Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 11 of 444
Found at i:3220751 original size:122 final size:124
Alignment explanation
Indices: 3220533--3220766 Score: 339
Period size: 122 Copynumber: 1.9 Consensus size: 124
3220523 TCGTGTCCTG
* *
3220533 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
3220598 TGCCCGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTTGAAAAACCAAAATAAAA
66 TGCCCGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTTGAAAAACCAAAATAAAA
* * * * * *
3220657 AGGCTTAACTCACCTCTCGTAGTATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* * *
3220719 TGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA
66 TG-CCCGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTTGAAAA
3220767 TAAAAATTAC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
121 23 0.23
122 49 0.50
123 1 0.01
124 25 0.26
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTTGAAAAACCAAAATAAAA
Found at i:3220770 original size:69 final size:71
Alignment explanation
Indices: 3220657--3220831 Score: 196
Period size: 71 Copynumber: 2.5 Consensus size: 71
3220647 CAAAATAAAA
* * * * * *
3220657 AGGCTTAACTCACCTCTCGTAGTATGAG-TCAATTTAAAACAT-AAACTAAAAATACCTCAGCGT
1 AGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTAAAACATAAAACTAAAAATACCTCAACGT
3220720 GTCCCG
66 GTCCCG
* * * *
3220726 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-ATAAAAATTACAAATACCTCAACG
1 AGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTAAAACAT-AAAACTAAAAATACCTCAACG
**
3220790 TGTCTTG
65 TGTCCCG
3220797 AGGCTCAACTCA-TCTCTCGTAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGTAATATGAGTTGATTT
3220832 CCCTTGAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
69 26 0.29
70 9 0.10
71 54 0.61
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (71 bp):
AGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTAAAACATAAAACTAAAAATACCTCAACGT
GTCCCG
Found at i:3220805 original size:193 final size:197
Alignment explanation
Indices: 3220380--3220831 Score: 551
Period size: 193 Copynumber: 2.3 Consensus size: 197
3220370 ATGAAGACAG
* *
3220380 AAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGA
1 AAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
** * * * *
3220445 AAAAGTAGAAATTAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAAT
65 AAAACCAGAAATAAAAGGTTCAACCCACCTCTCGCAATATGAGTTCAATCTTGACAAACAGAAAC
* * * *
3220510 TGAAATTACCTCATCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACA
130 TAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACA
3220575 CAA
195 CAA
* * *
3220578 AAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTTGAA
1 AAATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAA
* * * *
3220643 AAACCA-AAATAAAAAGGCTT-AACTCACCTCTCGTAGTATGAG-TCAAT-TT-A-AAACATAAA
66 AAACCAGAAAT-AAAAGG-TTCAACCCACCTCTCGCAATATGAGTTCAATCTTGACAAACAGAAA
* ** *
3220702 CTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-
129 CTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAC
*
3220766 ATAA
194 ACAA
* * * *
3220770 AAATT-ACAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGTAATATGAGTTGATTT
1 AAATTGA-AAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
3220832 CCCTTGAAAA
Statistics
Matches: 219, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
191 1 0.00
192 22 0.10
193 96 0.44
194 1 0.00
195 2 0.01
196 7 0.03
197 67 0.31
198 23 0.11
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27
Consensus pattern (197 bp):
AAATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAA
AAACCAGAAATAAAAGGTTCAACCCACCTCTCGCAATATGAGTTCAATCTTGACAAACAGAAACT
AAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACAC
AA
Found at i:3225854 original size:12 final size:12
Alignment explanation
Indices: 3225834--3225869 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3225824 TGGGATATGC
*
3225834 AATGTATGAATG
1 AATGCATGAATG
3225846 AATGCATGAATG
1 AATGCATGAATG
3225858 AATGCATGAATG
1 AATGCATGAATG
3225870 TCAAATGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:3227739 original size:2 final size:2
Alignment explanation
Indices: 3227732--3227770 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3227722 ATGTACAAAA
3227732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3227771 CGTATGTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3228462 original size:30 final size:32
Alignment explanation
Indices: 3228419--3228479 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
3228409 GGTGGCTAGG
*
3228419 TTTTTTTTATCTTTTTTT-TGTTAGGTTTTTC
1 TTTTTTCTATCTTTTTTTCTGTTAGGTTTTTC
*
3228450 TTTTTTCT-TCTTTTTTTCTTTTAGGTTTTT
1 TTTTTTCTATCTTTTTTTCTGTTAGGTTTTT
3228480 TTTGGGGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (32 bp):
TTTTTTCTATCTTTTTTTCTGTTAGGTTTTTC
Found at i:3228463 original size:27 final size:25
Alignment explanation
Indices: 3228415--3228464 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
3228405 GTTAGGTGGC
*
3228415 TAGGTTTTTTTTATCTTTTTTTTGT
1 TAGGTTTTTTTTATCTTCTTTTTGT
*
3228440 TAGGTTTTTCTTTTTTCTTCTTTTT
1 TAGG-TTTT-TTTTATCTTCTTTTT
3228465 TTCTTTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 4 0.19
27 13 0.62
ACGTcount: A:0.06, C:0.08, G:0.10, T:0.76
Consensus pattern (25 bp):
TAGGTTTTTTTTATCTTCTTTTTGT
Found at i:3228528 original size:47 final size:46
Alignment explanation
Indices: 3228440--3228534 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 46
3228430 TTTTTTTTGT
*
3228440 TAGGTTTTTCTTTTTTCTTCTTTTTTTCTTTTAGGTTTTTTTTGGGG
1 TAGGTTTTTCTTTTTCCTTCTTTTTTTCTTTTAGG-TTTTTTTGGGG
*
3228487 TAGGTTTTTCTTTTTCCTT-TTTTTTTCTTGGGTTTGGTTTTTTTGGGG
1 TAGGTTTTTCTTTTTCCTTCTTTTTTTCTT---TTAGGTTTTTTTGGGG
3228535 GGCATTTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
46 10 0.23
47 18 0.42
48 11 0.26
49 4 0.09
ACGTcount: A:0.03, C:0.08, G:0.20, T:0.68
Consensus pattern (46 bp):
TAGGTTTTTCTTTTTCCTTCTTTTTTTCTTTTAGGTTTTTTTGGGG
Found at i:3230404 original size:24 final size:24
Alignment explanation
Indices: 3230355--3230406 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3230345 AATCAATATC
**
3230355 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAACACT
*
3230379 AAATATATTATGCTCATAAACACT
1 AAATATATTATGCTAATAAACACT
3230403 AAAT
1 AAAT
3230407 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATATATTATGCTAATAAACACT
Found at i:3235670 original size:60 final size:60
Alignment explanation
Indices: 3235577--3235803 Score: 436
Period size: 60 Copynumber: 3.8 Consensus size: 60
3235567 ACCATAATCA
3235577 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTGGGAACTAGTATTT
1 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTGGGAACTAGTATTT
3235637 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTGGGAACTAGTATTT
1 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTGGGAACTAGTATTT
*
3235697 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATGTTCAAGCATTTGGGAACTAGTATTT
1 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTGGGAACTAGTATTT
*
3235757 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAACCATTTG
1 ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTG
3235804 AGTTCCGTTG
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 164 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (60 bp):
ATGGGTTCATAAAGAGGTGCAAATGCAATCCCATTTTCAAGCATTTGGGAACTAGTATTT
Found at i:3240190 original size:23 final size:24
Alignment explanation
Indices: 3240135--3240191 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
3240125 AGGTTCTTTG
* *
3240135 TGAACCTCCCGTTAAAGGCTCTCT
1 TGAACTTCCCGTTAAAGGCTCGCT
* * *
3240159 GGAATTTCCCGTT-AATGCTCGCT
1 TGAACTTCCCGTTAAAGGCTCGCT
3240182 TGAACTTCCC
1 TGAACTTCCC
3240192 ACTATATGGC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.32
Consensus pattern (24 bp):
TGAACTTCCCGTTAAAGGCTCGCT
Found at i:3244932 original size:46 final size:44
Alignment explanation
Indices: 3244828--3244935 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3244818 TGTCTTTGAC
** * * *
3244828 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3244872 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3244918 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3244936 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3251576 original size:21 final size:21
Alignment explanation
Indices: 3251552--3251592 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3251542 ACCTTTTTTA
*
3251552 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGACAAAACTATT
3251573 AAGTTAAAAGACAAAACTAT
1 AAGTTAAAAGACAAAACTAT
3251593 ATTGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGACAAAACTATT
Found at i:3256409 original size:22 final size:22
Alignment explanation
Indices: 3256384--3256426 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3256374 TATCCAAACA
3256384 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
3256406 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
3256427 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:3256430 original size:11 final size:11
Alignment explanation
Indices: 3256391--3256431 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3256381 ACAATAACAA
3256391 CAAAATAGTAG
1 CAAAATAGTAG
* *
3256402 CAACATAATAG
1 CAAAATAGTAG
*
3256413 TAAAATAGTAG
1 CAAAATAGTAG
3256424 CAAAATAG
1 CAAAATAG
3256432 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:3256547 original size:33 final size:34
Alignment explanation
Indices: 3256510--3256582 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 34
3256500 GGCCAAAAAT
*
3256510 GCCTTACCCGTGGCCCGGCCTA-TTTTTAAACAG
1 GCCTTACCCGAGGCCCGGCCTATTTTTTAAACAG
*
3256543 GCCTTACCCGAGGCCCGGCCTATTTTTTAAACGG
1 GCCTTACCCGAGGCCCGGCCTATTTTTTAAACAG
3256577 GCCTTA
1 GCCTTA
3256583 TTTTTTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.27
Consensus pattern (34 bp):
GCCTTACCCGAGGCCCGGCCTATTTTTTAAACAG
Found at i:3257358 original size:20 final size:20
Alignment explanation
Indices: 3257333--3257374 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3257323 ATTTTTTGTA
3257333 AATTTAAAATTTAATTTTTT
1 AATTTAAAATTTAATTTTTT
**
3257353 AATTTAATTTTTAATTTTTT
1 AATTTAAAATTTAATTTTTT
3257373 AA
1 AA
3257375 AGATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTAAAATTTAATTTTTT
Found at i:3257363 original size:12 final size:13
Alignment explanation
Indices: 3257340--3257369 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3257330 GTAAATTTAA
3257340 AATTTAATTTTTT
1 AATTTAATTTTTT
3257353 AATTTAA-TTTTT
1 AATTTAATTTTTT
3257365 AATTT
1 AATTT
3257370 TTTAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:3260388 original size:16 final size:18
Alignment explanation
Indices: 3260349--3260382 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3260339 TAAGTTTAGA
3260349 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
3260366 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
3260383 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:3262067 original size:12 final size:12
Alignment explanation
Indices: 3262050--3262080 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3262040 GATGAGGTAT
3262050 ATACATACATGC
1 ATACATACATGC
3262062 ATACATACATGC
1 ATACATACATGC
*
3262074 ATGCATA
1 ATACATA
3262081 GCTCTCTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (12 bp):
ATACATACATGC
Found at i:3262425 original size:2 final size:2
Alignment explanation
Indices: 3262418--3262461 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
3262408 TTGGGATCTG
*
3262418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3262458 AT AT
1 AT AT
3262462 TTAGAGGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3264160 original size:7 final size:8
Alignment explanation
Indices: 3264133--3264174 Score: 66
Period size: 8 Copynumber: 5.0 Consensus size: 8
3264123 ATATATATAT
3264133 AAATTCAAA
1 AAATT-AAA
3264142 AAATTATAA
1 AAATTA-AA
3264151 AAATTAAA
1 AAATTAAA
3264159 AAATTAAA
1 AAATTAAA
3264167 AAATTAAA
1 AAATTAAA
3264175 CTTTTTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 19 0.59
9 13 0.41
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATTAAA
Found at i:3264168 original size:16 final size:17
Alignment explanation
Indices: 3264128--3264174 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
3264118 TATATATATA
*
3264128 TATATAAATTCAAAAAAT
1 TATAAAAATT-AAAAAAT
3264146 TATAAAAATTAAAAAAT
1 TATAAAAATTAAAAAAT
3264163 TA-AAAAATTAAA
1 TATAAAAATTAAA
3264175 CTTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 10 0.36
17 9 0.32
18 9 0.32
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TATAAAAATTAAAAAAT
Found at i:3264608 original size:2 final size:2
Alignment explanation
Indices: 3264603--3264635 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3264593 CTTTTTTCTT
3264603 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 T
3264636 GTCTTACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3268769 original size:15 final size:16
Alignment explanation
Indices: 3268741--3268770 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3268731 TTTCCACCAT
3268741 ATTTGTTGTTAATTTC
1 ATTTGTTGTTAATTTC
3268757 ATTTGTT-TTAATTT
1 ATTTGTTGTTAATTT
3268771 TATTGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (16 bp):
ATTTGTTGTTAATTTC
Found at i:3276099 original size:18 final size:18
Alignment explanation
Indices: 3276074--3276166 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
3276064 ACCGTTTACG
3276074 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
3276092 GCACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
3276110 GTACTATTCACGTATACG
1 GTACTATTCACGTATACA
* * *
3276128 GTACTATTTACGAATACG
1 GTACTATTCACGTATACA
*
3276146 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
3276164 GTA
1 GTA
3276167 GTTGGGATTG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:3282031 original size:3 final size:3
Alignment explanation
Indices: 3282023--3282048 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3282013 GTATAGAAAA
3282023 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
3282049 ATGTATACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:3283644 original size:58 final size:59
Alignment explanation
Indices: 3283504--3283655 Score: 177
Period size: 59 Copynumber: 2.6 Consensus size: 59
3283494 TTAGTAATTT
* * *
3283504 TTCTCACATTGGGGTCTAAT-TTTTTTTTGTCCAAGTTAGGCTTTGAACTTGGCAACTA
1 TTCTCACATTGAGGTCTAATCTTTTTTTTGTCCAAATTAGGCTTTGAACTTGGCAAATA
** * *
3283562 TTCTCACATTGAGACCTAAACTTTTTTTTGTCCAAATTAGG-TGTTGAACTTGGTAAAT-
1 TTCTCACATTGAGGTCTAATCTTTTTTTTGTCCAAATTAGGCT-TTGAACTTGGCAAATA
*
3283620 TTC-CTAGATTGAGGTCTAATCTTTTTTTTTGTCCAA
1 TTCTC-ACATTGAGGTCTAATC-TTTTTTTTGTCCAA
3283656 GTTAATCATT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 32 0.41
59 46 0.58
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (59 bp):
TTCTCACATTGAGGTCTAATCTTTTTTTTGTCCAAATTAGGCTTTGAACTTGGCAAATA
Found at i:3309366 original size:43 final size:43
Alignment explanation
Indices: 3309305--3309391 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
3309295 CTAACTTGAT
3309305 TTGAAATTTAATTGGAGTCTAATGTGACTTGAATATTAAGAAG
1 TTGAAATTTAATTGGAGTCTAATGTGACTTGAATATTAAGAAG
3309348 TTGAAATTTAATTGGAGTCTAATGTGACTTGAATATTAAGAAG
1 TTGAAATTTAATTGGAGTCTAATGTGACTTGAATATTAAGAAG
3309391 T
1 T
3309392 AAAGGTTGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (43 bp):
TTGAAATTTAATTGGAGTCTAATGTGACTTGAATATTAAGAAG
Found at i:3320128 original size:3 final size:3
Alignment explanation
Indices: 3320120--3320151 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3320110 TAGCTGAAAA
3320120 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3320152 ATGTGAAGAA
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:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3320826 original size:17 final size:18
Alignment explanation
Indices: 3320804--3320846 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
3320794 AACTTATACT
*
3320804 TAAAATTTCAAAAT-TTA
1 TAAAATTACAAAATATTA
3320821 TAAAATTACAAAATATTA
1 TAAAATTACAAAATATTA
3320839 TAAAATTA
1 TAAAATTA
3320847 TTATAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATTACAAAATATTA
Found at i:3320827 original size:9 final size:9
Alignment explanation
Indices: 3320804--3320858 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 9
3320794 AACTTATACT
3320804 TAAAATTT-
1 TAAAATTTA
*
3320812 CAAAATTTA
1 TAAAATTTA
3320821 TAAAA-TTA
1 TAAAATTTA
*
3320829 CAAAATATTA
1 TAAAAT-TTA
3320839 TAAAATTATTA
1 TAAAA-T-TTA
3320850 TAAAATTTA
1 TAAAATTTA
3320859 CATAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 14 0.36
9 7 0.18
10 8 0.21
11 10 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAATTTA
Found at i:3325119 original size:27 final size:27
Alignment explanation
Indices: 3325081--3325132 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3325071 ACTTAATGAA
*
3325081 ATTAGATATCTCGGTGAAGTGCATTTC
1 ATTAGATATCTCGGTAAAGTGCATTTC
3325108 ATTAGATATCTCGGTAAAGTGCATT
1 ATTAGATATCTCGGTAAAGTGCATT
3325133 CCAGTACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (27 bp):
ATTAGATATCTCGGTAAAGTGCATTTC
Found at i:3325408 original size:15 final size:15
Alignment explanation
Indices: 3325390--3325421 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3325380 AAAAAGAATG
3325390 TAAAGATTATTATTT
1 TAAAGATTATTATTT
3325405 TAAAGATTATTATTT
1 TAAAGATTATTATTT
3325420 TA
1 TA
3325422 TAGAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TAAAGATTATTATTT
Found at i:3328344 original size:3 final size:3
Alignment explanation
Indices: 3328336--3328365 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3328326 ATTGCTGAAC
3328336 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3328366 GTGTAAATTA
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):
TTA
Found at i:3328591 original size:3 final size:3
Alignment explanation
Indices: 3328585--3328629 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
3328575 AAATAATAAG
* * *
3328585 AGA AGA AGA TGA AGA AGA AAA AGA AGA AGA AGA AGA ATA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3328630 GAAAAAATGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:3329468 original size:25 final size:25
Alignment explanation
Indices: 3329434--3329481 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3329424 GTTGCAATGG
3329434 TTGAGGAGTAAGCCTCTAAAATCAT
1 TTGAGGAGTAAGCCTCTAAAATCAT
* *
3329459 TTGAGGAGTAAGCTTTTAAAATC
1 TTGAGGAGTAAGCCTCTAAAATC
3329482 TCTAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (25 bp):
TTGAGGAGTAAGCCTCTAAAATCAT
Found at i:3329490 original size:34 final size:34
Alignment explanation
Indices: 3329447--3329515 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
3329437 AGGAGTAAGC
*
3329447 CTCTAAAATCATTTGAGGAGTAAGCTTTTAAAAT
1 CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT
3329481 CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT
1 CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT
3329515 C
1 C
3329516 ATTCTTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (34 bp):
CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT
Found at i:3332507 original size:36 final size:38
Alignment explanation
Indices: 3332429--3332511 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 38
3332419 CAAGTTGTTG
* *
3332429 ATTCAATTGGTCTATTTGTTTTGATTATTTTTTTTTAA
1 ATTCAATTGATCTATTTGTTTTGATTATTTATTTTTAA
*
3332467 ATTCAATTGATTTAATTT-TTTT-ATT-TTTATTTTTAA
1 ATTCAATTGATCT-ATTTGTTTTGATTATTTATTTTTAA
3332503 ATTCAATTG
1 ATTCAATTG
3332512 GTACGAACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
36 19 0.46
37 3 0.07
38 15 0.37
39 4 0.10
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (38 bp):
ATTCAATTGATCTATTTGTTTTGATTATTTATTTTTAA
Found at i:3339347 original size:16 final size:16
Alignment explanation
Indices: 3339322--3339352 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3339312 CCACTTATAT
*
3339322 TGTCTGCCATTAATGC
1 TGTCTCCCATTAATGC
3339338 TGTCTCCCATTAATG
1 TGTCTCCCATTAATG
3339353 TTAACAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (16 bp):
TGTCTCCCATTAATGC
Found at i:3353631 original size:10 final size:10
Alignment explanation
Indices: 3353616--3353644 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3353606 ACCACCCTGA
3353616 CAAACAGTAC
1 CAAACAGTAC
3353626 CAAACAGTAC
1 CAAACAGTAC
3353636 CAAACAGTA
1 CAAACAGTA
3353645 AAAAAACGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.28, G:0.10, T:0.10
Consensus pattern (10 bp):
CAAACAGTAC
Found at i:3353856 original size:8 final size:8
Alignment explanation
Indices: 3353843--3353881 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
3353833 GAAAAAGAGA
3353843 GAAGAAGG
1 GAAGAAGG
3353851 GAAGAAGG
1 GAAGAAGG
3353859 GAAGAAGG
1 GAAGAAGG
*
3353867 GAAGAAGA
1 GAAGAAGG
3353875 GAAGAAG
1 GAAGAAG
3353882 AAGAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (8 bp):
GAAGAAGG
Found at i:3353895 original size:16 final size:17
Alignment explanation
Indices: 3353830--3353897 Score: 50
Period size: 19 Copynumber: 3.8 Consensus size: 17
3353820 CATTTTCAGC
3353830 AAAGAA-AAAGAGAGAAG
1 AAAGAAGAAAGA-AGAAG
* *
3353847 AAGGGAAGAAGGGAAGAAGG
1 AA-AGAAGAA-AGAAGAA-G
*
3353867 GAAGAAGAGAAGAAGAAG
1 AAAGAAGA-AAGAAGAAG
3353885 AAAGAA-AAAGAAG
1 AAAGAAGAAAGAAG
3353898 GAGAGGAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
16 6 0.15
17 3 0.08
18 9 0.22
19 17 0.43
20 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAGAAGAAG
Found at i:3354273 original size:21 final size:21
Alignment explanation
Indices: 3354248--3354287 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3354238 AGATTTTTTT
3354248 AATTTATTTGATTTATTATAG
1 AATTTATTTGATTTATTATAG
* * *
3354269 AATTTTTTTTATTTTTTAT
1 AATTTATTTGATTTATTAT
3354288 TTTTTATGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
AATTTATTTGATTTATTATAG
Found at i:3354482 original size:22 final size:21
Alignment explanation
Indices: 3354434--3354483 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3354424 GTTTTTTTGT
3354434 TAAAATAATATAAAAAAAATA
1 TAAAATAATATAAAAAAAATA
*
3354455 TGAAAATAGTATAATTAAAAAA-A
1 T-AAAATAATATAA--AAAAAATA
3354478 TAAAAT
1 TAAAAT
3354484 TTGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 16 0.64
23 2 0.08
24 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAAATAATATAAAAAAAATA
Found at i:3355511 original size:72 final size:72
Alignment explanation
Indices: 3355418--3355558 Score: 246
Period size: 72 Copynumber: 2.0 Consensus size: 72
3355408 AGTCCGAGCG
*
3355418 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
3355483 GCTCGTC
66 GCTCGTC
* * *
3355490 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCAGGCAATGACAATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
3355555 GCTC
66 GCTC
3355559 ATCGGGGGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
GCTCGTC
Found at i:3355652 original size:33 final size:32
Alignment explanation
Indices: 3355606--3355678 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
3355596 GGGTCGTACA
3355606 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
1 CACCGCAGCATAGCA-CTGC-CCCGGCCCATATC
** *
3355639 CACCGCATTATAGCACTGCCCCGGCCCGTATC
1 CACCGCAGCATAGCACTGCCCCGGCCCATATC
*
3355671 CACTGCAG
1 CACCGCAG
3355679 TACTCCACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.21, C:0.45, G:0.18, T:0.16
Consensus pattern (32 bp):
CACCGCAGCATAGCACTGCCCCGGCCCATATC
Found at i:3359707 original size:15 final size:16
Alignment explanation
Indices: 3359688--3359749 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
3359678 TACCTTCTTT
3359688 TTTTCTTCTCCTTCT-
1 TTTTCTTCTCCTTCTA
*
3359703 TTTTCTTCTTTCTCTTCTC
1 TTTTCTTC--TC-CTTCTA
* *
3359722 CTTTCTT-TCCTTTTA
1 TTTTCTTCTCCTTCTA
3359737 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
3359750 GCTGCTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 18 0.47
16 7 0.18
17 2 0.05
18 5 0.13
19 6 0.16
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTA
Found at i:3359721 original size:24 final size:24
Alignment explanation
Indices: 3359682--3359729 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3359672 AAATTATACC
*
3359682 TTCTTTTTTTCTTCTCC-TTCTTT
1 TTCTTTTTCTCTTCTCCTTTCTTT
3359705 TTCTTCTTTCTCTTCTCCTTTCTTT
1 TTCTT-TTTCTCTTCTCCTTTCTTT
3359730 CCTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (24 bp):
TTCTTTTTCTCTTCTCCTTTCTTT
Found at i:3359919 original size:14 final size:15
Alignment explanation
Indices: 3359902--3359935 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3359892 TTTTTTTTCG
3359902 TTTTTCAG-CTTTTT
1 TTTTTCAGACTTTTT
*
3359916 TTTTTCAGAGTTTTT
1 TTTTTCAGACTTTTT
3359931 TTTTT
1 TTTTT
3359936 ACTGTTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (15 bp):
TTTTTCAGACTTTTT
Found at i:3361429 original size:18 final size:18
Alignment explanation
Indices: 3361394--3361431 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3361384 AATCGACCGA
*
3361394 TTAACCGAATTTGATCGG
1 TTAACCGAATTTAATCGG
3361412 TTAACCGAA-TTAATTCGG
1 TTAACCGAATTTAA-TCGG
3361430 TT
1 TT
3361432 TTACCTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (18 bp):
TTAACCGAATTTAATCGG
Found at i:3370872 original size:28 final size:27
Alignment explanation
Indices: 3370840--3370894 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3370830 AATAATAATG
*
3370840 AAATAT-TTTTTTTATATTTAATTGAACA
1 AAATATATATTTTT-TATTTAA-TGAACA
3370868 AAATATATATTTTTTATTTAATGAACA
1 AAATATATATTTTTTATTTAATGAACA
3370895 CTAATCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 13 0.52
29 6 0.24
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
AAATATATATTTTTTATTTAATGAACA
Found at i:3384416 original size:19 final size:19
Alignment explanation
Indices: 3384392--3384428 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3384382 AATTCATAGT
*
3384392 AATTATGAATAATTAATAA
1 AATTATGAATAACTAATAA
3384411 AATTATGAATAACTAATA
1 AATTATGAATAACTAATA
3384429 GATAGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AATTATGAATAACTAATAA
Found at i:3392010 original size:23 final size:23
Alignment explanation
Indices: 3391980--3392043 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
3391970 TGATCGGCAA
*
3391980 GTATTAGTGGAGGAATAGT-TTTT
1 GTATTAGTGGAGGAATA-TATTAT
*
3392003 GTATTAGTGGGGGAATATATTAT
1 GTATTAGTGGAGGAATATATTAT
*
3392026 GCATTAGTGGAGGAATAT
1 GTATTAGTGGAGGAATAT
3392044 TAATAGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.30, C:0.02, G:0.31, T:0.38
Consensus pattern (23 bp):
GTATTAGTGGAGGAATATATTAT
Found at i:3392334 original size:19 final size:19
Alignment explanation
Indices: 3392307--3392351 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3392297 TATTGGGGGT
* *
3392307 TAAGTTTAAAATAATGATA
1 TAAGATTAAAATAATGACA
* *
3392326 TAAGATTAAAATTATTACA
1 TAAGATTAAAATAATGACA
3392345 TAAGATT
1 TAAGATT
3392352 TTTGGGCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (19 bp):
TAAGATTAAAATAATGACA
Found at i:3395588 original size:315 final size:317
Alignment explanation
Indices: 3395010--3395641 Score: 1088
Period size: 315 Copynumber: 2.0 Consensus size: 317
3395000 ATATTTTTAA
* *
3395010 ACATTACAAATCAAATGGTATAATACTAAAAGCTAACATATTTGTTTATTTTAATTTCTTTTGCG
1 ACATTACAAATCAAATGGTATAATACTAAAAGCTAACATATTTGTTTATTTTAAGTTCTTGTGCG
* * * * *
3395075 ACGTGGATGTTTAGAGCGTCTTCTATCGAACAATATGTTTTCAATGTTTTAATGATAGTTAAGGT
66 ACATAGATGTTTAGACCGTCTTCCATCGAACAATATGTTTTCAATGCTTTAATGATAGTTAAGGT
*
3395140 ACTTAAGGAAGTGCAAGTTTTATAATTCTAAAACTTCTTAGTAGTTTGTTGGAAAATATGTTGTT
131 ACTTAAGGAAGTGCAAGTTTTATAATTCTAAAACTTCTTAGTAGTTTGTTGGAAAATATGTTATT
* *
3395205 GTAGACAAGGTGTTTGTGTATTGGTTGTAGAGACTAGGGCTTGATGTTCAAGATGAAAAGGGAAG
196 GTAGACAAGGTGTTTGTGTATTGGTTGTAGAAACTAGGGCTTGATGTTCAAGATGAAAAGCGAAG
3395270 GCAGTTCAATTATATTCCCTTGCTATTT-GTGTTTTTTT-TTACACGCAACAATCAC
261 GCAGTTCAATTATATTCCCTTGCTATTTGGTGTTTTTTTCTTACACGCAACAATCAC
* *
3395325 ACATTTCAAATCAAATGGTATAATACTAAAAGCTAACATCTTTGTTTATTTTAAGTTCTTGTGCG
1 ACATTACAAATCAAATGGTATAATACTAAAAGCTAACATATTTGTTTATTTTAAGTTCTTGTGCG
* *
3395390 ACATAGATGTTTAGACCGTCTTCCATCGAACAATATGTTTTCGATGCTTTAATGATTGTTAAGGT
66 ACATAGATGTTTAGACCGTCTTCCATCGAACAATATGTTTTCAATGCTTTAATGATAGTTAAGGT
3395455 ACTTAAGGAAGTGCAAGTTTTATAATTCTAAAACTTCTTAGTAGTTTGTTGGAAAATATGTTATT
131 ACTTAAGGAAGTGCAAGTTTTATAATTCTAAAACTTCTTAGTAGTTTGTTGGAAAATATGTTATT
*
3395520 GTAGACAAGGTGTTTGTGTTTTGGTTGTAGAAACTAGGGCTTGATGTTCAAGATGAAAAGCGAAG
196 GTAGACAAGGTGTTTGTGTATTGGTTGTAGAAACTAGGGCTTGATGTTCAAGATGAAAAGCGAAG
* *
3395585 GCAGTTCAATTATATTCTCTTGCTATTTGGGTTTTTTTTTCTTACACGCAACAATCA
261 GCAGTTCAATTATATTCCCTTGCTATTT-GGTGTTTTTTTCTTACACGCAACAATCA
3395642 TAAGAGTTTG
Statistics
Matches: 297, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
315 272 0.92
317 9 0.03
318 16 0.05
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (317 bp):
ACATTACAAATCAAATGGTATAATACTAAAAGCTAACATATTTGTTTATTTTAAGTTCTTGTGCG
ACATAGATGTTTAGACCGTCTTCCATCGAACAATATGTTTTCAATGCTTTAATGATAGTTAAGGT
ACTTAAGGAAGTGCAAGTTTTATAATTCTAAAACTTCTTAGTAGTTTGTTGGAAAATATGTTATT
GTAGACAAGGTGTTTGTGTATTGGTTGTAGAAACTAGGGCTTGATGTTCAAGATGAAAAGCGAAG
GCAGTTCAATTATATTCCCTTGCTATTTGGTGTTTTTTTCTTACACGCAACAATCAC
Found at i:3399480 original size:13 final size:13
Alignment explanation
Indices: 3399459--3399509 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
3399449 TATGTATACT
3399459 AATTAAAAATATG
1 AATTAAAAATATG
*
3399472 AAATAAAAATTATG
1 AATTAAAAA-TATG
3399486 AATTAATAAA-ATG
1 AATTAA-AAATATG
3399499 ATATTAAAAAT
1 A-ATTAAAAAT
3399510 TTAGCTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 15 0.47
14 14 0.44
15 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (13 bp):
AATTAAAAATATG
Found at i:3408615 original size:3 final size:3
Alignment explanation
Indices: 3408607--3408656 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
3408597 AAGCTGAAGA
*
3408607 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3408655 TA
1 TA
3408657 CTGAACTTAA
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:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3413603 original size:2 final size:2
Alignment explanation
Indices: 3413596--3413620 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3413586 TAAAGCTTGG
3413596 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3413621 AACAGACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3416316 original size:20 final size:20
Alignment explanation
Indices: 3416291--3416331 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3416281 TACTGCATTT
*
3416291 TTTTTTTGCACTCAATTGGG
1 TTTTTTTACACTCAATTGGG
3416311 TTTTTTTACACTCAATTGGG
1 TTTTTTTACACTCAATTGGG
3416331 T
1 T
3416332 ACTTAGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (20 bp):
TTTTTTTACACTCAATTGGG
Found at i:3416380 original size:3 final size:3
Alignment explanation
Indices: 3416372--3416397 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3416362 CTCAAACTTA
3416372 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3416398 AGCAATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3416594 original size:9 final size:9
Alignment explanation
Indices: 3416557--3416724 Score: 83
Period size: 9 Copynumber: 17.6 Consensus size: 9
3416547 CATGTGGCAA
3416557 AAAAATTAT
1 AAAAATTAT
*
3416566 AAAAA-AAT
1 AAAAATTAT
*
3416574 AAAAATCAAT
1 AAAAAT-TAT
*
3416584 AAAAGTTAT
1 AAAAATTAT
3416593 AAAAATTAT
1 AAAAATTAT
3416602 AAAAATTAT
1 AAAAATTAT
* *
3416611 TAAACTT-T
1 AAAAATTAT
3416619 AATAAACTATATTT
1 AA-AAA-T-TA--T
3416633 AAAATATT-T
1 AAAA-ATTAT
*
3416642 -AAAGTTCACT
1 AAAAATT-A-T
*
3416652 AAAAATTAA
1 AAAAATTAT
*
3416661 AAAAAATAT
1 AAAAATTAT
*
3416670 AGAAATTAT
1 AAAAATTAT
3416679 AAAAATATATAT
1 -AAAA-AT-TAT
3416691 AAAAAATTAT
1 -AAAAATTAT
*
3416701 AAAATTTTAT
1 AAAA-ATTAT
*
3416711 AAAAATCAT
1 AAAAATTAT
3416720 AAAAA
1 AAAAA
3416725 AATTTATAAG
Statistics
Matches: 123, Mismatches: 19, Indels: 34
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.02
8 12 0.10
9 58 0.47
10 25 0.20
11 10 0.08
12 9 0.07
13 3 0.02
14 4 0.03
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3416603 original size:18 final size:17
Alignment explanation
Indices: 3416557--3416723 Score: 57
Period size: 19 Copynumber: 8.8 Consensus size: 17
3416547 CATGTGGCAA
**
3416557 AAAAATTATAAAAAAAT
1 AAAAATTATAAAATTAT
*
3416574 AAAAATCAATAAAAGTTAT
1 AAAAAT-TATAAAA-TTAT
3416593 AAAAATTATAAAAATTATT
1 AAAAATTAT-AAAATTA-T
** *
3416612 AAACTTTAATAAACTATATTT
1 AAAAATT-ATAAA--AT-TAT
*
3416633 AAAATATT-TAAAGTTCACT
1 AAAA-ATTATAAAATT-A-T
* *
3416652 AAAAATTAAAAAAAATAT
1 AAAAATT-ATAAAATTAT
*
3416670 AGAAATTATAAAAATATATAT
1 AAAAATTAT--AAA-AT-TAT
3416691 AAAAAATTATAAAATTTTAT
1 -AAAAATTATAAAA--TTAT
*
3416711 AAAAATCATAAAA
1 AAAAATTATAAAA
3416724 AAATTTATAA
Statistics
Matches: 111, Mismatches: 19, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
17 8 0.07
18 22 0.20
19 43 0.39
20 17 0.15
21 10 0.09
22 11 0.10
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAATTATAAAATTAT
Found at i:3416690 original size:21 final size:20
Alignment explanation
Indices: 3416652--3416727 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
3416642 AAAGTTCACT
3416652 AAAAATTA-AAAAAAATAT-
1 AAAAATTATAAAAAAATATA
*
3416670 AGAAATTATAAAAATATATATA
1 AAAAATTATAAAAA-A-ATATA
***
3416692 AAAAATTATAAAATTTTAT-
1 AAAAATTATAAAAAAATATA
*
3416711 AAAAATCATAAAAAAAT
1 AAAAATTATAAAAAAAT
3416728 TTATAAGATG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 7 0.16
19 18 0.40
20 4 0.09
21 4 0.09
22 12 0.27
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAAAATATA
Found at i:3416693 original size:12 final size:11
Alignment explanation
Indices: 3416674--3416733 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
3416664 AAATATAGAA
3416674 ATTATAAAAAT
1 ATTATAAAAAT
3416685 ATATATAAAAA-
1 AT-TATAAAAAT
3416696 ATTAT-AAAAT
1 ATTATAAAAAT
*
3416706 TTTATAAAAAT
1 ATTATAAAAAT
*
3416717 CA-TAAAAAAAT
1 -ATTATAAAAAT
3416728 -TTATAA
1 ATTATAA
3416734 GATGCATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 4 0.10
10 11 0.28
11 17 0.43
12 8 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:3417031 original size:19 final size:20
Alignment explanation
Indices: 3417009--3417050 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3416999 TTAAAAAAAA
3417009 TTATAAT-TTTTTACT-ATTT
1 TTATAATATTTTT-CTAATTT
3417028 TTATAATATTTTTCTAATTT
1 TTATAATATTTTTCTAATTT
3417048 TTA
1 TTA
3417051 ATAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATAATATTTTTCTAATTT
Found at i:3417064 original size:29 final size:30
Alignment explanation
Indices: 3417032--3417091 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3417022 CTATTTTTAT
*
3417032 AATATTTT-TCTAATTTTTAATAAAAATTA
1 AATATTTTATATAATTTTTAATAAAAATTA
* * *
3417061 AATATTTTATATATTTTTTATTAAAATTTA
1 AATATTTTATATAATTTTTAATAAAAATTA
3417091 A
1 A
3417092 TAACTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
AATATTTTATATAATTTTTAATAAAAATTA
Found at i:3417086 original size:30 final size:29
Alignment explanation
Indices: 3417032--3417109 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
3417022 CTATTTTTAT
*
3417032 AATATTTTTCTAATTTTTAATAAAAATTA
1 AATATTTTTATAATTTTTAATAAAAATTA
* * *
3417061 AATA-TTTTATATATTTTTTATTAAAATTT
1 AATATTTTTATA-ATTTTTAATAAAAATTA
* *
3417090 AATAACTTTTATAACTTTTA
1 AAT-ATTTTTATAATTTTTA
3417110 TTTATTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 6 0.15
29 21 0.52
30 6 0.15
31 7 0.17
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
AATATTTTTATAATTTTTAATAAAAATTA
Found at i:3420130 original size:22 final size:20
Alignment explanation
Indices: 3420104--3420146 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
3420094 AAAGTGAAAT
*
3420104 TTGTGTAAAAATATAAGATTAA
1 TTGTG-AAAAATA-AAAATTAA
*
3420126 TTGTGAATAATAAAAATTAA
1 TTGTGAAAAATAAAAATTAA
3420146 T
1 T
3420147 CTCGGTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
TTGTGAAAAATAAAAATTAA
Found at i:3420532 original size:2 final size:2
Alignment explanation
Indices: 3420525--3420552 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3420515 GATTGAATTG
3420525 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
3420553 GTGTATGTGT
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:3429788 original size:5 final size:5
Alignment explanation
Indices: 3429778--3429803 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3429768 GATGCTATTT
3429778 TAAGC TAAGC TAAGC TAAGC TAAGC T
1 TAAGC TAAGC TAAGC TAAGC TAAGC T
3429804 CAGTACTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TAAGC
Found at i:3431529 original size:20 final size:19
Alignment explanation
Indices: 3431492--3431530 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3431482 AGGCTCTACC
*
3431492 AACACATTCAATGCATATT
1 AACACATTCAATGAATATT
*
3431511 AACACATGTTAATGAATATT
1 AACACAT-TCAATGAATATT
3431531 TTAATCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (19 bp):
AACACATTCAATGAATATT
Found at i:3443591 original size:10 final size:10
Alignment explanation
Indices: 3443576--3443614 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
3443566 AAGTTTCTTA
3443576 TTTTTATATT
1 TTTTTATATT
3443586 TTTTTATAATT
1 TTTTTAT-ATT
*
3443597 ATTTT-TATT
1 TTTTTATATT
3443606 TTTTTATAT
1 TTTTTATAT
3443615 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 7 0.28
10 11 0.44
11 7 0.28
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTATATT
Found at i:3443601 original size:22 final size:22
Alignment explanation
Indices: 3443573--3443616 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3443563 TATAAGTTTC
3443573 TTATTTTTATATTTTTT-TATAA
1 TTATTTTTAT-TTTTTTATATAA
3443595 TTATTTTTATTTTTTTATATAA
1 TTATTTTTATTTTTTTATATAA
3443617 AAAATTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATTTTTATTTTTTTATATAA
Found at i:3445220 original size:52 final size:52
Alignment explanation
Indices: 3445162--3445284 Score: 158
Period size: 52 Copynumber: 2.3 Consensus size: 52
3445152 ATGAAAATGA
*
3445162 AATAAAAAATTATATTTTGATGCCACCACATTATTTGGAGG-ATCCCAAATTG
1 AATAAAAAATTATTTTTTGATGCCACCACATTATTTGGAGGCA-CCCAAATTG
* * * * *
3445214 AATAAAAATTTATTTTTTGGTGCCGCCATATTATTTGGAGGCACTCAAATTG
1 AATAAAAAATTATTTTTTGATGCCACCACATTATTTGGAGGCACCCAAATTG
*
3445266 AATAAGAAAAATATTTTTT
1 AATAA-AAAATTATTTTTT
3445285 ATTTCTTCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
52 49 0.80
53 12 0.20
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (52 bp):
AATAAAAAATTATTTTTTGATGCCACCACATTATTTGGAGGCACCCAAATTG
Found at i:3448641 original size:38 final size:38
Alignment explanation
Indices: 3448590--3448668 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
3448580 TATGTGAAAA
*
3448590 TTTGTATCTATTAGTACTTAATTTCGAAAATTTTTTGT
1 TTTGTATCTATTAGTACTTAATTTCGAAAAATTTTTGT
3448628 TTTGTATCTATTAGTACTTAATTTCGAAAAATTTTTGT
1 TTTGTATCTATTAGTACTTAATTTCGAAAAATTTTTGT
3448666 TTT
1 TTT
3448669 CTTTCAGCTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.56
Consensus pattern (38 bp):
TTTGTATCTATTAGTACTTAATTTCGAAAAATTTTTGT
Found at i:3456159 original size:4 final size:4
Alignment explanation
Indices: 3456152--3456191 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
3456142 GGATGTCATT
3456152 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3456192 TAATCTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:3458651 original size:22 final size:23
Alignment explanation
Indices: 3458618--3458661 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3458608 ACCTACATTT
3458618 TAAATTTTCAAAAACAAAAAAAA
1 TAAATTTTCAAAAACAAAAAAAA
* *
3458641 TAAA-TTTCAAATATAAAAAAA
1 TAAATTTTCAAAAACAAAAAAA
3458662 TACAAGGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAATTTTCAAAAACAAAAAAAA
Found at i:3461400 original size:24 final size:24
Alignment explanation
Indices: 3461347--3461398 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3461337 TCATAAATTT
* * *
3461347 TAAATATAAAAATAAATTCAATAT
1 TAAATATAAAAATAAAATAAATAA
3461371 TAAATATAAAAATAATAATAAATAA
1 TAAATATAAAAATAA-AATAAATAA
3461396 TAA
1 TAA
3461399 TAACAACCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAATATAAAAATAAAATAAATAA
Found at i:3466304 original size:16 final size:16
Alignment explanation
Indices: 3466283--3466313 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3466273 GAAATAAATT
3466283 ATATATATTGTATATA
1 ATATATATTGTATATA
*
3466299 ATATATATTTTATAT
1 ATATATATTGTATAT
3466314 TAACAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATATTGTATATA
Found at i:3471103 original size:148 final size:149
Alignment explanation
Indices: 3470841--3471129 Score: 472
Period size: 148 Copynumber: 1.9 Consensus size: 149
3470831 GAATTTAGAT
* *
3470841 TATTAAGGAAGTTGAGATCAACTTAACTTTGTGAATAAGGTTTTGTGCTTATCCTTTGCACTTAT
1 TATTAAAGAAGTTGAGATCAACTTAACTTTGTCAATAAGGTTTTGTGCTTATCCTTTGCACTTAT
* ** * * *
3470906 CCTCGTAAATTTATGGGCTGATTTTAAGAAGATTAATCTTAATTTATCTTGAGATAAGATTGGAG
66 CCTCGTAAATTCACAGGCTAATTTTAAGAAGATTAATCTTAATTAATCTTCAGATAAGATTGGAG
*
3470971 GCTATTTATCCATTTAAAG
131 ACTATTTATCCATTTAAAG
*
3470990 TATTAAAGAAGTTGAGATCGACTTAACTTTGTCAATAAGG-TTTGTGCTTATCCTTTGCACTTAT
1 TATTAAAGAAGTTGAGATCAACTTAACTTTGTCAATAAGGTTTTGTGCTTATCCTTTGCACTTAT
*
3471054 CCTCGTAAATTCACAGGCTAATTTTAAGGAGATTAATCTTAATTAATCTTCAGATAAGATTGGAG
66 CCTCGTAAATTCACAGGCTAATTTTAAGAAGATTAATCTTAATTAATCTTCAGATAAGATTGGAG
3471119 ACTATTTATCC
131 ACTATTTATCC
3471130 TAATTATTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
148 92 0.71
149 37 0.29
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (149 bp):
TATTAAAGAAGTTGAGATCAACTTAACTTTGTCAATAAGGTTTTGTGCTTATCCTTTGCACTTAT
CCTCGTAAATTCACAGGCTAATTTTAAGAAGATTAATCTTAATTAATCTTCAGATAAGATTGGAG
ACTATTTATCCATTTAAAG
Found at i:3478899 original size:19 final size:18
Alignment explanation
Indices: 3478875--3478938 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
3478865 AGTTAAAAAC
3478875 AATATATAATAAATAATGA
1 AATATATAAT-AATAATGA
* *
3478894 AATATATGATTTAA-AATTA
1 AATATAT-A-ATAATAATGA
*
3478913 ATTA-ATAATAATATATGA
1 AATATATAATAATA-ATGA
3478931 AATATATA
1 AATATATA
3478939 CGACATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
16 3 0.09
17 2 0.06
18 8 0.24
19 17 0.50
20 3 0.09
21 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AATATATAATAATAATGA
Found at i:3480854 original size:16 final size:17
Alignment explanation
Indices: 3480833--3480866 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3480823 GGTTTTGATC
*
3480833 TAAGTC-ATTCTAAGTT
1 TAAGTCAATTCAAAGTT
3480849 TAAGTCAATTCAAAGTT
1 TAAGTCAATTCAAAGTT
3480866 T
1 T
3480867 GACTCACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TAAGTCAATTCAAAGTT
Found at i:3484396 original size:21 final size:22
Alignment explanation
Indices: 3484372--3484416 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3484362 AAATATTTTT
3484372 ATAATTTGTAT-GTTTTTAAAA
1 ATAATTTGTATAGTTTTTAAAA
* *
3484393 ATAATTTTTATAGTTTTTTAAA
1 ATAATTTGTATAGTTTTTAAAA
3484415 AT
1 AT
3484417 TCTTACATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
ATAATTTGTATAGTTTTTAAAA
Found at i:3485482 original size:18 final size:18
Alignment explanation
Indices: 3485450--3485501 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3485440 TAGACCCCTT
*
3485450 ATCTTAATA-TTAAATTCA
1 ATCTTGATACTTAAATT-A
*
3485468 AT-TTGATACTTAAATTT
1 ATCTTGATACTTAAATTA
*
3485485 TTCTTGATACTTAAATT
1 ATCTTGATACTTAAATT
3485502 TGACAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.21
18 23 0.79
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (18 bp):
ATCTTGATACTTAAATTA
Found at i:3503334 original size:9 final size:9
Alignment explanation
Indices: 3503322--3503352 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3503312 TTAAATTTTA
3503322 TTTTTAATT
1 TTTTTAATT
3503331 TTTTTAATT
1 TTTTTAATT
*
3503340 TTATTAATT
1 TTTTTAATT
3503349 TTTT
1 TTTT
3503353 AATGAGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTAATT
Found at i:3506134 original size:17 final size:18
Alignment explanation
Indices: 3506112--3506145 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3506102 TTATAATTTG
*
3506112 TAAATTT-ATAAAAAAAA
1 TAAATTTGAGAAAAAAAA
3506129 TAAATTTGAGAAAAAAA
1 TAAATTTGAGAAAAAAA
3506146 GTATTAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
TAAATTTGAGAAAAAAAA
Found at i:3507193 original size:20 final size:20
Alignment explanation
Indices: 3507128--3507193 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
3507118 ATCAGTTAAC
* *
3507128 AATTTTTTAAATTTATTTTTGT
1 AATTTTTAAAATTTA--TATGT
* * *
3507150 ATATTTTTAGATTTTATATAT
1 A-ATTTTTAAAATTTATATGT
*
3507171 AATTTTTAAAATTTGTATGT
1 AATTTTTAAAATTTATATGT
3507191 AAT
1 AAT
3507194 GCCTCGATGC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 18 0.53
21 4 0.12
22 1 0.03
23 11 0.32
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (20 bp):
AATTTTTAAAATTTATATGT
Found at i:3508899 original size:70 final size:70
Alignment explanation
Indices: 3508786--3508926 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
3508776 TGAGCTGCTT
3508786 TTGATACTGTTTGATTTGTTTAAAAACAATAATGGAAATATAGCCTAGGTCGAGAAATGGGAGAT
1 TTGATACTGTTTGATTTGTTTAAAAACAATAATGGAAATATAGCCTAGGTCGAGAAATGGGAGAT
3508851 GTAAA
66 GTAAA
3508856 TTGATACTGTTTGATTTGTTTAAAAACAATAATGGAAATATAGCCTAGGTCGAGAAATGGGAGAT
1 TTGATACTGTTTGATTTGTTTAAAAACAATAATGGAAATATAGCCTAGGTCGAGAAATGGGAGAT
3508921 GTAAA
66 GTAAA
3508926 T
1 T
3508927 GGTTTGGTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (70 bp):
TTGATACTGTTTGATTTGTTTAAAAACAATAATGGAAATATAGCCTAGGTCGAGAAATGGGAGAT
GTAAA
Found at i:3517439 original size:14 final size:15
Alignment explanation
Indices: 3517420--3517450 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3517410 AAGTTATATT
3517420 AACAAAA-AAAAAAA
1 AACAAAACAAAAAAA
3517434 AACAAAACAAAAAAA
1 AACAAAACAAAAAAA
3517449 AA
1 AA
3517451 AGCAAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AACAAAACAAAAAAA
Found at i:3517457 original size:16 final size:15
Alignment explanation
Indices: 3517420--3517457 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3517410 AAGTTATATT
3517420 AACAAA-AAAAAAAA
1 AACAAACAAAAAAAA
3517434 AACAAAACAAAAAAAA
1 AAC-AAACAAAAAAAA
3517450 AAGCAAAC
1 AA-CAAAC
3517458 CTTTATTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 3 0.14
16 14 0.67
17 1 0.05
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (15 bp):
AACAAACAAAAAAAA
Found at i:3519051 original size:18 final size:18
Alignment explanation
Indices: 3519028--3519063 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3519018 ATTTTTTTAT
3519028 TTATAAACTTAAATGGGC
1 TTATAAACTTAAATGGGC
3519046 TTATAAACTTAAATGGGC
1 TTATAAACTTAAATGGGC
3519064 CAAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
TTATAAACTTAAATGGGC
Found at i:3521606 original size:116 final size:116
Alignment explanation
Indices: 3521388--3521620 Score: 333
Period size: 116 Copynumber: 2.0 Consensus size: 116
3521378 TCTACTCTTT
* *
3521388 TTGACATAATGCCTAGAACTACCCATAGCCCCTCCCCAACCCATAAATAGGAGGATAATGTATTT
1 TTGACATAATGCCTAGAACTACCCATAGCCCCTCCCCAACCCATAAATAGGAGAATAATGCATTT
* * *
3521453 CAGCACACTCGAACCCACATCCTCTTGTATTAGCAACAATACCCATGCCAA
66 CAGCACACTCGAACCCACATCCTCCTATATTAGCAACAATACCCATACCAA
* * * * *
3521504 TTGATATAATGTCTAGAACTACCTATAGCTCCTCCCCAACTCATAAATAGGAGAATAATGCATTT
1 TTGACATAATGCCTAGAACTACCCATAGCCCCTCCCCAACCCATAAATAGGAGAATAATGCATTT
* * *
3521569 CAGTACACTCGAACCCACGTCCTCCTATATT-GACAACAATACCTATACCAA
66 CAGCACACTCGAACCCACATCCTCCTATATTAG-CAACAATACCCATACCAA
3521620 T
1 T
3521621 CGAGTAAGAC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
115 1 0.01
116 102 0.99
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (116 bp):
TTGACATAATGCCTAGAACTACCCATAGCCCCTCCCCAACCCATAAATAGGAGAATAATGCATTT
CAGCACACTCGAACCCACATCCTCCTATATTAGCAACAATACCCATACCAA
Found at i:3522383 original size:17 final size:17
Alignment explanation
Indices: 3522357--3522392 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3522347 TCCAGCTGAT
* *
3522357 AATATTTTTTTTTGTAA
1 AATATCTTTTTTTATAA
3522374 AATATCTTTTTTTATAA
1 AATATCTTTTTTTATAA
3522391 AA
1 AA
3522393 ATTTATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
AATATCTTTTTTTATAA
Found at i:3522880 original size:2 final size:2
Alignment explanation
Indices: 3522873--3522903 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3522863 TCACTCCCTT
3522873 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 T
3522904 TAAATCTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3524259 original size:20 final size:22
Alignment explanation
Indices: 3524220--3524259 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
3524210 AATTAAGATA
3524220 TTTTATATTTATTGTATATAGT
1 TTTTATATTTATTGTATATAGT
*
3524242 TTTTA-ATTT-TTTTATATA
1 TTTTATATTTATTGTATATA
3524260 ATGTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATATTTATTGTATATAGT
Found at i:3526241 original size:17 final size:19
Alignment explanation
Indices: 3526212--3526247 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3526202 AAACGTTTTA
3526212 AAATTTCTTTAAAT-TAAT
1 AAATTTCTTTAAATATAAT
3526230 AAATTT-TTTAAATATAAT
1 AAATTTCTTTAAATATAAT
3526248 TTATATCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTCTTTAAATATAAT
Found at i:3526275 original size:23 final size:23
Alignment explanation
Indices: 3526249--3526292 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3526239 AAATATAATT
*
3526249 TATA-TCCATTTTATTAATTTTAA
1 TATATTCCATATT-TTAATTTTAA
3526272 TATATTCCATATTTTAATTTT
1 TATATTCCATATTTTAATTTT
3526293 CGGTGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTCCATATTTTAATTTTAA
Found at i:3526896 original size:21 final size:20
Alignment explanation
Indices: 3526849--3526904 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
3526839 ACCTGATAAT
3526849 TAAAAAACA-TAAAAATTAGA
1 TAAAAAA-ATTAAAAATTAGA
* *
3526869 TATAAAATTCTAAAAATTAGGA
1 TAAAAAAAT-TAAAAATTA-GA
3526891 -AAAAAAATTAAAAA
1 TAAAAAAATTAAAAA
3526905 ATAAAGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 12 0.41
21 15 0.52
22 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAAAAAATTAAAAATTAGA
Found at i:3526897 original size:22 final size:21
Alignment explanation
Indices: 3526858--3526899 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3526848 TTAAAAAACA
* *
3526858 TAAAAATTAGATATAAAATTC
1 TAAAAATTAGAAAAAAAATTC
3526879 TAAAAATTAGGAAAAAAAATT
1 TAAAAATTA-GAAAAAAAATT
3526900 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
TAAAAATTAGAAAAAAAATTC
Found at i:3528948 original size:22 final size:24
Alignment explanation
Indices: 3528916--3528960 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3528906 TTTCCTGTTT
3528916 ATTATTATTATTTTTTA-AAAATA
1 ATTATTATTATTTTTTAGAAAATA
3528939 ATTATT-TTATTTTTTAGAAAAT
1 ATTATTATTATTTTTTAGAAAAT
3528961 TCTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTATTATTATTTTTTAGAAAATA
Found at i:3529172 original size:21 final size:22
Alignment explanation
Indices: 3529147--3529188 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3529137 GACGACGTTG
3529147 TATA-TTTAA-ATTTATAATTAT
1 TATATTTTAATATTTA-AATTAT
3529168 TATATTTTAATATTTAAATTA
1 TATATTTTAATATTTAAATTA
3529189 AAATATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTTAATATTTAAATTAT
Found at i:3529194 original size:22 final size:22
Alignment explanation
Indices: 3529151--3529194 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3529141 ACGTTGTATA
**
3529151 TTTAAATTTATAATTATTATAT
1 TTTAAATTTATAATTAAAATAT
3529173 TTTAATATTTA-AATTAAAATAT
1 TTTAA-ATTTATAATTAAAATAT
3529195 ACAAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATTTATAATTAAAATAT
Found at i:3531394 original size:12 final size:12
Alignment explanation
Indices: 3531377--3531406 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
3531367 TGTCATTTAC
3531377 TTTATGATGTCA
1 TTTATGATGTCA
3531389 TTTATGATGTCA
1 TTTATGATGTCA
3531401 TCTTAT
1 T-TTAT
3531407 TCATTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (12 bp):
TTTATGATGTCA
Found at i:3535066 original size:17 final size:18
Alignment explanation
Indices: 3535032--3535072 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 18
3535022 TTTAATTTAA
3535032 TTAAAATATATAAACTATT
1 TTAAAATATATAAACTA-T
3535051 TTAAAAT-TAT-AACTAT
1 TTAAAATATATAAACTAT
3535067 TTAAAA
1 TTAAAA
3535073 AATTCAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 5 0.23
18 3 0.14
19 7 0.32
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAATATATAAACTAT
Found at i:3535073 original size:17 final size:19
Alignment explanation
Indices: 3535034--3535073 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
3535024 TAATTTAATT
*
3535034 AAAATATATAAACTATTTT
1 AAAATATATAAACTATTTA
3535053 AAAAT-TAT-AACTATTTA
1 AAAATATATAAACTATTTA
3535070 AAAA
1 AAAA
3535074 ATTCAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 3 0.15
19 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATATAAACTATTTA
Found at i:3538184 original size:32 final size:32
Alignment explanation
Indices: 3538143--3538206 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3538133 AAAACTAAGT
3538143 GAATTTGATTTTTAATTTTTTATTATTATGTG
1 GAATTTGATTTTTAATTTTTTATTATTATGTG
3538175 GAATTTGATTTTTAATTTTTTATTATTATGTG
1 GAATTTGATTTTTAATTTTTTATTATTATGTG
3538207 CCATCATCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (32 bp):
GAATTTGATTTTTAATTTTTTATTATTATGTG
Found at i:3544341 original size:22 final size:25
Alignment explanation
Indices: 3544316--3544369 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
3544306 AGTCTATTTT
3544316 TAATTTTTTA-ATGACATTT-CA-A
1 TAATTTTTTATATGACATTTACATA
*
3544338 TAATTTTTTATATGTCATTTACATA
1 TAATTTTTTATATGACATTTACATA
3544363 TAATTTT
1 TAATTTT
3544370 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.36
23 8 0.29
24 2 0.07
25 8 0.29
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (25 bp):
TAATTTTTTATATGACATTTACATA
Found at i:3545540 original size:12 final size:12
Alignment explanation
Indices: 3545525--3545550 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3545515 GAAATTATGG
3545525 TTAAAATAAGTT
1 TTAAAATAAGTT
3545537 TTAAAATAAGTT
1 TTAAAATAAGTT
3545549 TT
1 TT
3545551 TTTTTCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
TTAAAATAAGTT
Found at i:3550730 original size:30 final size:30
Alignment explanation
Indices: 3550696--3550758 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
3550686 ACTTATTTTA
3550696 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
3550726 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
3550756 TTG
1 TTG
3550759 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:3550905 original size:12 final size:12
Alignment explanation
Indices: 3550884--3550917 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3550874 TATATCTTTT
*
3550884 AAAATTATATAA
1 AAAATAATATAA
3550896 AAAATAATATAA
1 AAAATAATATAA
*
3550908 AAATTAATAT
1 AAAATAATAT
3550918 GGTCGGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:3551467 original size:22 final size:24
Alignment explanation
Indices: 3551427--3551473 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
3551417 AAATATTACA
3551427 ATATAATTGTTACAAATTT-AAAT
1 ATATAATTGTTACAAATTTGAAAT
* *
3551450 ATATAA-TGTTATATATTTGAAAT
1 ATATAATTGTTACAAATTTGAAAT
3551473 A
1 A
3551474 AATTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (24 bp):
ATATAATTGTTACAAATTTGAAAT
Found at i:3551956 original size:24 final size:23
Alignment explanation
Indices: 3551901--3551956 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
3551891 TTAACATATG
* *
3551901 AAATATAAATTTTAAATATTTTT
1 AAATATAAATATTAAATATTTTA
* *
3551924 GAATAATAAATATTAATTATTTATA
1 AAAT-ATAAATATTAAATATTT-TA
3551949 AAATATAA
1 AAATATAA
3551957 TTAGAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.12
24 19 0.73
25 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATAAATATTAAATATTTTA
Found at i:3555961 original size:3 final size:3
Alignment explanation
Indices: 3555945--3555993 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
3555935 CGAGGTATAA
* *
3555945 TAT TAT CAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3555993 T
1 T
3555994 TTCGTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3560131 original size:33 final size:32
Alignment explanation
Indices: 3560085--3560154 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
3560075 TACATTGTCT
* *
3560085 TTTTTTCAATTATTTA-ATAAAATTTTATTAAA
1 TTTTTTCAATTATTAACATAAAATTTTAAT-AA
* *
3560117 TTTTTTCATGTTATTAACATATAATTTTAATAA
1 TTTTTTCA-ATTATTAACATAAAATTTTAATAA
3560150 TTTTT
1 TTTTT
3560155 AACCCTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 8 0.25
33 13 0.41
34 11 0.34
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (32 bp):
TTTTTTCAATTATTAACATAAAATTTTAATAA
Found at i:3564644 original size:12 final size:12
Alignment explanation
Indices: 3564616--3564654 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3564606 ATTCTGAATT
3564616 TTGAG-TCAAGC
1 TTGAGCTCAAGC
* *
3564627 TCGAGCTCGAGC
1 TTGAGCTCAAGC
3564639 TTGAGCTCAAGC
1 TTGAGCTCAAGC
3564651 TTGA
1 TTGA
3564655 CAGTATACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (12 bp):
TTGAGCTCAAGC
Found at i:3566325 original size:18 final size:19
Alignment explanation
Indices: 3566304--3566344 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3566294 TTAAGATAAA
3566304 AAAATAATTTAATAATA-T
1 AAAATAATTTAATAATATT
* *
3566322 AAAATATTTTAATTATATT
1 AAAATAATTTAATAATATT
3566341 AAAA
1 AAAA
3566345 ATAAAAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATAATTTAATAATATT
Found at i:3567026 original size:21 final size:21
Alignment explanation
Indices: 3567001--3567044 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3566991 ATTCGATCTG
3567001 AATTTAACTCAAACTAAAATT
1 AATTTAACTCAAACTAAAATT
3567022 AATTTAACTCAAACTAAAATT
1 AATTTAACTCAAACTAAAATT
3567043 AA
1 AA
3567045 CTTGATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTTAACTCAAACTAAAATT
Found at i:3567076 original size:18 final size:18
Alignment explanation
Indices: 3567039--3567073 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3567029 CTCAAACTAA
*
3567039 AATTAACTTGATTTATTT
1 AATTAACATGATTTATTT
3567057 AATTAACAT-ATTTATTT
1 AATTAACATGATTTATTT
3567074 TAAACTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTAACATGATTTATTT
Found at i:3568936 original size:12 final size:12
Alignment explanation
Indices: 3568884--3568942 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
3568874 GTTACTATAA
3568884 TTTA-TTTATTT
1 TTTATTTTATTT
* *
3568895 GTTTAATTTATTAA
1 -TTTATTTTATT-T
*
3568909 TTT-TTTGATATT
1 TTTATTTTAT-TT
3568921 TTTATTTTATTT
1 TTTATTTTATTT
3568933 TTTATTTTAT
1 TTTATTTTAT
3568943 AATATTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 23 0.61
13 15 0.39
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTT
Done.