Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011758.1 Corchorus capsularis cultivar CVL-1 contig11779, whole genome shotgun sequence
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: 128464
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1175 original size:22 final size:22
Alignment explanation
Indices: 1058--1200 Score: 100
Period size: 22 Copynumber: 6.6 Consensus size: 22
1048 TATAGGAAGA
** **
1058 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
1080 TTATCAAAATTT--TAAAGCGAGG
1 TTATCAAAATTTCATAAA--GAGG
* * * *
1102 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
*
1124 TTATCAGAATTTCATAGAAG-GG
1 TTATCAAAATTTCATA-AAGAGG
* * *
1146 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
1168 TTATC-AAA--TCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
1187 TTATCAAATTTTCA
1 TTATCAAAATTTCA
1201 AAATGTGATT
Statistics
Matches: 92, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
19 15 0.16
20 4 0.04
21 6 0.07
22 62 0.67
23 2 0.02
24 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:1183 original size:19 final size:19
Alignment explanation
Indices: 1159--1195 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1149 ACAAAATTTT
1159 ATAAAGAGGTTATCAAATC
1 ATAAAGAGGTTATCAAATC
1178 ATAAAGAGGTTATCAAAT
1 ATAAAGAGGTTATCAAAT
1196 TTTCAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (19 bp):
ATAAAGAGGTTATCAAATC
Found at i:1377 original size:22 final size:22
Alignment explanation
Indices: 1328--1386 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
1318 TCAGGGAAGA
***
1328 TATCAAAATTTCATACTTTAGT
1 TATCAAAATTTCATAAGATAGT
* *
1350 TTTCAAAATTTCATAAGATGGT
1 TATCAAAATTTCATAAGATAGT
1372 TATCAAAATTTCATA
1 TATCAAAATTTCATA
1387 GGGAGACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (22 bp):
TATCAAAATTTCATAAGATAGT
Found at i:1423 original size:22 final size:21
Alignment explanation
Indices: 1354--1423 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
1344 TTTAGTTTTC
*
1354 AAAATTTCATAAGATGGTTATC
1 AAAATTTCATAAGA-GGTTATA
* **
1376 AAAATTTCATAGGGAGACTA-A
1 AAAATTTCATA-AGAGGTTATA
1397 CAAAATTTCATAATGAGGTTATA
1 -AAAATTTCATAA-GAGGTTATA
1420 AAAA
1 AAAA
1424 AATCATAGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
22 34 0.92
23 3 0.08
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (21 bp):
AAAATTTCATAAGAGGTTATA
Found at i:1448 original size:44 final size:44
Alignment explanation
Indices: 1353--1436 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
1343 CTTTAGTTTT
* **
1353 CAAAATTTCATAAGATGGTTATCAAAATTTCATAGGGAGACTAA
1 CAAAATTTCATAAGATGGTTATAAAAAAATCATAGGGAGACTAA
1397 CAAAATTTCATAATGA-GGTTATAAAAAAATCATAGGGAGA
1 CAAAATTTCATAA-GATGGTTATAAAAAAATCATAGGGAGA
1437 TTATTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 34 0.94
45 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (44 bp):
CAAAATTTCATAAGATGGTTATAAAAAAATCATAGGGAGACTAA
Found at i:1481 original size:22 final size:22
Alignment explanation
Indices: 1451--1492 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1441 TAAAATTTGT
* *
1451 AGTTTTCAAGATTTAATAAGAA
1 AGTTATCAAAATTTAATAAGAA
*
1473 AGTTATCAAAATTTTATAAG
1 AGTTATCAAAATTTAATAAG
1493 GAGGTTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (22 bp):
AGTTATCAAAATTTAATAAGAA
Found at i:1501 original size:23 final size:23
Alignment explanation
Indices: 1475--1556 Score: 78
Period size: 25 Copynumber: 3.5 Consensus size: 23
1465 AATAAGAAAG
1475 TTATCAAAATTTTATAAGGAGGTT
1 TTATCAAAATTTTATAAGGAGG-T
*
1499 TATATCAAAATTTTAT-AGGAAGAT
1 T-TATCAAAATTTTATAAGG-AGGT
* * *
1523 TTATTAAAATTTCATAACGAGG-
1 TTATCAAAATTTTATAAGGAGGT
*
1545 TTATCACAATTT
1 TTATCAAAATTT
1557 CATGGTGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
22 10 0.21
23 14 0.29
24 8 0.17
25 16 0.33
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGGAGGT
Found at i:1508 original size:25 final size:25
Alignment explanation
Indices: 1476--1546 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
1466 ATAAGAAAGT
1476 TATCAAAATTTTATAAGGAGGTTTA
1 TATCAAAATTTTATAAGGAGGTTTA
*
1501 TATCAAAATTTTAT-AGGAAGATTTA
1 TATCAAAATTTTATAAGG-AGGTTTA
* *
1526 T-T-AAAATTTCATAACGAGGTT
1 TATCAAAATTTTATAAGGAGGTT
1547 ATCACAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 13 0.32
24 6 0.15
25 21 0.52
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (25 bp):
TATCAAAATTTTATAAGGAGGTTTA
Found at i:1791 original size:49 final size:49
Alignment explanation
Indices: 1719--1816 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
1709 CTCGTCTTTG
1719 TCCTCACTTTGATTACTTGATGAATCAGGTCATGAAGGTTTTCAAGATT
1 TCCTCACTTTGATTACTTGATGAATCAGGTCATGAAGGTTTTCAAGATT
* *
1768 TCCTCATTTTGATTACTTGATGAATCAGGTCATGGAGGTTTTCAAGATT
1 TCCTCACTTTGATTACTTGATGAATCAGGTCATGAAGGTTTTCAAGATT
1817 AAGGTAGAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (49 bp):
TCCTCACTTTGATTACTTGATGAATCAGGTCATGAAGGTTTTCAAGATT
Found at i:1954 original size:3 final size:3
Alignment explanation
Indices: 1948--1992 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1938 ATTGTGTTTT
*
1948 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1993 CTTTCATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2033 original size:16 final size:16
Alignment explanation
Indices: 2012--2043 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2002 ACGAACTACA
2012 TTTTTATTCACTTGTT
1 TTTTTATTCACTTGTT
*
2028 TTTTTATTGACTTGTT
1 TTTTTATTCACTTGTT
2044 ATAGGTTACA
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:0.12, C:0.09, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTTTATTCACTTGTT
Found at i:2315 original size:59 final size:59
Alignment explanation
Indices: 2238--2408 Score: 306
Period size: 59 Copynumber: 2.9 Consensus size: 59
2228 TCTTGGATCC
2238 CGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTAATTGATTTGAATCA
1 CGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTAATTGATTTGAATCA
* *
2297 CGCTATAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTAATTGATTTGAATCC
1 CGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTAATTGATTTGAATCA
* *
2356 CGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATGCTTGATTGATTT
1 CGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTAATTGATTT
2409 CATCAGTGTA
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 107 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (59 bp):
CGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTAATTGATTTGAATCA
Found at i:3881 original size:20 final size:21
Alignment explanation
Indices: 3853--3902 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
3843 AAATTAAAAT
* *
3853 AAATCAATAAAAGAGATATTA
1 AAATAAATAAAAGAGATATCA
3874 AAATAATAGTAAAAGAGATATCA
1 AAATAA-A-TAAAAGAGATATCA
*
3897 GAATAA
1 AAATAA
3903 CAAAAGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 1 0.04
23 18 0.75
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (21 bp):
AAATAAATAAAAGAGATATCA
Found at i:3890 original size:23 final size:25
Alignment explanation
Indices: 3845--3894 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
3835 GAGATATTAA
3845 ATTAAAATAAATCAATAAAAGAGAT
1 ATTAAAATAAATCAATAAAAGAGAT
*
3870 ATTAAAAT-AAT-AGTAAAAGAGAT
1 ATTAAAATAAATCAATAAAAGAGAT
3893 AT
1 AT
3895 CAGAATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 13 0.54
24 3 0.12
25 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (25 bp):
ATTAAAATAAATCAATAAAAGAGAT
Found at i:4370 original size:21 final size:21
Alignment explanation
Indices: 4345--4387 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4335 GCTGAGAAAT
4345 ATAATAGAAATTTAAATAAAA
1 ATAATAGAAATTTAAATAAAA
4366 ATAATAGAAATTTAAATAAAA
1 ATAATAGAAATTTAAATAAAA
4387 A
1 A
4388 AGAGATACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
ATAATAGAAATTTAAATAAAA
Found at i:5422 original size:16 final size:15
Alignment explanation
Indices: 5401--5431 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5391 CAACCGGCTT
5401 GAGCCGAGCCGCGTTC
1 GAGCCGAGCCG-GTTC
5417 GAGCCGAGCCGGTTC
1 GAGCCGAGCCGGTTC
5432 AAAAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.13, C:0.35, G:0.39, T:0.13
Consensus pattern (15 bp):
GAGCCGAGCCGGTTC
Found at i:6408 original size:15 final size:15
Alignment explanation
Indices: 6388--6421 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6378 ATTGGATTTA
6388 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
6403 TTATTATAACTTGTT
1 TTATTATAACTTGTT
6418 TTAT
1 TTAT
6422 GAACTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:7278 original size:24 final size:24
Alignment explanation
Indices: 7246--7294 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
7236 AATCCATAGA
7246 AACTAAATCTAAGAGTCTATCATT
1 AACTAAATCTAAGAGTCTATCATT
7270 AACTAAATCTAAGAGTCTATCATT
1 AACTAAATCTAAGAGTCTATCATT
7294 A
1 A
7295 GACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (24 bp):
AACTAAATCTAAGAGTCTATCATT
Found at i:8073 original size:29 final size:28
Alignment explanation
Indices: 8031--8120 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 28
8021 AGGACACAAT
* * *
8031 TAAACTTTTAAATTAAGAAAAAATTTAGA
1 TAAAATTTAAAATTAAG-AAAAATTTTGA
*
8060 TAAAATTTAAAATTAAGAAAATTTTTGA
1 TAAAATTTAAAATTAAGAAAAATTTTGA
* *
8088 TAAAATTTAAAATCAATAAAAATTTTGA
1 TAAAATTTAAAATTAAGAAAAATTTTGA
8116 TAAAA
1 TAAAA
8121 AACAAAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 39 0.72
29 15 0.28
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (28 bp):
TAAAATTTAAAATTAAGAAAAATTTTGA
Found at i:8489 original size:28 final size:28
Alignment explanation
Indices: 8449--8549 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 28
8439 TTAATGTCTT
*
8449 AAAAGAGAGAAGGGCATCGTTGTCAAAA
1 AAAAGAGAGAAGGGTATCGTTGTCAAAA
* * *
8477 AAAAGAGGGAAGGGTATCGTTCTAAAAA
1 AAAAGAGAGAAGGGTATCGTTGTCAAAA
* * *
8505 AAAAAAGAGAATGGTATCATTGTCAGAAA
1 AAAAGAGAGAAGGGTATCGTTGTCA-AAA
* *
8534 AAAAAAGAAAAGGGTA
1 AAAAGAGAGAAGGGTA
8550 GTGTAAGTCA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 43 0.72
29 17 0.28
ACGTcount: A:0.51, C:0.07, G:0.26, T:0.16
Consensus pattern (28 bp):
AAAAGAGAGAAGGGTATCGTTGTCAAAA
Found at i:9531 original size:21 final size:21
Alignment explanation
Indices: 9506--9549 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
9496 GCTAAGAAAT
9506 ATAATAGAAATTTAAATAAAA
1 ATAATAGAAATTTAAATAAAA
9527 ATAATAGAAATTTAAATAAAA
1 ATAATAGAAATTTAAATAAAA
9548 AT
1 AT
9550 GAGTTACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAATAGAAATTTAAATAAAA
Found at i:9899 original size:24 final size:24
Alignment explanation
Indices: 9860--9908 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
9850 AATCCATAGA
*
9860 AACTAAATCTATGAGTCTATCATT
1 AACTAAATCTAAGAGTCTATCATT
*
9884 AACTAAATTTAAGAGTCTATCATT
1 AACTAAATCTAAGAGTCTATCATT
9908 A
1 A
9909 GACATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (24 bp):
AACTAAATCTAAGAGTCTATCATT
Found at i:10693 original size:29 final size:28
Alignment explanation
Indices: 10651--10740 Score: 126
Period size: 28 Copynumber: 3.2 Consensus size: 28
10641 AGGACACAAT
* * *
10651 TAAACTTTTAAATTAAGAAAAAATTTAGA
1 TAAAATTTAAAATTAAG-AAAAATTTTGA
10680 TAAAATTTAAAATTAAGAAAAATTTTGA
1 TAAAATTTAAAATTAAGAAAAATTTTGA
* *
10708 TAAAATTTAAAATCAATAAAAATTTTGA
1 TAAAATTTAAAATTAAGAAAAATTTTGA
10736 TAAAA
1 TAAAA
10741 AAACAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 41 0.73
29 15 0.27
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (28 bp):
TAAAATTTAAAATTAAGAAAAATTTTGA
Found at i:10703 original size:17 final size:18
Alignment explanation
Indices: 10670--10704 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10660 AAATTAAGAA
*
10670 AAAATTTAGATAAAATTT
1 AAAATTAAGATAAAATTT
10688 AAAATTAAGA-AAAATTT
1 AAAATTAAGATAAAATTT
10705 TGATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
AAAATTAAGATAAAATTT
Found at i:11125 original size:30 final size:31
Alignment explanation
Indices: 11089--11149 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
11079 ATGTCTTAAA
* *
11089 AGAGAGAAGGGCATCGTTGTCA-AAAAAAAG
1 AGAGAGAACGGCATCATTGTCAGAAAAAAAG
*
11119 AGAGAGAACGGTATCATTGTCAGGAAAAAAA
1 AGAGAGAACGGCATCATTGTCA-GAAAAAAA
11150 AAGAAAAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.73
32 7 0.27
ACGTcount: A:0.48, C:0.10, G:0.28, T:0.15
Consensus pattern (31 bp):
AGAGAGAACGGCATCATTGTCAGAAAAAAAG
Found at i:11664 original size:23 final size:25
Alignment explanation
Indices: 11619--11670 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
11609 GAGATATTAA
11619 ATTAAAATAAATCAATAAAAGAGAT
1 ATTAAAATAAATCAATAAAAGAGAT
*
11644 ATTAAAAT-AAT-AGTAAAAGAGAT
1 ATTAAAATAAATCAATAAAAGAGAT
11667 ATTA
1 ATTA
11671 GAAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.58
24 3 0.12
25 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.27
Consensus pattern (25 bp):
ATTAAAATAAATCAATAAAAGAGAT
Found at i:12145 original size:21 final size:21
Alignment explanation
Indices: 12119--12162 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12109 GCTAAGAAAT
12119 ATAATAGAAATTTAAATAAAA
1 ATAATAGAAATTTAAATAAAA
*
12140 ATAATAGAAATTTAAATATAA
1 ATAATAGAAATTTAAATAAAA
12161 AT
1 AT
12163 GAGATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
ATAATAGAAATTTAAATAAAA
Found at i:12519 original size:24 final size:24
Alignment explanation
Indices: 12487--12535 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12477 AATCCATAGA
12487 AACTAAATCTAAGAGTCTATCATT
1 AACTAAATCTAAGAGTCTATCATT
12511 AACTAAATCTAAGAGTCTATCATT
1 AACTAAATCTAAGAGTCTATCATT
12535 A
1 A
12536 GACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (24 bp):
AACTAAATCTAAGAGTCTATCATT
Found at i:14672 original size:28 final size:27
Alignment explanation
Indices: 14640--14701 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
14630 CAATTAAACT
14640 TTTAAACTAAGAAAAAAATTAGATAAAA
1 TTTAAACTAAG-AAAAAATTAGATAAAA
* * *
14668 TTTAAAATTAAGAAAAATTTTGATAAAA
1 TTT-AAACTAAGAAAAAATTAGATAAAA
14696 TTTAAA
1 TTTAAA
14702 ATCAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 3 0.10
28 20 0.67
29 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (27 bp):
TTTAAACTAAGAAAAAATTAGATAAAA
Found at i:14676 original size:17 final size:17
Alignment explanation
Indices: 14654--14687 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
14644 AACTAAGAAA
14654 AAAATT-AGATAAAATTT
1 AAAATTAAGA-AAAATTT
14671 AAAATTAAGAAAAATTT
1 AAAATTAAGAAAAATTT
14688 TGATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAATTAAGAAAAATTT
Found at i:14702 original size:28 final size:28
Alignment explanation
Indices: 14647--14723 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
14637 ACTTTTAAAC
* *
14647 TAAGAAAAAAATTAGATAAAATTTAAAAT
1 TAAG-AAAAATTTTGATAAAATTTAAAAT
14676 TAAGAAAAATTTTGATAAAATTTAAAAT
1 TAAGAAAAATTTTGATAAAATTTAAAAT
* *
14704 CAATAAAAATTTTGATAAAA
1 TAAGAAAAATTTTGATAAAA
14724 ACAAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 40 0.91
29 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (28 bp):
TAAGAAAAATTTTGATAAAATTTAAAAT
Found at i:14730 original size:28 final size:28
Alignment explanation
Indices: 14671--14730 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
14661 GATAAAATTT
* ***
14671 AAAATTAAGAAAAATTTTGATAAAATTT
1 AAAATCAAGAAAAATTTTGATAAAAACA
*
14699 AAAATCAATAAAAATTTTGATAAAAACA
1 AAAATCAAGAAAAATTTTGATAAAAACA
14727 AAAA
1 AAAA
14731 AAAAACTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAATCAAGAAAAATTTTGATAAAAACA
Found at i:15099 original size:27 final size:27
Alignment explanation
Indices: 15069--15127 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
15059 TTAATGTCTT
*
15069 AAAAGAGAGAAGGGCATCGTTGTCAAA
1 AAAAAAGAGAAGGGCATCGTTGTCAAA
*
15096 AAAAAAGAGAAGGGTATCGTTGTCAAA
1 AAAAAAGAGAAGGGCATCGTTGTCAAA
15123 AAAAA
1 AAAAA
15128 TAAAAGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.25, T:0.15
Consensus pattern (27 bp):
AAAAAAGAGAAGGGCATCGTTGTCAAA
Found at i:15147 original size:35 final size:34
Alignment explanation
Indices: 15093--15167 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 34
15083 CATCGTTGTC
*
15093 AAAAAAA-A-AGAGAAGGGTATCGTTGTCAAAAA
1 AAAAAAAGAGAGAGAACGGTATCGTTGTCAAAAA
*
15125 AAATAAAAGAGAGAGAACGGTATCGTTGTCAGAAA
1 AAA-AAAAGAGAGAGAACGGTATCGTTGTCAAAAA
15160 AAAAAAAG
1 AAAAAAAG
15168 GTGGTGTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 3 0.08
33 4 0.11
34 6 0.16
35 25 0.66
ACGTcount: A:0.56, C:0.07, G:0.23, T:0.15
Consensus pattern (34 bp):
AAAAAAAGAGAGAGAACGGTATCGTTGTCAAAAA
Found at i:15307 original size:44 final size:46
Alignment explanation
Indices: 15231--15321 Score: 150
Period size: 44 Copynumber: 2.0 Consensus size: 46
15221 GATAATTATA
15231 TTTTTGTTGGTTTTTTTTTTTTGAGTGAGTACATATGAAATCTCATT
1 TTTTTGTTGG-TTTTTTTTTTTGAGTGAGTACATATGAAATCTCATT
*
15278 TTTTTGTTGG-TTTTTTTTTT-AGTGAGTACATGTGAAATCTCATT
1 TTTTTGTTGGTTTTTTTTTTTGAGTGAGTACATATGAAATCTCATT
15322 ACAATCAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
44 23 0.53
45 10 0.23
47 10 0.23
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.57
Consensus pattern (46 bp):
TTTTTGTTGGTTTTTTTTTTTGAGTGAGTACATATGAAATCTCATT
Found at i:15634 original size:25 final size:26
Alignment explanation
Indices: 15585--15634 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
15575 ACATTAAAAA
* *
15585 AAGTCTAATTGTCCAAGTACCGTAAG
1 AAGTCTAACTGTCCAAGTACAGTAAG
*
15611 AAGTCTAACT-TCTAAGTACAGTAA
1 AAGTCTAACTGTCCAAGTACAGTAA
15635 AAATCTATGG
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:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (26 bp):
AAGTCTAACTGTCCAAGTACAGTAAG
Found at i:18248 original size:902 final size:900
Alignment explanation
Indices: 16507--18769 Score: 4323
Period size: 902 Copynumber: 2.5 Consensus size: 900
16497 GAATCACCCA
* * * *
16507 ATTCTTGGAGGTTAAGTTTATGCTAGTATAAATAGAGAGTTTCTTTATAGAATTTTATATGCTCG
1 ATTCTTGGAGGTTAAGTTTATGCTAGTATACATAGAGAGTTTCTCTATAGAATTTTGTATGCTTG
* * *
16572 GAGAAAAGATGTAGTCTCAGGGTTGGATTTAGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
66 GAGAAAAGATGTACTCTCAGGGTTAGATTTGGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
16637 TCATGGGTGTGTGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAGAG
131 TCATGGGTGTGTGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAGAG
*
16702 ACCGAGCGAGAGTGCTAAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGATTGGGTTGAGT
196 ACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGATTGGGTTGAGT
*
16767 GATTGAGTGACAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTT
261 GATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTT
16832 CTCCTCCGTGGATGTAGGCAAGATCAGTGACGAACCACGTAAATTCTTTTGTCTTGTTTGGATGA
326 CTCCTCCGTGGATGTAGGCAAGATCAGTGACGAACCACGTAAATTCTTTTGTCTTGTTTGGATGA
16897 TTTATTATTTTAGTTGCTTCCGCTTGCATGATTAATTTGATAGATCATAGTTTAGGATATCCGGG
391 TTTATTATTTTAGTTGCTTCCGCTTGCATGATTAATTTGATAGATCATAGTTTAGGATATCCGGG
16962 TTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCGGTAGCCCAAACTTGA
456 TTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCGGTAGCCCAAACTTGA
*
17027 GTTATGGTTCGTCAGGTTTGGTTGTCGTGGAGATTGCCAAATTTTGCTGCTTGATGATTGTTTTG
521 GATATGGTTCGTCAGGTTTGGTTGTCGTGGAGATTGCCAAATTTTGCTGCTTGATGATTGTTTTG
17092 AAGATTGAAGTTGATTTTTCAAATCAGATTTAGATGAAAAGTAAGATCGGATTCGAAATTAAAGT
586 AAGATTGAAGTTGATTTTTCAAATCAGATTTAGATGAAAAGTAAGATCGGATTCGAAATTAAAGT
*
17157 TGAAGATGATGCAGTGAAGATGAAGACACATAAGAGAAGATTGCTTGAAGATTGGGAGACTTTCG
651 TGAAGATGATGCAGTGAAGATGAAGACACATAAGAGAAGATTGCTTGAAGATTGGGAGACTTTCA
17222 TTGCAGGTGGAACCATGCACGTCCTTGAAGATTGATTGAAGATTGAAGATTTGGTGGAATTTGAG
716 TTGCAGGTGGAACCATGCACGTCCTTGAAGATTGATTGAAGATTGAAGATTTGGTGGAATTTGAG
17287 TCAAGGTGGAGATTGTTAGGATCTTGCCTCAAATCCCAAATAGATTTGGATTGAGATTTTTCAAG
781 TCAAGGTGGAGATTGTTAGGATCTTGCCTCAAATCCCAAATAGATTTGGATTGAGATTTTTCAAG
17352 CCTATTGCTTGGTGGACAAAAAGACTTGGTAAACAAGAATCCTAGTAGGAAAGTG
846 CCTATTGCTTGGTGGACAAAAAGACTTGGTAAACAAGAATCCTAGTAGGAAAGTG
*
17407 ATTCTTGGAGGTTAAGTTTATGTTAGTATACATAGAGAGTTTCTCTATAGAATTTTGTATGCTTG
1 ATTCTTGGAGGTTAAGTTTATGCTAGTATACATAGAGAGTTTCTCTATAGAATTTTGTATGCTTG
17472 GAGAAAAGATGTACTCTCAGGGTTAGATTTGGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
66 GAGAAAAGATGTACTCTCAGGGTTAGATTTGGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
17537 TCATGGGTGTGTGTGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAG
131 TCAT-GG-GTGTGTGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAG
*
17602 AGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTTGTTTAGGATTGATTGTTAGATTGGGTTGA
194 AGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGATTGGGTTGA
17667 GTGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTC
259 GTGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTC
17732 TTCTCCTCCGTGGATGTAGGCAAGATCAGTGACGAACCACGTAAATTCTTTTGTCTTGTTTGGAT
324 TTCTCCTCCGTGGATGTAGGCAAGATCAGTGACGAACCACGTAAATTCTTTTGTCTTGTTTGGAT
17797 GATTTATTATTTTAGTTGCTTCCGCTTGCATGATTAATTTGATAGATCATAGTTTAGGATATCCG
389 GATTTATTATTTTAGTTGCTTCCGCTTGCATGATTAATTTGATAGATCATAGTTTAGGATATCCG
17862 GGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCGGTAGCCCAAACTT
454 GGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCGGTAGCCCAAACTT
17927 GAGATATGGTTCGTCAGGTTTGGTTGTCGTGGAGATTGCCAAATTTTGCTGCTTGATGATTGTTT
519 GAGATATGGTTCGTCAGGTTTGGTTGTCGTGGAGATTGCCAAATTTTGCTGCTTGATGATTGTTT
*
17992 TGAAGATTGAAGTTGATTTTTCAAATCAGATTTGGATGAAAAGTAAGATCGGATTCGAAATTAAA
584 TGAAGATTGAAGTTGATTTTTCAAATCAGATTTAGATGAAAAGTAAGATCGGATTCGAAATTAAA
18057 GTTGAAGATGATGCAGTGAAGATGAAGACACATAAGAGAAGATTGCTTGAAGATTGGGAGACTTT
649 GTTGAAGATGATGCAGTGAAGATGAAGACACATAAGAGAAGATTGCTTGAAGATTGGGAGACTTT
18122 CATTGCAGGTGGAACCATGCACGTCCTTGAAGATTGATTGAAGATTGAAGATTTGGTGGAATTTG
714 CATTGCAGGTGGAACCATGCACGTCCTTGAAGATTGATTGAAGATTGAAGATTTGGTGGAATTTG
18187 AGTCAAGGTGGAGATTGTTAGGATCTTGCCTCAAATCCCAAATAGATTTGGATTGAGATTTTTCA
779 AGTCAAGGTGGAGATTGTTAGGATCTTGCCTCAAATCCCAAATAGATTTGGATTGAGATTTTTCA
18252 AGCCTATTGCTTGGTGGACAAAAAGACTTGGTAAACAAGAATCCTAGTAGGAAAGTG
844 AGCCTATTGCTTGGTGGACAAAAAGACTTGGTAAACAAGAATCCTAGTAGGAAAGTG
18309 ATTCTTGGAGGTTAAGTTTATGCTAGTATACATAGAGAGTTTCTCTATAGAATTTTGTATGCTTG
1 ATTCTTGGAGGTTAAGTTTATGCTAGTATACATAGAGAGTTTCTCTATAGAATTTTGTATGCTTG
18374 GAGAAAAGATGTACTCTCAGGGTTAGATTTGGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
66 GAGAAAAGATGTACTCTCAGGGTTAGATTTGGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
18439 TCATGGGT-T-TGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAGAG
131 TCATGGGTGTGTGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAGAG
*
18502 ACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGATTGGGTTGAGA
196 ACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGATTGGGTTGAGT
18567 GATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTT
261 GATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTT
*
18632 CTCCTCCGTGGATGTAGGCAAGATCAGTGCCGAACCACGTAAATTCTTTTGTCTTGTTTGGATGA
326 CTCCTCCGTGGATGTAGGCAAGATCAGTGACGAACCACGTAAATTCTTTTGTCTTGTTTGGATGA
* * *
18697 TTTATTATTTTAGTTGTTTCCGCTTACATGATTAATTTGATAGATCATAGTTTGGGATATCCGGG
391 TTTATTATTTTAGTTGCTTCCGCTTGCATGATTAATTTGATAGATCATAGTTTAGGATATCCGGG
18762 TTACAACA
456 TTACAACA
18770 GCTTCCCCCT
Statistics
Matches: 1340, Mismatches: 21, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
898 316 0.24
899 1 0.00
900 128 0.10
901 4 0.00
902 891 0.66
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (900 bp):
ATTCTTGGAGGTTAAGTTTATGCTAGTATACATAGAGAGTTTCTCTATAGAATTTTGTATGCTTG
GAGAAAAGATGTACTCTCAGGGTTAGATTTGGGTGGAGGCACCCCATAGGACAAAAGGGTGGTCC
TCATGGGTGTGTGTGTGTGATTGTTTAGTTTGGTGTTTGGTGATGTGCTTGTTAGTTTGTTAGAG
ACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGATTGGGTTGAGT
GATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTT
CTCCTCCGTGGATGTAGGCAAGATCAGTGACGAACCACGTAAATTCTTTTGTCTTGTTTGGATGA
TTTATTATTTTAGTTGCTTCCGCTTGCATGATTAATTTGATAGATCATAGTTTAGGATATCCGGG
TTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCGGTAGCCCAAACTTGA
GATATGGTTCGTCAGGTTTGGTTGTCGTGGAGATTGCCAAATTTTGCTGCTTGATGATTGTTTTG
AAGATTGAAGTTGATTTTTCAAATCAGATTTAGATGAAAAGTAAGATCGGATTCGAAATTAAAGT
TGAAGATGATGCAGTGAAGATGAAGACACATAAGAGAAGATTGCTTGAAGATTGGGAGACTTTCA
TTGCAGGTGGAACCATGCACGTCCTTGAAGATTGATTGAAGATTGAAGATTTGGTGGAATTTGAG
TCAAGGTGGAGATTGTTAGGATCTTGCCTCAAATCCCAAATAGATTTGGATTGAGATTTTTCAAG
CCTATTGCTTGGTGGACAAAAAGACTTGGTAAACAAGAATCCTAGTAGGAAAGTG
Found at i:18488 original size:28 final size:25
Alignment explanation
Indices: 18445--18495 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
18435 GTCCTCATGG
18445 GTTTGTGTGTGATTGTTTAGTTTGGT
1 GTTTGTGTGTGATTG-TTAGTTTGGT
*
18471 GTTTGGTGATGTGCTTGTTAGTTTG
1 GTTT-GTG-TGTGATTGTTAGTTTG
18496 TTAGAGACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.08, C:0.02, G:0.35, T:0.55
Consensus pattern (25 bp):
GTTTGTGTGTGATTGTTAGTTTGGT
Found at i:20470 original size:31 final size:31
Alignment explanation
Indices: 20402--20543 Score: 133
Period size: 31 Copynumber: 4.5 Consensus size: 31
20392 GCGGCGTCCG
* * * **
20402 ACGTGGCATGCCACGTGCCATTTTTTGAAAC
1 ACGTGGCGTGCCACGTGTCACTTTTTGGTAC
* * *
20433 ATGTGGCATGCCATGTGTCACTTTTTGGTAC
1 ACGTGGCGTGCCACGTGTCACTTTTTGGTAC
* * *
20464 ACGTGGCGTGACATGTGGCAGGAC-TTTTGGTAC
1 ACGTGGCGTGCCACGTGTC---ACTTTTTGGTAC
* *
20497 ATGTGGCGTGCCACATGTCACTTTTTGGTAC
1 ACGTGGCGTGCCACGTGTCACTTTTTGGTAC
20528 ACGTGGCGTGCCACGT
1 ACGTGGCGTGCCACGT
20544 CGGACACCGT
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.02
31 63 0.70
33 23 0.26
34 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.31
Consensus pattern (31 bp):
ACGTGGCGTGCCACGTGTCACTTTTTGGTAC
Found at i:20987 original size:26 final size:25
Alignment explanation
Indices: 20936--20991 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
20926 AATATACCCC
20936 AAAAAAAAAACAAATACAAGCCAAAA
1 AAAAAAAAAACAAATACAAG-CAAAA
* * **
20962 AAAATAAAAACAAATTCTGGCAAAA
1 AAAAAAAAAACAAATACAAGCAAAA
20987 AAAAA
1 AAAAA
20992 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.73, C:0.12, G:0.05, T:0.09
Consensus pattern (25 bp):
AAAAAAAAAACAAATACAAGCAAAA
Found at i:35340 original size:17 final size:17
Alignment explanation
Indices: 35312--35368 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
35302 GTGGTTTTTT
35312 TTTTATTA-TTTTAATA
1 TTTTATTATTTTTAATA
*
35328 TTTTATTATTTTTAACA
1 TTTTATTATTTTTAATA
35345 TTTTATTATTTTTTAATA
1 TTTTATTA-TTTTTAATA
35363 TTTTAT
1 TTTTAT
35369 AAATTTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.22
17 15 0.41
18 14 0.38
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTATTTTTAATA
Found at i:40430 original size:30 final size:30
Alignment explanation
Indices: 40391--40469 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
40381 TTTCTCTATG
* *
40391 TCAATAGCATCTGATCCATGACCCTCAACA
1 TCAACAGCATCAGATCCATGACCCTCAACA
* * **
40421 TCAACAGCATCAGATCCATTACCTTCAATG
1 TCAACAGCATCAGATCCATGACCCTCAACA
*
40451 TCAACTGCATCAGATCCAT
1 TCAACAGCATCAGATCCAT
40470 CACCATCTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.33, C:0.32, G:0.10, T:0.25
Consensus pattern (30 bp):
TCAACAGCATCAGATCCATGACCCTCAACA
Found at i:40734 original size:12 final size:13
Alignment explanation
Indices: 40719--40779 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
40709 CTGTGGCTTC
40719 CACTGTCACTTG-
1 CACTGTCACTTGT
*
40731 CACTATCACTACTGT
1 CACTGTCACT--TGT
40746 CACTGTCAC-TGT
1 CACTGTCACTTGT
* *
40758 CACTATCAC-TGC
1 CACTGTCACTTGT
40770 CACTGTCACT
1 CACTGTCACT
40780 GGCACTATGC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 30 0.75
14 2 0.05
15 8 0.20
ACGTcount: A:0.21, C:0.36, G:0.11, T:0.31
Consensus pattern (13 bp):
CACTGTCACTTGT
Found at i:40745 original size:21 final size:21
Alignment explanation
Indices: 40720--40762 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40710 TGTGGCTTCC
40720 ACTGTCACT-TGCACTATCACT
1 ACTGTCACTGT-CACTATCACT
*
40741 ACTGTCACTGTCACTGTCACT
1 ACTGTCACTGTCACTATCACT
40762 A
1 A
40763 TCACTGCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.33, G:0.12, T:0.33
Consensus pattern (21 bp):
ACTGTCACTGTCACTATCACT
Found at i:40773 original size:6 final size:6
Alignment explanation
Indices: 40741--40785 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
40731 CACTATCACT
* * *
40741 ACTGTC ACTGTC ACTGTC ACTATC ACTGCC ACTGTC ACTGGC ACT
1 ACTGTC ACTGTC ACTGTC ACTGTC ACTGTC ACTGTC ACTGTC ACT
40786 ATGCGCCTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.36, G:0.16, T:0.29
Consensus pattern (6 bp):
ACTGTC
Found at i:41675 original size:2 final size:2
Alignment explanation
Indices: 41668--41705 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
41658 CTTAGTCTTA
* *
41668 CT CT CT CT CT CT CT CT CT CT CT GT GT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41706 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
CT
Found at i:45170 original size:20 final size:22
Alignment explanation
Indices: 45145--45185 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
45135 TTTTTAAAAA
45145 TATATA-C-ATACAATTTGAAG
1 TATATAGCAATACAATTTGAAG
45165 TATATAGCAATACAATTTGAA
1 TATATAGCAATACAATTTGAA
45186 TAAGATAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (22 bp):
TATATAGCAATACAATTTGAAG
Found at i:53384 original size:1 final size:1
Alignment explanation
Indices: 53378--53414 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
53368 TGTGTTGTAG
**
53378 TTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53415 ATGAATTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:61829 original size:42 final size:42
Alignment explanation
Indices: 61770--61850 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
61760 AGAATACCGT
**
61770 TAACGTGTTGTATTTTGATGACGATTTAAGAAAAATGAACGA
1 TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAACGA
*
61812 TAACGTGCCGTATTTTGATGACGATTTCAGAAAAATGAA
1 TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAA
61851 ATTTTTGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (42 bp):
TAACGTGCCGTATTTTGATGACGATTTAAGAAAAATGAACGA
Found at i:63008 original size:44 final size:44
Alignment explanation
Indices: 62945--63040 Score: 183
Period size: 44 Copynumber: 2.2 Consensus size: 44
62935 AGTTTAAGTG
62945 TTTAACCTCAAAAGCAGCTTCAATTTGCGGTAAAAGTAAATGAC
1 TTTAACCTCAAAAGCAGCTTCAATTTGCGGTAAAAGTAAATGAC
62989 TTTAACCTCAAAAGCAGCTTCAATTTGCGGTAAAAGTAAATGAC
1 TTTAACCTCAAAAGCAGCTTCAATTTGCGGTAAAAGTAAATGAC
*
63033 TTTTACCT
1 TTTAACCT
63041 TGTCATGTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (44 bp):
TTTAACCTCAAAAGCAGCTTCAATTTGCGGTAAAAGTAAATGAC
Found at i:63912 original size:16 final size:16
Alignment explanation
Indices: 63882--63912 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63872 GGGTATCATG
*
63882 GTCAAAATAGAAAAAT
1 GTCAAAATAAAAAAAT
63898 GTCAAAATAAAAAAA
1 GTCAAAATAAAAAAA
63913 CATGAATTTT
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:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (16 bp):
GTCAAAATAAAAAAAT
Found at i:76621 original size:9 final size:10
Alignment explanation
Indices: 76591--76620 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
76581 AAATGTTTGA
76591 TCTTTTTTTT
1 TCTTTTTTTT
76601 TCTTTTTTTT
1 TCTTTTTTTT
76611 TCTTTTTTTT
1 TCTTTTTTTT
76621 CCGGTTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:77959 original size:74 final size:74
Alignment explanation
Indices: 77837--77988 Score: 243
Period size: 74 Copynumber: 2.1 Consensus size: 74
77827 ATTAAGGAAT
* * * * *
77837 GTGTAATTACGAAAAATGGTAGAAGGAAAAGGAATGGGGGAAATTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
77902 ATCC-GAAAA
66 A-CCTGAAAA
77911 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
77976 ACCTGAAAA
66 ACCTGAAAA
77985 GTGT
1 GTGT
77989 GAAAAGACCA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 2 0.03
74 70 0.97
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (74 bp):
GTGTAATTACAAAAAAGGGTAGAAGGAAAAGAAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
ACCTGAAAA
Found at i:82563 original size:31 final size:29
Alignment explanation
Indices: 82520--82597 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
82510 TCGGACAGAG
* * *
82520 TTTTGGACGTTTTACCTCATGAACTTATACA
1 TTTTAGACGTTTTACCCCACGAACTT-TA-A
*
82551 TTTTAGACGTTTTACCCCCCGAACTTTAA
1 TTTTAGACGTTTTACCCCACGAACTTTAA
* *
82580 TTTTAGACATTTTGCCCC
1 TTTTAGACGTTTTACCCC
82598 CTAATTAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 17 0.41
30 2 0.05
31 22 0.54
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (29 bp):
TTTTAGACGTTTTACCCCACGAACTTTAA
Found at i:82592 original size:29 final size:31
Alignment explanation
Indices: 82540--82598 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
82530 TTTACCTCAT
*
82540 GAACTTATACATTTTAGACGTTTTACCCCCC
1 GAACTTATACATTTTAGACATTTTACCCCCC
*
82571 GAACTT-TA-ATTTTAGACATTTTGCCCCC
1 GAACTTATACATTTTAGACATTTTACCCCC
82599 TAATTAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
30 2 0.08
31 6 0.23
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.37
Consensus pattern (31 bp):
GAACTTATACATTTTAGACATTTTACCCCCC
Found at i:82718 original size:28 final size:30
Alignment explanation
Indices: 82667--82727 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
82657 AATGGAGGCT
* * * *
82667 AAAATTGAAAGTTTAGGAGGC-AAATGTCC
1 AAAATTGAAAGTTCAAGAGACAAAACGTCC
82696 AAAATTG-AAGTTCAAGAGACAAAACGTCC
1 AAAATTGAAAGTTCAAGAGACAAAACGTCC
82725 AAA
1 AAA
82728 CGCTACAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.20
Consensus pattern (30 bp):
AAAATTGAAAGTTCAAGAGACAAAACGTCC
Found at i:89623 original size:12 final size:12
Alignment explanation
Indices: 89608--89637 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
89598 TTAATTCAGC
89608 ATTAAATTACTA
1 ATTAAATTACTA
89620 ATTAAATTACTA
1 ATTAAATTACTA
89632 ATTAAA
1 ATTAAA
89638 GTCCAAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAATTACTA
Found at i:94526 original size:23 final size:23
Alignment explanation
Indices: 94496--94540 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
94486 CGATCTCAAC
94496 CTGGAGATTTGCATTTTCGTTTT
1 CTGGAGATTTGCATTTTCGTTTT
94519 CTGGAGATTTGCATTTTCGTTT
1 CTGGAGATTTGCATTTTCGTTT
94541 GATGTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.51
Consensus pattern (23 bp):
CTGGAGATTTGCATTTTCGTTTT
Found at i:95318 original size:28 final size:29
Alignment explanation
Indices: 95287--95341 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
95277 TAATAAAAGT
95287 TAAAGT-TAAAGAAATAAA-TTTGAGGAAC
1 TAAAGTGTAAA-AAATAAAGTTTGAGGAAC
* *
95315 TAAATTGTATAAAATAAAGTTTGAGGA
1 TAAAGTGTAAAAAATAAAGTTTGAGGA
95342 TTAAATTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.18, T:0.29
Consensus pattern (29 bp):
TAAAGTGTAAAAAATAAAGTTTGAGGAAC
Found at i:95346 original size:28 final size:28
Alignment explanation
Indices: 95298--95356 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
95288 AAAGTTAAAG
*
95298 AAATAAATTTGAGGAACTAAATTGTATA
1 AAATAAATTTGAGGAACTAAATTGCATA
*
95326 AAATAAAGTTTGAGG-ATTAAATTGCATA
1 AAATAAA-TTTGAGGAACTAAATTGCATA
95354 AAA
1 AAA
95357 GATAAATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (28 bp):
AAATAAATTTGAGGAACTAAATTGCATA
Found at i:103098 original size:2 final size:2
Alignment explanation
Indices: 103091--103119 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
103081 GAATGAATGC
103091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
103120 GAAGTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108345 original size:6 final size:6
Alignment explanation
Indices: 108330--108363 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
108320 CCAAATTCTG
108330 GAAAAA -AAAAA G-AAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
108364 CCATTCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:108350 original size:11 final size:11
Alignment explanation
Indices: 108330--108363 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
108320 CCAAATTCTG
*
108330 GAAAAAAAAAA
1 GAAAAGAAAAA
108341 GAAAAGAAAAA
1 GAAAAGAAAAA
108352 GAAAAAGAAAAA
1 G-AAAAGAAAAA
108364 CCATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:112519 original size:26 final size:25
Alignment explanation
Indices: 112483--112539 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
112473 TCAGTGTGGT
112483 AAATTTACTTGATGAGAACA-ATTGTA
1 AAATTTACTTGATGAGAA-ATATTG-A
*
112509 AAATTTTCTTGATGAGAAATATTGA
1 AAATTTACTTGATGAGAAATATTGA
112534 AAATTT
1 AAATTT
112540 CTTACTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (25 bp):
AAATTTACTTGATGAGAAATATTGA
Found at i:119128 original size:30 final size:31
Alignment explanation
Indices: 119076--119133 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
119066 TGTTTTCTGT
*
119076 TTGTACCATTATTTTTAAAACATATTTCCAA
1 TTGTACCATTATTTTAAAAACATATTTCCAA
119107 TTGTACCATT-TTTTAAAAACATATTTC
1 TTGTACCATTATTTTAAAAACATATTTC
119134 TAAATTGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (31 bp):
TTGTACCATTATTTTAAAAACATATTTCCAA
Found at i:119140 original size:31 final size:31
Alignment explanation
Indices: 119076--119140 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
119066 TGTTTTCTGT
* *
119076 TTGTACCATTATTTTTAAAACATATTTCCAA
1 TTGTACCATTATTTTAAAAACATATTTCAAA
119107 TTGTACCATT-TTTTAAAAACATATTTCTAAA
1 TTGTACCATTATTTTAAAAACATATTTC-AAA
119138 TTG
1 TTG
119141 CCATTACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (31 bp):
TTGTACCATTATTTTAAAAACATATTTCAAA
Found at i:119957 original size:18 final size:18
Alignment explanation
Indices: 119934--119972 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
119924 ATTCAATTTT
119934 AAGGTTAAGATTTAGTTA
1 AAGGTTAAGATTTAGTTA
119952 AAGGTTAAGATTTAGTTA
1 AAGGTTAAGATTTAGTTA
119970 AAG
1 AAG
119973 TAATTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (18 bp):
AAGGTTAAGATTTAGTTA
Found at i:120382 original size:22 final size:22
Alignment explanation
Indices: 120289--120393 Score: 106
Period size: 22 Copynumber: 4.8 Consensus size: 22
120279 TTTTTGTCCT
120289 AGGTTATCAAAATTAT-ATA-ATG
1 AGGTTATCAAAATT-TCATAGA-G
* *
120311 TGATTATCAAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
* * *
120333 GGGTCAACAAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
120355 AGGTTATCAAAATTTCATAAAG
1 AGGTTATCAAAATTTCATAGAG
* *
120377 AAGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCA
120394 AAATGTGATT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.01
22 67 0.97
23 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGAG
Found at i:120552 original size:44 final size:44
Alignment explanation
Indices: 120499--120662 Score: 126
Period size: 44 Copynumber: 3.7 Consensus size: 44
120489 TTATGAAATA
120499 ATCAAAATTTCA-AGGAGGATATCAAAATTTCATATATGAAGGTT
1 ATCAAAATTTCATAGGAGGATATCAAAATTTCATATATG-AGGTT
* * * *
120543 ATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCGTAGTATGTA-G--
1 ATCAAAATTTCATAG--GAGGATATCAAAATTTCATA-TATG-AGGTT
*
120587 ATCAAAATTTCATAGG-GAGATTAACAAAATTTCATA-ATGAGGTT
1 ATCAAAATTTCATAGGAG-GA-TATCAAAATTTCATATATGAGGTT
** * *
120631 ATCAAAAAATCATAGGGAAGTTATCAAAATTT
1 ATCAAAATTTCATA-GGAGGATATCAAAATTT
120663 GTAGTTATCA
Statistics
Matches: 93, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 1 0.01
44 61 0.66
45 5 0.05
46 15 0.16
47 6 0.06
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (44 bp):
ATCAAAATTTCATAGGAGGATATCAAAATTTCATATATGAGGTT
Found at i:120572 original size:22 final size:22
Alignment explanation
Indices: 120519--120601 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
120509 CAAGGAGGAT
*
120519 ATCAAAATTTCATA-TATGAAGG
1 ATCAAAATTTCATAGTATGTA-G
120541 TTATCAAAATTTCATAGT-T-TAG
1 --ATCAAAATTTCATAGTATGTAG
* *
120563 TTTTCAAAATTTCGTAGTATGTAG
1 --ATCAAAATTTCATAGTATGTAG
120587 ATCAAAATTTCATAG
1 ATCAAAATTTCATAG
120602 GGAGATTAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
22 30 0.59
23 2 0.04
24 18 0.35
25 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (22 bp):
ATCAAAATTTCATAGTATGTAG
Found at i:120614 original size:22 final size:22
Alignment explanation
Indices: 120587--120946 Score: 105
Period size: 22 Copynumber: 16.5 Consensus size: 22
120577 TAGTATGTAG
120587 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGATT
* ** *
120609 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATT
**
120631 ATCAAAAAATCATAGGGA-AGTT
1 ATCAAAATTTCATAGGGAGA-TT
*
120653 ATCAAAA-TT--T--GTAG-TT
1 ATCAAAATTTCATAGGGAGATT
* * *
120669 ATCAAGA-TTCAATAAGGAGGTT
1 ATCAAAATTTC-ATAGGGAGATT
* * *
120691 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGA-GATT
* * *
120714 ACCAAAATTTCATAGCGAGTTT
1 ATCAAAATTTCATAGGGAGATT
* * *
120736 ATCAAAATTTTATAGTGTGATT
1 ATCAAAATTTCATAGGGAGATT
* * * *
120758 ATTAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGATT
* * * *
120780 ACTGACAA-TTCATATGGAGGTT
1 A-TCAAAATTTCATAGGGAGATT
* * * ** * *
120802 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGATT
* * * *
120824 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGATT
* ** *
120846 ATCAACATCTT-ATAGTGTTGGTT
1 ATCAAAAT-TTCATAG-GGAGATT
** *
120869 ATCAAAATTTCATTTGCA-AGTT
1 ATCAAAATTTCATAGGGAGA-TT
* *
120891 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGAT-T
* * *
120914 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGATT
*
120935 AACAAAATTTCA
1 ATCAAAATTTCA
120947 CAAGAAAGTT
Statistics
Matches: 244, Mismatches: 75, Indels: 38
0.68 0.21 0.11
Matches are distributed among these distances:
16 10 0.04
17 2 0.01
19 2 0.01
21 8 0.03
22 183 0.75
23 39 0.16
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGATT
Found at i:120906 original size:45 final size:45
Alignment explanation
Indices: 120819--120907 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
120809 TTTCATAACG
* * * *
120819 TGGTTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGCAAGTTATCAAAATCTTATAGTGT
* *
120864 TGGTTATCAAAATTTCATTTGCAAGTTATCAAAAT-TTCATAGTG
1 TGGTTATCAAAATATCATATGCAAGTTATCAAAATCTT-ATAGTG
120908 AGGTCTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGCAAGTTATCAAAATCTTATAGTGT
Found at i:121023 original size:22 final size:22
Alignment explanation
Indices: 121005--121182 Score: 114
Period size: 22 Copynumber: 8.5 Consensus size: 22
120995 ATCGTTATTG
121005 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
121027 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
* *
121049 AAATTTCATAAGG-ACGTCAT-A
1 AAATTTCAT-AGGAAGGTTATCA
*
121070 AAA---AATAGTGTAA--TTATCA
1 AAATTTCATAG-G-AAGGTTATCA
* *
121089 TAATTTCATAGGAAGATTATCA
1 AAATTTCATAGGAAGGTTATCA
* *
121111 AAATTTCATAAGG-ACGTCATCA
1 AAATTTCAT-AGGAAGGTTATCA
121133 AAA----ATAGTGTAA--TTATCA
1 AAATTTCATAG-G-AAGGTTATCA
* *
121151 TAATTTAATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
*
121173 TAATTTCATA
1 AAATTTCATA
121183 TGAATATTTC
Statistics
Matches: 123, Mismatches: 13, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
17 4 0.03
18 16 0.13
19 3 0.02
20 6 0.05
21 6 0.05
22 82 0.67
23 6 0.05
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTTATCA
Found at i:121094 original size:62 final size:62
Alignment explanation
Indices: 121021--121182 Score: 279
Period size: 62 Copynumber: 2.6 Consensus size: 62
121011 CATAGGAAGG
*
121021 TTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAA
1 TTATCATAATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAA
* *
121083 TTATCATAATTTCATAGGAAGATTATCAAAATTTCATAAGGACGTCATCAAAAATAGTGTAA
1 TTATCATAATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAA
* *
121145 TTATCATAATTTAATAGGAAGGTTATCATAATTTCATA
1 TTATCATAATTTCATAGGAAGGTTATCAAAATTTCATA
121183 TGAATATTTC
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 94 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (62 bp):
TTATCATAATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAA
Found at i:122229 original size:20 final size:20
Alignment explanation
Indices: 122192--122230 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
122182 TACTATTATT
122192 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
122212 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
122231 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:122424 original size:22 final size:22
Alignment explanation
Indices: 122396--122625 Score: 170
Period size: 22 Copynumber: 10.5 Consensus size: 22
122386 TGTCTCTGTG
*
122396 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
122418 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
122441 -GGTTATGAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
122462 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
122485 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
*
122506 AGGTTATCAAAATTTC--AGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
122526 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
122548 TCAGGTTAT-TAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* * *
122571 AGGTTAAT-GAAATTTCATAGTA
1 TGGTT-ATCAAAATTTCATAGGA
* * *
122593 TGGTTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAGGA
*
122615 AGGTTATCAAA
1 TGGTTATCAAA
122626 GATATCAAAA
Statistics
Matches: 164, Mismatches: 30, Indels: 28
0.74 0.14 0.13
Matches are distributed among these distances:
20 15 0.09
21 13 0.08
22 115 0.70
23 16 0.10
24 5 0.03
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:122499 original size:66 final size:65
Alignment explanation
Indices: 122393--123456 Score: 394
Period size: 66 Copynumber: 16.3 Consensus size: 65
122383 TCTTGTCTCT
* * * * * *
122393 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATGAAAATTCCAT
1 GTGTGGTTATCAAAATTTCATAGGA-AGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCAT
122458 A
65 A
*
122459 GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTC-
1 GTGTGGTTATCAAAATTTCATA-GGAAGTTATCAAAATTTCATGAGG-AGGTTATCAAAATTTCA
122522 -A
64 TA
* * * *
122523 GTGTGGTTACCAAAATTTCATAGGATCAGGTTAT-TAAATTTC-TTAGGAAGGTTAAT-GAAATT
1 GTGTGGTTATCAAAATTTCATAGGA--A-GTTATCAAAATTTCATGAGG-AGGTT-ATCAAAATT
122585 TCATA
61 TCATA
* * * * *
122590 GTATGGTTATCACAATTTTATAGAAAGGTTATCAAAGATATCAAAATGTCATAGCGAGGTTAT-A
1 GTGTGGTTATCAAAATTTCATAGGAA-GTTATCAAA-ATTTC---ATG----AG-GAGGTTATCA
*
122654 GGAATTTCATA
56 -AAATTTCATA
* * * * * *
122665 ATGTGGTTAACAAAATTTCATAAGGAGGTTA-CTAATATATCATGGGGAGGTTATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCAT-AGGAAGTTATC-AAAATTTCATGAGGAGGTTATCAAAATTTCA
122729 TA
64 TA
** ** * *
122731 GTGTGGTTATCAAAATTTTTTAGTGTGGTTATCAAAATTTCAT-ATGAAGGTTAT-AAAAGTCTC
1 GTGTGGTTATCAAAATTTCATAG-GAAGTTATCAAAATTTCATGA-GGAGGTTATCAAAA-TTTC
122794 AATTTCA
63 -A--T-A
* * * * *
122801 -TGAGGAGTACCAAAATTTGATA-GAAGGTTATC-AAATTTCAT-A-GAGTGATTATCGAAATTT
1 GTGTGG-TTATCAAAATTTCATAGGAA-GTTATCAAAATTTCATGAGGAG-G-TTATCAAAATTT
122861 CATA
62 CATA
* * **
122865 GAGATCAGATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCAT-AGTGTTGTTATCAAAATT
1 GTG-T--GGTTATCAAAATTTCATAGGAAG-TTATCAAAATTTCATGAG-GAGGTTATCAAAATT
*
122928 TCAAA
61 TCATA
* * * * * * * *
122933 GCGAGATTATCAAAATTTCATAGAGAGGTCAACAAAATTTTAT-AGAGAGATTATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCATAG-GAAGTTATCAAAATTTCATGAG-GAGGTTATCAAAATTTCA
122997 TA
64 TA
** * * * * *
122999 AAGAGATTATCAAATTTTCA-A--AATGTGAATCAAAATTTCAT-A-GTGG-TAT-----TTT--
1 GTGTGGTTATCAAAATTTCATAGGAA-GT-TATCAAAATTTCATGAGGAGGTTATCAAAATTTCA
*
123051 TG
64 TA
* * * * * * * * *
123053 GGGAGGTTATCAAAATTTCATAGTATGGTTA-CCAAA-TT-A-G-GAAGGTTATTAAACTTTTAT
1 GTGTGGTTATCAAAATTTCATAGGA-AGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCA-
123113 TA
64 TA
* * * * *
123115 -TG-GAGTAATCAAAATTTCA-GGGAAGATATCAAAATTTCAT-ATGAAGGTTACCAAAATTTCA
1 GTGTG-GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATGA-GGAGGTTATCAAAATTTCA
123176 TA
64 TA
* * * ** * **
123178 GTTTAGTTTTCAAAATTTCATAGTTTAGTTTTCAAAATTTCAT-AAAAGGGTTATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCATAG-GAAGTTATCAAAATTTCATGAGGA-GGTTATCAAAATTTCA
123242 TA
64 TA
* * * * * * *
123244 GTAT-GTAGATCAAAAATTCATAGGGAGGTTAACAAAATTTCATGATGAGGTTATCAAAAAATT-
1 GTGTGGT-TATCAAAATTTCATA-GGAAGTTATCAAAATTTCATGAGGAGGTTATC-AAAATTTC
123307 ATA
63 ATA
* * * * * * * *
123310 GGGAGATTATCAAAA-TT--T--GTAGTTATCAAGATTTCATAATGAGGTTATCAAAATTTTATA
1 GTGTGGTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATA
* * * * *
123370 GGGAGGTTTATCAAAAATTT-ATA-GAAGGTTTATCAAAATTTCGTG-GCGAGGTTATTACAATT
1 GTGTGG-TTATC-AAAATTTCATAGGAA-G-TTATCAAAATTTCATGAG-GAGGTTATCAAAATT
123432 TCATA
61 TCATA
*
123437 GTGTGATTATCAAAATTTCA
1 GTGTGGTTATCAAAATTTCA
123457 GAGTGTGATT
Statistics
Matches: 759, Mismatches: 147, Indels: 184
0.70 0.13 0.17
Matches are distributed among these distances:
53 3 0.00
54 22 0.03
55 5 0.01
56 4 0.01
57 3 0.00
59 12 0.02
60 41 0.05
61 25 0.03
62 9 0.01
63 10 0.01
64 67 0.09
65 71 0.09
66 262 0.35
67 97 0.13
68 45 0.06
69 15 0.02
70 14 0.02
71 4 0.01
74 8 0.01
75 38 0.05
76 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (65 bp):
GTGTGGTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATGAGGAGGTTATCAAAATTTCATA
Found at i:122681 original size:22 final size:22
Alignment explanation
Indices: 122628--123043 Score: 172
Period size: 22 Copynumber: 18.8 Consensus size: 22
122618 TTATCAAAGA
* * *
122628 TATCAAAATGTCATAGCGAGGT
1 TATCAAAATTTCATAGTGTGGT
* *
122650 TAT-AGGAATTTCATAATGTGGT
1 TATCA-AAATTTCATAGTGTGGT
* *
122672 TAACAAAATTTCATAAG-GAGGT
1 TATCAAAATTTCAT-AGTGTGGT
* * * * *
122694 TA-CTAATATATCATGGGGAGGT
1 TATC-AAAATTTCATAGTGTGGT
122716 TATCAAAATTTCATAGTGTGGT
1 TATCAAAATTTCATAGTGTGGT
**
122738 TATCAAAATTTTTTAGTGTGGT
1 TATCAAAATTTCATAGTGTGGT
*
122760 TATCAAAATTTCATA-TGAAGGT
1 TATCAAAATTTCATAGTG-TGGT
* * *
122782 TAT-AAAAGTCTCAATTTCA-TGAGGAG
1 TATCAAAA-TTTC-A--T-AGTGTGG-T
* * **
122808 TACCAAAATTTGATAG-AAGGT
1 TATCAAAATTTCATAGTGTGGT
* *
122829 TATC-AAATTTCATAGAGTGAT
1 TATCAAAATTTCATAGTGTGGT
* * *
122850 TATCGAAATTTCATAGAGATCAGAT
1 TATCAAAATTTCATAGTG-T--GGT
* *
122875 TATCAAAATTT-ATAG-GAAGAT
1 TATCAAAATTTCATAGTG-TGGT
*
122896 TATCAAAATTTCATAGTGTTGT
1 TATCAAAATTTCATAGTGTGGT
* * * *
122918 TATCAAAATTTCAAAGCGAGAT
1 TATCAAAATTTCATAGTGTGGT
* *
122940 TATCAAAATTTCATAGAGAGGT
1 TATCAAAATTTCATAGTGTGGT
* * * * * *
122962 CAACAAAATTTTATAGAGAGAT
1 TATCAAAATTTCATAGTGTGGT
** * *
122984 TATCAAAATTTCATAAAGAGAT
1 TATCAAAATTTCATAGTGTGGT
* * *
123006 TATCAAATTTTCAAAATGT-G-
1 TATCAAAATTTCATAGTGTGGT
*
123026 AATCAAAATTTCATAGTG
1 TATCAAAATTTCATAGTG
123044 GTATTTTTGG
Statistics
Matches: 308, Mismatches: 64, Indels: 46
0.74 0.15 0.11
Matches are distributed among these distances:
20 24 0.08
21 32 0.10
22 210 0.68
23 9 0.03
24 4 0.01
25 18 0.06
26 7 0.02
27 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGGT
Found at i:122761 original size:44 final size:44
Alignment explanation
Indices: 122715--123635 Score: 256
Period size: 44 Copynumber: 21.4 Consensus size: 44
122705 CATGGGGAGG
* * * * *
122715 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
122759 TTATCAAAATTTCATA-TGAAGGTTAT-AAAAGTCTCAATT-TCATGAG-GA
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAA-T-T---TTAT-A-GAGAGA
* * * * * *
122807 GTACCAAAATTTGATAG-AAGGTTATC-AAATTTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
* * *
122849 TTATCGAAATTTCATAGAGATCAGATTATCAAAA-TTTATAG-GAAGA
1 TTATCAAAATTTCAT--AG-TGAGGTTATCAAAATTTTATAGAG-AGA
** * * *
122895 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
* * *
122939 TTATCAAAATTTCATAGAGAGGTCAACAAAATTTTATAGAGAGA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
** * * *
122983 TTATCAAAATTTCATAAAGAGATTATC-AAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTT-ATAGA-GAGA
* * *
123027 --ATCAAAATTTCATAGT--GG---T----ATTTT-TGGGGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
* * *
123059 TTATCAAAATTTCATAGT-ATGGTTA-CCAAA--TTA-GGA-AGG
1 TTATCAAAATTTCATAGTGA-GGTTATCAAAATTTTATAGAGAGA
* * * * * **
123098 TTATTAAACTTTTATTA-TG-GAGTAATCAAAATTTCAGGGA-AGA
1 TTATCAAAATTTCA-TAGTGAG-GTTATCAAAATTTTATAGAGAGA
* * **
123141 -TATCAAAATTTCATA-TGAAGGTTACCAAAATTTCATAGTTTAG-
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTTATAG-AGAGA
* * * * * *
123184 TTTTCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATA-AAAGGG
1 TTATCAAAATTTCATAG-TGAGGTTATCAAAATTTTATAGAGA-GA
* * * * * *
123228 TTATCAAAATTTCATAGT-ATGTAGATCAAAAATTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGGT-TATCAAAATTTTATAGAGAGA
* ** *
123272 TTAACAAAATTTCAT-GATGAGGTTATCAAAAAATTATAGGGAGA
1 TTATCAAAATTTCATAG-TGAGGTTATCAAAATTTTATAGAGAGA
* * *
123316 TTATCAAAA-TT--T-GT-A-GTTATCAAGATTTCATA-ATGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGA-GAGA
* * * *
123354 TTATCAAAATTTTATAGGGAGGTTTATCAAAAATTTATAGA-AGGT
1 TTATCAAAATTTCATAGTGAGG-TTATCAAAATTTTATAGAGA-GA
* * * * * * * *
123399 TTATCAAAATTTCGTGGCGAGGTTATTACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
* * * *
123443 TTATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATG-GAGA
1 TTATCAAAATTTCATAGTGAGGTTATC-AA-AATTTTATA-GAGAGA
* * * ** * * * * * *
123487 TTTTTAAATTTTCATAACGTGGTTATTAATATATCATATGA-AGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATA-GAGAGA
* * * * * * * *
123531 TTATCAACATCTCATAGTGTTGATTATTAAAATTTCATTG-GGGA
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTTATAGAGAGA
* *
123575 GTTATCAAAATTTCATAGTGAGGTCT-TCAAAATTCCT-TAGGGAGA
1 -TTATCAAAATTTCATAGTGAGGT-TATCAAAATT-TTATAGAGAGA
*
123620 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
123636 AGAAGGTTAA
Statistics
Matches: 653, Mismatches: 145, Indels: 158
0.68 0.15 0.17
Matches are distributed among these distances:
32 2 0.00
34 21 0.03
36 2 0.00
37 1 0.00
38 26 0.04
39 21 0.03
40 12 0.02
41 10 0.02
42 59 0.09
43 41 0.06
44 313 0.48
45 80 0.12
46 32 0.05
47 14 0.02
48 17 0.03
49 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGAGGTTATCAAAATTTTATAGAGAGA
Found at i:123191 original size:22 final size:22
Alignment explanation
Indices: 123166--123221 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
123156 TGAAGGTTAC
123166 CAAAATTTCATAGTTTAGTTTT
1 CAAAATTTCATAGTTTAGTTTT
123188 CAAAATTTCATAGTTTAGTTTT
1 CAAAATTTCATAGTTTAGTTTT
123210 CAAAATTTCATA
1 CAAAATTTCATA
123222 AAAGGGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (22 bp):
CAAAATTTCATAGTTTAGTTTT
Found at i:123279 original size:22 final size:22
Alignment explanation
Indices: 123226--123456 Score: 97
Period size: 22 Copynumber: 10.7 Consensus size: 22
123216 TTCATAAAAG
* *
123226 GGTTATCAAAATTTCATA-GTA
1 GGTTATCAAAAATTCATAGGGA
* *
123247 TGTAGATCAAAAATTCATAGGGA
1 GGT-TATCAAAAATTCATAGGGA
* * *
123270 GGTTAACAAAATTTCAT-GATGA
1 GGTTATCAAAAATTCATAG-GGA
123292 GGTTATCAAAAAATT-ATAGGGA
1 GGTTATC-AAAAATTCATAGGGA
* *
123314 GATTATC-AAAATT--T--GTA
1 GGTTATCAAAAATTCATAGGGA
* * **
123331 -GTTATCAAGATTTCATAATGA
1 GGTTATCAAAAATTCATAGGGA
* *
123352 GGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAAATTCATAGGGA
* *
123374 GGTTTATCAAAAATTTATA-GAA
1 GG-TTATCAAAAATTCATAGGGA
* *
123396 GGTTTATCAAAATTTCGT-GGCGA
1 GG-TTATCAAAAATTCATAGG-GA
* * * * *
123419 GGTTATTACAATTTCATAGTGT
1 GGTTATCAAAAATTCATAGGGA
* *
123441 GATTATCAAAATTTCA
1 GGTTATCAAAAATTCA
123457 GAGTGTGATT
Statistics
Matches: 158, Mismatches: 37, Indels: 29
0.71 0.17 0.13
Matches are distributed among these distances:
16 5 0.03
17 6 0.04
19 2 0.01
20 6 0.04
21 4 0.03
22 105 0.66
23 30 0.19
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAAATTCATAGGGA
Found at i:123354 original size:60 final size:61
Alignment explanation
Indices: 123271--123385 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 61
123261 TCATAGGGAG
*
123271 GTTAACAAAATTTCATGATGAGGTTATCAAAAAATTATAGGGA-GATTATCAAAATTTGTA
1 GTTAACAAAATTTCATAATGAGGTTATCAAAAAATTATAGGGAGGATTATCAAAATTTGTA
* * ** *
123331 GTTATCAAGATTTCATAATGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAA
1 GTTAACAAAATTTCATAATGAGGTTATCAAAAAATTATAGGGAGGATTATCAAAA
123386 ATTTATAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 38 0.79
61 10 0.21
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (61 bp):
GTTAACAAAATTTCATAATGAGGTTATCAAAAAATTATAGGGAGGATTATCAAAATTTGTA
Found at i:123478 original size:22 final size:23
Alignment explanation
Indices: 123426--123476 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
123416 CGAGGTTATT
*
123426 ACAATTTCATAGTGTGATTATCA
1 ACAATTTCAGAGTGTGATTATCA
123449 A-AATTTCAGAGTGTGATTA-CTA
1 ACAATTTCAGAGTGTGATTATC-A
123471 ACAATT
1 ACAATT
123477 CATATGGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 1 0.04
22 19 0.76
23 5 0.20
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (23 bp):
ACAATTTCAGAGTGTGATTATCA
Found at i:123645 original size:22 final size:22
Alignment explanation
Indices: 123575--123730 Score: 68
Period size: 22 Copynumber: 7.1 Consensus size: 22
123565 TCATTGGGGA
*
123575 GTTATCAAAATTTCAT-AGTGAG
1 GTTATCAAAATTTCATAAG-AAG
* * * *
123597 GTCT-TCAAAATTCCTTAGGGAG
1 GT-TATCAAAATTTCATAAGAAG
* *
123619 ATTAACAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAAGAAG
* * * * *
123641 GTTA-AAATAAATTAATAAAAAA
1 GTTATCAA-AATTTCATAAGAAG
* * * **
123663 GTTCTCGAAATTCCAT-AGTATC
1 GTTATCAAAATTTCATAAG-AAG
* * *
123685 GTTATTAAAATTTCATAGGAAT
1 GTTATCAAAATTTCATAAGAAG
123707 GTTATCAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAAGAAG
123729 GT
1 GT
123731 CATAAAAAAT
Statistics
Matches: 93, Mismatches: 34, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
21 4 0.04
22 85 0.91
23 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGAAG
Found at i:123738 original size:22 final size:22
Alignment explanation
Indices: 123691--123738 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
123681 TATCGTTATT
* * * *
123691 AAAATTTCATAGGAATGTTATC
1 AAAATTTCATAAGAAGGTCATA
123713 AAAATTTCATAAGAAGGTCATA
1 AAAATTTCATAAGAAGGTCATA
123735 AAAA
1 AAAA
123739 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTCATA
Found at i:125720 original size:14 final size:14
Alignment explanation
Indices: 125701--125729 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
125691 AAATTGTCTT
125701 ACTCATAATCAAGG
1 ACTCATAATCAAGG
125715 ACTCATAATCAAGG
1 ACTCATAATCAAGG
125729 A
1 A
125730 TAACTTCTTC
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:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ACTCATAATCAAGG
Found at i:127331 original size:32 final size:31
Alignment explanation
Indices: 127258--127390 Score: 131
Period size: 31 Copynumber: 4.3 Consensus size: 31
127248 GACGTGACAT
**
127258 GCCACGTGTACCAAAAAGTGACATGTGGCAC
1 GCCACGTGTACCAAAAAGTGACACATGGCAC
* * * *
127289 GCCACATGTACAAAAAAGTTAACACATGTCAC
1 GCCACGTGTACCAAAAAG-TGACACATGGCAC
*
127321 GCCACGTGTACCAAAAAGTGACACATGGCAT
1 GCCACGTGTACCAAAAAGTGACACATGGCAC
* ** * * * *
127352 GCCACATGTTTCAAAAAATGGCACCTGGCAT
1 GCCACGTGTACCAAAAAGTGACACATGGCAC
127383 GCCACGTG
1 GCCACGTG
127391 CATAAAAGGA
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
31 58 0.70
32 25 0.30
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGTGACACATGGCAC
Done.