Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold475
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: 1773841
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 10 of 12
Found at i:1468534 original size:164 final size:163
Alignment explanation
Indices: 1468054--1468698 Score: 509
Period size: 164 Copynumber: 3.9 Consensus size: 163
1468044 CTATCAATGA
* * * * * *
1468054 TTCTTATTC-ATTAACTCGTATTGTTTCGTTCTAATC-AACTCTTCTTATTCGTTGACTTGTATA
1 TTCTTATTCGA-TGACTCGTATGGTTTCGTCCTAGTCAAAC-CTTCTTATTCGTTGACAT-TATG
* * * * * * **
1468117 ATTTCAT-TTCGATCAACCTTTCTCATTTGTTGACTCAGATGGTTTCATCTCGGTTAACTATTTT
63 GTTTCATCTTAG-TTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCTCGGTCAACCCTTTT
* **
1468181 CATTCGTTGACTCGTAT-AGTTTTGTCCCAATCAATCC-
127 CATTCGTTAACTCGTATGA-TTTCATCCCAATCAA-CCT
* * ** * * * * * *
1468218 TTCTTATTCGTTGGCTCGTATCATTTTGTCCTGGTCAATCTTTCTTATTCATTGAC-TCATATGA
1 TTCTTATTCGATGACTCGTATGGTTTCGTCCTAGTCAAACCTTCTTATTCGTTGACAT--TATGG
* * * * * ** * *
1468282 TTTAATCTTAGCTAACCATTCTCATTCGTTGAC-CTGTATGATTTCATCTCAATCAATCCTTCTC
64 TTTCATCTTAGTTAACCTTTCTCATTCGTTGACTC-ATATGGTTTCATCTCGGTCAACCCTTTTC
* * *
1468346 ATTCGTTAACTCATATGGTTTCATCCCAGTCAACCT
128 ATTCGTTAACTCGTATGATTTCATCCCAATCAACCT
** * * *
1468382 TTCTTATTTAATGTCTCATATGGTTTCGTCCTAGTCAAACCTTCTCATTCGTTGACATGTATGGT
1 TTCTTATTCGATGACTCGTATGGTTTCGTCCTAGTCAAACCTTCTTATTCGTTGACAT-TATGGT
* *
1468447 TTCGTCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCTCGGTTAACCCTTTTCAT
65 TTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCTCGGTCAACCCTTTTCAT
* * *
1468512 TTGTTAACTTGTATGATTTCATCTCAATCAACCT
130 TCGTTAACTCGTATGATTTCATCCCAATCAACCT
* * * * * *
1468546 TT-TTCATTCGATAACTCGTATGGTTTCAG-CCCAATCAAATCTTCTTATTCGTTAGCGCA-CAT
1 TTCTT-ATTCGATGACTCGTATGGTTTC-GTCCTAGTCAAACCTTCTTATTCGTT-G-ACATTAT
* * * * * *
1468608 GGTTTCATCTTGGTTAAACTTTCTCATTTGTTAACTCCTATGGTTTCATCCCGGTCAACCCTTTT
62 GGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCTCGGTCAACCCTTTT
** * *
1468673 CATTCACTGACTAGTATGATTTCATC
127 CATTCGTTAACTCGTATGATTTCATC
1468699 TTGGCCAACC
Statistics
Matches: 376, Mismatches: 92, Indels: 26
0.76 0.19 0.05
Matches are distributed among these distances:
163 6 0.02
164 359 0.95
165 9 0.02
166 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (163 bp):
TTCTTATTCGATGACTCGTATGGTTTCGTCCTAGTCAAACCTTCTTATTCGTTGACATTATGGTT
TCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCTCGGTCAACCCTTTTCATT
CGTTAACTCGTATGATTTCATCCCAATCAACCT
Found at i:1468581 original size:41 final size:41
Alignment explanation
Indices: 1468059--1468677 Score: 179
Period size: 41 Copynumber: 15.1 Consensus size: 41
1468049 AATGATTCTT
* * * *
1468059 ATTCATTAACTCGTATTGTTTCGT-TCTAATCAACTCTTCTT-
1 ATTCGTTAACTCGTATGGTTTCATCTC-AATCAAC-CTTTTTC
* * ** * * *
1468100 ATTCGTTGACTTGTATAATTTCATTTCGATCAACCTTTCTC
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTTTTC
* * ** *
1468141 ATTTGTTGACTCAG-ATGGTTTCATCTCGGTTAA-CTATTTTC
1 ATTCGTTAACTC-GTATGGTTTCATCTCAATCAACCT-TTTTC
* * ** * *
1468182 ATTCGTTGACTCGTATAGTTTTGTCCCAATCAATCCTTCTT-
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAA-CCTTTTTC
** ** ** ** *
1468223 ATTCGTTGGCTCGTATCATTTTGTC-CTGGTCAATCTTTCTT-
1 ATTCGTTAACTCGTATGGTTTCATCTC-AATCAACCTTT-TTC
* * * * * * * * *
1468264 ATTCATTGACTCATATGATTTAATCT-TAGCTAACCATTCTC
1 ATTCGTTAACTCGTATGGTTTCATCTCAATC-AACCTTTTTC
* * *
1468305 ATTCGTTGAC-CTGTATGATTTCATCTCAATCAATCC-TTCTC
1 ATTCGTTAACTC-GTATGGTTTCATCTCAATCAA-CCTTTTTC
* * *
1468346 ATTCGTTAACTCATATGGTTTCATCCCAGTCAACCTTTCTT-
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTT-TTC
*** ** * * * *
1468387 ATTTAATGTCTCATATGGTTTCGTC-CTAGTCAAACC-TTCTC
1 ATTCGTTAACTCGTATGGTTTCATCTC-AATC-AACCTTTTTC
* * * * * *
1468428 ATTCGTTGACAT-GTATGGTTTCGTCTTAGTTAACCTTTCTC
1 ATTCGTTAAC-TCGTATGGTTTCATCTCAATCAACCTTTTTC
* * ** * *
1468469 ATTCGTTGACTCATATGGTTTCATCTCGGTTAACCCTTTTC
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTTTTC
* * *
1468510 ATTTGTTAACTTGTATGATTTCATCTCAATCAACCTTTTTC
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTTTTC
* * * * *
1468551 ATTCGATAACTCGTATGGTTTCAGCCCAATCAAATCTTCTT-
1 ATTCGTTAACTCGTATGGTTTCATCTCAATC-AACCTTTTTC
* * ** *** * * *
1468592 ATTCGTTAGCGCACATGGTTTCATCTTGGTTAAACTTTCTC
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTTTTC
* * * ** *
1468633 ATTTGTTAACTCCTATGGTTTCATCCCGGTCAACCCTTTTC
1 ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTTTTC
1468674 ATTC
1 ATTC
1468678 ACTGACTAGT
Statistics
Matches: 432, Mismatches: 119, Indels: 54
0.71 0.20 0.09
Matches are distributed among these distances:
40 29 0.07
41 377 0.87
42 24 0.06
43 2 0.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (41 bp):
ATTCGTTAACTCGTATGGTTTCATCTCAATCAACCTTTTTC
Found at i:1469576 original size:21 final size:21
Alignment explanation
Indices: 1469552--1469601 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1469542 ATTATCTCAA
1469552 GATTTCACTTTGAAAACAAGG
1 GATTTCACTTTGAAAACAAGG
*
1469573 GATTTCACTTTGAAAATAAGG
1 GATTTCACTTTGAAAACAAGG
*
1469594 TATTTCAC
1 GATTTCAC
1469602 GTTAAGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (21 bp):
GATTTCACTTTGAAAACAAGG
Found at i:1472332 original size:20 final size:20
Alignment explanation
Indices: 1472307--1472346 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1472297 ATTTGGAAGC
*
1472307 ATGTATCGATACATTTTCTT
1 ATGTATCAATACATTTTCTT
1472327 ATGTATCAATACATTTTCTT
1 ATGTATCAATACATTTTCTT
1472347 TCCAGAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (20 bp):
ATGTATCAATACATTTTCTT
Found at i:1472391 original size:21 final size:21
Alignment explanation
Indices: 1472367--1472422 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
1472357 AGGGTGGTTT
* *
1472367 TGTATCGATACATTTTAGGC-A
1 TGTATCGATACATTTCA-CCTA
*
1472388 TGTATCAATACA-TTCACCTA
1 TGTATCGATACATTTCACCTA
1472408 TGTATCGATACATTT
1 TGTATCGATACATTT
1472423 ACTGTTTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 15 0.52
21 13 0.45
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCACCTA
Found at i:1472412 original size:20 final size:21
Alignment explanation
Indices: 1472387--1472440 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1472377 CATTTTAGGC
1472387 ATGTATCAATACATTCAC-CT
1 ATGTATCAATACATTCACTCT
* * *
1472407 ATGTATCGATACATTTACTGT
1 ATGTATCAATACATTCACTCT
*
1472428 TTGTATCAATACA
1 ATGTATCAATACA
1472441 AATTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTATCAATACATTCACTCT
Found at i:1472434 original size:21 final size:20
Alignment explanation
Indices: 1472367--1472440 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
1472357 AGGGTGGTTT
* * *
1472367 TGTATCGATACATTTTAGGCA
1 TGTATCAATACA-TTTACGTA
* *
1472388 TGTATCAATACATTCACCTA
1 TGTATCAATACATTTACGTA
* *
1472408 TGTATCGATACATTTACTGTT
1 TGTATCAATACATTTAC-GTA
1472429 TGTATCAATACA
1 TGTATCAATACA
1472441 AATTGTAGAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 19 0.45
21 23 0.55
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
TGTATCAATACATTTACGTA
Found at i:1476560 original size:56 final size:56
Alignment explanation
Indices: 1476473--1476584 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 56
1476463 TATTGTGATA
* * *
1476473 AGCATTAAAATGTAAAAGACTAAGAGTAGCTAGTATGTTTCATCCCAATTGAAATT
1 AGCATTAAAATGTAAAAGACTAAAAGAAGCTAGTAGGTTTCATCCCAATTGAAATT
* * * * *
1476529 AGCATTGAAATG-AAAAGGTCTAAAAGAAGCTAGTGGGTTTCATCCTAGTTGAAATT
1 AGCATTAAAATGTAAAA-GACTAAAAGAAGCTAGTAGGTTTCATCCCAATTGAAATT
1476585 GGCACCAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
55 4 0.09
56 43 0.91
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (56 bp):
AGCATTAAAATGTAAAAGACTAAAAGAAGCTAGTAGGTTTCATCCCAATTGAAATT
Found at i:1476624 original size:56 final size:56
Alignment explanation
Indices: 1476550--1477043 Score: 232
Period size: 56 Copynumber: 8.9 Consensus size: 56
1476540 GAAAAGGTCT
* * * * *
1476550 AAAAGAAGCTAGTGGGTTTCATCCTAGTTGAAATTGGCACCAAAGAGAAAAAACCC
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGAGAAAAAGCCA
* * * * * * * **
1476606 AAGAGTAGCTGATAGGTTTCATCCAAGCTAAAATTGGGACCAAA-ATGAATAAGCTT
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGA-GAAAAAGCCA
* * * ** * *
1476662 AAAAGGAGTTAATAGGTTTCATCCTAGTTAAAATTACCACCAAAGTGAAAAAGCCT
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGAGAAAAAGCCA
* * ** * ** * * **
1476718 AAAAGTAGTTGATAGGTTT-GGCCTAATTGAAATTGGTGCTAAA-ATTAAAAATAGAAAA
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGA--GAAAA-AG-CCA
* * * * *
1476776 AAAAGTAACTATTAGGTTTCATCCAAGTTG----T--AACCAAA-ATGAAAAAGCCT
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGA-GAAAAAGCCA
* * ** * * ** *
1476826 AATAGTAACTGGTAGGTTTCGTCCTAGTTAAAATTGATAACAAAGAGAAAAAGCCA
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGAGAAAAAGCCA
* * * * *
1476882 AAAAGTAGCTAATAGGTTTTACCCCAGTTGAAATTGGTACAAAAGAGTAAAAA-CCA
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGAG-AAAAAGCCA
* ** * *
1476938 AAGAA-TAACTAATA-GTTTTTTCCCAGTTGAAATTGGCACCGAAA-TG-AAAAGCTC-
1 AA-AAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACC-AAAGAGAAAAAGC-CA
* * *
1476992 AAGAGTAGCTAGTAGGTTTCATCC-AATTGAAATTGGCACCAAAGTA-AAAAAG
1 AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAG-AGAAAAAG
1477044 TTCAAGAGTA
Statistics
Matches: 324, Mismatches: 90, Indels: 49
0.70 0.19 0.11
Matches are distributed among these distances:
50 24 0.07
51 2 0.01
52 5 0.02
53 13 0.04
54 26 0.08
55 53 0.16
56 170 0.52
57 10 0.03
58 15 0.05
59 6 0.02
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (56 bp):
AAAAGTAGCTAATAGGTTTCATCCTAGTTGAAATTGGCACCAAAGAGAAAAAGCCA
Found at i:1476963 original size:55 final size:56
Alignment explanation
Indices: 1476867--1476973 Score: 148
Period size: 55 Copynumber: 1.9 Consensus size: 56
1476857 AATTGATAAC
*
1476867 AAAGAGAAAAAGCCAAAAAGTAGCTAATAGGTTTTACCCCAGTTGAAATTGGTACA
1 AAAGAGAAAAAGCCAAAAAGTAACTAATAGGTTTTACCCCAGTTGAAATTGGTACA
**
1476923 AAAGAGTAAAAA-CCAAAGAA-TAACTAATA-GTTTTTTCCCAGTTGAAATTGG
1 AAAGAG-AAAAAGCCAAA-AAGTAACTAATAGGTTTTACCCCAGTTGAAATTGG
1476974 CACCGAAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 20 0.43
56 19 0.41
57 7 0.15
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (56 bp):
AAAGAGAAAAAGCCAAAAAGTAACTAATAGGTTTTACCCCAGTTGAAATTGGTACA
Found at i:1477053 original size:55 final size:53
Alignment explanation
Indices: 1476959--1477120 Score: 157
Period size: 55 Copynumber: 2.9 Consensus size: 53
1476949 ATAGTTTTTT
* *
1476959 CCCAGTTGAAATTGGCACCGAAATGAAAAGCTCAAGAGTAGCTAGTAGGTTTC-A
1 CCCAATTGAAATTGGCACC-AAATAAAAAG-TCAAGAGTAGCTAGTAGGTTTCGA
* ** *
1477013 TCCAATTGAAATTGGCACCAAAGTAAAAAAGTTCAAGAGTAGCTAGTAACTTTCGC
1 CCCAATTGAAATTGGCACCAAA-T-AAAAAG-TCAAGAGTAGCTAGTAGGTTTCGA
* * *
1477069 CCCAATT-AAATTGGCACCAAAATGAAAAAGCCTAAGAGTAGTTGGTAGGTTT
1 CCCAATTGAAATTGGCACC-AAAT-AAAAAGTC-AAGAGTAGCTAGTAGGTTT
1477121 TGATGTGCCA
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
53 3 0.03
54 19 0.21
55 58 0.65
56 9 0.10
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (53 bp):
CCCAATTGAAATTGGCACCAAATAAAAAGTCAAGAGTAGCTAGTAGGTTTCGA
Found at i:1477352 original size:29 final size:28
Alignment explanation
Indices: 1477318--1477400 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
1477308 AAGCTTTGGT
1477318 ATTTTAATTGACTTTTAATTCCTTTCAAA
1 ATTTTAATTGACTTTTAATTCCTTT-AAA
* * ***
1477347 ATTTTAGTTGACTTTTAAATCCATTTTTG
1 ATTTTAATTGACTTTTAATTCC-TTTAAA
*
1477376 AGTTTAAGTTGACTTTTAATTCCTT
1 ATTTTAA-TTGACTTTTAATTCCTT
1477401 AATTTACAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 27 0.61
30 17 0.39
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (28 bp):
ATTTTAATTGACTTTTAATTCCTTTAAA
Found at i:1480932 original size:13 final size:13
Alignment explanation
Indices: 1480914--1480997 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
1480904 AGCTTCGTAG
1480914 CGATACATTGTAT
1 CGATACATTGTAT
1480927 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1480946 CGATACATTGTAT
1 CGATACATTGTAT
1480959 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
*
1480978 CGATACATTATAT
1 CGATACATTGTAT
1480991 CGATACA
1 CGATACA
1480998 AATCGTTGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 24
0.70 0.01 0.29
Matches are distributed among these distances:
13 25 0.43
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.33
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1480946 original size:19 final size:18
Alignment explanation
Indices: 1480922--1480984 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1480912 AGCGATACAT
1480922 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1480941 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1480954 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1480973 TGTATCGATACA
1 TGTATCGATACA
1480985 TTATATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1480955 original size:32 final size:32
Alignment explanation
Indices: 1480914--1480999 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
1480904 AGCTTCGTAG
1480914 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1480946 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1480978 CGATACATTATATCGATACAAA
1 CGATACATTGTATCGATACAAA
1481000 TCGTTGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1481615 original size:59 final size:59
Alignment explanation
Indices: 1481517--1481633 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
1481507 CAAGAGGTTC
* *
1481517 GATTATTTACTTGATACACACTATGCACATGCATTTGCACTGGATTCCCACCAAACTCT
1 GATTATTTACTTGATACACACTATGCACATGCATATGCACTAGATTCCCACCAAACTCT
*
1481576 GATTGTTTACTTGATACACACTATGCACATGCATATGCACTAGATTCCCACCAAACTC
1 GATTATTTACTTGATACACACTATGCACATGCATATGCACTAGATTCCCACCAAACTC
1481634 CATGGTGAGG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (59 bp):
GATTATTTACTTGATACACACTATGCACATGCATATGCACTAGATTCCCACCAAACTCT
Found at i:1488849 original size:20 final size:20
Alignment explanation
Indices: 1488811--1488849 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1488801 ATAATCCAGA
**
1488811 GTATCGATACATAGGTATTT
1 GTATCGATACATAAATATTT
*
1488831 GTATTGATACATAAATATT
1 GTATCGATACATAAATATT
1488850 GACTTAAGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (20 bp):
GTATCGATACATAAATATTT
Found at i:1498966 original size:30 final size:31
Alignment explanation
Indices: 1498929--1499011 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
1498919 GAGTAGGATG
*
1498929 CTTACCAACCTCAGTCCTTAAAGAACAA-CA
1 CTTACCAACCTCAGTCCTCAAAGAACAAGCA
* *
1498959 TTTACCAACCTCAGTCCTCAAAGAGCAAGGCA
1 CTTACCAACCTCAGTCCTCAAAGAACAA-GCA
*
1498991 CTTACTAACCTCAGTCCTCAA
1 CTTACCAACCTCAGTCCTCAA
1499012 GTAGTAGGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 25 0.54
32 21 0.46
ACGTcount: A:0.35, C:0.34, G:0.10, T:0.22
Consensus pattern (31 bp):
CTTACCAACCTCAGTCCTCAAAGAACAAGCA
Found at i:1499065 original size:64 final size:64
Alignment explanation
Indices: 1498894--1499123 Score: 195
Period size: 64 Copynumber: 3.6 Consensus size: 64
1498884 CAAAAGTAGG
* * * * * * ***
1498894 ATGCTTACCTACCTTAGTCCTTAATGAGTAGGATGCTTACCAACCTCAGTCCTTAAAGAACAAC
1 ATGCCTACCCACCTTAGTCATTAAAGAATAGGATGCTTACCAACCTCAGTCCTCAAAGAGTGAC
* * * * * *
1498958 AT--TTACCAACCTCAGTCCTCAAAGAGCA-AGGCA--CTTACTAACCTCAGTCCTC-AAGTAGT
1 ATGCCTACCCACCTTAGTCATTAAAGA--ATAGG-ATGCTTACCAACCTCAGTCCTCAAAG-AGT
*
1499017 -AGG
62 GA-C
*
1499020 ATGCCTACCCACCTTAGTCATTAAAGAATAGGGTGCTTACCAACCTCAGTCCTCAAAGAGTGAC
1 ATGCCTACCCACCTTAGTCATTAAAGAATAGGATGCTTACCAACCTCAGTCCTCAAAGAGTGAC
* *
1499084 ATGCCTACCTACCTTAGTCCTTAAAGAATAGGATGCTTAC
1 ATGCCTACCCACCTTAGTCATTAAAGAATAGGATGCTTAC
1499124 TTACCTTAAT
Statistics
Matches: 133, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
61 4 0.03
62 40 0.30
63 6 0.05
64 79 0.59
65 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (64 bp):
ATGCCTACCCACCTTAGTCATTAAAGAATAGGATGCTTACCAACCTCAGTCCTCAAAGAGTGAC
Found at i:1499131 original size:32 final size:32
Alignment explanation
Indices: 1498890--1499123 Score: 176
Period size: 32 Copynumber: 7.4 Consensus size: 32
1498880 AAACCAAAAG
* * * *
1498890 TAGGATGCTTACCTACCTTAGTCCTTAATGAG
1 TAGGATGCTTACCAACCTCAGTCCTTAAAGAA
1498922 TAGGATGCTTACCAACCTCAGTCCTTAAAGAA
1 TAGGATGCTTACCAACCTCAGTCCTTAAAGAA
* ** *
1498954 CAACAT--TTACCAACCTCAGTCCTCAAAGAGCA
1 TAGGATGCTTACCAACCTCAGTCCTTAAAGA--A
* * *
1498986 -AGGCA--CTTACTAACCTCAGTCC-TCAAGTAG
1 TAGG-ATGCTTACCAACCTCAGTCCTTAAAG-AA
* * * *
1499016 TAGGATGCCTACCCACCTTAGTCATTAAAGAA
1 TAGGATGCTTACCAACCTCAGTCCTTAAAGAA
* * *
1499048 TAGGGTGCTTACCAACCTCAGTCCTCAAAGAG
1 TAGGATGCTTACCAACCTCAGTCCTTAAAGAA
* * * *
1499080 T-GACATGCCTACCTACCTTAGTCCTTAAAGAA
1 TAG-GATGCTTACCAACCTCAGTCCTTAAAGAA
1499112 TAGGATGCTTAC
1 TAGGATGCTTAC
1499124 TTACCTTAAT
Statistics
Matches: 154, Mismatches: 37, Indels: 22
0.72 0.17 0.10
Matches are distributed among these distances:
30 23 0.15
31 8 0.05
32 118 0.77
33 5 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (32 bp):
TAGGATGCTTACCAACCTCAGTCCTTAAAGAA
Found at i:1500409 original size:166 final size:164
Alignment explanation
Indices: 1500081--1500576 Score: 452
Period size: 166 Copynumber: 3.0 Consensus size: 164
1500071 ATATAATTTT
** * * * *
1500081 CATTAAATGAGTAATTCAAAATTCTTTTTGTTTCATGAATTTTTATTTTTTCTGGTGAAA-TCTT
1 CATTAAATGAGTTTTTCAAAATTCATTTTATTTCATGAGTTTTTATTTTTTCT-TTGAAATTCTT
* * * ** *
1500145 CT-TGTTTTCGAAATACTG-AGTTTTCTTCTCTGTAAATTTTTTTAGGAGAATTTTCATCAGTTT
65 CTAT-TTTT-GAAATACTGAAGTTTACTACTCTGTAAATGTTTTCGGGGGAATTTTC-TCAGTTT
* * * *
1500208 AAAAGTTTTAAAATTCATTAAATATTATTATTTAATTGC
127 AAAATTTTTAATATTCATTAAATATCATCATTTAATT-C
1500247 CATTAAATGAGTTTTTCAAAATTTC-TTTTATTTCATGAGTTTTTAATTTTTTCTTTGAAATTCT
1 CATTAAATGAGTTTTTCAAAA-TTCATTTTATTTCATGAGTTTTT-ATTTTTTCTTTGAAATTCT
* * * ** *
1500311 CCTATTTTTGAAATA-TGAAGTTTGCCACTCTGTAAATGTTTTCGGGGTGGGTTTTCTCAGTTCA
64 TCTATTTTTGAAATACTGAAGTTTACTACTCTGTAAATGTTTTCGGGG-GAATTTTCTCAGTTTA
* * *
1500375 TAATTTTTAATATTCATCAAATATCAACATTTAA-TC
128 AAATTTTTAATATTCATTAAATATCATCATTTAATTC
* * ** * * * *
1500411 CATAGTAAATTAATTTTGAAAAATTCATTTATTTTTC-TAAGTTTTGCATTTTTTC-TTAAAATT
1 CAT--TAAATGAGTTTTTCAAAATTCATTT-TATTTCATGAGTTTT-TATTTTTTCTTTGAAATT
* * * * * **
1500474 TTTCTATTCTCGAAAAACT-AAGTTTACTACTCTATAAATGTTTTTCGGGGGTTTTTTCTCAGTT
62 CTTCTATTTTTGAAATACTGAAGTTTACTACTCTGTAAATG-TTTTCGGGGGAATTTTCTCAGTT
1500538 TAAAATTTTTAATATTCATTAAATATCATCATTTAATTC
126 TAAAATTTTTAATATTCATTAAATATCATCATTTAATTC
1500577 ATAATAAACC
Statistics
Matches: 271, Mismatches: 45, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
164 4 0.01
165 87 0.32
166 147 0.54
167 32 0.12
168 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.49
Consensus pattern (164 bp):
CATTAAATGAGTTTTTCAAAATTCATTTTATTTCATGAGTTTTTATTTTTTCTTTGAAATTCTTC
TATTTTTGAAATACTGAAGTTTACTACTCTGTAAATGTTTTCGGGGGAATTTTCTCAGTTTAAAA
TTTTTAATATTCATTAAATATCATCATTTAATTC
Found at i:1500631 original size:165 final size:162
Alignment explanation
Indices: 1500195--1500632 Score: 425
Period size: 165 Copynumber: 2.6 Consensus size: 162
1500185 TTTAGGAGAA
* * * * *
1500195 TTTTCATCAGTTTAAAAGTTTTAAAATTCATTAAATATTATTATTTAATTGCCAT-TAAATGAGT
1 TTTTC-TCAGTTTAAAATTTTTAATATTCATTAAATATCATCATTTAATT--CATATAAATCA-T
* * * * * * * *
1500259 TTTTCAAAATTTCTTTTATTTCATGAGTTTTTAATTTTTTCTTTGAAATTCTCCTATTTTTGAAA
62 TTTTGAAAAATTCATTTATTTTATGAGTTTATAA-TTTTTC-TTAAAATTCTCCTATTCTCGAAA
* * *
1500324 TATGAAGTTTGCCACTCTGTAAATGTTTTCGGGGTGGG
125 AATGAAGTTTACCACTCTATAAATGTTTTCGGGGTGGG
* * * * * * *
1500362 TTTTCTCAGTTCATAATTTTTAATATTCATCAAATATCAACATTTAATCCATAGTAAATTAATTT
1 TTTTCTCAGTTTAAAATTTTTAATATTCATTAAATATCATCATTTAATTCATA-TAAATCATTTT
* * * * *
1500427 TGAAAAATTCATTTATTTTTCTAAGTTT-TGCATTTTTTCTTAAAATTTTTCTATTCTCGAAAAA
65 TGAAAAATTCATTTA-TTTTATGAGTTTAT--AATTTTTCTTAAAATTCTCCTATTCTCGAAAAA
* **
1500491 CT-AAGTTTACTACTCTATAAATGTTTTTCGGGG-GTT
127 -TGAAGTTTACCACTCTATAAATG-TTTTCGGGGTGGG
*
1500527 TTTTCTCAGTTTAAAATTTTTAATATTCATTAAATATCATCATTTAATTCATAATAAACCATTTT
1 TTTTCTCAGTTTAAAATTTTTAATATTCATTAAATATCATCATTTAATTCAT-ATAAATCATTTT
1500592 TGAAAAATTCAATTTATTTTATGAGTTCTATAATTTTTCTT
65 TGAAAAATTC-ATTTATTTTATGAGTT-TATAATTTTTCTT
1500633 GTTACCGAGA
Statistics
Matches: 220, Mismatches: 40, Indels: 24
0.77 0.14 0.08
Matches are distributed among these distances:
164 3 0.01
165 137 0.62
166 73 0.33
167 7 0.03
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (162 bp):
TTTTCTCAGTTTAAAATTTTTAATATTCATTAAATATCATCATTTAATTCATATAAATCATTTTT
GAAAAATTCATTTATTTTATGAGTTTATAATTTTTCTTAAAATTCTCCTATTCTCGAAAAATGAA
GTTTACCACTCTATAAATGTTTTCGGGGTGGG
Found at i:1501387 original size:11 final size:11
Alignment explanation
Indices: 1501368--1501422 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
1501358 TTTTGGGAGC
*
1501368 AAGAGAGAAAA
1 AAGAAAGAAAA
1501379 AAGAAAG-AAA
1 AAGAAAGAAAA
1501389 AAGAAAGAAAA
1 AAGAAAGAAAA
*
1501400 AAGAGAGAAAA
1 AAGAAAGAAAA
*
1501411 TA-AAA-AAAA
1 AAGAAAGAAAA
1501420 AAG
1 AAG
1501423 TTAAACTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
9 5 0.14
10 12 0.32
11 20 0.54
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:1501391 original size:10 final size:10
Alignment explanation
Indices: 1501376--1501410 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1501366 GCAAGAGAGA
1501376 AAAAAGAAAG
1 AAAAAGAAAG
1501386 AAAAAGAAAG
1 AAAAAGAAAG
*
1501396 AAAAAAGAGAG
1 -AAAAAGAAAG
1501407 AAAA
1 AAAA
1501411 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1501392 original size:21 final size:21
Alignment explanation
Indices: 1501368--1501422 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1501358 TTTTGGGAGC
*
1501368 AAGAGAGAAAAAAGAAAGAAA
1 AAGAAAGAAAAAAGAAAGAAA
*
1501389 AAGAAAGAAAAAAGAGAGAAA
1 AAGAAAGAAAAAAGAAAGAAA
1501410 ATA-AAA-AAAAAAG
1 A-AGAAAGAAAAAAG
1501423 TTAAACTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 7 0.23
21 23 0.74
22 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
AAGAAAGAAAAAAGAAAGAAA
Found at i:1507411 original size:20 final size:20
Alignment explanation
Indices: 1507386--1507442 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1507376 TACTGCCAGT
1507386 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
* *
1507406 TTCATGTATTGATACAA-TG
1 TTCATGTATCGATACAATTC
**
1507425 AACATGTATCGATACAAT
1 TTCATGTATCGATACAAT
1507443 GTATCGATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:1507446 original size:13 final size:13
Alignment explanation
Indices: 1507428--1507454 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1507418 TACAATGAAC
1507428 ATGTATCGATACA
1 ATGTATCGATACA
1507441 ATGTATCGATACA
1 ATGTATCGATACA
1507454 A
1 A
1507455 AGCGATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1510396 original size:128 final size:130
Alignment explanation
Indices: 1510146--1510378 Score: 355
Period size: 128 Copynumber: 1.8 Consensus size: 130
1510136 TGATGTATCG
* *
1510146 ATACAAAAATCCTCTAATTATTGTTTTGTCTACAACACTTATGCACAACAACTTCCCATGGATAT
1 ATACAAAAATCCTCTAATTATTGTATTGTCTACAACACTTATGCACAACAACTTCCCACGGATAT
* * * *
1510211 GTACTCTACCTCGGTTGTGGATAACGCAATACTATTTTGTATTTAATAGGAATATGATCCATGAT
66 GTACTCTACCTCGGTTGTAGATAACACAACACTATTTTGTATTT-ATAGGAACATGATCCATGAT
1510276 A
130 A
* * *
1510277 ATACCAAAATCCTCTAATTA-T-TATT-TCTACAATACTTATGCACAACAACTTCCTACGGATAT
1 ATACAAAAATCCTCTAATTATTGTATTGTCTACAACACTTATGCACAACAACTTCCCACGGATAT
1510339 GTACTCTACCTCGGTTGTAGATAACACAACACTATTTTGT
66 GTACTCTACCTCGGTTGTAGATAACACAACACTATTTTGT
1510379 TTCTTGGAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
128 71 0.76
129 3 0.03
130 1 0.01
131 19 0.20
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (130 bp):
ATACAAAAATCCTCTAATTATTGTATTGTCTACAACACTTATGCACAACAACTTCCCACGGATAT
GTACTCTACCTCGGTTGTAGATAACACAACACTATTTTGTATTTATAGGAACATGATCCATGATA
Found at i:1513635 original size:15 final size:15
Alignment explanation
Indices: 1513611--1513652 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1513601 CCTTTTCTAG
*
1513611 TTCAACAATTTTCTT
1 TTCAACAATTTTATT
*
1513626 TTCAAGAATTTTATT
1 TTCAACAATTTTATT
1513641 TTCAACAATTTT
1 TTCAACAATTTT
1513653 TTATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (15 bp):
TTCAACAATTTTATT
Found at i:1514088 original size:3 final size:3
Alignment explanation
Indices: 1514080--1514110 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1514070 CGAGTCAACT
*
1514080 TCA TCA TCA TCA TCG TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1514111 TATCTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1515873 original size:20 final size:21
Alignment explanation
Indices: 1515850--1515888 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1515840 CGAAGCAATA
1515850 TGTATCGATAC-TTCTAGGCT
1 TGTATCGATACTTTCTAGGCT
1515870 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
1515889 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCT
Found at i:1520222 original size:29 final size:29
Alignment explanation
Indices: 1520188--1520265 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
1520178 TCTAGTGTTC
1520188 TAGTTGACTTTTAATTCCTTTTAGTATTT
1 TAGTTGACTTTTAATTCCTTTTAGTATTT
* * * *
1520217 TAGTTGACATTTAATTCTTTTTCGTGTTT
1 TAGTTGACTTTTAATTCCTTTTAGTATTT
*
1520246 TACTTGACTTTTAATTCCTT
1 TAGTTGACTTTTAATTCCTT
1520266 AGCTTTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (29 bp):
TAGTTGACTTTTAATTCCTTTTAGTATTT
Found at i:1521533 original size:20 final size:21
Alignment explanation
Indices: 1521503--1521546 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1521493 ATCTGTACTA
*
1521503 ATACAATAAGTTAATGTATCG
1 ATACAATAAGTGAATGTATCG
1521524 ATAC-ATAAGTGAATGTATCG
1 ATACAATAAGTGAATGTATCG
1521544 ATA
1 ATA
1521547 TATGCTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (21 bp):
ATACAATAAGTGAATGTATCG
Found at i:1524261 original size:52 final size:51
Alignment explanation
Indices: 1524103--1524273 Score: 175
Period size: 50 Copynumber: 3.3 Consensus size: 51
1524093 CATCTCCGAG
* * *
1524103 GGGATACTCCAAGCCCATTTTTACTTATAAAACATTAAATTTTTTATCTCT
1 GGGATACTCCAACCCCATTTTTACTTATAAAACATCAAATTTTTCATCTCT
* * * ** * *
1524154 -AGATACTTCAACCCTATTTTTACTTCCAAAGCATCAAA-TTTTCTATCTTT
1 GGGATACTCCAACCCCATTTTTACTTATAAAACATCAAATTTTTC-ATCTCT
* * * *
1524204 AGGGATACTCCAACCCCATTTTTTACTTGTAAACCGTCAAATTTTTCAACTCT
1 -GGGATACTCCAACCCCA-TTTTTACTTATAAAACATCAAATTTTTCATCTCT
1524257 GGGATACTCCAACCCCA
1 GGGATACTCCAACCCCA
1524274 CTATCTCCGA
Statistics
Matches: 96, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
49 4 0.04
50 35 0.36
52 30 0.31
53 22 0.23
54 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (51 bp):
GGGATACTCCAACCCCATTTTTACTTATAAAACATCAAATTTTTCATCTCT
Found at i:1524341 original size:132 final size:131
Alignment explanation
Indices: 1524171--1524617 Score: 483
Period size: 133 Copynumber: 3.4 Consensus size: 131
1524161 TCAACCCTAT
* * *
1524171 TTTTACTTCCAAAGCATCAAA-TTTTCTATCTTTAGGGATACTCCAACCCCATTTTTTACTTGTA
1 TTTTACTTCCAAAGCATCAAATTTTTC-ATCTCTGGGGATACTCCAACCCCATTTTTTACTTCTA
* *
1524235 AACCGTCAAATTTTTCAACTCTGGGATACTCCAACCCCACTATCTCCGAAGGGATACTCTAACCT
65 AAACGTCAAATTTTTCATCTCTGGGATACTCCAACCCCACTATCTCCGAAGGGATACTCTAACCT
1524300 TG
130 TG
* *
1524302 TTTATACTTCCGAAGCATCTAATTTTTCATCTCTGGGGATACTCCAACCCCATTTTTTACTTCTA
1 TTT-TACTTCCAAAGCATCAAATTTTTCATCTCTGGGGATACTCCAACCCCATTTTTTACTTCTA
* * * * * *
1524367 AAATG-CTAAATTTTTCATCTTTGGGGATACTCCAACCCTACCATCTCCGAAGAGACACTCTAAC
65 AAACGTC-AAATTTTTCATCTCT-GGGATACTCCAACCCCACTATCTCCGAAGGGATACTCTAA-
*
1524431 CCCAT-
127 -CCTTG
* * * * * *
1524436 TTTTACATT-CAAAGCATCAAATTTTTTATCTTTGGAGATATTCTAACCCTATTTTTTACTTCTA
1 TTTTAC-TTCCAAAGCATCAAATTTTTCATCTCTGGGGATACTCCAACCCCATTTTTTACTTCTA
* ** * * * ** * *
1524500 AAACATTGAATTTTTCATCTCT-GGATATTCGAACCCCATTATCTCTAAAAGGATACTCCAACCT
65 AAACGTCAAATTTTTCATCTCTGGGATACTCCAACCCCACTATCTCCGAAGGGATACTCTAACCT
1524564 TG
130 TG
* *
1524566 CTTTTACTTTCGAAA-CATCAAATGTTTCATCTCTGGGGATACTCCAACCCCA
1 -TTTTAC-TTCCAAAGCATCAAATTTTTCATCTCTGGGGATACTCCAACCCCA
1524618 CCATCTCCAA
Statistics
Matches: 257, Mismatches: 48, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
129 3 0.01
131 70 0.27
132 69 0.27
133 107 0.42
134 5 0.02
135 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (131 bp):
TTTTACTTCCAAAGCATCAAATTTTTCATCTCTGGGGATACTCCAACCCCATTTTTTACTTCTAA
AACGTCAAATTTTTCATCTCTGGGATACTCCAACCCCACTATCTCCGAAGGGATACTCTAACCTT
G
Found at i:1524612 original size:211 final size:213
Alignment explanation
Indices: 1524338--1524834 Score: 553
Period size: 211 Copynumber: 2.3 Consensus size: 213
1524328 TCATCTCTGG
* * *
1524338 GGATACTCCAACCCCATTTTTTACTT-CTAAA-ATGCTAAATTTTTCATCTTTGGGGATACTCCA
1 GGATACTCCAACCCCA-TTTTCACTTCCAAAACAT-C-AAATTTTTCATCTCTGGGGATACTCCA
* * *
1524401 ACCCTACCATCTCCGAA-GAGACACTCTAACCCCATTTTTACATTCAAAGCATCAAATTTTTTAT
63 ACCCTACCATCTCC-AAGGAGACACTCTAACCCCATTTTTACATTCAAAACATCAAATTTTTCAA
** * * * *
1524465 CT-TTGGAGATATTCTAACCCTAT-TTTTTACTTCTAAAACATTGAATTTTTCATC-TC-TGGAT
127 CTCTAAG-GATACTCTAACCCTATATTTTTACTTCT-AAACATCGAATTCTTCATCTTCGGGGAT
**
1524526 ATTCGAACCCCATTATCTCTAAAA
190 ATTCGAACCCCACCATCTCTAAAA
* * * *
1524550 GGATACTCCAACCTTGC-TTTT-ACTTTCGAAACATCAAATGTTTCATCTCTGGGGATACTCCAA
1 GGATACTCCAACC--CCATTTTCACTTCCAAAACATCAAATTTTTCATCTCTGGGGATACTCCAA
* * * ** *
1524613 CCCCACCATCTCCAAGGGGATACTCTAACCCTGTTTTTACTTTCAAAACATCAAATTTTTCAACT
64 CCCTACCATCTCCAAGGAGACACTCTAACCCCATTTTTACATTCAAAACATCAAATTTTTCAACT
*
1524678 CTAAGGATACTCTAATCCTATATTTTTACTTCTAAACATCGAATTCTTCATCTTCGGGGATATTC
129 CTAAGGATACTCTAACCCTATATTTTTACTTCTAAACATCGAATTCTTCATCTTCGGGGATATTC
* * * **
1524743 TAATCCTACCATCTCTAAGG
194 GAACCCCACCATCTCTAAAA
* ** *
1524763 GGATACTTCAACCCCATTTTCACTTCCAAAACATTGAATTTTTCATCTCTAGGGATACTCCAACC
1 GGATACTCCAACCCCATTTTCACTTCCAAAACATCAAATTTTTCATCTCTGGGGATACTCCAACC
1524828 CTACCAT
66 CTACCAT
1524835 TTCTGAGGGG
Statistics
Matches: 238, Mismatches: 36, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
210 2 0.01
211 115 0.48
212 41 0.17
213 79 0.33
214 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (213 bp):
GGATACTCCAACCCCATTTTCACTTCCAAAACATCAAATTTTTCATCTCTGGGGATACTCCAACC
CTACCATCTCCAAGGAGACACTCTAACCCCATTTTTACATTCAAAACATCAAATTTTTCAACTCT
AAGGATACTCTAACCCTATATTTTTACTTCTAAACATCGAATTCTTCATCTTCGGGGATATTCGA
ACCCCACCATCTCTAAAA
Found at i:1524651 original size:80 final size:78
Alignment explanation
Indices: 1524472--1524689 Score: 222
Period size: 80 Copynumber: 2.7 Consensus size: 78
1524462 TATCTTTGGA
* * ** * *
1524472 GATATTCTAACCCTATTTTTTAC-TTCTAAAACATTGAATTTTTCATCTCTGGATATTCGAACCC
1 GATACTCTAACCCT-GTTTTTACTTTC-AAAACATCAAATTTTTCATCTCTGGATACTCCAACCC
** *
1524536 CATTATCTCTAAAAG
64 CACCATCTCCAAAAG
* * * * *
1524551 GATACTCCAACCTTGCTTTTACTTTCGAAACATCAAATGTTTCATCTCTGGGGATACTCCAACCC
1 GATACTCTAACCCTGTTTTTACTTTCAAAACATCAAATTTTTCATCTCT--GGATACTCCAACCC
**
1524616 CACCATCTCCAAGGG
64 CACCATCTCCAAAAG
*
1524631 GATACTCTAACCCTGTTTTTACTTTCAAAACATCAAATTTTTCAACTCTAAGGATACTC
1 GATACTCTAACCCTGTTTTTACTTTCAAAACATCAAATTTTTCATCTCT--GGATACTC
1524690 TAATCCTATA
Statistics
Matches: 112, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
78 25 0.22
79 14 0.12
80 73 0.65
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (78 bp):
GATACTCTAACCCTGTTTTTACTTTCAAAACATCAAATTTTTCATCTCTGGATACTCCAACCCCA
CCATCTCCAAAAG
Found at i:1524819 original size:133 final size:134
Alignment explanation
Indices: 1524567--1524822 Score: 322
Period size: 133 Copynumber: 1.9 Consensus size: 134
1524557 CCAACCTTGC
1524567 TTTTACTTTCGAAACATCAAATGTTTCATCTCTGGGGATACTCCAACCCCACCATCTCCAAGGGG
1 TTTTACTTTCGAAACATCAAATGTTTCATCTCTGGGGATACTCCAACCCCACCATCTCCAAGGGG
** * *
1524632 ATACTCTAACCCTGTTTTTACTTTCAAAACATCAAATTTTTCAACTCTAAGGATACTCTAATCCT
66 ATACTCTAACCCCATTTTCACTTCCAAAACATCAAATTTTTCAACTCTAAGGATACTCTAATCCT
1524697 ATAT
131 ATAT
* * * * * * *
1524701 TTTTAC-TTCTAAACATCGAAT-TCTTCATCT-TCGGGGATATTCTAATCCTACCATCTCTAAGG
1 TTTTACTTTCGAAACATCAAATGT-TTCATCTCT-GGGGATACTCCAACCCCACCATCTCCAAGG
** * *
1524763 GGATACT-TCAACCCCATTTTCACTTCCAAAACATTGAATTTTTCATCTCTAGGGATACTC
64 GGATACTCT-AACCCCATTTTCACTTCCAAAACATCAAATTTTTCAACTCTAAGGATACTC
1524823 CAACCCTACC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
132 3 0.03
133 95 0.91
134 6 0.06
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (134 bp):
TTTTACTTTCGAAACATCAAATGTTTCATCTCTGGGGATACTCCAACCCCACCATCTCCAAGGGG
ATACTCTAACCCCATTTTCACTTCCAAAACATCAAATTTTTCAACTCTAAGGATACTCTAATCCT
ATAT
Found at i:1528071 original size:58 final size:58
Alignment explanation
Indices: 1528009--1528171 Score: 149
Period size: 58 Copynumber: 2.8 Consensus size: 58
1527999 CACTTTAGTT
* * *
1528009 TCATTTTAGTAAATT-TCAATGATTTT-GGACCATTTATGC-ATTCTTATGTATTTTAAGG
1 TCATTTTAGTAAATTGTC-ACG-TTTTAGGACCATTTATGCAATT-TCATATATTTTAAGG
* *
1528067 TCATTCTT-GTAATTTGTCACGTTTTAGGACCATTTATGCAATTTCATATATTTTAGGG
1 TCATT-TTAGTAAATTGTCACGTTTTAGGACCATTTATGCAATTTCATATATTTTAAGG
** * *
1528125 TCATTTTAGT-AATCTACCATGTTTTAGGGA-CTTTTATGCAATTTCAT
1 TCATTTTAGTAAAT-TGTCACGTTTTA-GGACCATTTATGCAATTTCAT
1528172 GCATTTGAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
57 8 0.09
58 70 0.80
59 10 0.11
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (58 bp):
TCATTTTAGTAAATTGTCACGTTTTAGGACCATTTATGCAATTTCATATATTTTAAGG
Found at i:1528188 original size:58 final size:58
Alignment explanation
Indices: 1528099--1528234 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 58
1528089 TTTAGGACCA
** * * **
1528099 TTTATGCAATTTCATATATTTTAGGGTCATTTTAGTAATCTACCATGTTTTAGGGACT
1 TTTATGCAATTTCATGCATTTGAAGACCATTTTAGTAATCTACCATGTTTTAGGGACT
* * * ***
1528157 TTTATGCAATTTCATGCATTTGAAGACCATTTTGGTCATTTTTTATGTTTTAGGGACT
1 TTTATGCAATTTCATGCATTTGAAGACCATTTTAGTAATCTACCATGTTTTAGGGACT
*
1528215 ATTATGCAA-TTCATGCATTT
1 TTTATGCAATTTCATGCATTT
1528235 TAGCACTATT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
57 11 0.17
58 54 0.83
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (58 bp):
TTTATGCAATTTCATGCATTTGAAGACCATTTTAGTAATCTACCATGTTTTAGGGACT
Found at i:1530882 original size:20 final size:21
Alignment explanation
Indices: 1530857--1530907 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1530847 GCAAATAGTG
*
1530857 AATGTATCGATACATGAGT-A
1 AATGTATCGATACATGACTAA
*
1530877 AATGTATCGATACATGTCTAA
1 AATGTATCGATACATGACTAA
1530898 AATGTATCGA
1 AATGTATCGA
1530908 CAGAAGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACATGACTAA
Found at i:1531003 original size:51 final size:52
Alignment explanation
Indices: 1530948--1531086 Score: 163
Period size: 52 Copynumber: 2.7 Consensus size: 52
1530938 TCTGAAAAGA
* * *
1530948 AAATGTATCGTTACATTTTTCATTGTATCGATATATT-TTGGCTTTTAACCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGCTTTTAACCC
* * * * *
1530999 AAATGTATCAATACATTTTTCATTGTATCGCTACATTCTGGGTTTTTGACCT
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGCTTTTAACCC
* * * *
1531051 AAATGTATTGATACGTTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTTTTCATTGTATCGATACAT
1531087 GCAGCCTATT
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
51 33 0.45
52 40 0.55
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGCTTTTAACCC
Found at i:1532286 original size:20 final size:19
Alignment explanation
Indices: 1532243--1532292 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1532233 ACATCATGCT
**
1532243 TTGTATCGATACATGTTCA
1 TTGTATCGATACATACTCA
1532262 TTGTATCGATACATACTCAA
1 TTGTATCGATACATACTC-A
*
1532282 TTGTATTGATA
1 TTGTATCGATA
1532293 TATGAAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACATACTCA
Found at i:1532348 original size:20 final size:20
Alignment explanation
Indices: 1532323--1532397 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
1532313 CCCTAAGTGA
*
1532323 AATGTATCGATATATAGGAC
1 AATGTATCGATACATAGGAC
1532343 AATGTATCGATACATAGGAC
1 AATGTATCGATACATAGGAC
1532363 AATGTATCGATACATGAGGA-
1 AATGTATCGATACAT-AGGAC
* *
1532383 ACTATATCGATACAT
1 AATGTATCGATACAT
1532398 CATGTCCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 47 0.92
21 4 0.08
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACATAGGAC
Found at i:1538548 original size:13 final size:13
Alignment explanation
Indices: 1538530--1538569 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1538520 ACAATGTTCT
1538530 TTGTATCGATACA
1 TTGTATCGATACA
*
1538543 TTGTATCGATGCA
1 TTGTATCGATACA
* *
1538556 ATGTATCGGTACA
1 TTGTATCGATACA
1538569 T
1 T
1538570 GGGTTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1540420 original size:13 final size:13
Alignment explanation
Indices: 1540402--1540426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1540392 CATAAAGTGT
1540402 TGTATCGATACAA
1 TGTATCGATACAA
1540415 TGTATCGATACA
1 TGTATCGATACA
1540427 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1540424 original size:33 final size:33
Alignment explanation
Indices: 1540382--1540448 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1540372 TTCAACGATT
1540382 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1540415 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1540448 T
1 T
1540449 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1540507 original size:13 final size:13
Alignment explanation
Indices: 1540489--1540513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1540479 ATCACTTAAA
1540489 TGTATCGATACAT
1 TGTATCGATACAT
1540502 TGTATCGATACA
1 TGTATCGATACA
1540514 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1540578 original size:52 final size:52
Alignment explanation
Indices: 1540522--1540702 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
1540512 CACTGATCTT
*
1540522 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1540574 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1540626 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1540678 GGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1540703 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1544684 original size:19 final size:19
Alignment explanation
Indices: 1544622--1544709 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 19
1544612 ACCCTAAAAG
* * *
1544622 GTATCGATATATATCCAGAT
1 GTATCGATACATATTCA-TT
* *
1544642 GTATCGATACATCATGCTTT
1 GTATCGATACAT-ATTCATT
*
1544662 GTATCGATACATGTTCATT
1 GTATCGATACATATTCATT
*
1544681 GTATCGATACATACTCAATT
1 GTATCGATACATATTC-ATT
1544701 GTATCGATA
1 GTATCGATA
1544710 TATGAAACTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.32
20 36 0.63
21 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
GTATCGATACATATTCATT
Found at i:1544785 original size:33 final size:33
Alignment explanation
Indices: 1544742--1544807 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1544732 CTAAGTGAAA
1544742 TGTATCGATACATG-GGACAATGTATCAATACAT
1 TGTATCGATACATGAGGA-AATGTATCAATACAT
* * *
1544775 TGTATTGATACATGAGGAATTGTATCGATACAT
1 TGTATCGATACATGAGGAAATGTATCAATACAT
1544808 CATGTCCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGAGGAAATGTATCAATACAT
Found at i:1546735 original size:79 final size:79
Alignment explanation
Indices: 1546551--1546772 Score: 214
Period size: 79 Copynumber: 2.8 Consensus size: 79
1546541 TCACTTCTAT
* * * * *
1546551 AATATCGAATTTTTTACCATTGGGGATACTCCAACCCTGTTATTTTCAAGGAGATACTGCAATCT
1 AATATCG-ATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCAAGGAGATACTCCAACCT
*
1546616 CGTTTTTATTTCCAA
65 CATTTTTATTTCCAA
** * * * * * *
1546631 AATATTAAATTTTTCATC-GCAGGGATACTCTAACCTTGTTA-TTTCTGAGGGGATACTCCAACC
1 AATA-TCGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTC-AAGGAGATACTCCAACC
*
1546694 TCATTTTTATTTTCAA
64 TCATTTTTATTTCCAA
** * * * *
1546710 AATATCGATTTTTCACCATCGGGGATACTCTAACCCCATCACTTCCAAGGGGATACTCCAACC
1 AATATCGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCAAGGAGATACTCCAACC
1546773 CCGACTTTTA
Statistics
Matches: 112, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
78 14 0.12
79 82 0.73
80 15 0.13
81 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (79 bp):
AATATCGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCAAGGAGATACTCCAACCTC
ATTTTTATTTCCAA
Found at i:1548227 original size:59 final size:59
Alignment explanation
Indices: 1548093--1548402 Score: 240
Period size: 58 Copynumber: 5.3 Consensus size: 59
1548083 TTTGGTTTTA
* ** *
1548093 TTTTCGATGATTTAAGGACTATTATGCGTTTTCATCCA--TTTTAGGGTCATTTAAGTCAT
1 TTTTC-ATGATTTAAGGACTATTATACAATTTCATGCATTTTTTA-GGTCATTTAAGTCAT
* * * * * * *
1548152 TTTCCATGAGTTAAGGACAATTATACAATTTCACGTATTTTTTAGGCCATTTAAGTTAT
1 TTTTCATGATTTAAGGACTATTATACAATTTCATGCATTTTTTAGGTCATTTAAGTCAT
* * * ** * *
1548211 TTTTCGTGATTTAAGGATTATTA-AGCAATTTCATGCA-TTTTCAAATTATTTAAGTTAT
1 TTTTCATGATTTAAGGACTATTATA-CAATTTCATGCATTTTTTAGGTCATTTAAGTCAT
* * * * * *
1548269 TTTTCATGATTTAGGGACCATTGTGA-AATTT-ATGCAATATTT-GGCTCGTTTAAGTCAT
1 TTTTCATGATTTAAGGACTATTAT-ACAATTTCATGCATTTTTTAGG-TCATTTAAGTCAT
* * * * * *
1548327 TTTTCATGACTTAAGGATTATTATGCAATTTCATGTATTTTTAAGGTCATTTAAGCCA-
1 TTTTCATGATTTAAGGACTATTATACAATTTCATGCATTTTTTAGGTCATTTAAGTCAT
*
1548385 TTTTCATAATTTAAGGAC
1 TTTTCATGATTTAAGGAC
1548403 CATTTTGCTT
Statistics
Matches: 191, Mismatches: 50, Indels: 21
0.73 0.19 0.08
Matches are distributed among these distances:
57 5 0.03
58 116 0.61
59 62 0.32
60 8 0.04
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (59 bp):
TTTTCATGATTTAAGGACTATTATACAATTTCATGCATTTTTTAGGTCATTTAAGTCAT
Found at i:1553786 original size:14 final size:14
Alignment explanation
Indices: 1553767--1553808 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1553757 TTAAATGTTG
*
1553767 GTGTGTGTGTATGT
1 GTGTGTGTGTATAT
1553781 GTGTGTGTGTATAT
1 GTGTGTGTGTATAT
* *
1553795 GTGTATGTATATAT
1 GTGTGTGTGTATAT
1553809 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (14 bp):
GTGTGTGTGTATAT
Found at i:1553786 original size:16 final size:16
Alignment explanation
Indices: 1553767--1553798 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1553757 TTAAATGTTG
*
1553767 GTGTGTGTGTATGTGT
1 GTGTGTGTATATGTGT
1553783 GTGTGTGTATATGTGT
1 GTGTGTGTATATGTGT
1553799 ATGTATATAT
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:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (16 bp):
GTGTGTGTATATGTGT
Found at i:1554667 original size:3 final size:3
Alignment explanation
Indices: 1554648--1554697 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
1554638 TACAAAGCTT
*
1554648 TTA TT- TTA TT- TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1554694 TTA T
1 TTA T
1554698 CGTCGTCGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1556451 original size:29 final size:29
Alignment explanation
Indices: 1556419--1556480 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
1556409 TTTTATCTTT
1556419 AATAAATTATT-TT-TATTAATATTTTTAAA
1 AATAAATTATTATTATATT-AT-TTTTTAAA
*
1556448 AATAATTTATTAATTATATTATTTTTTAAA
1 AATAAATTATT-ATTATATTATTTTTTAAA
1556478 AAT
1 AAT
1556481 CATTTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 10 0.34
30 11 0.38
31 4 0.14
32 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
AATAAATTATTATTATATTATTTTTTAAA
Found at i:1556466 original size:26 final size:26
Alignment explanation
Indices: 1556416--1556494 Score: 72
Period size: 30 Copynumber: 2.9 Consensus size: 26
1556406 ATTTTTTATC
*
1556416 TTTAATAAATTATTTTTATTAATATT
1 TTTAATAAATAATTTTTATTAATATT
1556442 TTTAA-AAATAATTTATTAATTATATTATTT
1 TTTAATAAATAATTT-TT-ATTA-A-TA-TT
* *
1556472 TTTAA-AAATCATTTTAATTAATA
1 TTTAATAAATAATTTTTATTAATA
1556495 CTATATCTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
25 8 0.18
26 9 0.20
27 5 0.11
28 5 0.11
29 3 0.07
30 15 0.33
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTAATAAATAATTTTTATTAATATT
Found at i:1556977 original size:100 final size:99
Alignment explanation
Indices: 1556811--1557003 Score: 255
Period size: 100 Copynumber: 1.9 Consensus size: 99
1556801 GAGCTCCGAC
* * * *
1556811 AAAACTAATATTAATCCACTCCACTTCGTCAGTCGAAAATATAATATACTTTGAATTTGATGGGA
1 AAAACTAATATTAATCCACTCCACTTCATCAGTCAAAAATATAATATACTTTGAATTTAATAGGA
*
1556876 AATTTCTAAAATTAAGAATTTTTAATTTAAAAAA
66 AATTTCTAAAATTAAGAATTTATAATTTAAAAAA
* * * *
1556910 AAAATTAA-ATTAATCTACTCCACTTCATCAGTCATAAAAATATAATATGCTTTCG-TTTTAATA
1 AAAACTAATATTAATCCACTCCACTTCATCAGTC--AAAAATATAATATACTTT-GAATTTAATA
*
1556973 GGAAATTTTTAAAATTAAGAATTTATAATTT
63 GGAAATTTCTAAAATTAAGAATTTATAATTT
1557004 GACATCATAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
98 23 0.28
99 7 0.09
100 50 0.62
101 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (99 bp):
AAAACTAATATTAATCCACTCCACTTCATCAGTCAAAAATATAATATACTTTGAATTTAATAGGA
AATTTCTAAAATTAAGAATTTATAATTTAAAAAA
Found at i:1557045 original size:2 final size:2
Alignment explanation
Indices: 1557038--1557069 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1557028 GCAAAGCTTT
*
1557038 TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1557070 AATAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1558502 original size:5 final size:5
Alignment explanation
Indices: 1558492--1558549 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
1558482 TTTGTTCACA
* * *
1558492 ATAAT ATAAT ATAAT ATAAAA ATAACT AAAAT ATAAT ATAAC ATAA- A-AAT
1 ATAAT ATAAT ATAAT AT-AAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT
1558542 A-AAT ATAA
1 ATAAT ATAA
1558550 ATATTATACA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
3 2 0.05
4 6 0.14
5 29 0.66
6 7 0.16
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (5 bp):
ATAAT
Found at i:1558524 original size:27 final size:28
Alignment explanation
Indices: 1558494--1558553 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
1558484 TGTTCACAAT
* *
1558494 AATATAATATAATATAAAAATAACTA-A
1 AATATAATATAACATAAAAATAAATATA
1558521 AATATAATATAACATAAAAATAAATATA
1 AATATAATATAACATAAAAATAAATATA
1558549 AATAT
1 AATAT
1558554 TATACAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (28 bp):
AATATAATATAACATAAAAATAAATATA
Found at i:1558525 original size:22 final size:21
Alignment explanation
Indices: 1558491--1558565 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1558481 TTTTGTTCAC
*
1558491 AATAATATAATATAATATAAA
1 AATAATAAAATATAATATAAA
1558512 AATAACTAAAATATAATAT-AA
1 AATAA-TAAAATATAATATAAA
*
1558533 CAT-A-AAAATA-AATATAAA
1 AATAATAAAATATAATATAAA
* *
1558551 TATTATACAAATATA
1 AATAATA-AAATATA
1558566 TAAACTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 5 0.11
18 10 0.22
19 1 0.02
20 2 0.04
21 14 0.31
22 13 0.29
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAATAAAATATAATATAAA
Found at i:1558526 original size:17 final size:18
Alignment explanation
Indices: 1558504--1558549 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1558494 AATATAATAT
*
1558504 AATATAAAAATAAC-TAA
1 AATATAAATATAACATAA
1558521 AATAT-AATATAACATAA
1 AATATAAATATAACATAA
1558538 AA-ATAAATATAA
1 AATATAAATATAA
1558550 ATATTATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAATATAACATAA
Found at i:1558527 original size:11 final size:11
Alignment explanation
Indices: 1558492--1558549 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
1558482 TTTGTTCACA
1558492 ATAATAT-AAT
1 ATAATATAAAT
*
1558502 ATAATATAAAA
1 ATAATATAAAT
1558513 ATAACTA-AAAT
1 ATAA-TATAAAT
1558524 ATAATATAACAT
1 ATAATATAA-AT
*
1558536 A-AAAATAAAT
1 ATAATATAAAT
1558546 ATAA
1 ATAA
1558550 ATATTATACA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 12 0.30
11 23 0.57
12 5 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1558983 original size:20 final size:20
Alignment explanation
Indices: 1558944--1558991 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1558934 GATAATAAAT
1558944 ATTTTATTAATATTTAAAT-A
1 ATTTT-TTAATATTTAAATAA
*
1558964 ATTTTTTAATATTATCAATAA
1 ATTTTTTAATATT-TAAATAA
1558985 ATTTTTT
1 ATTTTTT
1558992 TATTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 9 0.36
21 8 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTAATATTTAAATAA
Found at i:1558987 original size:21 final size:19
Alignment explanation
Indices: 1558939--1558991 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1558929 TACGTGATAA
1558939 TAAAT-ATTTTATTAATATT
1 TAAATAATTTT-TTAATATT
1558958 TAAATAATTTTTTAATATT
1 TAAATAATTTTTTAATATT
*
1558977 ATCAATAAATTTTTT
1 -TAAAT-AATTTTTT
1558992 TATTTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 9 0.30
21 8 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAATAATTTTTTAATATT
Found at i:1558990 original size:22 final size:21
Alignment explanation
Indices: 1558937--1558993 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1558927 GTTACGTGAT
1558937 AATAAATATTTTATTAATATTTA
1 AATAAAT-TTTT-TTAATATTTA
*
1558960 AAT-AA-TTTTTTAATATTATC
1 AATAAATTTTTTTAATATT-TA
1558980 AATAAATTTTTTTA
1 AATAAATTTTTTTA
1558994 TTTATTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.27
20 8 0.27
21 2 0.07
22 9 0.30
23 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATAAATTTTTTTAATATTTA
Found at i:1559017 original size:15 final size:15
Alignment explanation
Indices: 1558999--1559053 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 15
1558989 TTTTATTTAT
*
1558999 TAAATTTTAAAAATA
1 TAAAATTTAAAAATA
*
1559014 TAAAAATT-AAAATA
1 TAAAATTTAAAAATA
*
1559028 TAAAATTTAATAATA
1 TAAAATTTAAAAATA
1559043 TAAAA-TTAAAA
1 TAAAATTTAAAA
1559054 TATTTACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 18 0.53
15 16 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATTTAAAAATA
Found at i:1559025 original size:14 final size:14
Alignment explanation
Indices: 1559008--1559056 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
1558998 TTAAATTTTA
1559008 AAAATATAAAAATT
1 AAAATATAAAAATT
*
1559022 AAAATATAAAATTT
1 AAAATATAAAAATT
1559036 AATAATAT-AAAATT
1 AA-AATATAAAAATT
1559050 AAAATAT
1 AAAATAT
1559057 TTACTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 5 0.16
14 22 0.69
15 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:1559052 original size:21 final size:21
Alignment explanation
Indices: 1559008--1559056 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1558998 TTAAATTTTA
1559008 AAAATATAAAAATTAAAATAT
1 AAAATATAAAAATTAAAATAT
* *
1559029 AAAATTTAATAATATAAAAT-T
1 AAAATATAAAAAT-TAAAATAT
1559050 AAAATAT
1 AAAATAT
1559057 TTACTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATAAAAATTAAAATAT
Found at i:1559064 original size:28 final size:29
Alignment explanation
Indices: 1558999--1559056 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1558989 TTTTATTTAT
*
1558999 TAAATTTTAAAAATATAAAAATTAAAATA
1 TAAAATTTAAAAATATAAAAATTAAAATA
*
1559028 TAAAATTTAATAATAT-AAAATTAAAATA
1 TAAAATTTAAAAATATAAAAATTAAAATA
1559056 T
1 T
1559057 TTACTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAAATTTAAAAATATAAAAATTAAAATA
Found at i:1560341 original size:11 final size:11
Alignment explanation
Indices: 1560320--1560370 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
1560310 ATAATATTAC
1560320 AAAATAAATATT
1 AAAA-AAATATT
1560332 AAAAAAATATT
1 AAAAAAATATT
*
1560343 AATTTAAAAT-TT
1 AA--AAAAATATT
1560355 AATAAAAATATT
1 AA-AAAAATATT
1560367 AAAA
1 AAAA
1560371 TATTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 17 0.50
12 12 0.35
13 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAAAATATT
Found at i:1560419 original size:12 final size:12
Alignment explanation
Indices: 1560402--1560427 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1560392 AATATATTTT
1560402 TTAAAAAATAAA
1 TTAAAAAATAAA
1560414 TTAAAAAATAAA
1 TTAAAAAATAAA
1560426 TT
1 TT
1560428 TTAAATAAAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TTAAAAAATAAA
Found at i:1560543 original size:5 final size:5
Alignment explanation
Indices: 1560525--1560569 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
1560515 ATAAAATATA
1560525 TTAAT ATTATAT TTAATT TTAATT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT -TTA-AT TTAA-T TTAA-T TTAAT TTAAT TTAAT TTAAT T
1560570 GTACAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.49
6 17 0.46
7 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:1560929 original size:21 final size:22
Alignment explanation
Indices: 1560905--1560946 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1560895 TTTTTATGAA
1560905 TAATT-ATAAA-ATATAATAATT
1 TAATTAATAAATATA-AATAATT
1560926 TAATTAATAAATATAAATAAT
1 TAATTAATAAATATAAATAAT
1560947 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 11 0.58
23 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTAATAAATATAAATAATT
Found at i:1560950 original size:30 final size:27
Alignment explanation
Indices: 1560914--1560968 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
1560904 ATAATTATAA
*
1560914 AATATAATAATTTAATTAATAAATATAAAT
1 AATATAAAAATTT--TTAA-AAATATAAAT
1560944 AATATAAAAATTTTTAAAAATATAA
1 AATATAAAAATTTTTAAAAATATAA
1560969 TATTAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
30 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AATATAAAAATTTTTAAAAATATAAAT
Found at i:1560964 original size:27 final size:29
Alignment explanation
Indices: 1560897--1560968 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
1560887 TGTGTATATT
* * *
1560897 TTTATGAATAATTAT-AA-AATATAATAA
1 TTTATTAATAAATATAAATAATATAAAAA
1560924 TTTAATTAATAAATATAAATAATATAAAAA
1 TTT-ATTAATAAATATAAATAATATAAAAA
1560954 TTT-TTAA-AAATATAA
1 TTTATTAATAAATATAA
1560969 TATTAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 11 0.28
28 14 0.36
29 2 0.05
30 12 0.31
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
TTTATTAATAAATATAAATAATATAAAAA
Found at i:1561027 original size:6 final size:6
Alignment explanation
Indices: 1561016--1561061 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
1561006 TTTAAAAAAT
* *
1561016 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAT ATATAT ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
1561062 GTAACACGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:1561596 original size:33 final size:33
Alignment explanation
Indices: 1561559--1561621 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1561549 GTTAAAAATA
* *
1561559 TTAAAATTTA-TATAATAAATTTATTAAATTTTT
1 TTAAAAATTATTAT-ATAAATTAATTAAATTTTT
1561592 TTAAAAATTATTATATAAATTAATTAAATT
1 TTAAAAATTATTATATAAATTAATTAAATT
1561622 AAATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTAAAAATTATTATATAAATTAATTAAATTTTT
Found at i:1561926 original size:3 final size:3
Alignment explanation
Indices: 1561918--1561943 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1561908 TGAACACTCC
1561918 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1561944 AATAACAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1562002 original size:6 final size:6
Alignment explanation
Indices: 1561991--1562024 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1561981 CAGATTGAGG
1561991 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCT
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCT
1562025 GTCCATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTCT
Found at i:1562920 original size:16 final size:16
Alignment explanation
Indices: 1562864--1562931 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
1562854 TTTGTTAAAT
*
1562864 TTTTAAATTTTTAATTA
1 TTTTAAA-TTTAAATTA
* *
1562881 TTTTTAATTTTAATT-
1 TTTTAAATTTAAATTA
1562896 TTTT--ATTTAAATTA
1 TTTTAAATTTAAATTA
*
1562910 TTTTAAATTTAAGTTGA
1 TTTTAAATTTAAATT-A
1562927 TTTTA
1 TTTTA
1562932 CTTATTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
13 8 0.18
14 4 0.09
15 4 0.09
16 16 0.36
17 12 0.27
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:1562992 original size:20 final size:21
Alignment explanation
Indices: 1562958--1563003 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1562948 ATTAAAATAA
* *
1562958 AAATATTAAATTTTTTCATTT
1 AAATATTAAAATTTTACATTT
*
1562979 AAAT-TTAAAATTTTAGATTT
1 AAATATTAAAATTTTACATTT
1562999 AAATA
1 AAATA
1563004 ATTTACCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATATTAAAATTTTACATTT
Found at i:1564333 original size:6 final size:6
Alignment explanation
Indices: 1564295--1564319 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1564285 TTTCTTTTAC
1564295 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
1564320 TACAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:1564899 original size:10 final size:9
Alignment explanation
Indices: 1564836--1564895 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
1564826 AAATAAATCT
1564836 AAATATAAA
1 AAATATAAA
1564845 AAATATAAA
1 AAATATAAA
*
1564854 ATTATATTAAA
1 A-AATA-TAAA
1564865 AAATTATGAAA
1 AAA-TAT-AAA
* *
1564876 TAAT-CAAA
1 AAATATAAA
1564884 AAATATAAA
1 AAATATAAA
1564893 AAA
1 AAA
1564896 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
8 6 0.15
9 16 0.40
10 6 0.15
11 12 0.30
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
AAATATAAA
Found at i:1565216 original size:26 final size:27
Alignment explanation
Indices: 1565168--1565225 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1565158 TTGATTTTAA
* *
1565168 TTTAGATTATTTTATATTATAAAAT-T
1 TTTAAATTATTTTAAATTATAAAATAT
*
1565194 TTTAAATTATTTTTAAATT-TAAATTAT
1 TTTAAATTA-TTTTAAATTATAAAATAT
1565221 TTTAA
1 TTTAA
1565226 GTTTTAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTAAATTATTTTAAATTATAAAATAT
Found at i:1565225 original size:16 final size:16
Alignment explanation
Indices: 1565194--1565263 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
1565184 TTATAAAATT
1565194 TTTAAATTATTTTTAAA
1 TTTAAATTA-TTTTAAA
*
1565211 TTTAAATTATTTTAAG
1 TTTAAATTATTTTAAA
* *
1565227 TTTTAATCATTTTAAA
1 TTTAAATTATTTTAAA
* * *
1565243 TTCAAATTACTTTAGA
1 TTTAAATTATTTTAAA
1565259 TTTAA
1 TTTAA
1565264 GTCATTTCGT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
16 34 0.79
17 9 0.21
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:1565250 original size:32 final size:32
Alignment explanation
Indices: 1565204--1565270 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1565194 TTTAAATTAT
* * *
1565204 TTTTAAATTTAAATTATTTTAAGTTTTAA-TCA
1 TTTTAAATTCAAATTACTTT-AGATTTAAGTCA
1565236 TTTTAAATTCAAATTACTTTAGATTTAAGTCA
1 TTTTAAATTCAAATTACTTTAGATTTAAGTCA
1565268 TTT
1 TTT
1565271 CGTATTTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (32 bp):
TTTTAAATTCAAATTACTTTAGATTTAAGTCA
Found at i:1565424 original size:22 final size:21
Alignment explanation
Indices: 1565387--1565427 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1565377 AACATTCGAG
*
1565387 TTAAATTAGGTTTAAGTCATT
1 TTAAATTAAGTTTAAGTCATT
1565408 TTAAATTTAAGTTTAAGTCA
1 TTAAA-TTAAGTTTAAGTCA
1565428 ATCGGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
TTAAATTAAGTTTAAGTCATT
Found at i:1566429 original size:16 final size:16
Alignment explanation
Indices: 1566410--1566466 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
1566400 TCGAGTTTAG
*
1566410 GTCATTTCGGATTCAA
1 GTCATTTCGGATTCGA
* *
1566426 GTCATTTTGGGTTCGA
1 GTCATTTCGGATTCGA
1566442 GTCA-TTCTGGATTCGA
1 GTCATTTC-GGATTCGA
1566458 GTCATTTCG
1 GTCATTTCG
1566467 AGTTCGGGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 2 0.06
16 29 0.85
17 3 0.09
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (16 bp):
GTCATTTCGGATTCGA
Found at i:1566472 original size:16 final size:16
Alignment explanation
Indices: 1566362--1566472 Score: 68
Period size: 16 Copynumber: 6.9 Consensus size: 16
1566352 AATTATTTGG
*
1566362 GTCATTTCGAGTTCTTA
1 GTCATTTCGAGTTC-GA
* * *
1566379 -TCATTTCAAATTCGG
1 GTCATTTCGAGTTCGA
* *
1566394 GTTATTTCGAGTT-TA
1 GTCATTTCGAGTTCGA
*
1566409 GGTCATTTCG-GATTCAA
1 -GTCATTTCGAG-TTCGA
* *
1566426 GTCATTTTGGGTTCGA
1 GTCATTTCGAGTTCGA
*
1566442 GTCATTCTGGA-TTCGA
1 GTCATT-TCGAGTTCGA
1566458 GTCATTTCGAGTTCG
1 GTCATTTCGAGTTCG
1566473 GGTCCGTTCG
Statistics
Matches: 71, Mismatches: 16, Indels: 15
0.70 0.16 0.15
Matches are distributed among these distances:
15 4 0.06
16 63 0.89
17 4 0.06
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (16 bp):
GTCATTTCGAGTTCGA
Found at i:1566472 original size:32 final size:33
Alignment explanation
Indices: 1566362--1566476 Score: 89
Period size: 32 Copynumber: 3.6 Consensus size: 33
1566352 AATTATTTGG
* ** *
1566362 GTCATTTCGAGTTCTTA--TCATTTCAAATTCGG
1 GTCATTTCGAGTTC-GAGGTCATTTCGGATTCGA
* * *
1566394 GTTATTTCGAGTT-TAGGTCATTTCGGATTCAA
1 GTCATTTCGAGTTCGAGGTCATTTCGGATTCGA
* *
1566426 GTCATTTTGGGTTCGA-GTCA-TTCTGGATTCGA
1 GTCATTTCGAGTTCGAGGTCATTTC-GGATTCGA
1566458 GTCATTTCGAGTTCG-GGTC
1 GTCATTTCGAGTTCGAGGTC
1566477 CGTTCGAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
30 2 0.03
31 3 0.05
32 60 0.91
33 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (33 bp):
GTCATTTCGAGTTCGAGGTCATTTCGGATTCGA
Found at i:1574729 original size:17 final size:19
Alignment explanation
Indices: 1574707--1574750 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1574697 TTATATTTAA
1574707 TTAATT-TT-TAGTTGTTT
1 TTAATTATTGTAGTTGTTT
*
1574724 TTAATTAGTTGTTGTTGTTT
1 TTAATTA-TTGTAGTTGTTT
1574744 TTAATTA
1 TTAATTA
1574751 GTTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (19 bp):
TTAATTATTGTAGTTGTTT
Found at i:1574742 original size:20 final size:21
Alignment explanation
Indices: 1574693--1574753 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
1574683 TTAGATGTTT
* * * *
1574693 TTAGTTATATTTAATTAATTT
1 TTAGTTGTTTTTAATTAGTTG
1574714 TTAGTTGTTTTTAATTAGTTG
1 TTAGTTGTTTTTAATTAGTTG
1574735 TT-GTTGTTTTTAATTAGTT
1 TTAGTTGTTTTTAATTAGTT
1574754 TTATTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (21 bp):
TTAGTTGTTTTTAATTAGTTG
Found at i:1576550 original size:98 final size:97
Alignment explanation
Indices: 1576344--1576575 Score: 365
Period size: 98 Copynumber: 2.4 Consensus size: 97
1576334 TTGAAAAATA
* * * * *
1576344 GGGTTGCAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCAATGATGACAATTTAGGCAAGG
1 GGGTTGAAGTATCCCCTCGGAGGAATGAGGTTCGAGTGTCCCCAACGATGACAATTTAGGCAAGG
1576409 TTAGATTCAAATCTTGACAAGTTTTAAAAACG
66 TTAGATTCAAATCTTGACAAGTTTTAAAAACG
* * * *
1576441 GGGTTAAAGTATCTCCTCAGAGGAATGAGGTTCGAGTGTCTCCAACGATGACAATTTAGGCAAGG
1 GGGTTGAAGTATCCCCTCGGAGGAATGAGGTTCGAGTGTCCCCAACGATGACAATTTAGGCAAGG
1576506 TTAAGATTCAAATCTTGACAAGTTTTAAAAACG
66 TT-AGATTCAAATCTTGACAAGTTTTAAAAACG
*
1576539 GGGTTGGAGTATCCCCTCGGAGGAATGAGGTTCGAGT
1 GGGTTGAAGTATCCCCTCGGAGGAATGAGGTTCGAGT
1576576 ATTCTCGATG
Statistics
Matches: 121, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
97 58 0.48
98 63 0.52
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (97 bp):
GGGTTGAAGTATCCCCTCGGAGGAATGAGGTTCGAGTGTCCCCAACGATGACAATTTAGGCAAGG
TTAGATTCAAATCTTGACAAGTTTTAAAAACG
Found at i:1577853 original size:20 final size:20
Alignment explanation
Indices: 1577828--1577879 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1577818 CTGGATATGT
1577828 TAAAAATGCATGGAACATAG
1 TAAAAATGCATGGAACATAG
1577848 TAAAAATGCATGGAACATAG
1 TAAAAATGCATGGAACATAG
1577868 TAAAAATGCATG
1 TAAAAATGCATG
1577880 ATCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAAAATGCATGGAACATAG
Found at i:1591891 original size:62 final size:61
Alignment explanation
Indices: 1591806--1592241 Score: 519
Period size: 62 Copynumber: 7.1 Consensus size: 61
1591796 TGAAACTTAA
* * * **
1591806 CACCCTTTTAGTCCTCAAAGAGCAGGACACATTTTTCTTAAAAAGCCCACACAAGTTGGTGG
1 CACCCGTTCAGTCCTCAAAGAGCAGGACGC-TTTTTCTTTTAAAGCCCACACAAGTTGGTGG
* *
1591868 CACCTGTTCAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTAGTGG
1 CACCCGTTCAGTCCTCAAAGAGCAGGACG-CTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
*
1591930 CACCCGTTCAGTCTTCAAAGAGCAGGACGTCTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCCGTTCAGTCCTCAAAGAGCAGGACG-CTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
* * * *
1591992 CACCCATTCAGTCCTCAAAGAGCAGGTCATCTTTTTCTTTTAAAGCTCACACAAGTTGGTGG
1 CACCCGTTCAGTCCTCAAAGAGCAGGAC-GCTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
* *
1592054 CACCCGTTCAGTCCTCAAAAAGCAGGACGTCTTTTTCTTTTAAAGCCCACATAAGTTGGTGG
1 CACCCGTTCAGTCCTCAAAGAGCAGGACG-CTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
* *
1592116 CA--C---C---CCTCAAAGAGCAGGACGCTTTTTTTTTTAAAAAAAAAACCCACACAAGTTGGT
1 CACCCGTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTT------AAAGCCCACACAAGTTGGT
1592173 GG
60 GG
* * * *
1592175 CACCCGTTTAGTCCTTAAAGAGCAGGATGCATTTTTCTTTTAAAGCCCATACAAGTTGGTGG
1 CACCCGTTCAGTCCTCAAAGAGCAGGACGC-TTTTTCTTTTAAAGCCCACACAAGTTGGTGG
*
1592237 AACCC
1 CACCC
1592242 CTTTTCAAAA
Statistics
Matches: 323, Mismatches: 33, Indels: 36
0.82 0.08 0.09
Matches are distributed among these distances:
53 10 0.03
54 16 0.05
57 1 0.00
59 21 0.07
60 1 0.00
61 1 0.00
62 247 0.76
63 1 0.00
67 16 0.05
68 9 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (61 bp):
CACCCGTTCAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1592940 original size:18 final size:18
Alignment explanation
Indices: 1592917--1592955 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1592907 AAAAGTTATG
*
1592917 AAAAAA-TAGAAACAAATA
1 AAAAAAGTACAAAC-AATA
1592935 AAAAAAGTACAAACAATA
1 AAAAAAGTACAAACAATA
1592953 AAA
1 AAA
1592956 CTTTCGGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAAAAGTACAAACAATA
Found at i:1594188 original size:11 final size:11
Alignment explanation
Indices: 1594172--1594222 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
1594162 TTTCTACAAA
1594172 AAATAAAAAAT
1 AAATAAAAAAT
1594183 AAATAAAAAAT
1 AAATAAAAAAT
*
1594194 AAA-AAGAAAGT
1 AAATAA-AAAAT
*
1594205 ATA-AAAAAAT
1 AAATAAAAAAT
1594215 -AATAAAAA
1 AAATAAAAA
1594223 GTGTTTTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 1 0.03
10 11 0.32
11 22 0.65
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:1594198 original size:24 final size:24
Alignment explanation
Indices: 1594170--1594223 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1594160 GATTTCTACA
*
1594170 AAAAATAAAAAATAAATAAAA-AAT
1 AAAAAGAAAAAATAAA-AAAATAAT
**
1594194 AAAAAGAAAGTATAAAAAAATAAT
1 AAAAAGAAAAAATAAAAAAATAAT
1594218 AAAAAG
1 AAAAAG
1594224 TGTTTTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAAAGAAAAAATAAAAAAATAAT
Found at i:1595728 original size:26 final size:27
Alignment explanation
Indices: 1595675--1595729 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1595665 GAAATATAAT
* **
1595675 AAATTAGTTAAAAGATATTTTTTTATA
1 AAATTAGTTAAAAGATATTTATAAATA
*
1595702 AAATTA-TTGAAAGATATTTATAAATA
1 AAATTAGTTAAAAGATATTTATAAATA
1595728 AA
1 AA
1595730 TTAAAACTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (27 bp):
AAATTAGTTAAAAGATATTTATAAATA
Found at i:1597551 original size:16 final size:16
Alignment explanation
Indices: 1597530--1597567 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1597520 AACTATCTTT
1597530 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
1597546 AATTATTATTAAGTTA
1 AATTATTATTAAATTA
*
1597562 TATTAT
1 AATTAT
1597568 AATTCAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:1597661 original size:20 final size:22
Alignment explanation
Indices: 1597638--1597678 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1597628 AAATGAATTT
1597638 ATTAA-AA-TATTATTATTTTA
1 ATTAATAATTATTATTATTTTA
1597658 ATTAATTAATTATTATTATTT
1 ATTAA-TAATTATTATTATTT
1597679 AAAAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTAATAATTATTATTATTTTA
Found at i:1600386 original size:27 final size:27
Alignment explanation
Indices: 1600347--1600408 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
1600337 TGCACAACTT
*
1600347 ATTTTT-T-TATTAAATTTAAAATTTA
1 ATTTTTATATATTAAAATTAAAATTTA
*
1600372 ATTTTTATATATTAAAATTAAAATTTT
1 ATTTTTATATATTAAAATTAAAATTTA
1600399 ATTATTTATA
1 ATT-TTTATA
1600409 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 6 0.19
26 1 0.03
27 19 0.59
28 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTTATATATTAAAATTAAAATTTA
Found at i:1600411 original size:21 final size:21
Alignment explanation
Indices: 1600351--1600411 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
1600341 CAACTTATTT
* *
1600351 TTTTATTAAATTTAAAATTTAAT
1 TTTTATT--ATTTAAAATTAAAA
1600374 TTTTA-TATATTAAAATTAAAA
1 TTTTATTAT-TTAAAATTAAAA
*
1600395 TTTTATTATTTATAATT
1 TTTTATTATTTAAAATT
1600412 TTTTATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 22 0.67
22 4 0.12
23 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTATTTAAAATTAAAA
Found at i:1600426 original size:15 final size:17
Alignment explanation
Indices: 1600395--1600426 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1600385 AAAATTAAAA
1600395 TTTTATTATTTATAATT
1 TTTTATTATTTATAATT
1600412 TTTTATT-TTTA-AATT
1 TTTTATTATTTATAATT
1600427 ATAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTATTTATAATT
Found at i:1600539 original size:14 final size:15
Alignment explanation
Indices: 1600513--1600541 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1600503 ATTTAATTTA
1600513 AATTTTATTTAAAAT
1 AATTTTATTTAAAAT
1600528 AATTTT-TTTAAAAT
1 AATTTTATTTAAAAT
1600542 TGATTGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTATTTAAAAT
Found at i:1601936 original size:21 final size:21
Alignment explanation
Indices: 1601912--1601958 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1601902 CGTGTTCATA
1601912 TCAAAGGATGGTATGTAATAT
1 TCAAAGGATGGTATGTAATAT
*
1601933 TCAAATGATGGTATGTAATAT
1 TCAAAGGATGGTATGTAATAT
1601954 TCAAA
1 TCAAA
1601959 ATTATTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (21 bp):
TCAAAGGATGGTATGTAATAT
Found at i:1602670 original size:17 final size:15
Alignment explanation
Indices: 1602632--1602672 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1602622 TAGTATTACT
1602632 GTTAAAAAAACTTAA
1 GTTAAAAAAACTTAA
*
1602647 GTTAAAAGAAATTTAA
1 GTTAAAA-AAACTTAA
1602663 GATTAAAAAA
1 G-TTAAAAAA
1602673 TATGTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (15 bp):
GTTAAAAAAACTTAA
Found at i:1606709 original size:21 final size:22
Alignment explanation
Indices: 1606685--1606734 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1606675 ATCAAATCTT
* *
1606685 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1606706 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1606728 --TCAAAAT
1 CTTCAAAAT
1606735 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1611798 original size:20 final size:20
Alignment explanation
Indices: 1611769--1611844 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
1611759 AAAAAGACAT
*
1611769 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
1611789 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
1611809 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
1611829 AATGTATCGATACATT
1 AATGTATCGATACATT
1611845 AGGGTAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 43 0.93
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:1611837 original size:40 final size:39
Alignment explanation
Indices: 1611766--1611844 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
1611756 GGTAAAAAGA
* *
1611766 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1611805 CATACATGTATCGATATATTGAAAAATGTATCGATACATT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACATT
1611845 AGGGTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1612739 original size:169 final size:167
Alignment explanation
Indices: 1612405--1612997 Score: 796
Period size: 169 Copynumber: 3.5 Consensus size: 167
1612395 AAAAAAAAAT
* ** *
1612405 GTGCCACTAACTTATGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTG
1 GTGCCACTGACTCGTGGGCTTTGAAAG-GTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTA
* * *
1612470 ACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG-AAAGAATGCCACTGACTC
65 ACTT--GTGGGCTTTGAAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAAG-GTGCCACTGACTC
* * * *
1612534 ATGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGA
125 GTGGGCTTTAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGA
* *
1612577 GTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGC-TTGAAAAGGTGCCACTG
1 GTGCCACTGACTCGTGGGCTTTG-AAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTA
* *
1612641 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCATGGGCTTTGAAAAGGTGCCACTGACTTGTGTG
65 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGAC-T-CGTG
*
1612706 GGCTTTAAAAGAATGCCACTGACTCGTGGGCTTTGAAAGA
128 GGCTTTAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGA
* * * * *
1612746 ATGCCATTGACTCGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTGAAAGGGTGCCACTA
1 GTGCCACTGACTCGTGGGCTTTGAAAGG-TGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTA
*
1612810 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACTCGTGGG
65 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGG
*
1612875 CTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
130 CTTT-AAAAGAATGCCACTGACTTGTGGGCTTTG-AAAGA
* * * * *
1612915 GTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTTGGAAGGGTGCCACTA
1 GTGCCACTGACTCGTGGGCTTTG-AAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTA
1612980 ACTTGTGGGCTTTGAAAG
65 ACTTGTGGGCTTTGAAAG
1612998 GGTTTGAACG
Statistics
Matches: 380, Mismatches: 32, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
167 29 0.08
168 39 0.10
169 210 0.55
170 39 0.10
171 21 0.06
172 38 0.10
173 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (167 bp):
GTGCCACTGACTCGTGGGCTTTGAAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAA
CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGC
TTTAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGA
Found at i:1612770 original size:197 final size:197
Alignment explanation
Indices: 1612408--1612996 Score: 809
Period size: 197 Copynumber: 3.0 Consensus size: 197
1612398 AAAAAATGTG
**
1612408 CCACTAACTTATGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACT
1 CCACTAACTCGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGAC-
* * *
1612473 TGCGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGAATGCCACTGACTCATG
65 T-CGTGGGCTTTGAAAA-GGTGCCACTGACTTGTGTGGGCTTTAAAAGAATGCCACTGACTCGTG
* * *
1612537 GGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAA
128 GGCTTTGAAAGAATGCCATTGACTTGTGAGCTTTGAAAG-GTGCCACTGACTTGTGGGCTTTGAA
1612602 AAGGTA
192 AAGGTA
* *
1612608 CCACTGACTCGTGGGC-TTGAAA-AGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGA
1 CCACTAACTCGTGGGCTTTGAAAGA-GTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGA
*
1612670 CTCATGGGCTTTGAAAAGGTGCCACTGACTTGTGTGGGCTTTAAAAGAATGCCACTGACTCGTGG
64 CTCGTGGGCTTTGAAAAGGTGCCACTGACTTGTGTGGGCTTTAAAAGAATGCCACTGACTCGTGG
*
1612735 GCTTTGAAAGAATGCCATTGACTCGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTGAAA
129 GCTTTGAAAGAATGCCATTGACTTGTGAGCTTTGAAAGG-TGCCACTGACTTGTGGGCTTTGAAA
* *
1612799 GGGTG
193 AGGTA
* *
1612804 CCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATGTGCCACTGACT
1 CCACTAACTCGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACT
* *
1612869 CGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
66 CGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGTGGGCTTT-AAAAGAATGCCACTGACTCGTGG
* * * *
1612932 GCTTTGAAA-AGGTGCCACTGACTTGT-AGGCTTTGGAAGGGTGCCACTAACTTGTGGGCTTTGA
129 GCTTTGAAAGA-ATGCCATTGACTTGTGA-GCTTT-GAAAGGTGCCACTGACTTGTGGGCTTTGA
1612995 AA
191 AA
1612997 GGGTTTGAAC
Statistics
Matches: 350, Mismatches: 26, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
196 36 0.10
197 226 0.65
198 36 0.10
199 39 0.11
200 13 0.04
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (197 bp):
CCACTAACTCGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACT
CGTGGGCTTTGAAAAGGTGCCACTGACTTGTGTGGGCTTTAAAAGAATGCCACTGACTCGTGGGC
TTTGAAAGAATGCCATTGACTTGTGAGCTTTGAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGG
TA
Found at i:1612998 original size:28 final size:28
Alignment explanation
Indices: 1612405--1613000 Score: 710
Period size: 28 Copynumber: 21.1 Consensus size: 28
1612395 AAAAAAAAAT
* * *
1612405 GTGCCACTAACTTATGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1612433 GTGCCACTGACTCGTGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1612461 GTGCCACTGACTTGCGTGGGCTTTAAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAGG
*
1612491 GTGCCACTGACTTGCGTGGGCTTTGAAAGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGG
* **
1612521 ATGCCACTGACTCATGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
1612549 ATGCCATTGACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1612577 GTGCCACTGACTCGTGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
1612605 GTACCACTGACTCGTGGGC-TTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1612632 GTGCCACTGACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
** *
1612660 GTGCCACTGACTCATGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1612688 GTGCCACTGACTTGTGTGGGCTTTAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGG
* * *
1612718 ATGCCACTGACTCGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
1612746 ATGCCATTGACTCGTGAGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1612774 ATGCCACTGACTTGTGGGC-TTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1612801 GTGCCACTAACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* **
1612829 GTGCCACTGACTCGTGGGCTTTGAAAAT
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1612857 GTGCCACTGACTCGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
1612886 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
1612915 GTGCCACTGACTTGTGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1612943 GTGCCACTGACTTGTAGGCTTTGGAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1612971 GTGCCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
1612999 GT
1 GT
1613001 TTGAACGTTC
Statistics
Matches: 497, Mismatches: 64, Indels: 14
0.86 0.11 0.02
Matches are distributed among these distances:
27 50 0.10
28 318 0.64
29 56 0.11
30 73 0.15
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:1614139 original size:13 final size:13
Alignment explanation
Indices: 1614121--1614211 Score: 65
Period size: 13 Copynumber: 6.1 Consensus size: 13
1614111 ACATAAAATG
1614121 TTGTATCGATACA
1 TTGTATCGATACA
1614134 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1614150 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1614166 TTGTATCGATACATAA
1 TTGTATCGATAC---A
1614182 GTGTTGTATCGATACA
1 ---TTGTATCGATACA
*
1614198 ATGTATCGATACA
1 TTGTATCGATACA
1614211 T
1 T
1614212 AAGTTTTGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
13 33 0.52
14 1 0.02
16 8 0.12
18 1 0.02
19 21 0.33
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1614190 original size:19 final size:18
Alignment explanation
Indices: 1614100--1614229 Score: 67
Period size: 19 Copynumber: 7.8 Consensus size: 18
1614090 AATTCAACGA
*
1614100 TTTGTATCGATACATAAAA
1 TTTGTATCGATACAT-AAG
1614119 TGTTGTATCGATAC---A-
1 T-TTGTATCGATACATAAG
*
1614134 -TTGTATCGATACA-ACAC
1 TTTGTATCGATACATA-AG
1614151 TTATGTATCGATAC---A-
1 TT-TGTATCGATACATAAG
1614166 -TTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1614183 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1614199 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
1614215 TTTTGTACCGATACA
1 -TTTGTATCGATACA
1614230 ATTTAAGCTA
Statistics
Matches: 91, Mismatches: 1, Indels: 38
0.70 0.01 0.29
Matches are distributed among these distances:
13 34 0.37
14 1 0.01
15 2 0.02
16 4 0.04
17 2 0.02
18 1 0.01
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1614227 original size:64 final size:65
Alignment explanation
Indices: 1614101--1614229 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 65
1614091 ATTCAACGAT
* *
1614101 TTGTATCGATACATAAAATGTTGTATCGATACATTGTATCGATACAACACTTATGTATCGATACA
1 TTGTATCGATACATAAAATGTTGTATCGATACAATGTATCGATACAACACTTATGTACCGATACA
* * *
1614166 TTGTATCGATACAT-AAGTGTTGTATCGATACAATGTATCGATACATA-AGTTTTGTACCGATAC
1 TTGTATCGATACATAAAATGTTGTATCGATACAATGTATCGATACA-ACACTTATGTACCGATAC
1614229 A
65 A
1614230 ATTTAAGCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
64 43 0.74
65 15 0.26
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (65 bp):
TTGTATCGATACATAAAATGTTGTATCGATACAATGTATCGATACAACACTTATGTACCGATACA
Found at i:1614230 original size:32 final size:32
Alignment explanation
Indices: 1614102--1614231 Score: 165
Period size: 32 Copynumber: 4.0 Consensus size: 32
1614092 TTCAACGATT
* *
1614102 TGTATCGATACATAAAATGTTGTATCGATACAT
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
* *
1614135 TGTATCGATACA-ACACT-TATGTATCGATACAT
1 TGTATCGATACATA-AGTGT-TGTATCGATACAA
1614167 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1614199 TGTATCGATACATAAGTTTTGTACCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1614231 T
1 T
1614232 TTAAGCTACT
Statistics
Matches: 88, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
31 2 0.02
32 72 0.82
33 14 0.16
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Done.