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 41 of 444
Found at i:10052375 original size:18 final size:18
Alignment explanation
Indices: 10052342--10052376 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10052332 TTTTTTATAT
**
10052342 TTTTATTATTTTAATTAA
1 TTTTATTATTCAAATTAA
10052360 TTTTATTATTCAAATTA
1 TTTTATTATTCAAATTA
10052377 TGCCATTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATTATTCAAATTAA
Found at i:10062015 original size:25 final size:26
Alignment explanation
Indices: 10061975--10062024 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
10061965 CTAAGTTTTT
* *
10061975 TTTTTTTCTGATTA-TTCTTAATTTA
1 TTTTTTTCTAAATATTTCTTAATTTA
*
10062000 TTTTTTTCTAAATATTTTTTAATTT
1 TTTTTTTCTAAATATTTCTTAATTT
10062025 TTAGGGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTTTCTAAATATTTCTTAATTTA
Found at i:10062226 original size:3 final size:3
Alignment explanation
Indices: 10062218--10062260 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
10062208 CCTGGGCAAT
* *
10062218 AGA AGA AGA AG- AGA AAA AGA AGA ATA AG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
10062261 GGAGGAGGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:10062240 original size:17 final size:17
Alignment explanation
Indices: 10062218--10062260 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
10062208 CCTGGGCAAT
10062218 AGAAGAAGAAGAGAAAA
1 AGAAGAAGAAGAGAAAA
* *
10062235 AGAAGAATAAGAGAAGA
1 AGAAGAAGAAGAGAAAA
10062252 AGAAGAAGA
1 AGAAGAAGA
10062261 GGAGGAGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAAA
Found at i:10063318 original size:21 final size:21
Alignment explanation
Indices: 10063292--10063334 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10063282 CAACGTGGCA
*
10063292 AGTTAATTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
**
10063313 AGTTAACTGGCCATGTCAGCT
1 AGTTAACTGGCCACATCAGCT
10063334 A
1 A
10063335 TCCCGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:10063908 original size:3 final size:3
Alignment explanation
Indices: 10063900--10063932 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
10063890 TACATATGTC
10063900 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10063933 TTAAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:10063971 original size:18 final size:18
Alignment explanation
Indices: 10063950--10063985 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10063940 TTAGGTACTC
10063950 TATAAAAATGACGATATA
1 TATAAAAATGACGATATA
10063968 TATAAAAATGACGATATA
1 TATAAAAATGACGATATA
10063986 CAATAGTAGA
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:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
TATAAAAATGACGATATA
Found at i:10064829 original size:20 final size:21
Alignment explanation
Indices: 10064795--10064839 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
10064785 ATTTTATAAT
10064795 ACATAAATTAAATAA-AAATA
1 ACATAAATTAAATAATAAATA
** *
10064815 ACATAAATTTTATAATAGATA
1 ACATAAATTAAATAATAAATA
10064836 ACAT
1 ACAT
10064840 TTATAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
ACATAAATTAAATAATAAATA
Found at i:10065637 original size:3 final size:3
Alignment explanation
Indices: 10065629--10065677 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
10065619 TCAAAACCTC
10065629 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10065677 A
1 A
10065678 ACTAAGGGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10071923 original size:97 final size:97
Alignment explanation
Indices: 10071815--10072009 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
10071805 TACTTGATTT
10071815 GGTTTTAAAATATTTCGATGCCACGCATGGATTTAATTTCATTAAATGTTATTATTCATTTTATA
1 GGTTTTAAAATATTTCGATGCCACGCATGGATTTAATTTCATTAAATGTTATTATTCATTTTATA
10071880 AACATTCAATTTTTAATGTATTAATGTCGTTG
66 AACATTCAATTTTTAATGTATTAATGTCGTTG
10071912 GGTTTTAAAATATTTCGATGCCACGCATGGATTTAATTTCATTAAATGTTATTATTCATTTTATA
1 GGTTTTAAAATATTTCGATGCCACGCATGGATTTAATTTCATTAAATGTTATTATTCATTTTATA
10071977 AACATTCAATTTTTAATGTATTAATGTCGTTG
66 AACATTCAATTTTTAATGTATTAATGTCGTTG
10072009 G
1 G
10072010 AATTCTGTTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (97 bp):
GGTTTTAAAATATTTCGATGCCACGCATGGATTTAATTTCATTAAATGTTATTATTCATTTTATA
AACATTCAATTTTTAATGTATTAATGTCGTTG
Found at i:10072347 original size:14 final size:14
Alignment explanation
Indices: 10072328--10072363 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
10072318 AAAGACGTAT
10072328 GAAAATTTCAATAA
1 GAAAATTTCAATAA
*
10072342 GAAAATTTCGATAA
1 GAAAATTTCAATAA
10072356 GAAAATTT
1 GAAAATTT
10072364 TACCGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (14 bp):
GAAAATTTCAATAA
Found at i:10073656 original size:25 final size:24
Alignment explanation
Indices: 10073626--10073673 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
10073616 AGCACAACTC
10073626 TTATGAGCGTCCTAATATAGGCTCT
1 TTATGAGCGTCCTAATAT-GGCTCT
* *
10073651 TTATGAGCTTCCTGATATGGCTC
1 TTATGAGCGTCCTAATATGGCTC
10073674 GCTTCAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TTATGAGCGTCCTAATATGGCTCT
Found at i:10078080 original size:2 final size:2
Alignment explanation
Indices: 10078073--10078098 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10078063 CTGTATGTAA
10078073 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
10078099 TAAATGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10079661 original size:5 final size:5
Alignment explanation
Indices: 10079642--10079675 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
10079632 GAAATACTAA
*
10079642 TATTT TA-TA TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
10079676 AACTTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:10079760 original size:3 final size:3
Alignment explanation
Indices: 10079752--10079776 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10079742 GCTGTCAAAT
10079752 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
10079777 GAGTGCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10083376 original size:14 final size:14
Alignment explanation
Indices: 10083357--10083383 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10083347 TTTCAAGAAA
10083357 TTAATCTTAAAATC
1 TTAATCTTAAAATC
10083371 TTAATCTTAAAAT
1 TTAATCTTAAAAT
10083384 AACTAACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATCTTAAAATC
Found at i:10095387 original size:34 final size:34
Alignment explanation
Indices: 10095342--10095414 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
10095332 TTTATGCCCT
* *
10095342 TTTTTTTTTTTTAATTTTATCTCCCTTCTACAAA
1 TTTTTTATTTTTAATTTTATCTCACTTCTACAAA
*
10095376 TTTTTTATTTTTAATTTTATTTCACTTCTACAAA
1 TTTTTTATTTTTAATTTTATCTCACTTCTACAAA
*
10095410 ATTTT
1 TTTTT
10095415 ACCTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTTTTATTTTTAATTTTATCTCACTTCTACAAA
Found at i:10099567 original size:12 final size:12
Alignment explanation
Indices: 10099552--10099577 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10099542 AATTAGACTA
10099552 CAAATTCCATTC
1 CAAATTCCATTC
10099564 CAAATTCCATTC
1 CAAATTCCATTC
10099576 CA
1 CA
10099578 TGTGACATCG
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:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (12 bp):
CAAATTCCATTC
Found at i:10100184 original size:15 final size:15
Alignment explanation
Indices: 10100151--10100207 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
10100141 AAATAATAGT
10100151 ATAAATTAATAAAT-A
1 ATAAA-TAATAAATAA
*
10100166 ATAACTAA-AAATAA
1 ATAAATAATAAATAA
10100180 CATAAATAATAAATAA
1 -ATAAATAATAAATAA
10100196 ATAAATAATAAA
1 ATAAATAATAAA
10100208 ATTAACAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 23 0.62
16 6 0.16
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAATAATAAATAA
Found at i:10100194 original size:4 final size:4
Alignment explanation
Indices: 10100151--10100207 Score: 52
Period size: 4 Copynumber: 15.2 Consensus size: 4
10100141 AAATAATAGT
* *
10100151 ATAA ATTA ATAA AT-A ATAA CT-A A-AA ATAA CATAA AT-A ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA
10100196 ATAA AT-A ATAA A
1 ATAA ATAA ATAA A
10100208 ATTAACAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
3 12 0.28
4 27 0.63
5 4 0.09
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:10100229 original size:34 final size:32
Alignment explanation
Indices: 10100157--10100244 Score: 92
Period size: 34 Copynumber: 2.7 Consensus size: 32
10100147 TAGTATAAAT
*
10100157 TAATAAAT-AATAACTAAAAATAACATAAATAA
1 TAATAAATAAATAA-TAAAATTAACATAAATAA
10100189 TAAATAAATAAATAATAAAATTAACAATACGAA-AA
1 T-AATAAATAAATAATAAAATTAAC-ATA--AATAA
10100224 TAAT-AATAAAATAATAAAATT
1 TAATAAAT-AAATAATAAAATT
10100245 CAAACTCAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
32 1 0.02
33 19 0.39
34 24 0.49
35 3 0.06
36 2 0.04
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (32 bp):
TAATAAATAAATAATAAAATTAACATAAATAA
Found at i:10100234 original size:11 final size:11
Alignment explanation
Indices: 10100157--10100240 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
10100147 TAGTATAAAT
10100157 TAAT-AAATAA
1 TAATAAAATAA
10100167 TAACT-AAA-AA
1 TAA-TAAAATAA
*
10100177 TAACATAAATAA
1 TAATA-AAATAA
10100189 TAA-ATAAATAAA
1 TAATA-AAAT-AA
10100201 TAATAAAATTAA
1 TAATAAAA-TAA
*
10100213 CAATACGAAAATAA
1 TAAT---AAAATAA
10100227 TAATAAAATAA
1 TAATAAAATAA
10100238 TAA
1 TAA
10100241 AATTCAAACT
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
10 8 0.13
11 23 0.38
12 18 0.30
13 2 0.03
14 6 0.10
15 4 0.07
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.25
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:10100519 original size:29 final size:29
Alignment explanation
Indices: 10100486--10100541 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
10100476 ACAAGAATGC
*
10100486 TTGATTTTATTGATTATGATTAGGTTTAG
1 TTGATTTTATTGATTAAGATTAGGTTTAG
* *
10100515 TTGATTTTATTGCTTAAGTTTAGGTTT
1 TTGATTTTATTGATTAAGATTAGGTTT
10100542 TTAGATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.20, T:0.57
Consensus pattern (29 bp):
TTGATTTTATTGATTAAGATTAGGTTTAG
Found at i:10106650 original size:18 final size:20
Alignment explanation
Indices: 10106627--10106664 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
10106617 ACATGGCAGT
10106627 CCAAC-TAGATTT-TAAATG
1 CCAACTTAGATTTCTAAATG
10106645 CCAACTTAGATTTCTAAATG
1 CCAACTTAGATTTCTAAATG
10106665 GGATGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
CCAACTTAGATTTCTAAATG
Found at i:10110702 original size:19 final size:20
Alignment explanation
Indices: 10110678--10110728 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
10110668 ATTGATATTA
10110678 TTTAAATAATATATTA-AAT
1 TTTAAATAATATATTATAAT
* *
10110697 TTTAAATATTATATTATATT
1 TTTAAATAATATATTATAAT
10110717 TTTAAAATAATA
1 TTT-AAATAATA
10110729 AAAATGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 15 0.56
20 5 0.19
21 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAATAATATATTATAAT
Found at i:10111041 original size:20 final size:21
Alignment explanation
Indices: 10111016--10111068 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
10111006 ATTTTCATCT
10111016 TAAAAATGATT-AAA-TTTAAA
1 TAAAAAT-ATTAAAATTTTAAA
*
10111036 TAAAAATTTTAAAATTTTAAA
1 TAAAAATATTAAAATTTTAAA
*
10111057 TAAAATTATTAA
1 TAAAAATATTAA
10111069 TGTAACATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 10 0.36
21 16 0.57
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAAATATTAAAATTTTAAA
Found at i:10111068 original size:21 final size:21
Alignment explanation
Indices: 10111016--10111068 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
10111006 ATTTTCATCT
*
10111016 TAAAAATGATT-AAATTTAAA
1 TAAAAATTATTAAAATTTAAA
10111036 TAAAAATT-TTAAAATTTTAAA
1 TAAAAATTATTAAAA-TTTAAA
10111057 T-AAAATTATTAA
1 TAAAAATTATTAA
10111069 TGTAACATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAAATTATTAAAATTTAAA
Found at i:10112374 original size:22 final size:23
Alignment explanation
Indices: 10112349--10112392 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
10112339 AATCATTGTT
10112349 AAAA-AATATATGAATT-TAAATA
1 AAAATAAT-TATGAATTGTAAATA
*
10112371 AAAATAATTGTGAATTGTAAAT
1 AAAATAATTATGAATTGTAAAT
10112393 CTTGAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
AAAATAATTATGAATTGTAAATA
Found at i:10114453 original size:21 final size:21
Alignment explanation
Indices: 10114429--10114506 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
10114419 TTTTATTCAG
* * *
10114429 CTCTCACGAGCCTCTGGTTAA
1 CTCTTACGAGCTTCTGTTTAA
* * *
10114450 CTCTTATGAGTTTCTGTTTAG
1 CTCTTACGAGCTTCTGTTTAA
10114471 CTCTTACGAGCTTCTGTTTAA
1 CTCTTACGAGCTTCTGTTTAA
*
10114492 CTCTTATGAGCTTCT
1 CTCTTACGAGCTTCT
10114507 CTTACGATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTTAA
Found at i:10114473 original size:42 final size:42
Alignment explanation
Indices: 10114399--10114506 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
10114389 TGCTTTGCTT
* * * * * *
10114399 TCTGGTTAGCTCTCACGAGCTTTTATTCAGCTCTCACGAGCC
1 TCTGGTTAACTCTTATGAGCTTCTGTTTAGCTCTCACGAGCC
* * *
10114441 TCTGGTTAACTCTTATGAGTTTCTGTTTAGCTCTTACGAGCT
1 TCTGGTTAACTCTTATGAGCTTCTGTTTAGCTCTCACGAGCC
*
10114483 TCTGTTTAACTCTTATGAGCTTCT
1 TCTGGTTAACTCTTATGAGCTTCT
10114507 CTTACGATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.42
Consensus pattern (42 bp):
TCTGGTTAACTCTTATGAGCTTCTGTTTAGCTCTCACGAGCC
Found at i:10118332 original size:21 final size:21
Alignment explanation
Indices: 10118279--10118347 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
10118269 CTTTACTTTT
* *
10118279 TGTTCAGCTCTCACGAGCTTC
1 TGTTCAACTCTTACGAGCTTC
*
10118300 TATTCAACTCTTACGAGCTTC
1 TGTTCAACTCTTACGAGCTTC
* * *
10118321 TGTTTAACTCTTATGAGTTTC
1 TGTTCAACTCTTACGAGCTTC
10118342 TGTTCA
1 TGTTCA
10118348 GCAGACGAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (21 bp):
TGTTCAACTCTTACGAGCTTC
Found at i:10124153 original size:22 final size:23
Alignment explanation
Indices: 10124125--10124186 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
10124115 ATTAACAATT
* *
10124125 AAATAAATATTTTAAAATC-TAA
1 AAATAAAAATATTAAAATCTTAA
* *
10124147 AAATAAAAATATTATATTCTTAA
1 AAATAAAAATATTAAAATCTTAA
*
10124170 AAATAAAAATATAAAAA
1 AAATAAAAATATTAAAA
10124187 CTAAAATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATAAAAATATTAAAATCTTAA
Found at i:10126460 original size:12 final size:12
Alignment explanation
Indices: 10126426--10126460 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
10126416 TGATATTATA
*
10126426 TGTATTTGTACC
1 TGTATTTGTATC
10126438 TGTATTTGTATC
1 TGTATTTGTATC
*
10126450 TGTATGTGTAT
1 TGTATTTGTAT
10126461 TTTCTGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.09, G:0.20, T:0.54
Consensus pattern (12 bp):
TGTATTTGTATC
Found at i:10126911 original size:18 final size:18
Alignment explanation
Indices: 10126890--10126951 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
10126880 CTGTGTCTGC
**
10126890 ATCTGTATCTAAATTTGA
1 ATCTGTATCTGTATTTGA
*
10126908 ATCT-TCATCTGTATCTGA
1 ATCTGT-ATCTGTATTTGA
*
10126926 AACTGTATCTGTATTTGA
1 ATCTGTATCTGTATTTGA
10126944 ATCTGTAT
1 ATCTGTAT
10126952 ATTATATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (18 bp):
ATCTGTATCTGTATTTGA
Found at i:10126923 original size:12 final size:12
Alignment explanation
Indices: 10126866--10126936 Score: 61
Period size: 12 Copynumber: 5.9 Consensus size: 12
10126856 TGGGGGTGGG
*
10126866 ATCTGTTTCTGC
1 ATCTGTATCTGC
*
10126878 ATCTGTGTCTGC
1 ATCTGTATCTGC
**
10126890 ATCTGTATCTAA
1 ATCTGTATCTGC
* * *
10126902 ATTTGAATCTTC
1 ATCTGTATCTGC
*
10126914 ATCTGTATCTGA
1 ATCTGTATCTGC
*
10126926 AACTGTATCTG
1 ATCTGTATCTG
10126937 TATTTGAATC
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (12 bp):
ATCTGTATCTGC
Found at i:10126932 original size:36 final size:36
Alignment explanation
Indices: 10126877--10126947 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
10126867 TCTGTTTCTG
* * *
10126877 CATCTGTGTCTGCATCTGTATCTAAATTTGAATCTT
1 CATCTGTATCTGAAACTGTATCTAAATTTGAATCTT
**
10126913 CATCTGTATCTGAAACTGTATCTGTATTTGAATCT
1 CATCTGTATCTGAAACTGTATCTAAATTTGAATCT
10126948 GTATATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (36 bp):
CATCTGTATCTGAAACTGTATCTAAATTTGAATCTT
Found at i:10129845 original size:29 final size:29
Alignment explanation
Indices: 10129821--10129942 Score: 154
Period size: 29 Copynumber: 4.2 Consensus size: 29
10129811 GACCGTATGT
*
10129821 GTCACGCGGCCGTGTGGTAGCCCGTGTGG
1 GTCACACGGCCGTGTGGTAGCCCGTGTGG
* *
10129850 GTCACATGGCGGTGTGGTAGCCCGTGTGG
1 GTCACACGGCCGTGTGGTAGCCCGTGTGG
*
10129879 GTCACACAGCCGTGTGGTAGCCCGTGTGG
1 GTCACACGGCCGTGTGGTAGCCCGTGTGG
* * * ** *
10129908 GTCACACGACCATGTAGTAAACCATGTGG
1 GTCACACGGCCGTGTGGTAGCCCGTGTGG
10129937 GTCACA
1 GTCACA
10129943 TGATCATGTA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.21
Consensus pattern (29 bp):
GTCACACGGCCGTGTGGTAGCCCGTGTGG
Found at i:10129950 original size:29 final size:29
Alignment explanation
Indices: 10129903--10129972 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
10129893 TGGTAGCCCG
10129903 TGTGGGTCACACGACCATGTAGTAAACCA
1 TGTGGGTCACACGACCATGTAGTAAACCA
* *
10129932 TGTGGGTCACATGATCATGTAGTAAACCA
1 TGTGGGTCACACGACCATGTAGTAAACCA
10129961 TGTGGGTCACAC
1 TGTGGGTCACAC
10129973 AACAATGTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (29 bp):
TGTGGGTCACACGACCATGTAGTAAACCA
Found at i:10133119 original size:2 final size:2
Alignment explanation
Indices: 10133112--10133270 Score: 214
Period size: 2 Copynumber: 80.5 Consensus size: 2
10133102 TATAGATTGT
*
10133112 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
10133154 AG AG GG AG GG AG GG A- AG GG AG AG AG AG AG AG AG AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
10133194 AG AG GG AG AG AG GG AG AG AG GG AG AG AG GG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10133236 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10133271 ATTAATAGAT
Statistics
Matches: 135, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
1 2 0.01
2 133 0.99
ACGTcount: A:0.45, C:0.01, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10134819 original size:16 final size:16
Alignment explanation
Indices: 10134800--10134830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10134790 CCTAAACTAA
*
10134800 TAAAGTAATAAATTAT
1 TAAACTAATAAATTAT
10134816 TAAACTAATAAATTA
1 TAAACTAATAAATTA
10134831 ATACATAAAT
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:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAACTAATAAATTAT
Found at i:10135849 original size:22 final size:22
Alignment explanation
Indices: 10135819--10135862 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10135809 ATTGTTAAAA
10135819 TACGCTGATGTGGCATTGACAT
1 TACGCTGATGTGGCATTGACAT
* *
10135841 TACGTTGATGTGGCATTTACAT
1 TACGCTGATGTGGCATTGACAT
10135863 GACATTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (22 bp):
TACGCTGATGTGGCATTGACAT
Found at i:10136505 original size:18 final size:19
Alignment explanation
Indices: 10136482--10136527 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
10136472 CTCAATAGTG
*
10136482 AAAAAAAATGCTGAAAA-C
1 AAAAAAAAAGCTGAAAATC
* *
10136500 AAAAAAAAAGTTGAAAATG
1 AAAAAAAAAGCTGAAAATC
10136519 AAAAAAAAA
1 AAAAAAAAA
10136528 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAGCTGAAAATC
Found at i:10136506 original size:19 final size:20
Alignment explanation
Indices: 10136482--10136528 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
10136472 CTCAATAGTG
10136482 AAAAAAAATGCTGAAAA-CA
1 AAAAAAAATGCTGAAAATCA
* *
10136501 AAAAAAAA-GTTGAAAATGA
1 AAAAAAAATGCTGAAAATCA
10136520 AAAAAAAAT
1 AAAAAAAAT
10136529 AAAAAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAAAAAATGCTGAAAATCA
Found at i:10136712 original size:15 final size:14
Alignment explanation
Indices: 10136676--10136753 Score: 63
Period size: 15 Copynumber: 5.4 Consensus size: 14
10136666 CAGCAGCAAG
10136676 GAGAAGAAAATA-AA
1 GAGAAGAAAA-AGAA
*
10136690 GGGAAAGAAAGAAGAA
1 GAG-AAGAAA-AAGAA
10136706 GAGAAGAAAAAGAA
1 GAGAAGAAAAAGAA
*
10136720 GGAGAAGGAAAA-AA
1 -GAGAAGAAAAAGAA
10136734 GA-AAGAAAAGAGAA
1 GAGAAGAAAA-AGAA
*
10136748 AAGAAG
1 GAGAAG
10136754 GTATAATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 6 0.12
13 3 0.06
14 12 0.23
15 26 0.50
16 5 0.10
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (14 bp):
GAGAAGAAAAAGAA
Found at i:10136712 original size:30 final size:31
Alignment explanation
Indices: 10136676--10136754 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
10136666 CAGCAGCAAG
*
10136676 GAGAAGAAAATA-AAGG-GAAAGAAAGAAGAA
1 GAGAAGAAAA-AGAAGGAGAAAGAAAAAAGAA
*
10136706 GAGAAGAAAAAGAAGGAGAAGGAAAAAAGAAA
1 GAGAAGAAAAAGAAGGAGAAAGAAAAAAG-AA
*
10136738 GAAAAGAGAAAAGAAGG
1 GAGAAGA-AAAAGAAGG
10136755 TATAATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.02
30 14 0.33
31 10 0.24
32 8 0.19
33 9 0.21
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (31 bp):
GAGAAGAAAAAGAAGGAGAAAGAAAAAAGAA
Found at i:10136719 original size:17 final size:17
Alignment explanation
Indices: 10136697--10136753 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
10136687 AAAGGGAAAG
10136697 AAAGAAGAAGAGAAGAA
1 AAAGAAGAAGAGAAGAA
*
10136714 AAAGAAG--GAGAAGGA
1 AAAGAAGAAGAGAAGAA
*
10136729 AAA-AAGAAAGAAAAGAGA
1 AAAGAAG-AAGAGAAGA-A
10136747 AAAGAAG
1 AAAGAAG
10136754 GTATAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
17 12 0.38
18 4 0.12
19 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAGAGAAGAA
Found at i:10136898 original size:26 final size:26
Alignment explanation
Indices: 10136842--10136899 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
10136832 TTTGTTAGTT
* *
10136842 ATTAATATTGTTAGTAAAAAACCCTT
1 ATTATTATTGTTAGTAAAAAACCCTA
10136868 ATTATTATTGTTAGTAAAAAACCCTA
1 ATTATTATTGTTAGTAAAAAACCCTA
10136894 ATTATT
1 ATTATT
10136900 GTTAGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (26 bp):
ATTATTATTGTTAGTAAAAAACCCTA
Found at i:10136901 original size:23 final size:25
Alignment explanation
Indices: 10136847--10136905 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 25
10136837 TAGTTATTAA
10136847 TATTGTTAGTAAAAAACCCTTATTAT
1 TATTGTTAGTAAAAAACCCTTA-TAT
10136873 TATTGTTAGTAAAAAACCC-TA-AT
1 TATTGTTAGTAAAAAACCCTTATAT
10136896 TATTGTTAGT
1 TATTGTTAGT
10136906 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.36
25 2 0.06
26 19 0.58
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (25 bp):
TATTGTTAGTAAAAAACCCTTATAT
Found at i:10142137 original size:9 final size:9
Alignment explanation
Indices: 10142119--10142190 Score: 54
Period size: 9 Copynumber: 8.9 Consensus size: 9
10142109 CTCCTCCTCC
10142119 CCTTCTTTTT
1 CCTTC-TTTT
10142129 CCTTC-TTT
1 CCTTCTTTT
*
10142137 --TTCTTCT
1 CCTTCTTTT
10142144 -CTTC-TTT
1 CCTTCTTTT
10142151 CCTTCTTTT
1 CCTTCTTTT
10142160 CCTTCTTTT
1 CCTTCTTTT
10142169 -C-T-TTTT
1 CCTTCTTTT
*
10142175 -CTTCTTCT
1 CCTTCTTTT
10142183 CCTTCTTT
1 CCTTCTTT
10142191 GTTCCCGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
6 8 0.16
7 6 0.12
8 14 0.27
9 18 0.35
10 5 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (9 bp):
CCTTCTTTT
Found at i:10142154 original size:22 final size:22
Alignment explanation
Indices: 10142122--10142188 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
10142112 CTCCTCCCCT
*
10142122 TCTT-TTTCCTTCTTTTTCTTC
1 TCTTCTTTCCTTCTTTTCCTTC
10142143 TCTTCTTTCCTTCTTTTCCTTC
1 TCTTCTTTCCTTCTTTTCCTTC
* * *
10142165 TTTTCTTTTTCTTCTTCTCCTTC
1 TCTTC-TTTCCTTCTTTTCCTTC
10142188 T
1 T
10142189 TTGTTCCCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.10
22 20 0.50
23 16 0.40
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (22 bp):
TCTTCTTTCCTTCTTTTCCTTC
Found at i:10142163 original size:31 final size:32
Alignment explanation
Indices: 10142119--10142190 Score: 103
Period size: 31 Copynumber: 2.2 Consensus size: 32
10142109 CTCCTCCTCC
10142119 CCTTCTTTTTCCTTCTTTT-TCTTCTCTTCTT-T
1 CCTTC-TTTTCCTTCTTTTCT-TTCTCTTCTTCT
*
10142151 CCTTCTTTTCCTTCTTTTCTTTTTCTTCTTCT
1 CCTTCTTTTCCTTCTTTTCTTTCTCTTCTTCT
10142183 CCTTCTTT
1 CCTTCTTT
10142191 GTTCCCGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (32 bp):
CCTTCTTTTCCTTCTTTTCTTTCTCTTCTTCT
Found at i:10158690 original size:21 final size:22
Alignment explanation
Indices: 10158666--10158706 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
10158656 TCCTTTTTTG
*
10158666 ATTTTTTTATT-TTTATTTAAA
1 ATTTTATTATTATTTATTTAAA
10158687 ATTTTATTATTATTTATTTA
1 ATTTTATTATTATTTATTTA
10158707 CTTAGGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTATTATTATTTATTTAAA
Found at i:10159890 original size:42 final size:42
Alignment explanation
Indices: 10159831--10159934 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
10159821 GGATTCTAAC
* *
10159831 GCTGGAATAGGACTGTTTGGCTGCAGAGATATAGCATTCTGG
1 GCTGGAATAGAACTGTTTGGCAGCAGAGATATAGCATTCTGG
* * *
10159873 GCTGGAATAGAACTGTTTGGCAGCAGGGATATGGCATTTTGG
1 GCTGGAATAGAACTGTTTGGCAGCAGAGATATAGCATTCTGG
*
10159915 GTTGGAATAGAACTGTTTGG
1 GCTGGAATAGAACTGTTTGG
10159935 TACCATGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.30
Consensus pattern (42 bp):
GCTGGAATAGAACTGTTTGGCAGCAGAGATATAGCATTCTGG
Found at i:10160058 original size:6 final size:6
Alignment explanation
Indices: 10160038--10160126 Score: 109
Period size: 6 Copynumber: 15.5 Consensus size: 6
10160028 ATTAATATTT
10160038 AAAT-A AAAT-A AAATAA AAAT-A AAAT-A AAATAA TAAATAA TAAA-AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA -AAATAA -AAATAA
*
10160083 AAA-AT AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
10160127 GAAAGATTGG
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
5 26 0.33
6 42 0.54
7 10 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:10160087 original size:41 final size:40
Alignment explanation
Indices: 10160042--10160126 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
10160032 ATATTTAAAT
10160042 AAAATAAAATAAAAAT-AAAAT-AAAATAATAAATAATAAAAA
1 AAAAT-AAATAAAAATAAAAATAAAAATAA-AAATAA-AAAAA
*
10160083 AAAATAAATAAAAATAAAAATAAAAATAAAAATAAAAATA
1 AAAATAAATAAAAATAAAAATAAAAATAAAAATAAAAAAA
10160123 AAAA
1 AAAA
10160127 GAAAGATTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
40 18 0.44
41 16 0.39
42 7 0.17
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (40 bp):
AAAATAAATAAAAATAAAAATAAAAATAAAAATAAAAAAA
Found at i:10163872 original size:27 final size:26
Alignment explanation
Indices: 10163842--10163903 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
10163832 AGATAATTAA
10163842 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
10163869 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
10163896 AATAAAAT
1 AATAAAAT
10163904 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:10172116 original size:23 final size:23
Alignment explanation
Indices: 10172086--10172133 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
10172076 TCAAGAAAAC
10172086 ACAATATTTATATATCATCATTT
1 ACAATATTTATATATCATCATTT
10172109 ACAATATTTATATATCATCATTT
1 ACAATATTTATATATCATCATTT
10172132 AC
1 AC
10172134 CATTCTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (23 bp):
ACAATATTTATATATCATCATTT
Found at i:10173970 original size:13 final size:13
Alignment explanation
Indices: 10173952--10173979 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10173942 TATTACTATA
10173952 TTTATAGTTAATT
1 TTTATAGTTAATT
10173965 TTTATAGTTAATT
1 TTTATAGTTAATT
10173978 TT
1 TT
10173980 AATCATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTATAGTTAATT
Found at i:10175188 original size:16 final size:16
Alignment explanation
Indices: 10175156--10175189 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10175146 TACACAAATC
*
10175156 AAAGAATTATTAGAAA
1 AAAGAATTAATAGAAA
10175172 AAAG-ATTAATAGAAA
1 AAAGAATTAATAGAAA
10175187 AAA
1 AAA
10175190 CTAATAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAGAATTAATAGAAA
Found at i:10176032 original size:18 final size:15
Alignment explanation
Indices: 10175987--10176023 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
10175977 TATCTGATGA
10175987 AGAAGAAACTTCTTC
1 AGAAGAAACTTCTTC
10176002 AGAAGAAACTTCTTC
1 AGAAGAAACTTCTTC
10176017 AGAAGAA
1 AGAAGAA
10176024 TCATCTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (15 bp):
AGAAGAAACTTCTTC
Found at i:10183504 original size:5 final size:5
Alignment explanation
Indices: 10183488--10183524 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
10183478 AGAGTTTTTT
10183488 GGCCC GGGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC -GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
10183525 AATTATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.00, C:0.57, G:0.43, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:10183665 original size:22 final size:22
Alignment explanation
Indices: 10183626--10183684 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
10183616 GTTTTAAGAA
*
10183626 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
10183647 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
10183669 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
10183685 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:10183715 original size:26 final size:26
Alignment explanation
Indices: 10183658--10183716 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
10183648 TGTTTTAATA
10183658 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATGTTTTTAAATATAT
* * *
10183683 TTGATTTATTATATTTTTTAAAT-TTT
1 TTTATTTATTAT-GTTTTTAAATATAT
10183709 TTTATTTA
1 TTTATTTA
10183717 ATGAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 6 0.21
26 13 0.46
27 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTATTTATTATGTTTTTAAATATAT
Found at i:10184126 original size:15 final size:15
Alignment explanation
Indices: 10184106--10184135 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10184096 GTCCTAAAAA
*
10184106 TTCTATTTCTGTTTT
1 TTCTATTTCTATTTT
10184121 TTCTATTTCTATTTT
1 TTCTATTTCTATTTT
10184136 CTTAGGACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.73
Consensus pattern (15 bp):
TTCTATTTCTATTTT
Found at i:10190991 original size:29 final size:29
Alignment explanation
Indices: 10190939--10191005 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
10190929 AGGTGGTTTT
* *
10190939 GGGTTTTAATGATTAGGTAAGATGGCTCG
1 GGGTTTAAATGATTAGGAAAGATGGCTCG
* *
10190968 GGGTTTAAATGATTA-GAAAGGATGGTTTG
1 GGGTTTAAATGATTAGGAAA-GATGGCTCG
10190997 GGGTTTAAA
1 GGGTTTAAA
10191006 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.03, G:0.34, T:0.34
Consensus pattern (29 bp):
GGGTTTAAATGATTAGGAAAGATGGCTCG
Found at i:10193598 original size:19 final size:17
Alignment explanation
Indices: 10193574--10193608 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
10193564 AGTAAAATAT
10193574 AAATTACAAACATAAAAAA
1 AAATTA-AAACA-AAAAAA
10193593 AAATTAAAACAAAAAA
1 AAATTAAAACAAAAAA
10193609 CTCCAACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (17 bp):
AAATTAAAACAAAAAAA
Found at i:10193845 original size:26 final size:25
Alignment explanation
Indices: 10193815--10193874 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
10193805 TACAAAACAA
*
10193815 AAAATATAATC-ATAAATATTAAATAT
1 AAAATATAA-CAAT-AATATAAAATAT
*
10193841 AAAATATAACAATAATGTAAAATAT
1 AAAATATAACAATAATATAAAATAT
10193866 AAACATATA
1 AAA-ATATA
10193875 TTTAATATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAATATAACAATAATATAAAATAT
Found at i:10194584 original size:2 final size:2
Alignment explanation
Indices: 10194577--10194611 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10194567 CAAACTTACT
10194577 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 T
10194612 TGTATAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10195246 original size:20 final size:20
Alignment explanation
Indices: 10195223--10195278 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
10195213 AAAAACAGAG
*
10195223 GCACAGAAGTGTAAACAAGA
1 GCACAGAAGTGCAAACAAGA
* *
10195243 GCACCA-AAGTGCAAACAGGG
1 GCA-CAGAAGTGCAAACAAGA
*
10195263 GCACCGAAGTGCAAAC
1 GCACAGAAGTGCAAAC
10195279 TTGTACAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.43, C:0.23, G:0.27, T:0.07
Consensus pattern (20 bp):
GCACAGAAGTGCAAACAAGA
Found at i:10197446 original size:13 final size:13
Alignment explanation
Indices: 10197428--10197466 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
10197418 AATGGCATAT
*
10197428 TATTCAAGCTCAA
1 TATTCAACCTCAA
10197441 TATTCAACCTCAA
1 TATTCAACCTCAA
10197454 TATTCAACCTCAA
1 TATTCAACCTCAA
10197467 GAAGAAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (13 bp):
TATTCAACCTCAA
Found at i:10201228 original size:27 final size:26
Alignment explanation
Indices: 10201176--10201228 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
10201166 TCATAAGTAT
* * *
10201176 TTTAAATTTGTATTTTGTTTCCTTAA
1 TTTAAATTTCTATTTTATTTCATTAA
*
10201202 TTTAAATATTCTATTTTATTTTATTAA
1 TTTAAAT-TTCTATTTTATTTCATTAA
10201229 CTCTAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTAAATTTCTATTTTATTTCATTAA
Found at i:10201362 original size:13 final size:13
Alignment explanation
Indices: 10201344--10201369 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10201334 AATGACATAT
10201344 TATTCAAGCTCAA
1 TATTCAAGCTCAA
10201357 TATTCAAGCTCAA
1 TATTCAAGCTCAA
10201370 GAGGAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TATTCAAGCTCAA
Found at i:10210801 original size:16 final size:16
Alignment explanation
Indices: 10210776--10210807 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10210766 ATAAATGCTA
10210776 AGCTTCAATCTCTTCT
1 AGCTTCAATCTCTTCT
*
10210792 AGCTTTAATCTCTTCT
1 AGCTTCAATCTCTTCT
10210808 CAATTAGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (16 bp):
AGCTTCAATCTCTTCT
Found at i:10211747 original size:2 final size:2
Alignment explanation
Indices: 10211740--10211764 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10211730 ACATGCGTAA
10211740 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
10211765 ATCATATTAG
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:10212513 original size:18 final size:18
Alignment explanation
Indices: 10212492--10212545 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
10212482 CCACCACTAA
10212492 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
10212510 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
10212522 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
10212540 CTCCAC
1 CTCCAC
10212546 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:10212518 original size:30 final size:30
Alignment explanation
Indices: 10212482--10212550 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
10212472 CTAGCCTTTG
*
10212482 CCACCACTAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
10212512 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
10212542 CCACCACCA
1 CCACCACCA
10212551 CTTGTACCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.51, G:0.06, T:0.16
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:10215379 original size:16 final size:15
Alignment explanation
Indices: 10215352--10215381 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10215342 GACTAACATT
10215352 CATTTATCATTCATA
1 CATTTATCATTCATA
10215367 CATTTATTCATTCAT
1 CATTTA-TCATTCAT
10215382 TGCATATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (15 bp):
CATTTATCATTCATA
Found at i:10218478 original size:26 final size:26
Alignment explanation
Indices: 10218442--10218493 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10218432 CGAGGGAGAA
10218442 GAAGACATTATCGCATCTATCTCTGC
1 GAAGACATTATCGCATCTATCTCTGC
10218468 GAAGACATTATCGCATCTATCTCTGC
1 GAAGACATTATCGCATCTATCTCTGC
10218494 TGATGCGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (26 bp):
GAAGACATTATCGCATCTATCTCTGC
Found at i:10223739 original size:73 final size:73
Alignment explanation
Indices: 10223642--10224160 Score: 749
Period size: 73 Copynumber: 7.1 Consensus size: 73
10223632 TGATGTTTTT
* * ** * * *
10223642 ATTTCTATTT-TCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
10223706 TAATTTCA
66 TAATTTCA
*
10223714 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCATGCTGAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
10223779 TAATTTCA
66 TAATTTCA
* * * *
10223787 TTTTCTGTTTATCAAAACA-CAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAG
1 ATTTCTGTTTGTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
10223851 GTAATTTCA
65 GTAATTTCA
*
10223860 ATTTCTGTTTGTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
10223925 TAATTTCA
66 TAATTTCA
*
10223933 ATTTCTGTTTGTC-AAAATACAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGCTGAG
1 ATTTCTGTTTGTCAAAAAT-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
10223997 GTAATTTCA
65 GTAATTTCA
*
10224006 ATTTCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
**
10224071 TGCTTTTCA
66 T-AATTTCA
* ** *
10224080 AGTTCTGCTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATATGCTG
1 ATTTCTG-TTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTG
* *
10224144 AGGTATTTTTA
63 AGGTAATTTCA
10224155 ATTTCT
1 ATTTCT
10224161 ATTTTTTTCA
Statistics
Matches: 406, Mismatches: 32, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
72 15 0.04
73 310 0.76
74 19 0.05
75 13 0.03
76 49 0.12
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (73 bp):
ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
TAATTTCA
Found at i:10224173 original size:16 final size:15
Alignment explanation
Indices: 10224149--10224182 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
10224139 TGCTGAGGTA
*
10224149 TTTTTAATTTCTATT
1 TTTTTAATTTATATT
10224164 TTTTTCAATTTATATT
1 TTTTT-AATTTATATT
10224180 TTT
1 TTT
10224183 CAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTAATTTATATT
Found at i:10224233 original size:89 final size:88
Alignment explanation
Indices: 10224095--10224309 Score: 358
Period size: 89 Copynumber: 2.4 Consensus size: 88
10224085 TGCTTTTCAA
* * *
10224095 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATATGCTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
10224160 TATTTTTTTCAATTTATATTTTTC
66 TATTTTTTTCAATTTATA-TTTTC
*
10224184 AAAAATCAACTCATATTGCGAGAGGTGAGTTTAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
10224249 TATTTTTTTCAATTTATATTTTC
66 TATTTTTTTCAATTTATATTTTC
* * *
10224272 AAAAATTAATTCATATTGCGAGAGATGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
10224310 GGGGCACATG
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 39 0.33
89 79 0.67
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TATTTTTTTCAATTTATATTTTC
Found at i:10224259 original size:16 final size:16
Alignment explanation
Indices: 10224238--10224270 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10224228 CGCTGAGGTA
*
10224238 TTTTCAATTTCTATTT
1 TTTTCAATTTATATTT
10224254 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
10224270 T
1 T
10224271 CAAAAATTAA
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:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:10225171 original size:18 final size:18
Alignment explanation
Indices: 10225148--10225237 Score: 53
Period size: 18 Copynumber: 5.7 Consensus size: 18
10225138 CCACCACCAA
10225148 CTCCACTAACCACACTTG
1 CTCCACTAACCACACTTG
*
10225166 CTCCAC-CACCA-A----
1 CTCCACTAACCACACTTG
*
10225178 CTCCACTAGCCACACTTG
1 CTCCACTAACCACACTTG
*
10225196 CTCCACT------ACTTA
1 CTCCACTAACCACACTTG
*
10225208 CTCCACTAGCCACACTTG
1 CTCCACTAACCACACTTG
10225226 CTCCACT-ACCAC
1 CTCCACTAACCAC
10225238 TTGTACCTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 25
0.64 0.07 0.29
Matches are distributed among these distances:
12 17 0.31
13 3 0.06
14 1 0.02
16 1 0.02
17 8 0.15
18 24 0.44
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.21
Consensus pattern (18 bp):
CTCCACTAACCACACTTG
Found at i:10225174 original size:30 final size:30
Alignment explanation
Indices: 10225138--10225236 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
10225128 CTAGCCTTTG
*
10225138 CCACCACCAACTCCACTAACCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
10225168 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* **
10225198 CCACTACTTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
10225228 CCACTACCA
1 CCACCACCA
10225237 CTTGTACCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.27, C:0.48, G:0.05, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:10227838 original size:15 final size:15
Alignment explanation
Indices: 10227820--10227852 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
10227810 TATATATATA
10227820 TTATAT-TTTTAGATT
1 TTATATATTTTA-ATT
10227835 TTATATATTTTAATT
1 TTATATATTTTAATT
10227850 TTA
1 TTA
10227853 AAATGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATATATTTTAATT
Found at i:10232914 original size:46 final size:46
Alignment explanation
Indices: 10232862--10233175 Score: 423
Period size: 46 Copynumber: 6.8 Consensus size: 46
10232852 AATGTGCTCT
* *
10232862 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
10232908 CTGATATGAAATGTGTACGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
10232954 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
10233000 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
10233046 CTGACATGAAATGAGTAAGACCATGGTTGAAAGAAACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** * *
10233092 ATGACGGGAAAATGAATAAGACAATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
10233139 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
10233176 TATGACATCA
Statistics
Matches: 245, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 205 0.84
47 40 0.16
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:10239683 original size:18 final size:18
Alignment explanation
Indices: 10239660--10239696 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10239650 TACCTAGCTT
*
10239660 TCAATATCAATACCAAAA
1 TCAATATCAACACCAAAA
*
10239678 TCAATATCGACACCAAAA
1 TCAATATCAACACCAAAA
10239696 T
1 T
10239697 TGAAACACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.22
Consensus pattern (18 bp):
TCAATATCAACACCAAAA
Found at i:10243193 original size:22 final size:24
Alignment explanation
Indices: 10243163--10243208 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
10243153 ACCAAAGAAG
*
10243163 AAATAGAAC-TGACGTCACGATGA
1 AAATAGAACACGACGTCACGATGA
*
10243186 AAAT-GAACACGACGTCATGATGA
1 AAATAGAACACGACGTCACGATGA
10243209 CGCGACGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (24 bp):
AAATAGAACACGACGTCACGATGA
Found at i:10244956 original size:49 final size:50
Alignment explanation
Indices: 10244869--10244966 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 50
10244859 TGAAATATGT
* **
10244869 ATTGATTAATGGAATCTGGTTTTCAGACCAAAGAATGATTCATGAATAAA
1 ATTGATTAATGGAATCTAGTAATCAGACCAAAGAATGATTCATGAATAAA
10244919 ATTGATTAATGGAATCTAG-AATCAGACCAAAGAATGATTCATGAATAA
1 ATTGATTAATGGAATCTAGTAATCAGACCAAAGAATGATTCATGAATAA
10244967 GTCAACTAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 27 0.60
50 18 0.40
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (50 bp):
ATTGATTAATGGAATCTAGTAATCAGACCAAAGAATGATTCATGAATAAA
Found at i:10245698 original size:16 final size:17
Alignment explanation
Indices: 10245668--10245703 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
10245658 TCAGAAAACT
10245668 AAAAGTCTTCCAGTTTC
1 AAAAGTCTTCCAGTTTC
*
10245685 AAAA-TCTTCTAGTTTC
1 AAAAGTCTTCCAGTTTC
10245701 AAA
1 AAA
10245704 GTCCAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
AAAAGTCTTCCAGTTTC
Found at i:10249602 original size:14 final size:14
Alignment explanation
Indices: 10249583--10249612 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10249573 CATTTGCTCA
10249583 TTCTTTTCTTTCTT
1 TTCTTTTCTTTCTT
*
10249597 TTCTTTTCTTTGTT
1 TTCTTTTCTTTCTT
10249611 TT
1 TT
10249613 GTTTGGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TTCTTTTCTTTCTT
Found at i:10252267 original size:20 final size:20
Alignment explanation
Indices: 10252231--10252280 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
10252221 GATCTTAATC
10252231 ATAAAAAATTATCTAAAAAT
1 ATAAAAAATTATCTAAAAAT
*
10252251 ATATAAAAATT-TTTAAAAAT
1 ATA-AAAAATTATCTAAAAAT
*
10252271 CTAAAAAATT
1 ATAAAAAATT
10252281 CAAAAAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 13 0.48
21 7 0.26
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAAAATTATCTAAAAAT
Found at i:10253068 original size:2 final size:2
Alignment explanation
Indices: 10253063--10253099 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10253053 AATTTTTTTG
*
10253063 TA TA TA TT 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 T
10253100 TTAATTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:10253849 original size:18 final size:18
Alignment explanation
Indices: 10253828--10253862 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10253818 AATTATACTT
*
10253828 TTTATAAAATTATTAAAA
1 TTTATAAAAATATTAAAA
10253846 TTTATAAAAATATTAAA
1 TTTATAAAAATATTAAA
10253863 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTATAAAAATATTAAAA
Found at i:10254517 original size:18 final size:19
Alignment explanation
Indices: 10254489--10254534 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
10254479 TTATTTTTAA
10254489 ATAAA-TTTAATAAT-TTT
1 ATAAATTTTAATAATATTT
10254506 ATAAATTTTAATAATATTT
1 ATAAATTTTAATAATATTT
10254525 -TAAAATTTTA
1 AT-AAATTTTA
10254535 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAAATTTTAATAATATTT
Found at i:10254537 original size:18 final size:21
Alignment explanation
Indices: 10254496--10254534 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
10254486 TAAATAAATT
10254496 TAATAATTTTATAAATTTTAA
1 TAATAATTTTATAAATTTTAA
10254517 TAAT-ATTTTA-AAATTTTA
1 TAATAATTTTATAAATTTTA
10254535 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATAATTTTATAAATTTTAA
Found at i:10254565 original size:14 final size:13
Alignment explanation
Indices: 10254537--10254562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10254527 AAATTTTATA
10254537 AAAAATATTTTTT
1 AAAAATATTTTTT
10254550 AAAAATATTTTTT
1 AAAAATATTTTTT
10254563 TAATTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:10256416 original size:22 final size:23
Alignment explanation
Indices: 10256370--10256415 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
10256360 TTAGATTATA
*
10256370 TATTTTTCTATTTTTAAATATTT
1 TATTTTTCAATTTTTAAATATTT
10256393 TATTTTT-AATTTTATAAATATTT
1 TATTTTTCAATTTT-TAAATATTT
10256416 AAAGTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTTCAATTTTTAAATATTT
Found at i:10256423 original size:23 final size:22
Alignment explanation
Indices: 10256379--10256423 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
10256369 ATATTTTTCT
* **
10256379 ATTTTTAAATATTTTATTTTTA
1 ATTTTTAAATATTTAAAGTTTA
10256401 ATTTTATAAATATTTAAAGTTTA
1 ATTTT-TAAATATTTAAAGTTTA
10256424 TATATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTTAAATATTTAAAGTTTA
Found at i:10256578 original size:24 final size:23
Alignment explanation
Indices: 10256551--10256595 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
10256541 TAACAATATT
*
10256551 TTAAGTATCAAATTAGAAAAAAAA
1 TTAAATATCAAATT-GAAAAAAAA
*
10256575 TTAAATATCAACTTGAAAAAA
1 TTAAATATCAAATTGAAAAAA
10256596 TAATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (23 bp):
TTAAATATCAAATTGAAAAAAAA
Found at i:10260705 original size:2 final size:2
Alignment explanation
Indices: 10260698--10260730 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10260688 TTTATTGGCT
10260698 TC TC TC 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 T
10260731 TTCTATCTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10269339 original size:28 final size:27
Alignment explanation
Indices: 10269287--10269342 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
10269277 AAATTCGACT
*
10269287 TTTTAAAAAATAAAATACAATAAAATA
1 TTTTAAAAAATAAAATACAAAAAAATA
* *
10269314 TTTTAAAAAATAAATTGATAAAAAAATA
1 TTTTAAAAAATAAAAT-ACAAAAAAATA
10269342 T
1 T
10269343 AAATATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
TTTTAAAAAATAAAATACAAAAAAATA
Found at i:10272988 original size:29 final size:29
Alignment explanation
Indices: 10272930--10272992 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
10272920 AATTTATATA
* *
10272930 TTTATAATTTTTAAATGATCAAATCAAAT
1 TTTATAATTTTTAAAGGATCAAATAAAAT
* *
10272959 TTTATAA-TTTTAAAGGGTTAAATAATAAT
1 TTTATAATTTTTAAAGGATCAAATAA-AAT
10272988 TTTAT
1 TTTAT
10272993 TTTTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (29 bp):
TTTATAATTTTTAAAGGATCAAATAAAAT
Found at i:10275247 original size:26 final size:26
Alignment explanation
Indices: 10275218--10275272 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
10275208 TCTTTCTAAA
10275218 AAATGATA-ATTAACATTTCCAACGCC
1 AAAT-ATATATTAACATTTCCAACGCC
* *
10275244 AAATTTATATTAACATTTCCAATGCC
1 AAATATATATTAACATTTCCAACGCC
10275270 AAA
1 AAA
10275273 CTTTGATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (26 bp):
AAATATATATTAACATTTCCAACGCC
Found at i:10275289 original size:26 final size:26
Alignment explanation
Indices: 10275226--10275281 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
10275216 AAAAATGATA
10275226 ATTAACATTTCCAACGCCAAATTTAT
1 ATTAACATTTCCAACGCCAAATTTAT
*
10275252 ATTAACATTTCCAATGCCAAACTTTGAT
1 ATTAACATTTCCAACGCCAAA-TTT-AT
10275280 AT
1 AT
10275282 GCATTTCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 20 0.74
27 3 0.11
28 4 0.15
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (26 bp):
ATTAACATTTCCAACGCCAAATTTAT
Found at i:10278610 original size:14 final size:14
Alignment explanation
Indices: 10278591--10278619 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10278581 TAAAGCTCTG
10278591 TTTGGTTGCGGCGT
1 TTTGGTTGCGGCGT
10278605 TTTGGTTGCGGCGT
1 TTTGGTTGCGGCGT
10278619 T
1 T
10278620 CGCTACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.41, T:0.45
Consensus pattern (14 bp):
TTTGGTTGCGGCGT
Found at i:10285144 original size:34 final size:34
Alignment explanation
Indices: 10285101--10285169 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
10285091 GGGCCCCTCC
* *
10285101 ACCTATTACCAAGCGGTTTTAGGTTTGATGCTTA
1 ACCTATTACCAAGCGGTATTAGGTTTGATACTTA
*
10285135 ACCTATTACCAAGTGGTATTAGGTTTGATACTTA
1 ACCTATTACCAAGCGGTATTAGGTTTGATACTTA
10285169 A
1 A
10285170 TAACAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (34 bp):
ACCTATTACCAAGCGGTATTAGGTTTGATACTTA
Found at i:10291230 original size:25 final size:25
Alignment explanation
Indices: 10291202--10291251 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
10291192 TAACAAAAAA
10291202 TATTTCTTGCTTAGCCTAGTTTAAC
1 TATTTCTTGCTTAGCCTAGTTTAAC
10291227 TATTTCTTGCTTAGCCTAGTTTAAC
1 TATTTCTTGCTTAGCCTAGTTTAAC
10291252 CCGTCTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (25 bp):
TATTTCTTGCTTAGCCTAGTTTAAC
Found at i:10298250 original size:11 final size:12
Alignment explanation
Indices: 10298227--10298264 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10298217 CATTGTACCA
*
10298227 TTTTCTCTCTCT
1 TTTTCTCTTTCT
10298239 TTTT-TCTTTCT
1 TTTTCTCTTTCT
*
10298250 TTTTCTTTTTCT
1 TTTTCTCTTTCT
10298262 TTT
1 TTT
10298265 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTCT
Found at i:10299380 original size:3 final size:3
Alignment explanation
Indices: 10299374--10299407 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
10299364 AAAGAGGAGG
*
10299374 AGA AGA AGA AGA AGA AGA AGT AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
10299408 AGAGAAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:10300548 original size:21 final size:21
Alignment explanation
Indices: 10300499--10300549 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
10300489 GGCAGCTTAT
*
10300499 TGAGTTGGGGTATTCTCTTGC
1 TGAGTTGGGGTACTCTCTTGC
*
10300520 T-AGTTTGGGGTAGCT-TGTTGC
1 TGAG-TTGGGGTA-CTCTCTTGC
10300541 TGAGTTGGG
1 TGAGTTGGG
10300550 ACACCAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.10, C:0.10, G:0.39, T:0.41
Consensus pattern (21 bp):
TGAGTTGGGGTACTCTCTTGC
Found at i:10301395 original size:89 final size:89
Alignment explanation
Indices: 10301293--10301471 Score: 259
Period size: 89 Copynumber: 2.0 Consensus size: 89
10301283 GGTAAATAAA
* * ** *
10301293 AAATTTTGATTTTGCCACATACAATATAGCAGCTTGGATACAAACAATGACAGATATACGTAGCA
1 AAATTTTGATTTTGCCACATACAATATAGCAGCTGGGATACAAACAATGACAGACATACACAACA
*
10301358 AACATCAATTTGATAATGGCATTC
66 AACATCAATTTGATAATGACATTC
* * *
10301382 AAATTTTGATTTTGCTACATACAATATAGCAGCTGGGATACAAACAATGGCAGGCATACACAACA
1 AAATTTTGATTTTGCCACATACAATATAGCAGCTGGGATACAAACAATGACAGACATACACAACA
* *
10301447 AATATCAGTTTGATAATGACATTC
66 AACATCAATTTGATAATGACATTC
10301471 A
1 A
10301472 TACAATGACA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (89 bp):
AAATTTTGATTTTGCCACATACAATATAGCAGCTGGGATACAAACAATGACAGACATACACAACA
AACATCAATTTGATAATGACATTC
Found at i:10301606 original size:18 final size:17
Alignment explanation
Indices: 10301583--10301660 Score: 93
Period size: 18 Copynumber: 4.4 Consensus size: 17
10301573 GAGTGTTTCA
10301583 AAATAGAAATCAAAATCG
1 AAATA-AAATCAAAATCG
*
10301601 AAATAGAAATCAAAATCA
1 AAATA-AAATCAAAATCG
*
10301619 AAATCAAAATCAGAATCG
1 AAAT-AAAATCAAAATCG
*
10301637 AAATTAAAATTAAAATCG
1 AAA-TAAAATCAAAATCG
10301655 AAATAA
1 AAATAA
10301661 CCCTAAATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.06
18 48 0.91
19 2 0.04
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.19
Consensus pattern (17 bp):
AAATAAAATCAAAATCG
Found at i:10301674 original size:6 final size:6
Alignment explanation
Indices: 10301580--10301658 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
10301570 AGTGAGTGTT
*
10301580 TCAAAA T-AGAAA TCAAAA TCGAAA T-AGAAA TCAAAA TCAAAA TCAAAA
1 TCAAAA TCA-AAA TCAAAA TCAAAA TCA-AAA TCAAAA TCAAAA TCAAAA
* * * * *
10301628 TCAGAA TCGAAA TTAAAA TTAAAA TCGAAA T
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA T
10301659 AACCCTAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
5 1 0.02
6 57 0.95
7 2 0.03
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.20
Consensus pattern (6 bp):
TCAAAA
Found at i:10302108 original size:21 final size:21
Alignment explanation
Indices: 10302082--10302121 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10302072 AACGCGGCAA
10302082 GTTAACTTGCCACATCAGCAG
1 GTTAACTTGCCACATCAGCAG
*
10302103 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
10302122 GGTCCCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCAG
Found at i:10302223 original size:30 final size:31
Alignment explanation
Indices: 10302164--10302224 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
10302154 TCAGTGACCA
* *
10302164 TTTTGTCACTTTTTCATAACGTTAGTGACTG
1 TTTTGTAACTTTTTCATAAAGTTAGTGACTG
10302195 TTTTGTAACTTTTT-A-AAAGTTGAGTGACTG
1 TTTTGTAACTTTTTCATAAAGTT-AGTGACTG
10302225 AAATGAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 5 0.19
30 9 0.33
31 13 0.48
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (31 bp):
TTTTGTAACTTTTTCATAAAGTTAGTGACTG
Found at i:10309911 original size:12 final size:12
Alignment explanation
Indices: 10309891--10309922 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10309881 TGGAACCTGC
*
10309891 TAGTGCCTACCA
1 TAGTACCTACCA
10309903 TAGTACCTACCA
1 TAGTACCTACCA
10309915 TAGTACCT
1 TAGTACCT
10309923 TGTAGGTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.28
Consensus pattern (12 bp):
TAGTACCTACCA
Found at i:10323329 original size:12 final size:12
Alignment explanation
Indices: 10323314--10323354 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
10323304 TTTTAAAATT
10323314 TTTAAAATTAAA
1 TTTAAAATTAAA
**
10323326 TTTAATGTTAAA
1 TTTAAAATTAAA
10323338 TTTAAAATTAAA
1 TTTAAAATTAAA
10323350 TTTAA
1 TTTAA
10323355 TGTTAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:10323330 original size:6 final size:6
Alignment explanation
Indices: 10323314--10323363 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
10323304 TTTTAAAATT
* *
10323314 TTTAAA ATTAAA TTT-AA TGTTAAA TTTAAA ATTAAA TTT-AA TGTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
10323362 TT
1 TT
10323364 AACTCGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
5 6 0.17
6 24 0.67
7 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:10323346 original size:24 final size:24
Alignment explanation
Indices: 10323314--10323363 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
10323304 TTTTAAAATT
10323314 TTTAAAATTAAATTTAATGTTAAA
1 TTTAAAATTAAATTTAATGTTAAA
10323338 TTTAAAATTAAATTTAATGTTAAA
1 TTTAAAATTAAATTTAATGTTAAA
10323362 TT
1 TT
10323364 AACTCGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTAAAATTAAATTTAATGTTAAA
Done.