1771276 TTATCAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 6 0.12
20 6 0.12
21 38 0.75
22 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTTAATATAAAATTAC
Found at i:1771276 original size:21 final size:21
Alignment explanation
Indices: 1771210--1771275 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
1771200 ATATATTTAT
*
1771210 ATATAAAATTATATATTATCA
1 ATATAAAATTACATATTATCA
1771231 ATATAAAATTACATATTATCA
1 ATATAAAATTACATATTATCA
1771252 ATATAAAATTACATATT-T-A
1 ATATAAAATTACATATTATCA
1771271 ATATA
1 ATATA
1771276 TTATCAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 6 0.14
20 1 0.02
21 37 0.84
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAAATTACATATTATCA
Found at i:1776246 original size:25 final size:23
Alignment explanation
Indices: 1776199--1776265 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 23
1776189 AATATTATTT
*
1776199 TAAAAT-AATATAATAT-AAAAA
1 TAAAATAAATTTAATATAAAAAA
1776220 TAAAATAAATTTAATATAACAAGAA
1 TAAAATAAATTTAATATAA-AA-AA
*
1776245 TAACATAAATATTATATATAA
1 TAAAATAAAT-TTA-ATATAA
1776266 TATTTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.16
22 9 0.24
23 1 0.03
24 2 0.05
25 11 0.29
26 3 0.08
27 6 0.16
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (23 bp):
TAAAATAAATTTAATATAAAAAA
Found at i:1776354 original size:19 final size:17
Alignment explanation
Indices: 1776329--1776492 Score: 73
Period size: 17 Copynumber: 10.6 Consensus size: 17
1776319 TGTAAATTTA
*
1776329 ATAATTTATGTTATATTT
1 ATAATTTATATTATA-TT
*
1776347 ATATATTTTTATTATATT
1 ATA-ATTTATATTATATT
1776365 ATAATTTAT-TTA-A--
1 ATAATTTATATTATATT
*
1776378 ATTA-TTATA-TATA-T
1 ATAATTTATATTATATT
*
1776392 A-AATTTAGA-TATATT
1 ATAATTTATATTATATT
1776407 AATAATTTATATTATA-T
1 -ATAATTTATATTATATT
* *
1776424 A-AATTTA-A--AAAAT
1 ATAATTTATATTATATT
*
1776437 AT-ATTTATATTATGTT
1 ATAATTTATATTATATT
*
1776453 AT-A-TAATATT-T-TT
1 ATAATTTATATTATATT
1776466 ATAATTT-TATATATATT
1 ATAATTTATAT-TATATT
1776483 AT-ATTTATAT
1 ATAATTTATAT
1776493 AATTATGTTA
Statistics
Matches: 113, Mismatches: 13, Indels: 41
0.68 0.08 0.25
Matches are distributed among these distances:
12 8 0.07
13 16 0.14
14 16 0.14
15 16 0.14
16 15 0.13
17 20 0.18
18 12 0.11
19 10 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATAATTTATATTATATT
Found at i:1776374 original size:21 final size:24
Alignment explanation
Indices: 1776350--1776398 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1776340 TATATTTATA
1776350 TATTT-TTATTATAT-TAT-AATT
1 TATTTATTATTATATATATAAATT
1776371 TATTTAAATTATTATATATATAAATT
1 TATTT--ATTATTATATATATAAATT
1776397 TA
1 TA
1776399 GATATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.22
24 9 0.39
25 3 0.13
26 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTATTATTATATATATAAATT
Found at i:1776381 original size:16 final size:17
Alignment explanation
Indices: 1776329--1776396 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 17
1776319 TGTAAATTTA
* *
1776329 ATAATTTATGTTATATTT
1 ATAATTTATATTA-AATT
* *
1776347 ATATATTTTTATTATATT
1 ATA-ATTTATATTAAATT
1776365 ATAATTTAT-TTAAATT
1 ATAATTTATATTAAATT
* *
1776381 ATTATATATA-TAAATT
1 ATAATTTATATTAAATT
1776397 TAGATATATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
16 19 0.47
17 5 0.12
18 8 0.20
19 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (17 bp):
ATAATTTATATTAAATT
Found at i:1776407 original size:26 final size:24
Alignment explanation
Indices: 1776355--1776407 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
1776345 TTATATATTT
**
1776355 TTATTATATTATAATTTATTTAAA
1 TTATTATATTATAATTTAGATAAA
*
1776379 TTATTATATATATAAATTTAGATATA
1 TTATTATAT-TAT-AATTTAGATAAA
1776405 TTA
1 TTA
1776408 ATAATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 3 0.12
26 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATTATATTATAATTTAGATAAA
Found at i:1776461 original size:21 final size:20
Alignment explanation
Indices: 1776435--1776487 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1776425 AATTTAAAAA
1776435 ATATATTTATATTATGTTAT
1 ATATATTTATATTATGTTAT
* * *
1776455 ATAATATTTTTATAATTTTAT
1 AT-ATATTTATATTATGTTAT
1776476 ATATA-TTATATT
1 ATATATTTATATT
1776488 TATATAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 17 0.63
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATATTTATATTATGTTAT
Found at i:1776498 original size:23 final size:23
Alignment explanation
Indices: 1776359--1776498 Score: 69
Period size: 23 Copynumber: 6.0 Consensus size: 23
1776349 ATATTTTTAT
*
1776359 TATATTATAATTTATTTAAATTATTA
1 TATATTAT-ATTTATAT-AATTA-TA
* *
1776385 TATATATAAATTTAGATATATTA-A
1 TATAT-TATATTTATATA-ATTATA
1776409 TA-ATT-TATATTATATAAATT-TA
1 TATATTATAT-TTATAT-AATTATA
* * * *
1776431 AAAAATATATTTATATTATGT-TA
1 TATATTATATTTATATAAT-TATA
*
1776454 TATA--ATATTTTTATAATTTTATA
1 TATATTATATTTATATAA--TTATA
1776477 TATATTATATTTATATAATTAT
1 TATATTATATTTATATAATTAT
1776499 GTTAATATTA
Statistics
Matches: 88, Mismatches: 13, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
21 12 0.14
22 14 0.16
23 27 0.31
24 6 0.07
25 12 0.14
26 15 0.17
27 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TATATTATATTTATATAATTATA
Found at i:1776506 original size:25 final size:25
Alignment explanation
Indices: 1776445--1776509 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1776435 ATATATTTAT
* *
1776445 ATTATGTT-ATATAATATTTTTATA
1 ATTATGTTAATATTATATTTATATA
1776469 ATT-T-TATATATATTATATTTATATA
1 ATTATGT-TA-ATATTATATTTATATA
1776494 ATTATGTTAATATTAT
1 ATTATGTTAATATTAT
1776510 GAGCTTTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 1 0.03
23 2 0.06
24 3 0.09
25 24 0.71
26 3 0.09
27 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
ATTATGTTAATATTATATTTATATA
Found at i:1776713 original size:25 final size:23
Alignment explanation
Indices: 1776685--1776745 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
1776675 GATTATTTAT
1776685 TAATTTTTTTAAAATTAAATATAAA
1 TAATTTTTTTAAAATT-AATA-AAA
*
1776710 TAATTTTATTT-TAATTAATAAAA
1 TAATTTT-TTTAAAATTAATAAAA
*
1776733 TAATATTATTTAA
1 TAAT-TTTTTTAA
1776746 TTTATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 10 0.33
24 6 0.20
25 11 0.37
26 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATTTTTTTAAAATTAATAAAA
Found at i:1776733 original size:23 final size:24
Alignment explanation
Indices: 1776697--1776747 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1776687 ATTTTTTTAA
*
1776697 AATTAAATATAAATAATTTTATTTT
1 AATTAAATATAAATAATATTA-TTT
1776722 AATT-AATA-AAATAATATTATTT
1 AATTAAATATAAATAATATTATTT
1776744 AATT
1 AATT
1776748 TATTTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 4 0.16
25 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTAAATATAAATAATATTATTT
Found at i:1776791 original size:25 final size:25
Alignment explanation
Indices: 1776763--1776813 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1776753 AATAATATAT
*
1776763 AAATTTATATA-TTATTAATTTATTA
1 AAATTTATATACTT-TTAATTCATTA
*
1776788 AAATTTTTATACTTTTAATTCATTA
1 AAATTTATATACTTTTAATTCATTA
1776813 A
1 A
1776814 TTTGTACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATTTATATACTTTTAATTCATTA
Found at i:1776828 original size:23 final size:24
Alignment explanation
Indices: 1776775--1776831 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
1776765 ATTTATATAT
* * *
1776775 TATTAATTTATTAAAATTTTTATAC
1 TATTAATTCATT-AAATTTGTACAC
*
1776800 TTTTAATTCATT-AATTTGTACAC
1 TATTAATTCATTAAATTTGTACAC
1776823 TATTAATTC
1 TATTAATTC
1776832 TTCAGTTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 17 0.63
25 10 0.37
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTAATTCATTAAATTTGTACAC
Found at i:1777063 original size:2 final size:2
Alignment explanation
Indices: 1777056--1777080 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1777046 TTGGATGATG
1777056 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1777081 CAGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1785087 original size:3 final size:3
Alignment explanation
Indices: 1785081--1785117 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1785071 TTTTTTACAG
*
1785081 TAA TAA TCA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1785118 GATTTAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1785546 original size:2 final size:2
Alignment explanation
Indices: 1785541--1785576 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1785531 AGAAAAAAAC
1785541 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1785577 GCCGTTTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1795480 original size:3 final size:3
Alignment explanation
Indices: 1795466--1795508 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1795456 GGAGTGAGTG
*
1795466 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1795509 GAAGAAGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1796270 original size:36 final size:39
Alignment explanation
Indices: 1796222--1796298 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 39
1796212 TTTCAAAAAT
1796222 ATATATAATT-AAATTAAAAATAAATTAA-AAT-ATTTA
1 ATATATAATTAAAATTAAAAATAAATTAATAATAATTTA
* * *
1796258 ATATATACTTAAAATTAAATATAACTTAATAATAATTTA
1 ATATATAATTAAAATTAAAAATAAATTAATAATAATTTA
1796297 AT
1 AT
1796299 TTAACAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 9 0.26
37 16 0.46
38 3 0.09
39 7 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (39 bp):
ATATATAATTAAAATTAAAAATAAATTAATAATAATTTA
Found at i:1796386 original size:8 final size:9
Alignment explanation
Indices: 1796365--1796408 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1796355 AAATTTTTTG
1796365 AATAAAAAT
1 AATAAAAAT
1796374 AATAAAAAT
1 AATAAAAAT
1796383 -ATAAAAATT
1 AATAAAAA-T
*
1796392 AATAATTAAT
1 AATAA-AAAT
1796402 AATAAAA
1 AATAAAA
1796409 TATTTATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.23
9 11 0.37
10 10 0.33
11 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AATAAAAAT
Found at i:1796450 original size:14 final size:14
Alignment explanation
Indices: 1796431--1796457 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1796421 CATTTAAAAT
1796431 TAATTTAAAAATAA
1 TAATTTAAAAATAA
1796445 TAATTTAAAAATA
1 TAATTTAAAAATA
1796458 TATATATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTTAAAAATAA
Found at i:1796534 original size:30 final size:29
Alignment explanation
Indices: 1796468--1796534 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1796458 TATATATTTG
*
1796468 ATAAAAATAAATAAATATTTTTTTAATATT
1 ATAAAAATAAAT-AATATTTTTTTAAAATT
*
1796498 AAAAAAATAAAT-ATATTTTTTATAAAAATT
1 ATAAAAATAAATAATATTTTTT-T-AAAATT
*
1796528 TTAAAAA
1 ATAAAAA
1796535 ATCTTTAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 9 0.29
29 1 0.03
30 21 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAAAAATAAATAATATTTTTTTAAAATT
Found at i:1800932 original size:2 final size:2
Alignment explanation
Indices: 1800925--1800958 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1800915 AAATAAAGGA
1800925 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
1800959 TAATAAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1808986 original size:2 final size:2
Alignment explanation
Indices: 1808979--1809028 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1808969 GGTTACTACA
*
1808979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1809021 AT AT AT AT
1 AT AT AT AT
1809029 TCTATAACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1810389 original size:5 final size:5
Alignment explanation
Indices: 1810379--1810412 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1810369 CTCCCACTCC
*
1810379 AATAT AATAT AGTAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
1810413 GGCCTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1812034 original size:42 final size:43
Alignment explanation
Indices: 1811963--1812085 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 43
1811953 AAATAAAAAA
1811963 ATTTATATATTTACGTATTTATGTATTATTTTTATATAAATTTATAA-T
1 ATTTATATA-TTA--TATTTA--TATTATTTTTATATAAATTT-TAATT
*
1812011 -TTTATATATTAT-TTTATATTTATTTTTAT-TATATTTTAATT
1 ATTTATATATTATATTTATA-TTATTTTTATATAAATTTTAATT
*
1812052 ATTTTTATATTATATTTATATTATTTTTTATATA
1 ATTTATATATTATATTTATATTA-TTTTTATATA
1812086 TTAAAATATT
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
40 3 0.04
41 9 0.13
42 24 0.36
43 17 0.25
44 3 0.04
46 3 0.04
47 8 0.12
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (43 bp):
ATTTATATATTATATTTATATTATTTTTATATAAATTTTAATT
Found at i:1812035 original size:11 final size:11
Alignment explanation
Indices: 1812009--1812084 Score: 70
Period size: 12 Copynumber: 6.8 Consensus size: 11
1811999 TAAATTTATA
1812009 ATTTTATATATT
1 ATTTTATAT-TT
1812021 ATTTTATATTT
1 ATTTTATATTT
1812032 ATTTT-TATTAT
1 ATTTTATATT-T
1812043 ATTTTA-A-TT
1 ATTTTATATTT
1812052 ATTTT-TATATT
1 ATTTTATAT-TT
1812063 ATATTTATATTAT
1 AT-TTTATATT-T
*
1812076 TTTTTATAT
1 ATTTTATAT
1812085 ATTAAAATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
9 7 0.13
10 5 0.09
11 18 0.33
12 20 0.36
13 5 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:1812048 original size:22 final size:23
Alignment explanation
Indices: 1811986--1812088 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 23
1811976 CGTATTTATG
*
1811986 TATTATTTTTATATA--AATTTA
1 TATTATTTTTATATATTATTTTA
1812007 TA--A-TTTTATATATTATTTTA
1 TATTATTTTTATATATTATTTTA
1812027 TATTTATTTTTAT-TA-TATTTTA
1 TA-TTATTTTTATATATTATTTTA
1812049 -ATTA-TTTT-TATATTATATTTA
1 TATTATTTTTATATATTAT-TTTA
1812070 TATTATTTTTTATATATTA
1 TATTA-TTTTTATATATTA
1812089 AAATATTATA
Statistics
Matches: 68, Mismatches: 1, Indels: 22
0.75 0.01 0.24
Matches are distributed among these distances:
18 10 0.15
19 7 0.10
20 13 0.19
21 7 0.10
22 11 0.16
23 3 0.04
24 10 0.15
25 7 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTATTTTTATATATTATTTTA
Found at i:1812053 original size:31 final size:33
Alignment explanation
Indices: 1811987--1812081 Score: 103
Period size: 33 Copynumber: 3.0 Consensus size: 33
1811977 GTATTTATGT
*
1811987 ATTATTTTTATA-TAAATTTATA--AT-TTTATA
1 ATTATTTTTATATTATATTTATATTATATTT-TA
*
1812017 TATTA-TTTTATATT-TATTTTTATTATATTTTA
1 -ATTATTTTTATATTATATTTATATTATATTTTA
*
1812049 ATTATTTTTATATTATATTTATATTATTTTTTA
1 ATTATTTTTATATTATATTTATATTATATTTTA
1812082 TATATTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
30 13 0.24
31 9 0.17
32 13 0.24
33 19 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (33 bp):
ATTATTTTTATATTATATTTATATTATATTTTA
Found at i:1812059 original size:17 final size:16
Alignment explanation
Indices: 1812017--1812067 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1812007 TAATTTTATA
1812017 TATTA-TTTTATA-TT
1 TATTATTTTTATATTT
1812031 TATT-TTTATTATATTT
1 TATTATTT-TTATATTT
*
1812047 TAATTATTTTTATATTA
1 T-ATTATTTTTATATTT
1812064 TATT
1 TATT
1812068 TATATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 6 0.19
17 11 0.35
18 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTATATTT
Found at i:1812086 original size:42 final size:40
Alignment explanation
Indices: 1811986--1812131 Score: 120
Period size: 43 Copynumber: 3.5 Consensus size: 40
1811976 CGTATTTATG
*
1811986 TATTATTTTTATATAAATTTATAATTTTATATATTATTTTA
1 TATTATTTTT-TATATATTTATAATTTTATATATTATTTTA
*
1812027 TATT-TATTTTTATTATATTT-TAATTATTTTTATATTATATTTA
1 TATTAT-TTTTTA-TATATTTATAA-T-TTTATATATTAT-TTTA
* * *
1812070 TATTATTTTTTATATA-TTAAAATATTATAAATTTATATAAATTA
1 TATTATTTTTTATATATTTATAATTTTATATA-TTAT-T---TTA
1812114 -ATTATTTTTTATATATTT
1 TATTATTTTTTATATATTT
1812132 TGATATATTA
Statistics
Matches: 87, Mismatches: 6, Indels: 21
0.76 0.05 0.18
Matches are distributed among these distances:
40 11 0.13
41 24 0.28
42 17 0.20
43 29 0.33
44 6 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (40 bp):
TATTATTTTTTATATATTTATAATTTTATATATTATTTTA
Found at i:1812087 original size:20 final size:20
Alignment explanation
Indices: 1811986--1812131 Score: 95
Period size: 22 Copynumber: 7.0 Consensus size: 20
1811976 CGTATTTATG
*
1811986 TATTATTTTTATATAAATTTA
1 TATTATTTTT-TATATATTTA
*
1812007 TA--ATTTTATATATTATTTTA
1 TATTATTTTTTATA-TA-TTTA
1812027 TATT-TATTTTTATTATATTT-
1 TATTAT-TTTTTA-TATATTTA
1812047 TAATTATTTTTATATTATATTTA
1 T-ATTATTTTT-TA-TATATTTA
*
1812070 TATTATTTTTTATATATTAAAA
1 TATTATTTTTTATATATT--TA
** *
1812092 TATTATAAATTTATATAAATTA
1 TATTAT-TTTTTATAT-ATTTA
1812114 -ATTATTTTTTATATATTT
1 TATTATTTTTTATATATTT
1812132 TGATATATTA
Statistics
Matches: 100, Mismatches: 11, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
18 4 0.04
19 9 0.09
20 20 0.20
21 20 0.20
22 35 0.35
23 10 0.10
24 2 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTTTTTATATATTTA
Found at i:1812894 original size:17 final size:18
Alignment explanation
Indices: 1812869--1812922 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 18
1812859 TAAATTTATT
*
1812869 TATATAAAAT-TTTAAAA
1 TATAAAAAATATTTAAAA
1812886 TATAAAAAATATTTAAATA
1 TATAAAAAATATTTAAA-A
* * *
1812905 AATAATAATTATTTAAAA
1 TATAAAAAATATTTAAAA
1812923 GTGTTAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 15 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAAAAATATTTAAAA
Found at i:1813313 original size:2 final size:2
Alignment explanation
Indices: 1813308--1813361 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
1813298 ATGGAGAAGA
* * *
1813308 AT AT AT AT AG AT AT AG AT AT AT AT ACT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
1813351 AG AT AT AT AT A
1 AT AT AT AT AT A
1813362 CCATCGTGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1824295 original size:23 final size:23
Alignment explanation
Indices: 1824269--1824345 Score: 88
Period size: 22 Copynumber: 3.4 Consensus size: 23
1824259 TTTACACAAA
*
1824269 AATATAAATATATTTTATTTTAT
1 AATATAAATATATTATATTTTAT
**
1824292 AATATAAATATAAAAT-TTTTAT
1 AATATAAATATATTATATTTTAT
*
1824314 AACATAAA-ATATTCATATTTTAT
1 AATATAAATATATT-ATATTTTAT
1824337 -ATATAAATA
1 AATATAAATA
1824346 CAAAATAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 3 0.07
22 21 0.48
23 20 0.45
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATAAATATATTATATTTTAT
Found at i:1824378 original size:28 final size:28
Alignment explanation
Indices: 1824317--1824388 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1824307 TTTTTATAAC
* *
1824317 ATAAAATATTCATATTTTATATATAAAT
1 ATAAAATAATAATATTTTATATATAAAT
*
1824345 ACAAAATAATAATATTTTA-ATAATAAAT
1 ATAAAATAATAATATTTTATAT-ATAAAT
*
1824373 TTAAAAATTAATAATA
1 AT-AAAA-TAATAATA
1824389 AGATGATCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.06
28 22 0.61
29 4 0.11
30 8 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAAAATAATAATATTTTATATATAAAT
Found at i:1825264 original size:2 final size:2
Alignment explanation
Indices: 1825259--1825338 Score: 60
Period size: 2 Copynumber: 40.0 Consensus size: 2
1825249 AAAATGTATC
* *
1825259 AT AT AT AT AT AT AA AT AT AT A- AT -T AGT AT -T CAT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT
* *
1825300 AT AT -T GAT GAT AT AT AA AT TT 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
1825339 GTGAATTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
1 4 0.06
2 52 0.83
3 7 0.11
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1825441 original size:30 final size:30
Alignment explanation
Indices: 1825407--1825465 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1825397 ACATAATTTA
*
1825407 ATTAA-ATAATAATATATAAATTTATATATG
1 ATTAACATAATAA-ATATAAATTTACATATG
*
1825437 ATTAACATATTAAATATAAATTTACATAT
1 ATTAACATAATAAATATAAATTTACATAT
1825466 TTCATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
ATTAACATAATAAATATAAATTTACATATG
Found at i:1826282 original size:2 final size:2
Alignment explanation
Indices: 1826275--1826305 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1826265 CTCCACCCCC
1826275 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
1826306 CATACATACT
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:1828406 original size:2 final size:2
Alignment explanation
Indices: 1828399--1828425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1828389 TCTGTCTGTT
1828399 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1828426 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1838595 original size:2 final size:2
Alignment explanation
Indices: 1838588--1838627 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1838578 TCTAAGTGAA
1838588 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
1838628 TATTCTGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1839797 original size:1 final size:1
Alignment explanation
Indices: 1839791--1839817 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1839781 ATTCGAGCTC
1839791 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1839818 GTTTCTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1840146 original size:13 final size:13
Alignment explanation
Indices: 1840130--1840154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1840120 TAATAGTAAT
1840130 AAGTAATAATCTA
1 AAGTAATAATCTA
1840143 AAGTAATAATCT
1 AAGTAATAATCT
1840155 TAACTTGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
AAGTAATAATCTA
Found at i:1850294 original size:179 final size:178
Alignment explanation
Indices: 1849323--1850570 Score: 2214
Period size: 178 Copynumber: 7.0 Consensus size: 178
1849313 TTTGTTTCTC
* *
1849323 AATGTCTATTCTAGTTGTAAGTAATAATAAATAGCTTCTATTACTAACAACATTCTTATGTAA-A
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
* * ***
1849387 GTACGTCCGAGATAGACAATCAAACATATCCTCGCTCTTTTTCTTCTATTTCTCTCCTAGAACTA
66 -TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTA
*
1849452 GCTTTAAGTATCTAACTAGATCATTGTGTATATTATAAATTTTAAGTTG
130 GCTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
1849501 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAA-A
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
* * *
1849565 GTACGTCCAAGATACACAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTA
66 -TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTA
1849630 GCTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
130 GCTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
1849679 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
* *
1849744 TACGTCCGAGACAGAAAATTAAACATTTCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
66 TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
1849809 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
131 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
1849857 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAA-A
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
* * *
1849921 GTACGTCCAAGATACACAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTA
66 -TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTA
1849986 GCTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
130 GCTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
1850035 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
* *
1850100 TACGTCCGAGACAGAAAATTAAACATTTCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
66 TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
1850165 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTTAAGTTG
131 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAA-TTTTAAGTTG
*
1850214 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCATATGTAACA
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
*
1850279 TACGTCCGAGACAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
66 TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
1850344 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTTAAGTTG
131 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAA-TTTTAAGTTG
*
1850393 AATGTCTATTCTAGTTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
1 AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
1850458 TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
66 TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
* *
1850523 CTTTAAGTATCAAACTAGATCGTTGCGTATATTATAAATTTTTAAGTT
131 CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAA-TTTTAAGTT
1850571 AGTTGAATCT
Statistics
Matches: 1035, Mismatches: 31, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
177 1 0.00
178 672 0.65
179 362 0.35
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (178 bp):
AATGTCTATTCTAATTGTAAGTAATAATAAATAGCCTCTATTACTAACAACATTCTTATGTAACA
TACGTCCGAGATAGAAAATTAAACATATCCTTATTCTTTTTCTTCTATTTCTCTCCTAGAACTAG
CTTTAAGTATCTAACTAGATCGTTGTGTATATTATAAATTTTAAGTTG
Found at i:1853193 original size:21 final size:21
Alignment explanation
Indices: 1853169--1853208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1853159 AAATAATAAA
*
1853169 AAATATTAAATTATTATTTTT
1 AAATATTAAATTAATATTTTT
*
1853190 AAATATTATATTAATATTT
1 AAATATTAAATTAATATTT
1853209 ATTTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATATTAAATTAATATTTTT
Found at i:1853221 original size:22 final size:21
Alignment explanation
Indices: 1853169--1853221 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1853159 AAATAATAAA
* * *
1853169 AAATATTAAATTATTATTTTT
1 AAATAATATATTAATATTTTT
*
1853190 AAATATTATATTAATATTTATT
1 AAATAATATATTAATATTT-TT
*
1853212 TAATAATATA
1 AAATAATATA
1853222 AATAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATAATATATTAATATTTTT
Found at i:1853297 original size:16 final size:16
Alignment explanation
Indices: 1853276--1853307 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1853266 TATATTTATA
*
1853276 TTAATTTTTAAAATAT
1 TTAATTTTAAAAATAT
1853292 TTAATTTTAAAAATAT
1 TTAATTTTAAAAATAT
1853308 AATATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTTTAAAAATAT
Found at i:1854243 original size:2 final size:2
Alignment explanation
Indices: 1854236--1854261 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1854226 AGTAATGACC
1854236 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
1854262 TTGTTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1860971 original size:5 final size:5
Alignment explanation
Indices: 1860961--1860994 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1860951 AATAAAGCAA
*
1860961 TAATC TAATC TAATC TAATC TAATGC TGATC TAA
1 TAATC TAATC TAATC TAATC TAAT-C TAATC TAA
1860995 AAGCATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (5 bp):
TAATC
Found at i:1862791 original size:2 final size:2
Alignment explanation
Indices: 1862784--1862819 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1862774 AATTCATGTC
1862784 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
1862820 GCATTCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1863285 original size:3 final size:3
Alignment explanation
Indices: 1863277--1863304 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1863267 TAATCATTCT
1863277 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1863305 AGTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1863469 original size:3 final size:3
Alignment explanation
Indices: 1863461--1863492 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1863451 CTTAGCTTTG
*
1863461 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1863493 AGCATACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1864329 original size:28 final size:29
Alignment explanation
Indices: 1864282--1864347 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 29
1864272 TTAAAAGTAC
*
1864282 AAAAATTAAAATTTTAATTT-AATAATAT
1 AAAAATTAAAATCTTAATTTGAATAATAT
1864310 AAAAATTAAAATACTT-ATTTGAGAATAATAT
1 AAAAATTAAAAT-CTTAATTT--GAATAATAT
1864341 AAAAATT
1 AAAAATT
1864348 CATAATAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 16 0.48
29 2 0.06
31 15 0.45
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATTAAAATCTTAATTTGAATAATAT
Found at i:1865372 original size:4 final size:4
Alignment explanation
Indices: 1865363--1865388 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1865353 ATTATGTCAC
1865363 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1865389 GATTTCGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1872391 original size:2 final size:2
Alignment explanation
Indices: 1872379--1872432 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1872369 CAACCCAAAT
*
1872379 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1872421 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1872433 GTGATTAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1873177 original size:4 final size:4
Alignment explanation
Indices: 1873153--1873195 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
1873143 GATAAGAACC
* * *
1873153 ATAT CTAT ATAT CTAT CTAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1873196 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:1873200 original size:2 final size:2
Alignment explanation
Indices: 1873195--1873219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1873185 ATATATATAT
1873195 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 A
1873220 AAAGCACCTC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1875466 original size:24 final size:24
Alignment explanation
Indices: 1875416--1875466 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1875406 GTCCAGGCAT
* *
1875416 GCTGTTATCTTTTTATAATAATAA
1 GCTGTTATCTTATTATAATAACAA
*
1875440 GCTGTTATCATTATTATAA-AACCA
1 GCTGTTATC-TTATTATAATAACAA
1875464 GCT
1 GCT
1875467 AGGGAGCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (24 bp):
GCTGTTATCTTATTATAATAACAA
Found at i:1877823 original size:19 final size:19
Alignment explanation
Indices: 1877782--1877824 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1877772 ATTTAAATAC
* *
1877782 AAAATATATATTAGATTTG
1 AAAATATATATTAGAGTTA
1877801 AAAATATATATTTAG-GTTA
1 AAAATATATA-TTAGAGTTA
1877820 AAAAT
1 AAAAT
1877825 GGAATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (19 bp):
AAAATATATATTAGAGTTA
Found at i:1877909 original size:22 final size:24
Alignment explanation
Indices: 1877884--1877935 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
1877874 TTTATTAATT
1877884 TTAAAGATAAATA-TATA-ATATA
1 TTAAAGATAAATATTATAGATATA
*
1877906 TTAAATATAAATATTATATGATATA
1 TTAAAGATAAATATTATA-GATATA
1877931 TTAAA
1 TTAAA
1877936 TAATTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.46
23 4 0.15
25 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TTAAAGATAAATATTATAGATATA
Found at i:1883636 original size:2 final size:2
Alignment explanation
Indices: 1883624--1883682 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
1883614 AACAGAATGA
1883624 AT AT AT A- AT AT AT A- AT AT AT AT AT AT AT AT A- 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
1883663 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1883683 CACTTTCTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1890114 original size:2 final size:2
Alignment explanation
Indices: 1890107--1890145 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1890097 AATTGAAATG
* * *
1890107 TA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1890146 GCATAGAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1890124 original size:12 final size:12
Alignment explanation
Indices: 1890107--1890145 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1890097 AATTGAAATG
*
1890107 TATATATATATA
1 TATATATATAGA
1890119 TATATATATAGA
1 TATATATATAGA
*
1890131 TATAGATATAGA
1 TATATATATAGA
1890143 TAT
1 TAT
1890146 GCATAGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TATATATATAGA
Found at i:1890601 original size:3 final size:3
Alignment explanation
Indices: 1890593--1890622 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1890583 TTAAGAAGCA
1890593 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1890623 GAATGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1892042 original size:16 final size:16
Alignment explanation
Indices: 1892017--1892079 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
1892007 TTTAAGGTCG
1892017 TTTATATTTTTTTATAA
1 TTTAT-TTTTTTTATAA
** *
1892034 TTTATTTTTTAAACAA
1 TTTATTTTTTTTATAA
* * *
1892050 TATATATTTTTTAAAA
1 TTTATTTTTTTTATAA
*
1892066 TTTAATTTTTTTAT
1 TTTATTTTTTTTAT
1892080 TATAATTTAA
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
16 29 0.85
17 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTTTTTTTATAA
Found at i:1892135 original size:38 final size:38
Alignment explanation
Indices: 1892093--1892165 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
1892083 AATTTAATTT
1892093 AATTTTCAATATGTACATTATAACATAAAATATATGTA
1 AATTTTCAATATGTACATTATAACATAAAATATATGTA
* * * *
1892131 AATTTTTAATATTTATATTATAATATAAAATATAT
1 AATTTTCAATATGTACATTATAACATAAAATATAT
1892166 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (38 bp):
AATTTTCAATATGTACATTATAACATAAAATATATGTA
Found at i:1892312 original size:18 final size:18
Alignment explanation
Indices: 1892289--1892341 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
1892279 AGGCTCAATC
1892289 TTTTTAATTAAATTTTAT
1 TTTTTAATTAAATTTTAT
1892307 TTTTT-ATCTAAA-TTTAT
1 TTTTTAAT-TAAATTTTAT
1892324 TTTTTAAATTAATATTTT
1 TTTTT-AATTAA-ATTTT
1892342 TATCTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 12 0.40
18 12 0.40
19 3 0.10
20 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAATTAAATTTTAT
Found at i:1892333 original size:31 final size:29
Alignment explanation
Indices: 1892296--1892360 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
1892286 ATCTTTTTAA
*
1892296 TTAAATTTTAT-TTTTTATCTAAATTTATTTT
1 TTAAATTTAATATTTTTATCT-AA-TT-TTTT
1892327 TTAAA-TTAATATTTTTATCTAATTTTTT
1 TTAAATTTAATATTTTTATCTAATTTTTT
1892355 TTAAAT
1 TTAAAT
1892361 CTGCGTCAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 9 0.29
29 2 0.06
30 6 0.19
31 14 0.45
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
TTAAATTTAATATTTTTATCTAATTTTTT
Found at i:1895171 original size:4 final size:4
Alignment explanation
Indices: 1895164--1895190 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1895154 CCCAAACAAC
1895164 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
1895191 TAAAAAGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1899738 original size:2 final size:2
Alignment explanation
Indices: 1899707--1899767 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
1899697 AGCATCATAC
* * * *
1899707 TA TA TC TA TA TC TA TA TC TA TA TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1899749 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
1899768 CACCAACAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1907069 original size:3 final size:3
Alignment explanation
Indices: 1907063--1907094 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1907053 TCCTAAATAA
*
1907063 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1907095 ATGATATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1907219 original size:18 final size:18
Alignment explanation
Indices: 1907196--1907243 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1907186 ATTGCGATGG
1907196 CGATGGCAATGCCGGTGC
1 CGATGGCAATGCCGGTGC
1907214 CGATGGCAATGCCGGTGC
1 CGATGGCAATGCCGGTGC
*
1907232 CAATGGCAATGC
1 CGATGGCAATGC
1907244 TATGCTGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.21, C:0.27, G:0.35, T:0.17
Consensus pattern (18 bp):
CGATGGCAATGCCGGTGC
Found at i:1910428 original size:2 final size:2
Alignment explanation
Indices: 1910421--1910450 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1910411 ATGTCTGCAC
1910421 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
1910451 TGTGTGTTAA
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:1910758 original size:47 final size:47
Alignment explanation
Indices: 1910704--1910794 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
1910694 GAATTTTTAT
* *
1910704 GTATTCAATTCTCCATTAAGAACCAAATGAGTAAGGGCATACTTGTA
1 GTATTCAATTCTCCACTAAGAACCAAAAGAGTAAGGGCATACTTGTA
*
1910751 GTATTCAATTCTCTACTAAGAACCAAAAGAGTAAGGGCATACTT
1 GTATTCAATTCTCCACTAAGAACCAAAAGAGTAAGGGCATACTT
1910795 ATAATTAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (47 bp):
GTATTCAATTCTCCACTAAGAACCAAAAGAGTAAGGGCATACTTGTA
Found at i:1911305 original size:96 final size:96
Alignment explanation
Indices: 1911141--1911333 Score: 325
Period size: 96 Copynumber: 2.0 Consensus size: 96
1911131 GAAGATTAAA
* * *
1911141 TAAATTTTGATTGATAATGAATCTACCATCAATATTCTTCCTCTAAAGATAATGAAAGAGTTTGG
1 TAAATTCTGATTGATAATGAATCTACCATCAACATTCTTCCTCTAAAGATAATGAAAGAGCTTGG
1911206 AGTTCCTTTAGATGAATTGGTAC-GAAGTTGC
66 AGTTCCTTTAGATGAATTGGTACAG-AGTTGC
* *
1911237 TAAATTCTGATTGATAATGAATCTACTATCAACATTCTTCCTCTTAAGATAATGAAAGAGCTTGG
1 TAAATTCTGATTGATAATGAATCTACCATCAACATTCTTCCTCTAAAGATAATGAAAGAGCTTGG
1911302 AGTTCCTTTAGATGAATTGGTACAGAGTTGC
66 AGTTCCTTTAGATGAATTGGTACAGAGTTGC
1911333 T
1 T
1911334 TGGTGATTCA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 90 0.99
97 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (96 bp):
TAAATTCTGATTGATAATGAATCTACCATCAACATTCTTCCTCTAAAGATAATGAAAGAGCTTGG
AGTTCCTTTAGATGAATTGGTACAGAGTTGC
Found at i:1913851 original size:2 final size:2
Alignment explanation
Indices: 1913844--1913880 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1913834 TTCATGCACG
1913844 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 A
1913881 AGATGCAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1914307 original size:2 final size:2
Alignment explanation
Indices: 1914302--1914326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1914292 TGTGTCTGTG
1914302 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1914327 CATTTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1914433 original size:2 final size:2
Alignment explanation
Indices: 1914428--1914462 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1914418 ATATATATAT
1914428 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1914463 ATAGCTGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1914807 original size:4 final size:4
Alignment explanation
Indices: 1914798--1914824 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1914788 ACAATTTTGC
1914798 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1914825 TTTCGGGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1914947 original size:2 final size:2
Alignment explanation
Indices: 1914942--1914966 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1914932 TTCATTTCCT
1914942 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1914967 TTGGTTATAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1915051 original size:2 final size:2
Alignment explanation
Indices: 1915044--1915068 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1915034 TTTAAGCTCC
1915044 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 C
1915069 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1915104 original size:2 final size:2
Alignment explanation
Indices: 1915068--1915093 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1915058 CTCTCTCTCT
1915068 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
1915094 GATAAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1916015 original size:6 final size:6
Alignment explanation
Indices: 1916004--1916040 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1915994 GGTGCTTATT
* *
1916004 TTTCCC TTTCCC TTCCCC TTTCCC TTTCTC TTTCCC T
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC T
1916041 CCCTCCCGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTCCC
Found at i:1921689 original size:48 final size:48
Alignment explanation
Indices: 1921618--1921717 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 48
1921608 AAATTACTTT
** *
1921618 ATATCTAGCAAGCAATTAACAAACTTTGTGGAAAGTAATTTGAGTTTA
1 ATATCTAGCAAGCAATTAACAAACTTCCTGGAAAGTAATTTAAGTTTA
*
1921666 ATATCTAGC-AGCTAATTAACAAACTTCCTGGAAAGTAATTTAATTTTA
1 ATATCTAGCAAGC-AATTAACAAACTTCCTGGAAAGTAATTTAAGTTTA
1921714 ATAT
1 ATAT
1921718 AAATCCAGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
47 3 0.06
48 44 0.94
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (48 bp):
ATATCTAGCAAGCAATTAACAAACTTCCTGGAAAGTAATTTAAGTTTA
Found at i:1928458 original size:24 final size:24
Alignment explanation
Indices: 1928426--1928473 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1928416 TGATCAATAC
1928426 CACTCATGATTTGCACAAAACTAA
1 CACTCATGATTTGCACAAAACTAA
1928450 CACTCATGATTTGCACAAAACTAA
1 CACTCATGATTTGCACAAAACTAA
1928474 GGCATGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (24 bp):
CACTCATGATTTGCACAAAACTAA
Found at i:1929751 original size:13 final size:13
Alignment explanation
Indices: 1929733--1929759 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1929723 ACAGAGATCA
1929733 AATGTATCGATAC
1 AATGTATCGATAC
1929746 AATGTATCGATAC
1 AATGTATCGATAC
1929759 A
1 A
1929760 TTTAAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1929836 original size:19 final size:18
Alignment explanation
Indices: 1929812--1929874 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1929802 AGCGATACAT
1929812 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
1929831 TGTATCTATAC--A--T-
1 TGTATCGATACAAACTTA
1929844 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1929863 TGTATCGATACA
1 TGTATCGATACA
1929875 GTTACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1929847 original size:32 final size:32
Alignment explanation
Indices: 1929804--1929874 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1929794 AGCTTCGTAG
1929804 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1929836 CTATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1929868 CGATACA
1 CGATACA
1929875 GTTACGGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1930337 original size:16 final size:16
Alignment explanation
Indices: 1930316--1930348 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1930306 TATAAAAGAA
1930316 AGGGTTGATGAAATAG
1 AGGGTTGATGAAATAG
1930332 AGGGTTGATGAAATAG
1 AGGGTTGATGAAATAG
1930348 A
1 A
1930349 AAAGGGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.24
Consensus pattern (16 bp):
AGGGTTGATGAAATAG
Found at i:1932266 original size:21 final size:21
Alignment explanation
Indices: 1932219--1932267 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1932209 TTAACTTTAA
* *
1932219 AAATATA-TTTTTTATTTAAT
1 AAATATATTTTTTTATCTAAC
*
1932239 AATTATATTTTTTTATCTAAC
1 AAATATATTTTTTTATCTAAC
1932260 AAATATAT
1 AAATATAT
1932268 AATTTTATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATATATTTTTTTATCTAAC
Found at i:1932273 original size:22 final size:22
Alignment explanation
Indices: 1932221--1932273 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1932211 AACTTTAAAA
* * *
1932221 ATATATTTTTTATTTAATAATT
1 ATATATTTTTTATCTAACAAAT
1932243 ATAT-TTTTTTATCTAACAAAT
1 ATATATTTTTTATCTAACAAAT
*
1932264 ATATAATTTT
1 ATATATTTTT
1932274 ATTCAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATTTTTTATCTAACAAAT
Found at i:1937482 original size:159 final size:159
Alignment explanation
Indices: 1937193--1937512 Score: 588
Period size: 159 Copynumber: 2.0 Consensus size: 159
1937183 TATTATGTGT
* *
1937193 CCTTGTTCTTGCTTCATTGTTTAGCGGATAATCAAAGCATTAGTTTTGTTTCTTTGATTCGCTAT
1 CCTTGTTCTTGCTTCATGGTTGAGCGGATAATCAAAGCATTAGTTTTGTTTCTTTGATTCGCTAT
1937258 ATTGGTTTGCTTTTAAGGTGAACTAAACTAATTTCCATGCTGTTATTTTGTTTTATCCCTTAGTT
66 ATTGGTTTGCTTTTAAGGTGAACTAAACTAATTTCCATGCTGTTATTTTGTTTTATCCCTTAGTT
1937323 TAACATCACCCTTCTTTCTACTTCTTTTA
131 TAACATCACCCTTCTTTCTACTTCTTTTA
*
1937352 CCTTGTTCTTGCTTCATGGTTGAGCGGATAATCAAAGCATTAGTTTTGTTTCTTTGATTCGCTCT
1 CCTTGTTCTTGCTTCATGGTTGAGCGGATAATCAAAGCATTAGTTTTGTTTCTTTGATTCGCTAT
*
1937417 ATTGGTTTGCATTTT-ATGTGAACTAAACTAATTTCCATGCTGTTATTTTGTTTTATCCCTTAGT
66 ATTGGTTTGC-TTTTAAGGTGAACTAAACTAATTTCCATGCTGTTATTTTGTTTTATCCCTTAGT
1937481 TTAACATCACCCTTCTTTCTACTTCTTTTA
130 TTAACATCACCCTTCTTTCTACTTCTTTTA
1937511 CC
1 CC
1937513 AGTAATTTAT
Statistics
Matches: 156, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
159 152 0.97
160 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (159 bp):
CCTTGTTCTTGCTTCATGGTTGAGCGGATAATCAAAGCATTAGTTTTGTTTCTTTGATTCGCTAT
ATTGGTTTGCTTTTAAGGTGAACTAAACTAATTTCCATGCTGTTATTTTGTTTTATCCCTTAGTT
TAACATCACCCTTCTTTCTACTTCTTTTA
Found at i:1938491 original size:1 final size:1
Alignment explanation
Indices: 1938485--1938509 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1938475 TGGGAGAAGT
1938485 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1938510 CCACTTAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1947504 original size:14 final size:15
Alignment explanation
Indices: 1947480--1947508 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1947470 TCAGCATATT
1947480 CCCCCCGGCCCCCCG
1 CCCCCCGGCCCCCCG
1947495 CCCCCC-GCCCCCCG
1 CCCCCCGGCCCCCCG
1947509 GGAGCGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.83, G:0.17, T:0.00
Consensus pattern (15 bp):
CCCCCCGGCCCCCCG
Found at i:1948877 original size:2 final size:2
Alignment explanation
Indices: 1948870--1948900 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1948860 ATACCAATTT
*
1948870 TA TA TA TA TA TC 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 T
1948901 GTGTGTGTGT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1955321 original size:28 final size:30
Alignment explanation
Indices: 1955280--1955359 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
1955270 ATATATAAAA
*
1955280 AATTTTACTCAAATAAATATTTATATT-T-T
1 AATTTTA-TTAAATAAATATTTATATTATAT
* **
1955309 AATTTTATTAAATACATAAATATATTATAGT
1 AATTTTATTAAATAAATATTTATATTATA-T
*
1955340 AATGTTATTAAATAAATATT
1 AATTTTATTAAATAAATATT
1955360 AAAATAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 15 0.38
29 8 0.20
31 17 0.43
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (30 bp):
AATTTTATTAAATAAATATTTATATTATAT
Found at i:1957945 original size:6 final size:6
Alignment explanation
Indices: 1957934--1957971 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1957924 CCTAAATTAC
* *
1957934 GATGGT GATGGT GAAGGT GATGGT GAAGGT GATGGT GA
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GA
1957972 AAGGCAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.50, T:0.26
Consensus pattern (6 bp):
GATGGT
Found at i:1957954 original size:12 final size:12
Alignment explanation
Indices: 1957937--1957972 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
1957927 AAATTACGAT
1957937 GGTGATGGTGAA
1 GGTGATGGTGAA
1957949 GGTGATGGTGAA
1 GGTGATGGTGAA
1957961 GGTGATGGTGAA
1 GGTGATGGTGAA
1957973 AGGCAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (12 bp):
GGTGATGGTGAA
Found at i:1958042 original size:5 final size:5
Alignment explanation
Indices: 1958031--1958067 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
1958021 GTACCGTAAA
* *
1958031 TCATC ACATC ACATC TCATC TCATC TCATC TCATC TC
1 TCATC TCATC TCATC TCATC TCATC TCATC TCATC TC
1958068 GGAGGCGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (5 bp):
TCATC
Found at i:1958478 original size:17 final size:17
Alignment explanation
Indices: 1958458--1958521 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
1958448 ATAAAAAAAT
*
1958458 TAAAATTATAAATATTA
1 TAAAATTATATATATTA
*
1958475 TAAAATAATATATA-TA
1 TAAAATTATATATATTA
*
1958491 TAATATTA-ATATA-T-
1 TAAAATTATATATATTA
1958505 TAAAATT-TATATATTA
1 TAAAATTATATATATTA
1958521 T
1 T
1958522 GTATTATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 11 0.28
15 7 0.18
16 9 0.23
17 12 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATTATATATATTA
Found at i:1958542 original size:22 final size:22
Alignment explanation
Indices: 1958508--1958552 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1958498 AATATATTAA
* *
1958508 AATTTATATATTATGTATTATT
1 AATTTATATATTATATATAATT
1958530 AATTTATCA-ATTATATATAATT
1 AATTTAT-ATATTATATATAATT
1958552 A
1 A
1958553 TTGACCCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTATATATTATATATAATT
Found at i:1963189 original size:3 final size:3
Alignment explanation
Indices: 1963183--1963220 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1963173 AATAATAAAT
1963183 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1963221 TTTCCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1963942 original size:6 final size:6
Alignment explanation
Indices: 1963931--1963959 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1963921 GAGAGATTCC
1963931 TAGTCT TAGTCT TAGTCT TAGTCT TAGTC
1 TAGTCT TAGTCT TAGTCT TAGTCT TAGTC
1963960 ATAGCCTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
TAGTCT
Found at i:1965849 original size:3 final size:3
Alignment explanation
Indices: 1965841--1965869 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1965831 AATCAAACCC
1965841 ACT ACT ACT ACT ACT ACT ACT ACT ACT AC
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT AC
1965870 CGAACTGTCT
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:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
ACT
Done.