Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 24 of 97
Found at i:10310591 original size:28 final size:28
Alignment explanation
Indices: 10310536--10310591 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
10310526 AATGGCCTTT
***
10310536 TTTCTTCTTTTTCTATTTATCTTTTTCC
1 TTTCTTCTTTTTCTATTTATCCGATTCC
* *
10310564 TTTCTTGTTTTTCTCTTTATCCGATTCC
1 TTTCTTCTTTTTCTATTTATCCGATTCC
10310592 AGAGTGCATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.07, C:0.23, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTCTTCTTTTTCTATTTATCCGATTCC
Found at i:10314845 original size:34 final size:35
Alignment explanation
Indices: 10314776--10314849 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
10314766 AAATTTAAAT
* *
10314776 TTAAATAATCAAAAACAAATATCTTAAATATCAAC
1 TTAAATAATCAAAAACAAATATCTCAAATAACAAC
10314811 TTAAATAA-CTAAAAACAAATATC-CAAATAACAAC
1 TTAAATAATC-AAAAACAAATATCTCAAATAACAAC
10314845 TTAAA
1 TTAAA
10314850 CAACATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (35 bp):
TTAAATAATCAAAAACAAATATCTCAAATAACAAC
Found at i:10319467 original size:23 final size:22
Alignment explanation
Indices: 10319436--10319478 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
10319426 CATTATCCTA
* *
10319436 AACATAACATAGATTGACTCATC
1 AACAAAACATA-ACTGACTCATC
10319459 AACAAAACATAACTGACTCA
1 AACAAAACATAACTGACTCA
10319479 CTAGACATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (22 bp):
AACAAAACATAACTGACTCATC
Found at i:10330330 original size:2 final size:2
Alignment explanation
Indices: 10330318--10330346 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10330308 AAAGGCCTAG
10330318 AT AT A- 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
10330347 GAAATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10331724 original size:21 final size:21
Alignment explanation
Indices: 10331672--10331724 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
10331662 AGAATTAAAT
* *
10331672 GAAGAAAATGAAAACGATATC
1 GAAGAAAATGAAAACGAGAAC
* ** *
10331693 GATGATGATGAAAATGAGAAC
1 GAAGAAAATGAAAACGAGAAC
10331714 GAAGAAAATGA
1 GAAGAAAATGA
10331725 GCTCACTTCT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.25, T:0.15
Consensus pattern (21 bp):
GAAGAAAATGAAAACGAGAAC
Found at i:10332836 original size:2 final size:2
Alignment explanation
Indices: 10332829--10332869 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10332819 AATACGTGTT
10332829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10332870 GTTGCTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10333567 original size:20 final size:20
Alignment explanation
Indices: 10333542--10333579 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10333532 TCTGCAGTTA
10333542 TTACTGACGAAATTCATCAG
1 TTACTGACGAAATTCATCAG
* *
10333562 TTACTGATGGAATTCATC
1 TTACTGACGAAATTCATC
10333580 CATTATTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TTACTGACGAAATTCATCAG
Found at i:10339174 original size:22 final size:22
Alignment explanation
Indices: 10339133--10339177 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
10339123 ATCATTTTAT
10339133 AATTTATAAAATTAAGCATCTA
1 AATTTATAAAATTAAGCATCTA
10339155 AATTATATATAAA-TAA-CATCTA
1 AATT-TATA-AAATTAAGCATCTA
10339177 A
1 A
10339178 TATCTAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 11 0.52
23 7 0.33
24 3 0.14
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTTATAAAATTAAGCATCTA
Found at i:10340199 original size:11 final size:11
Alignment explanation
Indices: 10340183--10340207 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10340173 TGTACAACCC
10340183 ATTATTTATTT
1 ATTATTTATTT
10340194 ATTATTTATTT
1 ATTATTTATTT
10340205 ATT
1 ATT
10340208 TAATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:10340361 original size:19 final size:19
Alignment explanation
Indices: 10340314--10340357 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
10340304 TTATTGATAT
10340314 TAAATATTATAATATTTGA
1 TAAATATTATAATATTTGA
*
10340333 TAAATATTATGATATTT-A
1 TAAATATTATAATATTTGA
10340351 T-AATATT
1 TAAATATT
10340358 TTATATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 16 0.67
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TAAATATTATAATATTTGA
Found at i:10350466 original size:15 final size:15
Alignment explanation
Indices: 10350446--10350477 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10350436 GGCAGGTCTC
10350446 TTCAATGGATATGTT
1 TTCAATGGATATGTT
10350461 TTCAATGGATATGTT
1 TTCAATGGATATGTT
10350476 TT
1 TT
10350478 TGCTTGTTAA
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:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTCAATGGATATGTT
Found at i:10355779 original size:15 final size:15
Alignment explanation
Indices: 10355761--10355792 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10355751 GTATGGTTAG
10355761 TATTTGAAAGAGACT
1 TATTTGAAAGAGACT
10355776 TATTTGAAAGAGACT
1 TATTTGAAAGAGACT
10355791 TA
1 TA
10355793 CTCATGAAAT
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:0.06, G:0.19, T:0.34
Consensus pattern (15 bp):
TATTTGAAAGAGACT
Found at i:10359914 original size:2 final size:2
Alignment explanation
Indices: 10359901--10360017 Score: 216
Period size: 2 Copynumber: 58.0 Consensus size: 2
10359891 CAACTCCATG
*
10359901 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10359943 AT AT AT AT AT AT AT AT AT AT ANT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
10359986 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
10360018 GACCAACTTA
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
2 110 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10361764 original size:13 final size:14
Alignment explanation
Indices: 10361743--10361799 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
10361733 TTTTAAGATG
*
10361743 TAAAATTTT-TAAT
1 TAAATTTTTATAAT
10361756 TAAATTTTTATAGA-
1 TAAATTTTTATA-AT
10361770 TAAATTTTTATAAT
1 TAAATTTTTATAAT
*
10361784 ATATATTTTTTATAAT
1 -TA-AATTTTTATAAT
10361800 ATATTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 9 0.24
14 14 0.38
15 3 0.08
16 11 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAAATTTTTATAAT
Found at i:10364004 original size:30 final size:30
Alignment explanation
Indices: 10363970--10364028 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
10363960 CATCTCAATT
*
10363970 ATGATTTCTATGATCATTTTGAATCTCTTC
1 ATGATTTCTAAGATCATTTTGAATCTCTTC
*
10364000 ATGATTTTTAAGATCATTTTGAATCTCTT
1 ATGATTTCTAAGATCATTTTGAATCTCTT
10364029 TATTAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (30 bp):
ATGATTTCTAAGATCATTTTGAATCTCTTC
Found at i:10364870 original size:17 final size:17
Alignment explanation
Indices: 10364850--10364884 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10364840 TACTTTTGAC
*
10364850 TTTTATATATTTTTTAAT
1 TTTTA-ATAATTTTTAAT
10364868 TTTTAATAATTTTTAAT
1 TTTTAATAATTTTTAAT
10364885 ATAATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATAATTTTTAAT
Found at i:10367233 original size:16 final size:17
Alignment explanation
Indices: 10367214--10367246 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10367204 GGTTTTCTAA
*
10367214 TTATTGTTT-TTTTATT
1 TTATTCTTTATTTTATT
10367230 TTATTCTTTATTTTATT
1 TTATTCTTTATTTTATT
10367247 AGCAAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTCTTTATTTTATT
Found at i:10404890 original size:20 final size:20
Alignment explanation
Indices: 10404867--10404912 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
10404857 CTTCTAAACC
*
10404867 TCAAATCATACTTCAATAAG
1 TCAAATCATACTCCAATAAG
*
10404887 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
10404907 TCAAAT
1 TCAAAT
10404913 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:10405472 original size:15 final size:15
Alignment explanation
Indices: 10405452--10405489 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
10405442 ACACACTTTA
10405452 TTTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
*
10405467 TTTCTTTTTCTTTTT
1 TTTCTTTTTCTTTTC
10405482 TTTCTTTT
1 TTTCTTTT
10405490 ACACCCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:10406148 original size:22 final size:23
Alignment explanation
Indices: 10406105--10406148 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
10406095 AATAAAACAT
10406105 GCAAAACATAACTTAAAATAAAA
1 GCAAAACATAACTTAAAATAAAA
10406128 GCAAAA-ATAA-TTAAAAGTAAA
1 GCAAAACATAACTTAAAA-TAAA
10406149 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.66, C:0.09, G:0.07, T:0.18
Consensus pattern (23 bp):
GCAAAACATAACTTAAAATAAAA
Found at i:10410871 original size:16 final size:18
Alignment explanation
Indices: 10410824--10410878 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
10410814 TTAAATAAAC
* *
10410824 ATAAAATTAAAATAAATTT
1 ATAAAAATAAACTAAA-TT
10410843 ATAAAAATAAACT-AATT
1 ATAAAAATAAACTAAATT
10410860 ATAAAAAT-AACTAAATT
1 ATAAAAATAAACTAAATT
10410877 AT
1 AT
10410879 TATTAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 4 0.12
17 16 0.48
18 2 0.06
19 11 0.33
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATAAACTAAATT
Found at i:10414263 original size:15 final size:16
Alignment explanation
Indices: 10414243--10414273 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
10414233 CCACTGAGGC
10414243 TATAACAT-GCATTCA
1 TATAACATAGCATTCA
10414258 TATAACATAGCATTCA
1 TATAACATAGCATTCA
10414274 CATCAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (16 bp):
TATAACATAGCATTCA
Found at i:10422244 original size:2 final size:2
Alignment explanation
Indices: 10422237--10422324 Score: 97
Period size: 2 Copynumber: 44.0 Consensus size: 2
10422227 CCCCACGCTG
* ** * *
10422237 CT CT CT CT CT CT TT CT CT AA CT CT C- CA CGT GT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT
* *
10422279 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10422321 CT CT
1 CT CT
10422325 AACTCCCCAC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.03, C:0.44, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10422902 original size:3 final size:3
Alignment explanation
Indices: 10422891--10422925 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
10422881 TTTTAAATTA
10422891 ATT ATTT ATT ATT ATT ATT ATT ATT ATT -TT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10422926 AAAAAAAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:10432753 original size:39 final size:39
Alignment explanation
Indices: 10432699--10432779 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
10432689 AGTAAGCAGA
*
10432699 TCTGGTTTACAATAAACCAGATCTGCTTATTTCACACTT
1 TCTGGTTTACAATAAACCAGATCTGCTTACTTCACACTT
10432738 TCTGGTTTACAATAAACCAGATCTGCTTACTTCACACTT
1 TCTGGTTTACAATAAACCAGATCTGCTTACTTCACACTT
10432777 TCT
1 TCT
10432780 TAATATCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (39 bp):
TCTGGTTTACAATAAACCAGATCTGCTTACTTCACACTT
Found at i:10434574 original size:22 final size:22
Alignment explanation
Indices: 10434549--10434597 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
10434539 GAAATTGATT
10434549 AGACTGATTTTTAAGTATTATG
1 AGACTGATTTTTAAGTATTATG
* *
10434571 AGACTGATTTTTAGGTGTTATG
1 AGACTGATTTTTAAGTATTATG
*
10434593 TGACT
1 AGACT
10434598 TAATCACTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (22 bp):
AGACTGATTTTTAAGTATTATG
Found at i:10434662 original size:21 final size:21
Alignment explanation
Indices: 10434608--10434662 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
10434598 TAATCACTGT
* *
10434608 GTGACTAGTTTTTAGGCATTAC
1 GTGACT-GATTTTAAGCATTAC
* * *
10434630 GTAATTGGTTTTAAGCATTAC
1 GTGACTGATTTTAAGCATTAC
10434651 GTGACTGATTTT
1 GTGACTGATTTT
10434663 TAAACAATGC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.44
Consensus pattern (21 bp):
GTGACTGATTTTAAGCATTAC
Found at i:10434701 original size:23 final size:23
Alignment explanation
Indices: 10434675--10434734 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
10434665 AACAATGCCT
* *
10434675 AAGTCACATAATGCTTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
** *
10434698 AAGTCATGCAATGCCTTGCTAAC
1 AAGTCACACAATGCCTTACTAAC
10434721 AAGTCA-AGCAATGC
1 AAGTCACA-CAATGC
10434735 TTATCAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (23 bp):
AAGTCACACAATGCCTTACTAAC
Found at i:10434753 original size:22 final size:22
Alignment explanation
Indices: 10434722--10434822 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 22
10434712 CTTGCTAACA
*
10434722 AGTCAAGCAATGCTTATCAACT
1 AGTCACGCAATGCTTATCAACT
* * *
10434744 AGTCATGCAATGTCATATCAACC
1 AGTCACGCAATG-CTTATCAACT
* * * **
10434767 AATCACACAATACTTAAAAACT
1 AGTCACGCAATGCTTATCAACT
* *
10434789 AGTCACGCAATGCCTA--AAGT
1 AGTCACGCAATGCTTATCAACT
10434809 CAGTCACGCAATGC
1 -AGTCACGCAATGC
10434823 CCAAAGTCAG
Statistics
Matches: 61, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
20 3 0.05
21 13 0.21
22 29 0.48
23 16 0.26
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTCACGCAATGCTTATCAACT
Found at i:10434815 original size:21 final size:21
Alignment explanation
Indices: 10434789--10434848 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
10434779 CTTAAAAACT
10434789 AGTCACGCAATGCCTAAAGTC
1 AGTCACGCAATGCCTAAAGTC
*
10434810 AGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATGCCTAAAGTC
10434831 AGTCACGCAATGCCTAAA
1 AGTCACGCAATGCCTAAA
10434849 AACTAATCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.17
Consensus pattern (21 bp):
AGTCACGCAATGCCTAAAGTC
Found at i:10437703 original size:19 final size:19
Alignment explanation
Indices: 10437679--10437716 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10437669 ACTTCTAAAT
10437679 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
10437698 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
10437717 AATCAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:10444477 original size:53 final size:52
Alignment explanation
Indices: 10444391--10444495 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 52
10444381 GGTCATGACC
* *
10444391 ATGGTGACTTCCTAATTTCTATTTCTAGATTTTGCATCTTCAAGTTATTGAT
1 ATGGTGACTTCCTAATTTCTATTACTAGATTTTGCATCCTCAAGTTATTGAT
* *
10444443 ATGGTGACTTCCTAATTTTCTATTACTAGATTTTGCGTCCTCTAGTTATTGAT
1 ATGGTGACTTCCTAA-TTTCTATTACTAGATTTTGCATCCTCAAGTTATTGAT
10444496 GTTTTCACTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
52 15 0.31
53 33 0.69
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (52 bp):
ATGGTGACTTCCTAATTTCTATTACTAGATTTTGCATCCTCAAGTTATTGAT
Found at i:10449360 original size:75 final size:75
Alignment explanation
Indices: 10449237--10449387 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
10449227 TCTAATGAAT
* *
10449237 TGTCCAGACTCTTACATATAGACTAAATTAGAGTAATTACTCATGATCAGTTACAACAAGAGTGA
1 TGTCCAGACTCTTACATATAGACTAAATTACAGTAATTACTCATGATCAGTTACAACAAGAGTCA
*
10449302 TTAGTAGACA
66 TTAGAAGACA
*
10449312 TGTCCAGACTCTTATATATAGACTAAATTACAGTAATTACTCATGATCAGTTACAACAAGAGTCA
1 TGTCCAGACTCTTACATATAGACTAAATTACAGTAATTACTCATGATCAGTTACAACAAGAGTCA
10449377 TTAGAAGACA
66 TTAGAAGACA
10449387 T
1 T
10449388 CATGATAGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (75 bp):
TGTCCAGACTCTTACATATAGACTAAATTACAGTAATTACTCATGATCAGTTACAACAAGAGTCA
TTAGAAGACA
Found at i:10452614 original size:9 final size:9
Alignment explanation
Indices: 10452600--10452635 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
10452590 ATGATAATCG
10452600 AAATATAAA
1 AAATATAAA
10452609 AAATATAAA
1 AAATATAAA
10452618 AAA-ATAAA
1 AAATATAAA
*
10452626 AAAAATAAA
1 AAATATAAA
10452635 A
1 A
10452636 TTGTTATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAATATAAA
Found at i:10466777 original size:9 final size:9
Alignment explanation
Indices: 10466763--10466801 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
10466753 ATGATAATCG
10466763 AAATATAAA
1 AAATATAAA
10466772 AAATAT-AA
1 AAATATAAA
10466780 AAATAATAAA
1 AAAT-ATAAA
*
10466790 TAATATAAA
1 AAATATAAA
10466799 AAA
1 AAA
10466802 AAAGAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 6 0.23
9 15 0.58
10 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATATAAA
Found at i:10469052 original size:15 final size:16
Alignment explanation
Indices: 10469032--10469072 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
10469022 ATTTTACTAG
10469032 GAATATGATT-ATAGA
1 GAATATGATTGATAGA
*
10469047 GAATATGATTGCTAGA
1 GAATATGATTGATAGA
10469063 -AATATGATTG
1 GAATATGATTG
10469073 TTGAGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATATGATTGATAGA
Found at i:10469079 original size:16 final size:16
Alignment explanation
Indices: 10469033--10469080 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
10469023 TTTTACTAGG
* *
10469033 AATATGATTATAGAG-
1 AATATGATTGTTGAGA
*
10469048 AATATGATTGCT-AGA
1 AATATGATTGTTGAGA
10469063 AATATGATTGTTGAGA
1 AATATGATTGTTGAGA
10469079 AA
1 AA
10469081 ATAACTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 2 0.07
15 20 0.74
16 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (16 bp):
AATATGATTGTTGAGA
Found at i:10469725 original size:17 final size:17
Alignment explanation
Indices: 10469703--10469735 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10469693 TTAGATCCTA
10469703 AATCTATCCTTATTTTT
1 AATCTATCCTTATTTTT
*
10469720 AATCTATCTTTATTTT
1 AATCTATCCTTATTTT
10469736 GTTCAAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (17 bp):
AATCTATCCTTATTTTT
Found at i:10483119 original size:16 final size:16
Alignment explanation
Indices: 10483079--10483111 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10483069 TTTTAAGTAA
*
10483079 GCCTTTCAAGGTTGAT
1 GCCTTTCAAGCTTGAT
10483095 GCCTTTCAAGCTTGAT
1 GCCTTTCAAGCTTGAT
10483111 G
1 G
10483112 TTTTTCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (16 bp):
GCCTTTCAAGCTTGAT
Found at i:10485310 original size:21 final size:21
Alignment explanation
Indices: 10485286--10485325 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10485276 ACTTTCCATC
10485286 TTTC-AAAAATCGACTTCTTAT
1 TTTCTAAAAATCGA-TTCTTAT
*
10485307 TTTCTCAAAATCGATTCTT
1 TTTCTAAAAATCGATTCTT
10485326 CACTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTCTAAAAATCGATTCTTAT
Found at i:10487473 original size:2 final size:2
Alignment explanation
Indices: 10487466--10487493 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10487456 CTTGAACTCG
10487466 CA 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 CA
10487494 TATATAACTA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:10491557 original size:18 final size:17
Alignment explanation
Indices: 10491534--10491589 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 17
10491524 TCAAGCTTCC
10491534 AAAAAGAGAGAAAAGACA
1 AAAAAGAGAGAAAAGA-A
10491552 AAAAAGAAAGAGAAGAAGAA
1 AAAAAG--AGAGAA-AAGAA
10491572 AGAAAAG-GAGAAAGAGAA
1 A-AAAAGAGAGAAA-AGAA
10491590 GGAAGAGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.03
18 15 0.45
20 8 0.24
21 9 0.27
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAGAAAAGAA
Found at i:10491572 original size:12 final size:12
Alignment explanation
Indices: 10491555--10491595 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
10491545 AAAGACAAAA
10491555 AAGAAAGAGAAG
1 AAGAAAGAGAAG
*
10491567 AAGAAAGAAAAG
1 AAGAAAGAGAAG
*
10491579 GAGAAAGAGAAGG
1 AAGAAAGAGAA-G
10491592 AAGA
1 AAGA
10491596 GAGTGGGGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGAAAGAGAAG
Found at i:10491692 original size:12 final size:12
Alignment explanation
Indices: 10491675--10491714 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
10491665 CTCGGGGAGA
10491675 AGAAAAAGAAAG
1 AGAAAAAGAAAG
10491687 AGAAAAAGAAAG
1 AGAAAAAGAAAG
10491699 AGAAAGAGAGAAAG
1 AGAAA-A-AGAAAG
10491713 AG
1 AG
10491715 CATGATGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 17 0.65
13 1 0.04
14 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAG
Found at i:10491697 original size:18 final size:18
Alignment explanation
Indices: 10491674--10491713 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
10491664 TCTCGGGGAG
10491674 AAGAAAAAGAAAGAGAAA
1 AAGAAAAAGAAAGAGAAA
* *
10491692 AAGAAAGAGAAAGAGAGA
1 AAGAAAAAGAAAGAGAAA
10491710 AAGA
1 AAGA
10491714 GCATGATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAAGAGAAA
Found at i:10492190 original size:2 final size:2
Alignment explanation
Indices: 10492174--10492210 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
10492164 ACTATGTCCT
10492174 TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10492211 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10492796 original size:60 final size:60
Alignment explanation
Indices: 10492701--10492926 Score: 276
Period size: 60 Copynumber: 3.8 Consensus size: 60
10492691 AAGAAAGACC
* * * * **
10492701 TGAAGCCTCGATTTATATTTAGTGACGTGGATAGTTCCCACGCGTAGGCAAAGGGGGACT
1 TGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACAAGTAGGCAAAGGGGGACT
* * * *
10492761 TGAAGCCCCGATTTATATTTGGTGACGTGGGTAGTTTCCACAAGTAGGTAAAAGGGGACT
1 TGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACAAGTAGGCAAAGGGGGACT
* * * *
10492821 TGAAGTCTCGATTTATATTTGGTGACGTGAGTAATTCCCACAAGTAGGCAAAGGGGGACC
1 TGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACAAGTAGGCAAAGGGGGACT
* * * *
10492881 TGAAGCCCCGATTCATA--TGGTGGCGTGGGCAATTCCCACTAGTAGG
1 TGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACAAGTAGG
10492927 TGATGATGTC
Statistics
Matches: 143, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
58 25 0.17
60 118 0.83
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (60 bp):
TGAAGCCCCGATTTATATTTGGTGACGTGGGTAATTCCCACAAGTAGGCAAAGGGGGACT
Found at i:10502068 original size:16 final size:15
Alignment explanation
Indices: 10502023--10502077 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
10502013 GCCAAAAAAG
10502023 GAGAAAAGACAAGAAA
1 GAGAAAAGA-AAGAAA
10502039 GAAAGAAAAG-AAGAAA
1 G--AGAAAAGAAAGAAA
10502055 GAGAAAAGGAAAGAGAA
1 GAGAAAA-GAAAGA-AA
10502072 G-GAAAA
1 GAGAAAA
10502078 TAGTGGGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.18
15 1 0.03
16 17 0.50
17 3 0.09
18 7 0.21
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (15 bp):
GAGAAAAGAAAGAAA
Found at i:10502111 original size:15 final size:16
Alignment explanation
Indices: 10502091--10502125 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10502081 TGGGGAGCCT
10502091 GAAAGG-AAAAAAAAA
1 GAAAGGAAAAAAAAAA
10502106 GAAAGGAAAAAAAAAA
1 GAAAGGAAAAAAAAAA
10502122 GAAA
1 GAAA
10502126 AAAGAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAGGAAAAAAAAAA
Found at i:10502117 original size:12 final size:12
Alignment explanation
Indices: 10502100--10502133 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
10502090 TGAAAGGAAA
*
10502100 AAAAAAGAAAGG
1 AAAAAAGAAAAG
10502112 AAAAAA-AAAAG
1 AAAAAAGAAAAG
10502123 AAAAAAGAAAA
1 AAAAAAGAAAA
10502134 AGGGGGAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:10502120 original size:18 final size:18
Alignment explanation
Indices: 10502092--10502134 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
10502082 GGGGAGCCTG
*
10502092 AAAGGAAAAAAAAAG--A
1 AAAGAAAAAAAAAAGAAA
*
10502108 AAGGAAAAAAAAAAGAAA
1 AAAGAAAAAAAAAAGAAA
10502126 AAAGAAAAA
1 AAAGAAAAA
10502135 GGGGGAGCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAAGAAA
Found at i:10502232 original size:48 final size:48
Alignment explanation
Indices: 10502163--10502275 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 48
10502153 GGAGAAGAAA
* ** *
10502163 AAAAAAAAGAGAAA-AAGAGCACGGCAACAAGGAGAATAAGGAGAGGG
1 AAAAAAAAGAGAAAGAAGAGCACGACAACAAAAAGAAGAAGGAGAGGG
* *
10502210 AAGAAAAAAGAGAAAGGA-AGCACGACGACAAAAAGAAGAAGGAGAGGG
1 AA-AAAAAAGAGAAAGAAGAGCACGACAACAAAAAGAAGAAGGAGAGGG
10502258 AAAAAAGAAGAGAAAGAA
1 AAAAAA-AAGAGAAAGAA
10502276 AAAAAAGAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
47 6 0.11
48 49 0.88
49 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.31, T:0.01
Consensus pattern (48 bp):
AAAAAAAAGAGAAAGAAGAGCACGACAACAAAAAGAAGAAGGAGAGGG
Found at i:10502297 original size:20 final size:19
Alignment explanation
Indices: 10502239--10502298 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
10502229 GCACGACGAC
**
10502239 AAAAAGAAGAAGGAGAGGGA
1 AAAAAGAAGAA-GAGAGAAA
*
10502259 AAAAAGAAG-AGAAAGAAA
1 AAAAAGAAGAAGAGAGAAA
*
10502277 AAAAAGAAGAATGAGATAAA
1 AAAAAGAAGAA-GAGAGAAA
10502297 AA
1 AA
10502299 GCAGTGGTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 14 0.42
19 2 0.06
20 17 0.52
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (19 bp):
AAAAAGAAGAAGAGAGAAA
Found at i:10502319 original size:31 final size:31
Alignment explanation
Indices: 10502281--10502354 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
10502271 AAGAAAAAAA
* **
10502281 AGAAGAATGAGATAAAA-AGCAGTGGTAGAGG
1 AGAAGAATGAGA-AAAAGAGCAGCGACAGAGG
10502312 AGAAGAATGAGAAAAAGAGCAGCGACAGAGG
1 AGAAGAATGAGAAAAAGAGCAGCGACAGAGG
*
10502343 AGAAGAAAGAGA
1 AGAAGAATGAGA
10502355 GAGGGAGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.53, C:0.05, G:0.35, T:0.07
Consensus pattern (31 bp):
AGAAGAATGAGAAAAAGAGCAGCGACAGAGG
Found at i:10502363 original size:31 final size:31
Alignment explanation
Indices: 10502307--10502368 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
10502297 AAGCAGTGGT
* *
10502307 AGAGGAGAAGAATGAGAAAAAGAGCAGCGAC
1 AGAGGAGAAGAAAGAGAAAAAGAGCAACGAC
* **
10502338 AGAGGAGAAGAAAGAGAGAGGGAGCAACGAC
1 AGAGGAGAAGAAAGAGAAAAAGAGCAACGAC
10502369 GGTGCCAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.39, T:0.02
Consensus pattern (31 bp):
AGAGGAGAAGAAAGAGAAAAAGAGCAACGAC
Found at i:10502415 original size:20 final size:21
Alignment explanation
Indices: 10502386--10502425 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
10502376 GAGGAGAAAG
10502386 AGGAAGAAGAGAAAG-GAAGA
1 AGGAAGAAGAGAAAGAGAAGA
*
10502406 AGGAATAAGAGAAAGAGAAG
1 AGGAAGAAGAGAAAGAGAAG
10502426 TGCCGACTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.03
Consensus pattern (21 bp):
AGGAAGAAGAGAAAGAGAAGA
Found at i:10502701 original size:2 final size:2
Alignment explanation
Indices: 10502696--10502731 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10502686 TTTTTTTTAA
*
10502696 AT AT AT GT 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
10502732 CTACATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10503191 original size:60 final size:59
Alignment explanation
Indices: 10503105--10503306 Score: 185
Period size: 60 Copynumber: 3.4 Consensus size: 59
10503095 TAAAAAAGAA
* * *
10503105 GACCTAAAGCCCCGATTTATATTTGGTGATG-TGGATAATTTCCACAAGTAGGCAAAAGGG
1 GACCTAAAG-CCCGATTTATATTTGGTGACGTTGG-TAATTCCCACAAGTAAGCAAAAGGG
* * * *
10503165 GACCAAAAGTCCCGATTTATATTTGGTGACGTTGGTAGTTCCCACAAGTAAGTAAAGGGG
1 GACCTAAAG-CCCGATTTATATTTGGTGACGTTGGTAATTCCCACAAGTAAGCAAAAGGG
* * * * * *
10503225 GACCTGAAGCTCCAATTTATATTTGGTAACG-TGAGTAATTCCCACGAGTAGGTC-AAGGGG
1 GACCTAAAGC-CCGATTTATATTTGGTGACGTTG-GTAATTCCCACAAGTAAG-CAAAAGGG
* *
10503285 GACCTGAAGCCCCGATTCATAT
1 GACCTAAAG-CCCGATTTATAT
10503307 GGTGGCATGG
Statistics
Matches: 119, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.03
60 112 0.94
61 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (59 bp):
GACCTAAAGCCCGATTTATATTTGGTGACGTTGGTAATTCCCACAAGTAAGCAAAAGGG
Found at i:10506106 original size:19 final size:19
Alignment explanation
Indices: 10506065--10506103 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
10506055 AAAAATAAAT
10506065 AACATAAAAGAAACAAAAG
1 AACATAAAAGAAACAAAAG
10506084 AACA-AAAATGAAA-AAAAG
1 AACATAAAA-GAAACAAAAG
10506102 AA
1 AA
10506104 ACAGCTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.77, C:0.08, G:0.10, T:0.05
Consensus pattern (19 bp):
AACATAAAAGAAACAAAAG
Found at i:10507387 original size:39 final size:39
Alignment explanation
Indices: 10507294--10507431 Score: 203
Period size: 39 Copynumber: 3.6 Consensus size: 39
10507284 CATCCTCAAC
* *
10507294 TCAAC-TCATGTGCACTCTCACACCGCACATAGC-TA-A
1 TCAACATCATGTGCACTCCCACACCGCACATGGCATATA
*
10507330 T-ACCATCATGTGCACTCCCACACCGCACATGGCATATA
1 TCAACATCATGTGCACTCCCACACCGCACATGGCATATA
*
10507368 TCATCATCATGTGCACTCCCACACCGCACATGGCATATA
1 TCAACATCATGTGCACTCCCACACCGCACATGGCATATA
*
10507407 TCAACATCGTGTGCACTCCCACACC
1 TCAACATCATGTGCACTCCCACACC
10507432 ATACACCACC
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
35 2 0.02
36 27 0.29
37 2 0.02
38 2 0.02
39 59 0.64
ACGTcount: A:0.28, C:0.38, G:0.12, T:0.22
Consensus pattern (39 bp):
TCAACATCATGTGCACTCCCACACCGCACATGGCATATA
Found at i:10514648 original size:116 final size:116
Alignment explanation
Indices: 10514444--10514673 Score: 415
Period size: 116 Copynumber: 2.0 Consensus size: 116
10514434 TTAATAATAT
10514444 ATTATTTTATTCTAAAAATTTTATCTTATCTCTTTGGTTCCCAAAGTTCCTTATTATGCCTCAAT
1 ATTATTTTATTCTAAAAATTTTATCTTATCTCTTTGGTTCCCAAAGTTCCTTATTATGCCTCAAT
* *
10514509 TCGCATCCGGCCAACTTTATTTATCACTATATCAAAGTATGGGGCATTTTA
66 TCGCATCCGACCAACTTTATTTATCACCATATCAAAGTATGGGGCATTTTA
*
10514560 ATTATTTTATTTTAAAAATTTTATCTTATCTCTTTGGTTCCCAAAGTTCCTTATTATGCCTCAAT
1 ATTATTTTATTCTAAAAATTTTATCTTATCTCTTTGGTTCCCAAAGTTCCTTATTATGCCTCAAT
**
10514625 TCGCATTTGACCAACTTTATTTATCACCATATCAAAGTATGGGGCATTT
66 TCGCATCCGACCAACTTTATTTATCACCATATCAAAGTATGGGGCATTT
10514674 CATAAATTCA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 109 1.00
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (116 bp):
ATTATTTTATTCTAAAAATTTTATCTTATCTCTTTGGTTCCCAAAGTTCCTTATTATGCCTCAAT
TCGCATCCGACCAACTTTATTTATCACCATATCAAAGTATGGGGCATTTTA
Found at i:10515798 original size:12 final size:13
Alignment explanation
Indices: 10515756--10515798 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
10515746 TTAGTCATAG
10515756 GAAAAATAGACTAA
1 GAAAAATA-ACTAA
10515770 GAAAAA-AACTAA
1 GAAAAATAACTAA
*
10515782 AAAAAATAA-TAA
1 GAAAAATAACTAA
10515794 GAAAA
1 GAAAA
10515799 TAGATAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 17 0.65
13 3 0.12
14 6 0.23
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (13 bp):
GAAAAATAACTAA
Found at i:10521543 original size:21 final size:21
Alignment explanation
Indices: 10521518--10521561 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10521508 AATTATCATT
10521518 AAATAAGAT-TTAAATTTCACA
1 AAATAA-ATCTTAAATTTCACA
* *
10521539 AAATAAATCTTAACTTTTACA
1 AAATAAATCTTAAATTTCACA
10521560 AA
1 AA
10521562 TAGTTAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATAAATCTTAAATTTCACA
Found at i:10529132 original size:2 final size:2
Alignment explanation
Indices: 10529125--10529174 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
10529115 CCTTTCAATT
10529125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10529167 TA TA TA TA
1 TA TA TA TA
10529175 CTACTATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10529712 original size:39 final size:38
Alignment explanation
Indices: 10529657--10529771 Score: 101
Period size: 39 Copynumber: 3.0 Consensus size: 38
10529647 TATTTTTTAA
*
10529657 AAAAATTAATTAAAAATATATAATATAAAAAATTATATT
1 AAAAATTAAAT-AAAATATATAATATAAAAAATTATATT
* * * *
10529696 AAGAATTAAATGAAAATA-A-AATATATAAGATTATAATA
1 AAAAATTAAAT-AAAATATATAATATAAAAAATTAT-ATT
* * *
10529734 AAAAATAACAATAAAATATATGATATTAAAAA-TATATT
1 AAAAATTA-AATAAAATATATAATATAAAAAATTATATT
10529772 TAACATGTGA
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
37 13 0.22
38 17 0.29
39 22 0.37
40 7 0.12
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (38 bp):
AAAAATTAAATAAAATATATAATATAAAAAATTATATT
Found at i:10529737 original size:26 final size:28
Alignment explanation
Indices: 10529665--10529746 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 28
10529655 AAAAAAATTA
* * *
10529665 ATTAAAAATATATAATATAAA-AAATTAT
1 ATTAAGAAT-TATAATAAAAATAAAATAT
*
10529693 ATTAAGAATTA-AATGAAAATAAAATAT
1 ATTAAGAATTATAATAAAAATAAAATAT
10529720 A-TAAG-ATTATAATAAAAAATAACAATA
1 ATTAAGAATTATAAT-AAAAATAA-AATA
10529747 AAATATATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
25 4 0.09
26 13 0.29
27 16 0.36
28 12 0.27
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (28 bp):
ATTAAGAATTATAATAAAAATAAAATAT
Found at i:10530450 original size:8 final size:8
Alignment explanation
Indices: 10530437--10530474 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
10530427 GTTACAATGC
10530437 ATAATTCT
1 ATAATTCT
*
10530445 ATAATTCA
1 ATAATTCT
10530453 ATAATTCT
1 ATAATTCT
10530461 ATAATTCT
1 ATAATTCT
10530469 ATAATT
1 ATAATT
10530475 TATTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (8 bp):
ATAATTCT
Found at i:10536905 original size:2 final size:2
Alignment explanation
Indices: 10536900--10536941 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10536890 AGAATTAGAA
*
10536900 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10536942 GTAGANAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10536989 original size:2 final size:2
Alignment explanation
Indices: 10536984--10537025 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10536974 AAATTAAGAA
*
10536984 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10537026 GTAGAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10554902 original size:57 final size:57
Alignment explanation
Indices: 10554814--10554928 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
10554804 AAGAGATCAT
* *
10554814 AATCATGCAATCTTTGTATACAAGATGCACCTAAGGATATGTATTTAAAATTATTCA
1 AATCATGCAATCTTTGTATAAAAGATGCACCTAAGGAAATGTATTTAAAATTATTCA
** * *
10554871 AATCATGTGATCTTTGTATAAAAGATGCACCTATGGAAATGTGTTTAAAATTATTCA
1 AATCATGCAATCTTTGTATAAAAGATGCACCTAAGGAAATGTATTTAAAATTATTCA
10554928 A
1 A
10554929 GCTCTTCTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (57 bp):
AATCATGCAATCTTTGTATAAAAGATGCACCTAAGGAAATGTATTTAAAATTATTCA
Found at i:10557911 original size:30 final size:30
Alignment explanation
Indices: 10557826--10557904 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
10557816 AATTATTAAT
* *
10557826 TATAAAAATTTATTTGAATTAAAATAAAAA
1 TATAAAAATTTATTTAAATTATAATAAAAA
* *
10557856 TATAAAAATTTAATTAAAATATAATAAAAA
1 TATAAAAATTTATTTAAATTATAATAAAAA
10557886 -ATAAAAATTTATTTAAATT
1 TATAAAAATTTATTTAAATT
10557905 TTTAATATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 17 0.40
30 26 0.60
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
TATAAAAATTTATTTAAATTATAATAAAAA
Found at i:10559188 original size:26 final size:26
Alignment explanation
Indices: 10559162--10559211 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
10559152 AATAATTATA
*
10559162 AAAAAAATTATA-ACAAAAAAATAAT
1 AAAAAAATTAGATACAAAAAAATAAT
* *
10559187 AATAAAATTAGATACAACAAAATAA
1 AAAAAAATTAGATACAAAAAAATAA
10559212 AAGTTCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (26 bp):
AAAAAAATTAGATACAAAAAAATAAT
Found at i:10562083 original size:19 final size:18
Alignment explanation
Indices: 10562050--10562086 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10562040 GAAAGATGTA
10562050 TTGAAATGCTTTGAATAT
1 TTGAAATGCTTTGAATAT
*
10562068 TTGAACATGTTTTGAATAT
1 TTGAA-ATGCTTTGAATAT
10562087 AAACGATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (18 bp):
TTGAAATGCTTTGAATAT
Found at i:10563790 original size:33 final size:33
Alignment explanation
Indices: 10563748--10563815 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
10563738 GGTTATACCT
10563748 TAACCAATTGAAAAAGTAGTTTTTGAGTGGTTA
1 TAACCAATTGAAAAAGTAGTTTTTGAGTGGTTA
*
10563781 TAACCAATTGAAAAGGTAGTTTTTGAGTGGTTA
1 TAACCAATTGAAAAAGTAGTTTTTGAGTGGTTA
10563814 TA
1 TA
10563816 CTTTAAGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (33 bp):
TAACCAATTGAAAAAGTAGTTTTTGAGTGGTTA
Found at i:10568593 original size:41 final size:41
Alignment explanation
Indices: 10568548--10568663 Score: 205
Period size: 41 Copynumber: 2.8 Consensus size: 41
10568538 GTTACGAAAT
*
10568548 GTGGATTTTGAGAAGGCATATGATAGTTTATGTTATTAAAG
1 GTGGATTTTAAGAAGGCATATGATAGTTTATGTTATTAAAG
*
10568589 GTGGATTTTAAGAAGGCACATGATAGTTTATGTTATTAAAG
1 GTGGATTTTAAGAAGGCATATGATAGTTTATGTTATTAAAG
*
10568630 GTGGATTTTAAGAAGGCATATGATAGTGTATGTT
1 GTGGATTTTAAGAAGGCATATGATAGTTTATGTT
10568664 GGTATTTTCT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (41 bp):
GTGGATTTTAAGAAGGCATATGATAGTTTATGTTATTAAAG
Found at i:10571835 original size:35 final size:34
Alignment explanation
Indices: 10571773--10571904 Score: 130
Period size: 35 Copynumber: 3.9 Consensus size: 34
10571763 GAAAAGTTAG
* * ** *
10571773 TTGTTG-GGTTTTGGTTGATCCCGTGAAAAATCA
1 TTGTTGAGGTTGTGGTTGAGCCTTTGAAAAACCA
10571806 TTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGTTG-AGGTTGTGGTTGAGCCTTTGAAAAACCA
* *
10571841 CT-TTGA-GTTTTGGTTGAG-CTTGTGAAAAACCA
1 TTGTTGAGGTTGTGGTTGAGCCTT-TGAAAAACCA
10571873 TTG-TGAAAGGTTGTGGTTGAGCCTTTGAAAAA
1 TTGTTG--AGGTTGTGGTTGAGCCTTTGAAAAA
10571905 TCGCTTTGGA
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
31 3 0.04
32 24 0.29
33 7 0.09
34 4 0.05
35 41 0.50
36 3 0.04
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (34 bp):
TTGTTGAGGTTGTGGTTGAGCCTTTGAAAAACCA
Found at i:10571857 original size:67 final size:66
Alignment explanation
Indices: 10571779--10571961 Score: 217
Period size: 67 Copynumber: 2.7 Consensus size: 66
10571769 TTAGTTGTTG
* *
10571779 GGTTTTGGTTGATCCCGTGAAAAATCATTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAACCACT
1 GGTTTTGGTTGATCCCGTGAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACT
10571843 TT
65 TT
* ** * *
10571845 GAGTTTTGGTTGAGCTTGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCGCT
1 G-GTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACT
10571910 TT
65 TT
* * * *
10571912 GGATTTTAGTTGATCCCGAT-AAAAACTATTGTGAAAGGTTTTGGCTGAGC
1 GG-TTTTGGTTGATCCCG-TGAAAAACCATTGTGAAAGGTTGTGGTTGAGC
10571962 TTGGTAAAAG
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
66 4 0.04
67 94 0.95
68 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (66 bp):
GGTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
T
Found at i:10582048 original size:17 final size:17
Alignment explanation
Indices: 10582026--10582062 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10582016 AGCAAAATAT
*
10582026 GCACACACTAAGTGGGA
1 GCACACACTAAGGGGGA
*
10582043 GCACACACTTAGGGGGA
1 GCACACACTAAGGGGGA
10582060 GCA
1 GCA
10582063 ATCCCCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.11
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:10582995 original size:35 final size:34
Alignment explanation
Indices: 10582956--10583067 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 34
10582946 GTTGATCCCG
*
10582956 TGAAAAACCATTATTGTAGGTTGTGGTTGAGCTTT
1 TGAAAAACCATT-TTGTAGGTTGTGGTTGAGCCTT
* * * *
10582991 TGAAAAATCA-CTT-TAGGTTTTGGTTGAGCCTG
1 TGAAAAACCATTTTGTAGGTTGTGGTTGAGCCTT
*
10583023 TGAAAAACCATTGTGTAAGGTTGTGGTTGAGCCTT
1 TGAAAAACCATTTTGT-AGGTTGTGGTTGAGCCTT
*
10583058 TAAAAAACCA
1 TGAAAAACCA
10583068 CTTTAGGTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
32 25 0.40
33 3 0.05
34 1 0.02
35 34 0.54
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (34 bp):
TGAAAAACCATTTTGTAGGTTGTGGTTGAGCCTT
Found at i:10583015 original size:32 final size:32
Alignment explanation
Indices: 10582972--10583076 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
10582962 ACCATTATTG
* *
10582972 TAGGTTGTGGTTGAGCTTTTGAAAAATCACTT
1 TAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
* * *
10583004 TAGGTTTTGGTTGAGCCTGTGAAAAACCATTGT
1 TAGGTTGTGGTTGAGCCTTTGAAAAACCACT-T
*
10583037 GTAAGGTTGTGGTTGAGCCTTTAAAAAACCACTT
1 -T-AGGTTGTGGTTGAGCCTTTGAAAAACCACTT
10583071 TAGGTT
1 TAGGTT
10583077 TTAGTTTATC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 31 0.51
33 2 0.03
34 2 0.03
35 26 0.43
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (32 bp):
TAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
Found at i:10583096 original size:67 final size:67
Alignment explanation
Indices: 10582939--10583111 Score: 213
Period size: 67 Copynumber: 2.6 Consensus size: 67
10582929 TTAGTTATTG
* * * *
10582939 GGTTTTAGTTGATCCCGTGAAAAACCATTATTGT-AGGTTGTGGTTGAGCTTTTGAAAAATCACT
1 GGTTTTAGTTGATCCCGTGAAAAACCATT-GTGTAAGGTTGTGGTTGAGCCTTTAAAAAACCACT
10583003 TTA
65 TTA
* * *
10583006 GGTTTTGGTTGAGCCTGTGAAAAACCATTGTGTAAGGTTGTGGTTGAGCCTTTAAAAAACCACTT
1 GGTTTTAGTTGATCCCGTGAAAAACCATTGTGTAAGGTTGTGGTTGAGCCTTTAAAAAACCACTT
10583071 TA
66 TA
* *** * *
10583073 GGTTTTAGTTTATCCCAAAAAAAACTATTGTGAAAGGTT
1 GGTTTTAGTTGATCCCGTGAAAAACCATTGTGTAAGGTT
10583112 TTGGCTAAGC
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
66 3 0.03
67 86 0.97
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (67 bp):
GGTTTTAGTTGATCCCGTGAAAAACCATTGTGTAAGGTTGTGGTTGAGCCTTTAAAAAACCACTT
TA
Found at i:10583662 original size:18 final size:18
Alignment explanation
Indices: 10583639--10583697 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
10583629 ATTTAAAAAT
10583639 TTAAAATATATATTTATA
1 TTAAAATATATATTTATA
*
10583657 TTAAAAT-TATCA-ATAT-
1 TTAAAATATAT-ATTTATA
*
10583673 TTTAAATATAT-TTTATAA
1 TTAAAATATATATTTAT-A
10583691 TTAAAAT
1 TTAAAAT
10583698 TAAATATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 9 0.28
17 9 0.28
18 14 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAATATATATTTATA
Found at i:10583704 original size:32 final size:32
Alignment explanation
Indices: 10583631--10583704 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 32
10583621 ATATTACTAT
*
10583631 TTAAAAATTTAAAATATATATTTATATTAAAA
1 TTAAATATTTAAAATATATATTTATATTAAAA
*
10583663 TTATCAATATTTTAAATATAT-TTTATAATTAAAA
1 TTA--AATATTTAAAATATATATTTAT-ATTAAAA
10583697 TTAAATAT
1 TTAAATAT
10583705 AACAGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
32 8 0.22
33 5 0.14
34 24 0.65
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
TTAAATATTTAAAATATATATTTATATTAAAA
Found at i:10585995 original size:2 final size:2
Alignment explanation
Indices: 10585990--10586024 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10585980 AATTTTTTTT
*
10585990 GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
10586025 GGGGGGATGG
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:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10586917 original size:2 final size:2
Alignment explanation
Indices: 10586907--10586950 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
10586897 GAGGTGAAGG
10586907 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10586950 A
1 A
10586951 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10587500 original size:2 final size:2
Alignment explanation
Indices: 10587493--10587543 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
10587483 AATTCAAACC
10587493 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10587534 AT AT AT AT AT
1 AT AT AT AT AT
10587544 TGTCTATATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10587701 original size:2 final size:2
Alignment explanation
Indices: 10587694--10587724 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10587684 AATTTTTGGT
*
10587694 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10587725 TTAGGGTGAT
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:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10589037 original size:57 final size:57
Alignment explanation
Indices: 10588949--10589057 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
10588939 TTGAAAAATT
* *
10588949 TTGGAAAACTAGTTTCAGCTTTTTCCATCATGAAATAAAAAACTTTAGGGTAATTAA
1 TTGGAAAACAAGTTTCAGCTATTTCCATCATGAAATAAAAAACTTTAGGGTAATTAA
* * *
10589006 TTGGAAAACAAGTTTTAGCTATTTCCTTCATGAAATAATAAACTTTAGGGTA
1 TTGGAAAACAAGTTTCAGCTATTTCCATCATGAAATAAAAAACTTTAGGGTA
10589058 GCTAATGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (57 bp):
TTGGAAAACAAGTTTCAGCTATTTCCATCATGAAATAAAAAACTTTAGGGTAATTAA
Found at i:10603560 original size:3 final size:3
Alignment explanation
Indices: 10603554--10603622 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
10603544 TTATTGTTGT
* ** * *
10603554 TTA TTA TTA -TA TTC TTAA TTA TCG TTA TTA TTA TTT TTG TTCA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT-A TTA
10603600 CTT- TTA TTA TTA TTA TTA TTA TT
1 -TTA TTA TTA TTA TTA TTA TTA TT
10603623 TATTTTAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:10603615 original size:40 final size:40
Alignment explanation
Indices: 10603538--10603615 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
10603528 TATATCATTT
* * *
10603538 TTATTGTTATTGTTGTTTATTATTATATTCTTAATTATCG
1 TTATTATTATTGTTGTTCATTATTATATTATTAATTATCG
* *
10603578 TTATTATTATTTTTGTTCATTACTTTTATTATT-ATTAT
1 TTATTATTATTGTTGTTCATTA-TTATATTATTAATTAT
10603616 TATTATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.65
Consensus pattern (40 bp):
TTATTATTATTGTTGTTCATTATTATATTATTAATTATCG
Found at i:10604256 original size:14 final size:16
Alignment explanation
Indices: 10604219--10604259 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
10604209 AATAATCGGC
*
10604219 TCTCTCTCTCTCTCTA
1 TCTCTCCCTCTCTCTA
10604235 TCTCTCCCTCTCTCT-
1 TCTCTCCCTCTCTCTA
10604250 TCT-TCCCTCT
1 TCTCTCCCTCT
10604260 TTTTGGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 7 0.29
15 3 0.12
16 14 0.58
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (16 bp):
TCTCTCCCTCTCTCTA
Found at i:10604948 original size:13 final size:14
Alignment explanation
Indices: 10604930--10605005 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 14
10604920 ATCCATTTTT
10604930 TTTATTTTTTTA-A
1 TTTATTTTTTTATA
*
10604943 TTTA-TTTTTTATT
1 TTTATTTTTTTATA
* *
10604956 TTTATTTTTTGTTTT
1 TTTATTTTTT-TATA
10604971 TTTATTATATTTTATTA
1 TTTATT-T-TTTTA-TA
10604988 TTATATTATTTTTATA
1 TT-TATT-TTTTTATA
10605004 TT
1 TT
10605006 ATATATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
12 7 0.13
13 8 0.15
14 5 0.10
15 9 0.17
16 6 0.12
17 11 0.21
18 6 0.12
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTATTTTTTTATA
Found at i:10604950 original size:18 final size:17
Alignment explanation
Indices: 10604924--10604999 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 17
10604914 CTGTTCATCC
*
10604924 ATTTTTTTTATTTTTTT
1 ATTTATTTTATTTTTTT
10604941 AATTTATTTT-TTATTTTT
1 -ATTTATTTTATT-TTTTT
*
10604959 A-TT-TTTTGTTTTTTT
1 ATTTATTTTATTTTTTT
* *
10604974 ATTATATTTTATTATTAT
1 ATT-TATTTTATTTTTTT
10604992 A-TTATTTT
1 ATTTATTTT
10605000 TATATTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 5 0.10
18 23 0.47
ACGTcount: A:0.20, C:0.00, G:0.01, T:0.79
Consensus pattern (17 bp):
ATTTATTTTATTTTTTT
Found at i:10604963 original size:11 final size:10
Alignment explanation
Indices: 10604925--10605000 Score: 57
Period size: 11 Copynumber: 7.4 Consensus size: 10
10604915 TGTTCATCCA
10604925 TTTTTTTTA-
1 TTTTTTTTAT
*
10604934 TTTTTTTAAT
1 TTTTTTTTAT
10604944 TTATTTTTTAT
1 TT-TTTTTTAT
10604955 TTTTATTTT-T
1 TTTT-TTTTAT
10604965 TGTTTTTTTAT
1 T-TTTTTTTAT
* *
10604976 TATATTTTAT
1 TTTTTTTTAT
* *
10604986 TATTATATTAT
1 T-TTTTTTTAT
10604997 TTTT
1 TTTT
10605001 ATATTATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
9 8 0.15
10 20 0.37
11 26 0.48
ACGTcount: A:0.18, C:0.00, G:0.01, T:0.80
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:10604965 original size:33 final size:36
Alignment explanation
Indices: 10604927--10605005 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 36
10604917 TTCATCCATT
10604927 TTTTTTATTTTTTTAATT-TATTTT-TTATT-T-TTA
1 TTTTTTATTTTTTT-ATTATATTTTATTATTATATTA
*
10604960 TTTTTTGTTTTTTTATTATATTTTATTATTATATTA
1 TTTTTTATTTTTTTATTATATTTTATTATTATATTA
10604996 TTTTTATATT
1 TTTTT-TATT
10605006 ATATATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 3 0.08
33 19 0.49
34 5 0.13
35 1 0.03
36 8 0.21
37 3 0.08
ACGTcount: A:0.20, C:0.00, G:0.01, T:0.78
Consensus pattern (36 bp):
TTTTTTATTTTTTTATTATATTTTATTATTATATTA
Found at i:10604984 original size:31 final size:33
Alignment explanation
Indices: 10604927--10604991 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
10604917 TTCATCCATT
* *
10604927 TTTTTTATTTTTTTAATTTATTTTTTATTTTTA
1 TTTTTTATTTTTTTAATTTATATTTTATTATTA
*
10604960 TTTTTTGTTTTTTT-A-TTATATTTTATTATTA
1 TTTTTTATTTTTTTAATTTATATTTTATTATTA
10604991 T
1 T
10604992 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 15 0.52
32 1 0.03
33 13 0.45
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (33 bp):
TTTTTTATTTTTTTAATTTATATTTTATTATTA
Found at i:10605505 original size:32 final size:32
Alignment explanation
Indices: 10605469--10605579 Score: 116
Period size: 32 Copynumber: 3.4 Consensus size: 32
10605459 TTTATCGGGA
*
10605469 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* **
10605501 TCAACCACAACCTTTCACAA-TGGTTTTTCACGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
* *
10605536 TTAACCAAAACCCAAAGTGATTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
*
10605568 TCAACCACAACC
1 TCAACCAAAACC
10605580 TACAACAATG
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
31 2 0.03
32 34 0.54
35 25 0.40
36 2 0.03
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:10605546 original size:67 final size:67
Alignment explanation
Indices: 10605430--10605619 Score: 240
Period size: 67 Copynumber: 2.8 Consensus size: 67
10605420 GACTTTTACC
* * * * * *
10605430 AGGCTCAACCAAAACTTTTTACAATAGTTTTT-ATCGGGATCAACTAAAACCCAAAGTGGTTTTT
1 AGGCTCAACCACAACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGATTTTT
10605494 CAA
65 CAA
* *
10605497 AGGCTCAACCACAACCTTTCACAATGGTTTTTCACGGGCTTAACCAAAACCCAAAGTGATTTTTC
1 AGGCTCAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGATTTTTC
10605562 AA
66 AA
* *
10605564 AGGCTCAACCACAACC-TACAACAATGATTTTTCTCACGGGATCAACCAAAACCCAA
1 AGGCTCAACCACAACCTTTC-ACAATG-GTTTT-TCACGGGATCAACCAAAACCCAA
10605620 CAACTAACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
66 2 0.02
67 79 0.74
68 5 0.05
69 21 0.20
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (67 bp):
AGGCTCAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGATTTTTC
AA
Found at i:10605621 original size:35 final size:33
Alignment explanation
Indices: 10605464--10605622 Score: 108
Period size: 32 Copynumber: 4.7 Consensus size: 33
10605454 TAGTTTTTAT
* * * *
10605464 CGGGATCAACTAAAACCCAA-AGTGGTTTTTCA
1 CGGGCTCAACCAAAACCCAACAATGATTTTTCA
** * *
10605496 AAGGCTCAACCACAACCTTTC-ACAATGGTTTTTCA
1 CGGGCTCAACCAAAACC---CAACAATGATTTTTCA
* *
10605531 CGGGCTTAACCAAAACCCAA-AGTGATTTTTCA
1 CGGGCTCAACCAAAACCCAACAATGATTTTTCA
** *
10605563 AAGGCTCAACCACAACCTACAACAATGATTTTTCTCA
1 CGGGCTCAACCAAAACC--CAACAATGA-TTTT-TCA
*
10605600 CGGGATCAACCAAAACCCAACAA
1 CGGGCTCAACCAAAACCCAACAA
10605623 CTAACTTTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 17
0.72 0.16 0.13
Matches are distributed among these distances:
32 36 0.38
33 1 0.01
34 4 0.04
35 35 0.36
36 4 0.04
37 16 0.17
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (33 bp):
CGGGCTCAACCAAAACCCAACAATGATTTTTCA
Found at i:10608868 original size:329 final size:328
Alignment explanation
Indices: 10608269--10608915 Score: 1285
Period size: 329 Copynumber: 2.0 Consensus size: 328
10608259 GCTTTCGGAA
10608269 ATTTAGATTTGAATATGTGTGGGTGTGAAAATGGTAGTTGCTCAAACTTATAAATTGTAAAACAA
1 ATTTAGATTTGAATATGTGTGGGTGTGAAAATGGTAGTTGCTCAAACTTATAAATTGTAAAACAA
10608334 AATGAGTTTATATTTTATATGCTGTTAATATATGGATTCTATACATTATCATTGAATCAAATAAT
66 AATGAGTTTATATTTTATATGCTGTTAATATATGGATTCTATACATTATCATTGAATCAAATAAT
10608399 ATTATTTTATTAATAAATAAATATAAAAGTTGGGACATAAAGACTTTTGAACTTTTACTTTTACA
131 ATTATTTTATTAATAAATAAATATAAAAGTTGGGACATAAAGACTTTTGAACTTTTACTTTTACA
10608464 CATTTAAGGAGTGACACTCTATGATTTACTAATAAGGTATTAGATGTTATATACTAATAGTACAT
196 CATTTAAGGAGTGACACTCTATGATTTACTAATAAGGTATTAGATGTTATATACTAATAGTACAT
10608529 CCAATATAAACTCAGAATTAAATAATCATCTTGAACATGATATTGATATATATATATAAAATAAT
261 CCAATATAAACTCAGAATTAAATAATCATCTTGAACATGATATTGATATATATATATAAAATAAT
10608594 ATG
326 ATG
10608597 ANTTTAGATTTGAATATGTGTGGGTGTGAAAATGGTAGTTGCTCAAACTTATAAATTGTAAAACA
1 A-TTTAGATTTGAATATGTGTGGGTGTGAAAATGGTAGTTGCTCAAACTTATAAATTGTAAAACA
10608662 AAATGAGTTTATATTTTATATGCTGTTAATATATGGATTCTATACATTATCATTGAATCAAATAA
65 AAATGAGTTTATATTTTATATGCTGTTAATATATGGATTCTATACATTATCATTGAATCAAATAA
10608727 TATTATTTTATTAATAAATAAATATAAAAGTTGGGACATAAAGACTTTTGAACTTTTACTTTTAC
130 TATTATTTTATTAATAAATAAATATAAAAGTTGGGACATAAAGACTTTTGAACTTTTACTTTTAC
10608792 ACATTTAAGGAGTGACACTCTATGATTTACTAATAAGGTATTAGATGTTATATACTAATAGTACA
195 ACATTTAAGGAGTGACACTCTATGATTTACTAATAAGGTATTAGATGTTATATACTAATAGTACA
10608857 TCCAATATAAACTCAGAATTAAATAATCATCTTGAACATGATATTGATATATATATATA
260 TCCAATATAAACTCAGAATTAAATAATCATCTTGAACATGATATTGATATATATATATA
10608916 TATATAAATA
Statistics
Matches: 318, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
328 1 0.00
329 317 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (328 bp):
ATTTAGATTTGAATATGTGTGGGTGTGAAAATGGTAGTTGCTCAAACTTATAAATTGTAAAACAA
AATGAGTTTATATTTTATATGCTGTTAATATATGGATTCTATACATTATCATTGAATCAAATAAT
ATTATTTTATTAATAAATAAATATAAAAGTTGGGACATAAAGACTTTTGAACTTTTACTTTTACA
CATTTAAGGAGTGACACTCTATGATTTACTAATAAGGTATTAGATGTTATATACTAATAGTACAT
CCAATATAAACTCAGAATTAAATAATCATCTTGAACATGATATTGATATATATATATAAAATAAT
ATG
Found at i:10608910 original size:2 final size:2
Alignment explanation
Indices: 10608903--10608937 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10608893 CATGATATTG
*
10608903 AT AT AT AT AT AT AT AT AT AA 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 A
10608938 ATAAATAGTG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10617151 original size:6 final size:6
Alignment explanation
Indices: 10617140--10617169 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
10617130 TTATTATCTA
*
10617140 AGAAGG AGAAGG AGAAGG AGAAGA AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
10617170 GAGGAAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:10621191 original size:3 final size:3
Alignment explanation
Indices: 10621177--10621211 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
10621167 CCTACCCCCC
* *
10621177 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCG TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
10621212 GTCTCTCACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:10628467 original size:13 final size:14
Alignment explanation
Indices: 10628449--10628482 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
10628439 TTTTAAAATG
10628449 AAAAAAAATTATA-
1 AAAAAAAATTATAT
10628462 AAAAAAAATTATAT
1 AAAAAAAATTATAT
10628476 AAAAAAA
1 AAAAAAA
10628483 CAAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTATAT
Found at i:10635579 original size:2 final size:2
Alignment explanation
Indices: 10635574--10635614 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
10635564 TCTCTCTCTC
*
10635574 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10635615 GATGAAGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10636303 original size:11 final size:11
Alignment explanation
Indices: 10636287--10636312 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10636277 TGCACTGCCT
10636287 TTTTTTTTTTG
1 TTTTTTTTTTG
10636298 TTTTTTTTTTG
1 TTTTTTTTTTG
10636309 TTTT
1 TTTT
10636313 GGCTTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:10636661 original size:2 final size:2
Alignment explanation
Indices: 10636656--10636689 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10636646 ACACATGTAC
10636656 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
10636690 GTCATTCTCA
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:10640315 original size:137 final size:137
Alignment explanation
Indices: 10640069--10640342 Score: 530
Period size: 137 Copynumber: 2.0 Consensus size: 137
10640059 ATAGCATTAG
10640069 CCAATAACTAATTTAAATCAAGGAAATACAATTCTTGAAGATGAGAAAACAAGTCAAAACCAAAT
1 CCAATAACTAATTTAAATCAAGGAAATACAATTCTTGAAGATGAGAAAACAAGTCAAAACCAAAT
* *
10640134 TAATAATTTTAAACGATGCATAACTAAGTTATAGATTCCATACAGTCTACATTGAACCATCACAG
66 TAATAATTTTAAAAGATGCATAACTAAATTATAGATTCCATACAGTCTACATTGAACCATCACAG
10640199 TAAAGAT
131 TAAAGAT
10640206 CCAATAACTAATTTAAATCAAGGAAATACAATTCTTGAAGATGAGAAAACAAGTCAAAACCAAAT
1 CCAATAACTAATTTAAATCAAGGAAATACAATTCTTGAAGATGAGAAAACAAGTCAAAACCAAAT
10640271 TAATAATTTTAAAAGATGCATAACTAAATTATAGATTCCATACAGTCTACATTGAACCATCACAG
66 TAATAATTTTAAAAGATGCATAACTAAATTATAGATTCCATACAGTCTACATTGAACCATCACAG
10640336 TAAAGAT
131 TAAAGAT
10640343 AAATTTTCTT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (137 bp):
CCAATAACTAATTTAAATCAAGGAAATACAATTCTTGAAGATGAGAAAACAAGTCAAAACCAAAT
TAATAATTTTAAAAGATGCATAACTAAATTATAGATTCCATACAGTCTACATTGAACCATCACAG
TAAAGAT
Found at i:10647964 original size:4 final size:4
Alignment explanation
Indices: 10647957--10647982 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
10647947 CATACATACA
10647957 TACG TACG TACG TACG TACG TACG TA
1 TACG TACG TACG TACG TACG TACG TA
10647983 TTTACATATA
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:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (4 bp):
TACG
Found at i:10663190 original size:15 final size:14
Alignment explanation
Indices: 10663162--10663200 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
10663152 AAAGAAGACA
10663162 AAATATATAATATTT
1 AAATAT-TAATATTT
*
10663177 TAATATTAATTATTT
1 AAATATTAA-TATTT
10663192 AAATATTAA
1 AAATATTAA
10663201 AATATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATATTAATATTT
Found at i:10663696 original size:23 final size:23
Alignment explanation
Indices: 10663666--10663711 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
10663656 TTCCTACAAG
10663666 GGTGAGAAGAAT-GAAAAAAAAA
1 GGTGAGAAGAATAGAAAAAAAAA
* *
10663688 GGTGAAGAAGTATAGAACAAAAAA
1 GGTG-AGAAGAATAGAAAAAAAAA
10663712 TAGAAGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.61, C:0.02, G:0.26, T:0.11
Consensus pattern (23 bp):
GGTGAGAAGAATAGAAAAAAAAA
Found at i:10664957 original size:2 final size:2
Alignment explanation
Indices: 10664944--10664978 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10664934 GTTCTTTTGT
*
10664944 TC TC TC TT 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 TC TC TC TC T
10664979 GAAAGATAAT
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:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:10667020 original size:21 final size:22
Alignment explanation
Indices: 10666990--10667064 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
10666980 GTATCTTTAG
* *
10666990 TTTTTTAGTATTGCGTGACT-A
1 TTTTTAAGTATTGCGTGATTGA
* * *
10667011 GTTTTAAGTATTACATGATTGA
1 TTTTTAAGTATTGCGTGATTGA
10667033 TTTTTAAGTATTGCGTGATTGA
1 TTTTTAAGTATTGCGTGATTGA
10667055 TTTTTAAGTA
1 TTTTTAAGTA
10667065 ACGCCTAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 15 0.33
22 30 0.67
ACGTcount: A:0.25, C:0.05, G:0.19, T:0.51
Consensus pattern (22 bp):
TTTTTAAGTATTGCGTGATTGA
Found at i:10667142 original size:22 final size:22
Alignment explanation
Indices: 10667114--10667155 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10667104 ATGCTTTACT
*
10667114 AACCAATCACGTAATACCTATC
1 AACCAATCACGCAATACCTATC
10667136 AACCAATCACGCAATACCTA
1 AACCAATCACGCAATACCTA
10667156 AAAATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.33, G:0.05, T:0.19
Consensus pattern (22 bp):
AACCAATCACGCAATACCTATC
Found at i:10667165 original size:22 final size:22
Alignment explanation
Indices: 10667140--10667222 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
10667130 CCTATCAACC
10667140 AATCACGCAATACCTAAAAATT
1 AATCACGCAATACCTAAAAATT
* * *
10667162 AATCACGCACT-GCTTAAAATT
1 AATCACGCAATACCTAAAAATT
* * ** * *
10667183 AATAATGCAATATTTTAAAACT
1 AATCACGCAATACCTAAAAATT
*
10667205 AATCACGTAATACCTAAA
1 AATCACGCAATACCTAAA
10667223 TGCTTATTAC
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
21 16 0.36
22 29 0.64
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (22 bp):
AATCACGCAATACCTAAAAATT
Found at i:10667606 original size:9 final size:9
Alignment explanation
Indices: 10667592--10667639 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
10667582 ACATGATTAA
*
10667592 TAACACGTT
1 TAACACGAT
10667601 TAACACGAT
1 TAACACGAT
*
10667610 TAACACAAT
1 TAACACGAT
* *
10667619 TAATACGTT
1 TAACACGAT
*
10667628 TAACATGAT
1 TAACACGAT
10667637 TAA
1 TAA
10667640 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:10673951 original size:3 final size:3
Alignment explanation
Indices: 10673943--10673974 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10673933 ATGAATGTGT
10673943 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10673975 GGTTCTTATG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10677034 original size:31 final size:30
Alignment explanation
Indices: 10676993--10677054 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
10676983 GACTTAGATG
*
10676993 AAAGGTATGTTATTTTAATCATATGTAATT
1 AAAGGTATGTTACTTTAATCATATGTAATT
*
10677023 AAAGGTTATGTTACTTTAATCGTATGTAATT
1 AAAGG-TATGTTACTTTAATCATATGTAATT
10677054 A
1 A
10677055 TAAGAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (30 bp):
AAAGGTATGTTACTTTAATCATATGTAATT
Found at i:10679427 original size:2 final size:2
Alignment explanation
Indices: 10679420--10679501 Score: 73
Period size: 2 Copynumber: 41.5 Consensus size: 2
10679410 TCTTTTTAAG
* *
10679420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TA CTA TA -A GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* *
10679462 TA CA NA -A GTA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10679502 CTTACTATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
1 4 0.06
2 61 0.90
3 3 0.04
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10683411 original size:20 final size:20
Alignment explanation
Indices: 10683386--10683429 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
10683376 TTTAAAAAAT
10683386 CAATCACCAATCGATGTATG
1 CAATCACCAATCGATGTATG
10683406 CAATCACCAATCGATGTATG
1 CAATCACCAATCGATGTATG
10683426 CAAT
1 CAAT
10683430 TACCCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (20 bp):
CAATCACCAATCGATGTATG
Done.