Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold265
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: 864291
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 1 of 6
Found at i:1453 original size:9 final size:9
Alignment explanation
Indices: 1418--1452 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1408 TGTAAATGTT
1418 TTTTTTTAA
1 TTTTTTTAA
1427 TTTTTTTAA
1 TTTTTTTAA
* *
1436 ATTTTTTAC
1 TTTTTTTAA
1445 TTTTTTTA
1 TTTTTTTA
1453 CACCTCCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:1528 original size:16 final size:16
Alignment explanation
Indices: 1507--1537 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1497 ACAGTAATAT
*
1507 AATTTAAATTCATTAA
1 AATTTAAATTAATTAA
1523 AATTTAAATTAATTA
1 AATTTAAATTAATTA
1538 CCTTTAAGGA
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATTAATTAA
Found at i:2163 original size:2 final size:2
Alignment explanation
Indices: 2151--2186 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2141 TGCTGGTCTA
*
2151 TC TC GC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2187 TCTTTTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:6403 original size:22 final size:21
Alignment explanation
Indices: 6353--6393 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6343 TTTAATAAAA
*
6353 AATAATTATTATTTTTATATT
1 AATATTTATTATTTTTATATT
6374 AATATTTATATATTTTTATA
1 AATATTTAT-TATTTTTATA
6394 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AATATTTATTATTTTTATATT
Found at i:6582 original size:3 final size:3
Alignment explanation
Indices: 6574--6627 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
6564 GTCCTCACAC
6574 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
6620 A-A ATA ATA
1 ATA ATA ATA
6628 TAAAACCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:6922 original size:21 final size:21
Alignment explanation
Indices: 6898--6945 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
6888 AGATATCTTA
6898 AATATTAAAACAATA-AAATAC
1 AATATTAAAA-AATATAAATAC
* *
6919 AATATCAAAATATATAAATAC
1 AATATTAAAAAATATAAATAC
*
6940 ATTATT
1 AATATT
6946 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATTAAAAAATATAAATAC
Found at i:7199 original size:34 final size:34
Alignment explanation
Indices: 7156--7227 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
7146 AAAAAAAGGA
7156 TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
1 TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
*
7190 TTTGGATGTATCCGAAGCTAGTTCCTGGTTTTAC
1 TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
7224 TTTG
1 TTTG
7228 AATCATTAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (34 bp):
TTTGGATGTATCAGAAGCTAGTTCCTGGTTTTAC
Found at i:10602 original size:15 final size:17
Alignment explanation
Indices: 10582--10615 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10572 TTTAATAATT
10582 TTAAAAA-T-ATTTTTA
1 TTAAAAACTCATTTTTA
10597 TTAAAAACTCATTTTTA
1 TTAAAAACTCATTTTTA
10614 TT
1 TT
10616 TTTTAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAACTCATTTTTA
Found at i:11001 original size:22 final size:22
Alignment explanation
Indices: 10973--11015 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10963 AAAAATAAAA
10973 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
10995 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
11016 AATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:11189 original size:3 final size:3
Alignment explanation
Indices: 11181--11211 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11171 GTCCATACAC
11181 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11212 TTATGAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16213 original size:20 final size:21
Alignment explanation
Indices: 16177--16215 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16167 TTTGTTTTAA
16177 CATTTTTTATTTAATTTTATT
1 CATTTTTTATTTAATTTTATT
16198 CATTGTTTT-TTT-ATTTTA
1 CATT-TTTTATTTAATTTTA
16216 CAAAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (21 bp):
CATTTTTTATTTAATTTTATT
Found at i:17596 original size:67 final size:68
Alignment explanation
Indices: 17522--17650 Score: 190
Period size: 70 Copynumber: 1.9 Consensus size: 68
17512 TACAAAAATG
* * *
17522 GAGTTGCAACG-TATTGTCTTAAAATA-CTTGTTTACAAAATAAAATTGAACAAGTTCATATACT
1 GAGTTGCAACGTTATTGTCTTAAAACAGC-CGTTCACAAAATAAAATTGAACAAGTTCATATACT
17585 GAAA
65 GAAA
17589 GAGTTGCAACGTATTATTGTCTTAAAACAGCCGTTCACAAAATAAAATTGAACAAGTTCATA
1 GAGTTGCAACG--TTATTGTCTTAAAACAGCCGTTCACAAAATAAAATTGAACAAGTTCATA
17651 CAATGAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
67 11 0.20
70 43 0.78
71 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (68 bp):
GAGTTGCAACGTTATTGTCTTAAAACAGCCGTTCACAAAATAAAATTGAACAAGTTCATATACTG
AAA
Found at i:22798 original size:19 final size:20
Alignment explanation
Indices: 22766--22804 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
22756 TTATAATTAA
22766 ATTTAAATAAAAATA-TATT
1 ATTTAAATAAAAATACTATT
22785 ATTT-AATATAAAATACTATT
1 ATTTAAATA-AAAATACTATT
22805 TTAATCTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAATAAAAATACTATT
Found at i:24120 original size:2 final size:2
Alignment explanation
Indices: 24113--24159 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
24103 CTATACATAC
24113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24155 AT AT A
1 AT AT A
24160 GTCTTATGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24945 original size:2 final size:2
Alignment explanation
Indices: 24938--24985 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
24928 AAAAACAAGA
24938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24980 AT AT AT
1 AT AT AT
24986 CTTGGCAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25832 original size:2 final size:2
Alignment explanation
Indices: 25825--25867 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
25815 AAGCTTCTGG
25825 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
25867 T
1 T
25868 TTTCTTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:31792 original size:1 final size:1
Alignment explanation
Indices: 31788--31812 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
31778 TATTTTTCTC
31788 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
31813 CATTTTGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33380 original size:16 final size:16
Alignment explanation
Indices: 33370--33411 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
33360 ATTTTGATTA
33370 TAAGTCATTTTAAATT
1 TAAGTCATTTTAAATT
33386 TAAGTCA--TTAAATT
1 TAAGTCATTTTAAATT
*
33400 TAGGT-ATTTTAA
1 TAAGTCATTTTAA
33412 GTTTGGATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 11 0.48
15 4 0.17
16 7 0.30
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (16 bp):
TAAGTCATTTTAAATT
Found at i:33473 original size:30 final size:31
Alignment explanation
Indices: 33408--33478 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
33398 TTTAGGTATT
*
33408 TTAAGTTTGGATCATTTCGATTTCAAAGTAT
1 TTAAGTTTGGATCATTTCGATTTCAAAGTAG
* * *
33439 TTAAGTTTGGATTATTTTGA-TTCAAGGTAG
1 TTAAGTTTGGATCATTTCGATTTCAAAGTAG
33469 TTAAGGTTTG
1 TTAA-GTTTG
33479 AGTTTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (31 bp):
TTAAGTTTGGATCATTTCGATTTCAAAGTAG
Found at i:33569 original size:17 final size:16
Alignment explanation
Indices: 33526--33573 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
33516 TTAATTATTT
*
33526 ATATTATTTTAAATTC
1 ATATTATTTTGAATTC
*
33542 AGATTATTTTGAATTC
1 ATATTATTTTGAATTC
33558 ATATTGATTTTGAATT
1 ATATT-ATTTTGAATT
33574 GTTGATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (16 bp):
ATATTATTTTGAATTC
Found at i:34019 original size:76 final size:76
Alignment explanation
Indices: 33934--34087 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
33924 TTAAACGGTA
33934 TATAAGTTTTTTAGTTAACTTGAGTTTGAATTAAGGAAAAAAAAAAATTCCCAAGCCAACTATTA
1 TATAAGTTTTTTAGTTAACTTGAGTTTGAATTAAGGAAAAAAAAAAATTCCCAAGCCAACTATTA
33999 ACACCTCTAAT
66 ACACCTCTAAT
*
34010 TATAAGTTTTTTAGTTAACTTGAGTTTGAATTAAGGAAAAAAAAAATTTCCCAAGCCAACTATTA
1 TATAAGTTTTTTAGTTAACTTGAGTTTGAATTAAGGAAAAAAAAAAATTCCCAAGCCAACTATTA
34075 ACACCTCTAAT
66 ACACCTCTAAT
34086 TA
1 TA
34088 CTACACGTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (76 bp):
TATAAGTTTTTTAGTTAACTTGAGTTTGAATTAAGGAAAAAAAAAAATTCCCAAGCCAACTATTA
ACACCTCTAAT
Found at i:38319 original size:15 final size:16
Alignment explanation
Indices: 38287--38323 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
38277 GCAATTGCTG
*
38287 CTTC-TCTTCTATTGT
1 CTTCTTCTTCTAATGT
38302 CTTCTTCTTCTAAT-T
1 CTTCTTCTTCTAATGT
38317 CTTCTTC
1 CTTCTTC
38324 CACCTTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.08, C:0.30, G:0.03, T:0.59
Consensus pattern (16 bp):
CTTCTTCTTCTAATGT
Found at i:38472 original size:16 final size:16
Alignment explanation
Indices: 38453--38489 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
38443 ATTCGATTGA
38453 AAGAAGATTTCTGTTG
1 AAGAAGATTTCTGTTG
38469 AAGAAGATTTCTGTTG
1 AAGAAGATTTCTGTTG
38485 AAGAA
1 AAGAA
38490 TGCCCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (16 bp):
AAGAAGATTTCTGTTG
Found at i:39333 original size:12 final size:12
Alignment explanation
Indices: 39318--39369 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
39308 GAATTAAAAT
39318 ATTAAATATATA
1 ATTAAATATATA
39330 ATTAAATAGTA-A
1 ATTAAATA-TATA
39342 A-TAAATAT-TA
1 ATTAAATATATA
39352 ATTATAATATATA
1 ATTA-AATATATA
*
39365 TTTAA
1 ATTAA
39370 TAAAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 3 0.09
11 8 0.24
12 16 0.47
13 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
ATTAAATATATA
Found at i:39377 original size:17 final size:17
Alignment explanation
Indices: 39321--39384 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
39311 TTAAAATATT
* *
39321 AAATATATAATTAAATAGT
1 AAATATAT-ATTTAATA-A
* *
39340 AAATAAATA-TTAATTA
1 AAATATATATTTAATAA
*
39356 TAATATATATTTAATAA
1 AAATATATATTTAATAA
39373 AAATATATATTT
1 AAATATATATTT
39385 TATTAAGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 7 0.19
17 21 0.58
18 1 0.03
19 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATATATATTTAATAA
Found at i:41304 original size:19 final size:19
Alignment explanation
Indices: 41244--41305 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
41234 TTTTAAATTA
* *
41244 TTTAATATTAATAAAATTT
1 TTTAATTTTAATAAAATAT
41263 ATTTAATTTATAAATAAAA-AT
1 -TTTAATTT-T-AATAAAATAT
*
41284 TTTAATTTTATTAAAATAT
1 TTTAATTTTAATAAAATAT
41303 TTT
1 TTT
41306 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 15 0.42
21 2 0.06
22 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATTTTAATAAAATAT
Found at i:41317 original size:13 final size:14
Alignment explanation
Indices: 41286--41320 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
41276 ATAAAAATTT
41286 TAATTTTATTAAAA
1 TAATTTTATTAAAA
41300 T-ATTTT-TTAAAA
1 TAATTTTATTAAAA
41312 TAATTTTAT
1 TAATTTTAT
41321 GTAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.37
13 10 0.53
14 2 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTTTATTAAAA
Found at i:41957 original size:16 final size:16
Alignment explanation
Indices: 41889--41950 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
41879 TTGAATTCAG
41889 ATTATTTTAATTTTAA
1 ATTATTTTAATTTTAA
* *
41905 ATCATTTTGATTTTAA
1 ATTATTTTAATTTTAA
*
41921 ATTATTTTAAGTTTAA
1 ATTATTTTAATTTTAA
41937 ATTATTTTAATTTT
1 ATTATTTTAATTTT
41951 GAGTTATGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTATTTTAATTTTAA
Found at i:42485 original size:16 final size:16
Alignment explanation
Indices: 42455--42513 Score: 77
Period size: 15 Copynumber: 3.8 Consensus size: 16
42445 TGAATTCAGG
42455 TTATTTTAA-TTTAAA
1 TTATTTTAATTTTAAA
* *
42470 TCATTTTGATTTTAAA
1 TTATTTTAATTTTAAA
*
42486 TTA-TTTAAGTTTAAA
1 TTATTTTAATTTTAAA
42501 TTATTTTAATTTT
1 TTATTTTAATTTT
42514 GAGTTATGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 20 0.56
16 16 0.44
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATTTTAATTTTAAA
Found at i:42505 original size:46 final size:47
Alignment explanation
Indices: 42404--42512 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 47
42394 TGGTTTTAGA
* * *
42404 TTAAATTATTTTGA-TTAAGTCATTTTAGGTTTTAAAATTTTTGAAT
1 TTAAATTATTTTAATTTAAATCATTTTAGATTTTAAAATTTTTGAAT
* **
42450 TCAGGTTATTTTAATTTAAATCATTTT-GATTTT-AAATTATTT-AAGT
1 TTAAATTATTTTAATTTAAATCATTTTAGATTTTAAAATT-TTTGAA-T
42496 TTAAATTATTTTAATTT
1 TTAAATTATTTTAATTT
42513 TGAGTTATGA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
45 7 0.14
46 33 0.65
47 11 0.22
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (47 bp):
TTAAATTATTTTAATTTAAATCATTTTAGATTTTAAAATTTTTGAAT
Found at i:42872 original size:563 final size:567
Alignment explanation
Indices: 41742--42871 Score: 2129
Period size: 563 Copynumber: 2.0 Consensus size: 567
41732 AATAAGTTGA
41742 TTTTTGAATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATATT
1 TTTTTGAATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATATT
41807 TGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTTT
66 TGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTTT
41872 AAAATTTTTGAATTCAGATTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTAA
131 AAAATTTTTGAATTCAGATTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTAA
41937 ATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATTT
196 ATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATTT
42002 AAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAAC
261 AAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAAC
42067 ATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAAC
326 ATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAAC
42132 TACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTTG
391 TACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTTG
42197 AATCATTATTCATTAAACTAACTTTGATCCATTTGAAAATTTCAACATTGAACTTGATAAGCCAA
456 AATCATTATTCATTAAACTAACTTTGATCCATTTGAAAATTTCAACATTGAACTTGATAAGCCAA
42262 GTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTTT
521 GTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTTT
*
42309 TTTTTGTATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATATT
1 TTTTTGAATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATATT
42374 TGTAAATTGTAT-GGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGG-TTTT
66 TGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTTT
*
42437 AAAATTTTTGAATTCAGGTTATTTTAA-TTTAAATCATTTTGATTTTAAATTA-TTTAAGTTTAA
131 AAAATTTTTGAATTCAGATTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTAA
42500 ATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATTT
196 ATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATTT
42565 AAATGAATTATTT-ATC-TTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAAC
261 AAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAAC
42628 ATAATTGAT-AAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAAC
326 ATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAAC
42692 TACAAAATAGAAA-AAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTTG
391 TACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTTG
* *
42756 AATCATTATTCATT-TACTAAC-TTGATCTATTTGAAAATTTC-ACATTGAACTTGATAAGCCCA
456 AATCATTATTCATTAAACTAACTTTGATCCATTTGAAAATTTCAACATTGAACTTGATAAG-CCA
42818 AGTTATGTTAACCAAATCCAAACACAAACATATTTTTATTCGATTTTTT
520 AGTTATGTTAACCAAATCCAAACA-AAACATATTTTTATTCGATTTTTT
42867 TTTTT
1 TTTTT
42872 TGTATCCACT
Statistics
Matches: 557, Mismatches: 4, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
556 17 0.03
557 46 0.08
558 35 0.06
559 65 0.12
560 68 0.12
561 56 0.10
562 3 0.01
563 89 0.16
564 25 0.04
565 30 0.05
566 47 0.08
567 76 0.14
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (567 bp):
TTTTTGAATTTTGAGGATATTTTAAAATCCCAATTTTCTTTGAGAGGATTTTGGATGAGTATATT
TGTAAATTGTATGGGTTAAGTTGGTTTTAGATTAAATTATTTTGATTAAGTCATTTTAGGTTTTT
AAAATTTTTGAATTCAGATTATTTTAATTTTAAATCATTTTGATTTTAAATTATTTTAAGTTTAA
ATTATTTTAATTTTGAGTTATGATTATGTTTTCTAATTAAATTGATTTAGATTAAGTTTAAATTT
AAATGAATTATTTAATCATTTTAGATTTAAATAAAAATTAAAAAATATATGAACGTGAAAAGAAC
ATAATTGATAAAGATTTATATTTTGATTGTATATTAATCTTCCATATAAAAATTATATTGATAAC
TACAAAATAGAAATAAATTAAATTGTCGAAGTATTATTTAAGCTCTATTTGGTTAAATTAACTTG
AATCATTATTCATTAAACTAACTTTGATCCATTTGAAAATTTCAACATTGAACTTGATAAGCCAA
GTTATGTTAACCAAATCCAAACAAAACATATTTTTATTCGATTTTTT
Found at i:43143 original size:17 final size:16
Alignment explanation
Indices: 43090--43144 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
43080 TTTTTAAATT
43090 TTTATTTTAAATAAAAAA
1 TTTA-TTTAAAT-AAAAA
* *
43108 TTAATATAAATAAAAA
1 TTTATTTAAATAAAAA
43124 TTTATTTAAATATAAAA
1 TTTATTTAAATA-AAAA
43141 TTTA
1 TTTA
43145 AATAAAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 15 0.47
17 14 0.44
18 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTATTTAAATAAAAA
Found at i:43150 original size:17 final size:16
Alignment explanation
Indices: 43097--43150 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
43087 ATTTTTATTT
*
43097 TAAATAAAAAATTAATA
1 TAAATAAAAATTTAA-A
**
43114 TAAATAAAAATTTATT
1 TAAATAAAAATTTAAA
43130 TAAATATAAAATTTAAA
1 TAAATA-AAAATTTAAA
43147 TAAA
1 TAAA
43151 GAGATAAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATAAAAATTTAAA
Found at i:43438 original size:11 final size:11
Alignment explanation
Indices: 43412--43496 Score: 50
Period size: 11 Copynumber: 7.7 Consensus size: 11
43402 TTTTAAAAAT
*
43412 ATATAATTTTTA
1 ATATAA-TTATA
43424 ATATAATTATA
1 ATATAATTATA
**
43435 ATATAAAAATA
1 ATATAATTATA
* * *
43446 ATTTAAATAAA
1 ATATAATTATA
43457 ATATAAATATATA
1 ATAT-AAT-TATA
43470 A-ATAATT-TA
1 ATATAATTATA
*
43479 ATTTAATT-TA
1 ATATAATTATA
*
43489 ATTTAATT
1 ATATAATT
43497 TTTTAATTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
9 3 0.05
10 16 0.27
11 27 0.45
12 10 0.17
13 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATAATTATA
Found at i:43496 original size:5 final size:5
Alignment explanation
Indices: 43472--43507 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
43462 AATATATAAA
43472 TAATT TAATT TAATT TAATT TAATT T--TT TAATT TAA
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAA
43508 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
5 26 0.90
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TAATT
Found at i:43511 original size:15 final size:13
Alignment explanation
Indices: 43472--43518 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 13
43462 AATATATAAA
43472 TAATTTAATTTAATT
1 TAATTTAATTT--TT
43487 TAATTTAATTTTT
1 TAATTTAATTTTT
43500 TAATTTAAAATTTTT
1 TAATTT--AATTTTT
43515 TAAT
1 TAAT
43519 ATTTAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.27
15 22 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATTTAATTTTT
Found at i:43556 original size:20 final size:20
Alignment explanation
Indices: 43533--43592 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
43523 AATAATTATA
43533 TTAAATAAATTATTTAAAAT
1 TTAAATAAATTATTTAAAAT
*
43553 TTAAATAAA--A-TTAAATT
1 TTAAATAAATTATTTAAAAT
* * *
43570 TTAAATGAATTTTTTAATAT
1 TTAAATAAATTATTTAAAAT
43590 TTA
1 TTA
43593 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 14 0.44
18 1 0.03
20 17 0.53
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATAAATTATTTAAAAT
Found at i:43563 original size:25 final size:26
Alignment explanation
Indices: 43518--43569 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
43508 AATTTTTTAA
* *
43518 TATTTAATAATTATATTAAA-TAAAT
1 TATTTAATAATTAAATAAAATTAAAT
43543 TATTTAA-AATTTAAATAAAATTAAAT
1 TATTTAATAA-TTAAATAAAATTAAAT
43569 T
1 T
43570 TTAAATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 15 0.65
26 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTTAATAATTAAATAAAATTAAAT
Found at i:44811 original size:14 final size:14
Alignment explanation
Indices: 44794--44823 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44784 TTGAATGATC
*
44794 ATATCACGTTCTCA
1 ATATCACGTGCTCA
44808 ATATCACGTGCTCA
1 ATATCACGTGCTCA
44822 AT
1 AT
44824 CCGAATGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (14 bp):
ATATCACGTGCTCA
Found at i:49517 original size:12 final size:12
Alignment explanation
Indices: 49495--49530 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
49485 TGATTATATT
49495 TTTTGTTTTTTTC
1 TTTT-TTTTTTTC
49508 TTTTTTTTTTTC
1 TTTTTTTTTTTC
*
49520 TCTTTTTTTTT
1 TTTTTTTTTTT
49531 AATTTTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:49517 original size:14 final size:14
Alignment explanation
Indices: 49493--49530 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
49483 AATGATTATA
*
49493 TTTTTTGTTTTTTTC
1 TTTTTT-TTTTTCTC
49508 TTTTTTTTTTTCTC
1 TTTTTTTTTTTCTC
49522 TTTTTTTTT
1 TTTTTTTTT
49531 AATTTTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTTCTC
Found at i:62221 original size:32 final size:33
Alignment explanation
Indices: 62169--62253 Score: 106
Period size: 32 Copynumber: 2.6 Consensus size: 33
62159 TATTATTTTT
62169 ATATTAAT-TA-TTATATTTATATAAAATTTAATA
1 ATATTAATATATTTATA-TTATATAAAATTTAA-A
*
62202 A-GTTAATA-ATTTATATTATATAAAATTTAAA
1 ATATTAATATATTTATATTATATAAAATTTAAA
*
62233 ATATTCATATATTTATATTAT
1 ATATTAATATATTTATATTAT
62254 TTTTATATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
31 2 0.04
32 26 0.58
33 17 0.38
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTAATATATTTATATTATATAAAATTTAAA
Found at i:62261 original size:25 final size:25
Alignment explanation
Indices: 62233--62287 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
62223 AAAATTTAAA
62233 ATATT-CA-TATATTTATATTATTTTT
1 ATATTACATTATATTTA-ATT-TTTTT
*
62258 ATATTATATTATATTTAATTTTTTT
1 ATATTACATTATATTTAATTTTTTT
62283 ATATT
1 ATATT
62288 TAATATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 15 0.56
26 4 0.15
27 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATATTACATTATATTTAATTTTTTT
Found at i:62297 original size:25 final size:27
Alignment explanation
Indices: 62239--62293 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
62229 TAAAATATTC
62239 ATATATTTATATTATTTTTATATTATA
1 ATATATTTATATTATTTTTATATTATA
*
62266 TTATATTTA-ATT-TTTTTATATT-TA
1 ATATATTTATATTATTTTTATATTATA
62290 ATAT
1 ATAT
62294 TATTAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 10 0.38
26 3 0.12
27 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
ATATATTTATATTATTTTTATATTATA
Found at i:62303 original size:27 final size:25
Alignment explanation
Indices: 62253--62305 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
62243 ATTTATATTA
*
62253 TTTTTATATTATATTATATTTAATT
1 TTTTTATATTATATTATATGTAATT
62278 TTTTTATATTTAATATTAT-TAGTAATT
1 TTTTTATA-TT-ATATTATAT-GTAATT
62305 T
1 T
62306 ACCATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
26 3 0.12
27 13 0.54
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTTATATTATATTATATGTAATT
Found at i:62681 original size:18 final size:18
Alignment explanation
Indices: 62640--62684 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
62630 AAAATTAAAT
* *
62640 TAATTTTATATATTTTTA
1 TAATTTTATATATATTCA
62658 TAATTTTATATATGATTCA
1 TAATTTTATATAT-ATTCA
62677 T-ATTTTAT
1 TAATTTTAT
62685 TAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TAATTTTATATATATTCA
Found at i:62981 original size:8 final size:9
Alignment explanation
Indices: 62910--63007 Score: 63
Period size: 10 Copynumber: 10.1 Consensus size: 9
62900 AAATAAATAT
62910 AAATTATATAA
1 AAATT-TAT-A
62921 AAATTTATA
1 AAATTTATA
*
62930 TAAATATATA
1 -AAATTTATA
* *
62940 AAATTAATT
1 AAATTTATA
* *
62949 AATTTTAAA
1 AAATTTATA
62958 CAAATATATATA
1 -AAAT-T-TATA
62970 AAATTT-TA
1 AAATTTATA
62978 AAATATTATA
1 AAAT-TTATA
62988 AAATTTATA
1 AAATTTATA
*
62997 TAAATTAATA
1 -AAATTTATA
63007 A
1 A
63008 TTAGGCATAG
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.09
9 21 0.30
10 29 0.42
11 10 0.14
12 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATTTATA
Found at i:63669 original size:13 final size:13
Alignment explanation
Indices: 63651--63686 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
63641 AGGAATAAAA
63651 AAATAATGAAGGG
1 AAATAATGAAGGG
63664 AAATAATGAAGGG
1 AAATAATGAAGGG
63677 AAATAA-GAAG
1 AAATAATGAAG
63687 AGATGGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (13 bp):
AAATAATGAAGGG
Found at i:64126 original size:17 final size:17
Alignment explanation
Indices: 64088--64144 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
64078 AATTAAATAA
*
64088 ATGAAACAAAAA-AAATT
1 ATGAAA-AAAAATAAAAT
* * *
64105 CTGAAATAAGATAAAAT
1 ATGAAAAAAAATAAAAT
64122 ATGAAAAAAAATAAAAT
1 ATGAAAAAAAATAAAAT
64139 AT-AAAA
1 ATGAAAA
64145 GTTAAATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 7 0.22
17 25 0.78
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.19
Consensus pattern (17 bp):
ATGAAAAAAAATAAAAT
Found at i:67967 original size:2 final size:2
Alignment explanation
Indices: 67962--68008 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
67952 AAGGAGTGAA
67962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68004 AT AT A
1 AT AT A
68009 AAATAGACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70375 original size:19 final size:20
Alignment explanation
Indices: 70346--70399 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
70336 TACATCAAAT
*
70346 ATAAACTCTAAAATTAAAGA
1 ATAAACACTAAAATTAAAGA
* * *
70366 A-AAACCCTAAAA-GAAATA
1 ATAAACACTAAAATTAAAGA
70384 ATAAACACTAAAATTA
1 ATAAACACTAAAATTA
70400 TAACACATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 5 0.19
19 20 0.74
20 2 0.07
ACGTcount: A:0.63, C:0.13, G:0.04, T:0.20
Consensus pattern (20 bp):
ATAAACACTAAAATTAAAGA
Found at i:70462 original size:6 final size:6
Alignment explanation
Indices: 70451--70516 Score: 78
Period size: 6 Copynumber: 11.0 Consensus size: 6
70441 GTAAGCTTAG
* * *
70451 TATATT TATATT TATATT TATATT TATATT TATATA TATATA TATATA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
* * *
70499 TATGTA TGTATT TATATT
1 TATATT TATATT TATATT
70517 CTTTAAGAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:70474 original size:18 final size:18
Alignment explanation
Indices: 70451--70516 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
70441 GTAAGCTTAG
*
70451 TATATTTATATTTATATT
1 TATATTTATATTTATATA
70469 TATATTTATATTTATATA
1 TATATTTATATTTATATA
* * *
70487 TATATATATATATATGTA
1 TATATTTATATTTATATA
*
70505 TGTATTTATATT
1 TATATTTATATT
70517 CTTTAAGAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATTTATATTTATATA
Found at i:70849 original size:17 final size:18
Alignment explanation
Indices: 70829--70863 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
70819 GATTATAATA
70829 TAAAAATAAAA-TAAATT
1 TAAAAATAAAATTAAATT
*
70846 TAAAATTAAAATTAAATT
1 TAAAAATAAAATTAAATT
70864 ATTATAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAATAAAATTAAATT
Found at i:71123 original size:138 final size:137
Alignment explanation
Indices: 70834--71091 Score: 356
Period size: 138 Copynumber: 1.9 Consensus size: 137
70824 TAATATAAAA
* * * *
70834 ATAAAATAAATTTAAAATTAAAATTAAATTATTATAACAAACAATATAAAGTATCTTAATTTGAG
1 ATAAAATGAATTTAAAATTAAAATTAAATTATTATAACAAACAATATAAAATATCTTAACTTAAG
* *
70899 GACAACTTTTAAATTAAAATATGGATATAAGATAACACAAATACAACATAAATAAACACAAATCT
66 GACAACTTTTAAAGTAAAATA-GGATATAAAATAACACAAATACAACATAAATAAACACAAATCT
70964 AATCTATT
130 AATCTATT
* * * * ** *
70972 ATAAAATGAATTTAGAATTAAAATTGAATTATTATGATAAATTATGTAAAATATCTTAACTTAAG
1 ATAAAATGAATTTAAAATTAAAATTAAATTATTATAACAAACAATATAAAATATCTTAACTTAAG
* * *
71037 GATAACTTTTAAAGTAAAGTA-GATATAAAATAACACAAATACAACATGAATAAAC
66 GACAACTTTTAAAGTAAAATAGGATATAAAATAACACAAATACAACATAAATAAAC
71092 GCGACTCTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
136 32 0.31
138 72 0.69
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.31
Consensus pattern (137 bp):
ATAAAATGAATTTAAAATTAAAATTAAATTATTATAACAAACAATATAAAATATCTTAACTTAAG
GACAACTTTTAAAGTAAAATAGGATATAAAATAACACAAATACAACATAAATAAACACAAATCTA
ATCTATT
Found at i:71804 original size:13 final size:13
Alignment explanation
Indices: 71786--71823 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
71776 ATATGTAATA
71786 TATAAAATAAAAT
1 TATAAAATAAAAT
71799 TATAAAATAAAAT
1 TATAAAATAAAAT
*
71812 TATAATATAAAA
1 TATAAAATAAAA
71824 GTAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAAATAAAAT
Found at i:72103 original size:14 final size:14
Alignment explanation
Indices: 72086--72123 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
72076 AAAATTTTAA
72086 ATTTATTAAATATT
1 ATTTATTAAATATT
72100 ATTT-TTAAA-ATT
1 ATTTATTAAATATT
72112 ATTTATATAAAT
1 ATTTAT-TAAAT
72124 TAATTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.33
13 6 0.29
14 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:74320 original size:15 final size:15
Alignment explanation
Indices: 74300--74361 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
74290 ATAAAACTTG
74300 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
74315 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
* *
74330 TAAGTTAAATTTAAAC
1 -AATTTAAATTTAAAA
*
74346 AATTTAAATCTAAAA
1 AATTTAAATTTAAAA
74361 A
1 A
74362 TTTTTATTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
15 28 0.68
16 13 0.32
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (15 bp):
AATTTAAATTTAAAA
Found at i:74869 original size:20 final size:20
Alignment explanation
Indices: 74846--74883 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
74836 ATTTAATATT
74846 TATTTAACATTAAAATTATA
1 TATTTAACATTAAAATTATA
* *
74866 TATTTAATATTTAAATTA
1 TATTTAACATTAAAATTA
74884 CTTTTAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTAACATTAAAATTATA
Found at i:75551 original size:9 final size:8
Alignment explanation
Indices: 75537--75582 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
75527 TATTTAATTT
75537 TTATTTGTA
1 TTATTT-TA
75546 TTATTTTAA
1 TTATTTT-A
75555 TT-TTTTA
1 TTATTTTA
75562 TTATTTTA
1 TTATTTTA
*
75570 ATATTTT-
1 TTATTTTA
75577 TTATTT
1 TTATTT
75583 AATATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 8 0.24
8 16 0.48
9 9 0.27
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:75565 original size:16 final size:16
Alignment explanation
Indices: 75538--75587 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
75528 ATTTAATTTT
75538 TATTTGTATTATTTTAA
1 TATTT-TATTATTTTAA
*
75555 TTTTTTATTATTTTAA
1 TATTTTATTATTTTAA
75571 TATTTT-TTA-TTTAA
1 TATTTTATTATTTTAA
75585 TAT
1 TAT
75588 ATATTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 16 0.52
17 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TATTTTATTATTTTAA
Found at i:75654 original size:9 final size:9
Alignment explanation
Indices: 75618--75669 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
75608 TTATATAATT
75618 TATTAAATA
1 TATTAAATA
*
75627 TA-TAAAAA
1 TATTAAATA
*
75635 AATTAAA-A
1 TATTAAATA
75643 TATTAAATA
1 TATTAAATA
75652 TATT---TA
1 TATTAAATA
75658 TATTAAATA
1 TATTAAATA
75667 TAT
1 TAT
75670 CTATTTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
6 6 0.17
8 13 0.37
9 16 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TATTAAATA
Found at i:78170 original size:21 final size:24
Alignment explanation
Indices: 78134--78188 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
78124 AAATGTTTTT
* *
78134 CAAATATATAGCTTATTTTCA-ATA
1 CAAATATATA-CTTATATACATATA
78158 -AAATATATA-TTATATACATATA
1 CAAATATATACTTATATACATATA
78180 CAAATATAT
1 CAAATATAT
78189 TTTCATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.26
22 3 0.11
23 17 0.63
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (24 bp):
CAAATATATACTTATATACATATA
Found at i:79181 original size:14 final size:15
Alignment explanation
Indices: 79148--79182 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
79138 ACAAATGTTG
79148 AATTCTTAAAATTATT
1 AATT-TTAAAATTATT
79164 AATTTTAAAATT-TT
1 AATTTTAAAATTATT
79178 AATTT
1 AATTT
79183 AATTAGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 8 0.42
16 4 0.21
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTAAAATTATT
Found at i:80749 original size:28 final size:28
Alignment explanation
Indices: 80668--80749 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
80658 TTTTGGAGAT
*
80668 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
80696 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
80724 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
80750 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:80892 original size:51 final size:51
Alignment explanation
Indices: 80732--80902 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
80722 GAAATAACGA
* * *
80732 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
80784 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
80837 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
80888 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
80903 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:80976 original size:27 final size:28
Alignment explanation
Indices: 80885--80988 Score: 158
Period size: 28 Copynumber: 3.8 Consensus size: 28
80875 AAAATAAAGT
*
80885 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
80913 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
80941 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
80968 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
80989 TGTGAAGAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 25 0.35
28 47 0.65
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:83421 original size:13 final size:13
Alignment explanation
Indices: 83403--83428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
83393 ACAAAGATCC
83403 ATGTATCGATACA
1 ATGTATCGATACA
83416 ATGTATCGATACA
1 ATGTATCGATACA
83429 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:83424 original size:33 final size:33
Alignment explanation
Indices: 83382--83448 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
83372 AAAATTTCCA
***
83382 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
83415 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
83448 A
1 A
83449 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:83492 original size:19 final size:18
Alignment explanation
Indices: 83468--83535 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
83458 CAGTAGCTAA
83468 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
83487 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
83502 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
83519 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
83536 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:83508 original size:13 final size:13
Alignment explanation
Indices: 83490--83514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83480 ACAATACTTA
83490 TGTATCGATACAT
1 TGTATCGATACAT
83503 TGTATCGATACA
1 TGTATCGATACA
83515 AAACTTATGT
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:83512 original size:32 final size:32
Alignment explanation
Indices: 83471--83533 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
83461 TAGCTAATTA
*
83471 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
83503 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
83534 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:83615 original size:21 final size:21
Alignment explanation
Indices: 83591--83647 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
83581 CATTTGTAGG
83591 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
83612 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
83633 ATGTATCGATACATT
1 ATGTATCGATACATT
83648 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:83658 original size:1 final size:1
Alignment explanation
Indices: 83652--83699 Score: 69
Period size: 1 Copynumber: 48.0 Consensus size: 1
83642 TACATTTAAA
***
83652 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
83700 CAAACACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:85848 original size:31 final size:31
Alignment explanation
Indices: 85805--85867 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
85795 TTTGGTATTT
*
85805 TACTTAAGTATTGATGGAAATCTCTTATGTG
1 TACTCAAGTATTGATGGAAATCTCTTATGTG
85836 TACTCAAGTATTGATGGAAATCTCTTATGTG
1 TACTCAAGTATTGATGGAAATCTCTTATGTG
85867 T
1 T
85868 CAGTAGTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (31 bp):
TACTCAAGTATTGATGGAAATCTCTTATGTG
Found at i:95581 original size:81 final size:81
Alignment explanation
Indices: 95446--95607 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
95436 AAAAAATTAA
95446 ACTAGGCCTAAATACATGTACCATAGGACTTTTAAACCATAATTAATAGCATATATGTTTCCTTA
1 ACTAGGCCTAAATACATGTACCATAGGACTTTTAAACCATAATTAATAGCATATATGTTTCCTTA
95511 AAATTAGACTTTTTAC
66 AAATTAGACTTTTTAC
* * *
95527 ACTAGGCCTAAATGCATGTACCATAGGACTTTTAAATCATAATTAATAGCATATATGTTTTCTTA
1 ACTAGGCCTAAATACATGTACCATAGGACTTTTAAACCATAATTAATAGCATATATGTTTCCTTA
*
95592 AAATTAGTCTTTTTAC
66 AAATTAGACTTTTTAC
95608 TTTAAATTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (81 bp):
ACTAGGCCTAAATACATGTACCATAGGACTTTTAAACCATAATTAATAGCATATATGTTTCCTTA
AAATTAGACTTTTTAC
Found at i:95834 original size:140 final size:135
Alignment explanation
Indices: 95593--96160 Score: 477
Period size: 140 Copynumber: 4.0 Consensus size: 135
95583 GTTTTCTTAA
* * * *
95593 AATTAGTCTTTTTACTTTAAATT--AATCAATAAGATTTCAATTAGATTTTTTTTTAACTAATAT
1 AATTAGACTTTTTA-TTT-AATTGAAATTAATAGGATTTCAATTAGA---CTTTTT-ACTAATAT
** * *
95656 GATTTTTTTGGTTAGATTTTTTTAATTTAATTGGAATTAATTA-AATTTCAATTAGACTTTGTTA
60 GATTTTTTTAATTAGA-TATTTTAATTTAATTGGAATTAA-TAGGATTTCAATTAGACTTT-TTA
*
95720 GTAAACTGTTTTTTT
122 CTAAA-TGTTTTTTT
* *
95735 AATTAGACTTTTTACATTAATTGAAATTAATAGGATTTTAATTAGACTTTTTACTAATATGATTT
1 AATTAGACTTTTTA-TTTAATTGAAATTAATAGGATTTCAATTAGACTTTTTACTAATATGA--T
* * * * *
95800 TTTTTTAATTAGATATTTTATTTTAACTGCAATTAATAGGATTTCAATTAGACTTTTCAACTGAT
63 TTTTTTAATTAGATATTTTAATTTAATTGGAATTAATAGGATTTCAATTAGACTTTT-TACT-AA
**
95865 ATAATTTTTT
126 ATGTTTTTTT
* * * *
95875 AATTAGAATTTTTATTTTAGTT-ATAGTTAATAGGATTTCAATTAAACCTTTTTACTAATATGA-
1 AATTAGACTTTTTA-TTTAATTGA-AATTAATAGGATTTCAATTAGA-CTTTTTACTAATATGAT
* * *
95938 TATTTTAATTAGA-ATTTTTACTTTAATTGGAATTAATAGGATTTCAATTTGACTTTTTTACTAA
63 TTTTTTAATTAGATA-TTTTAATTTAATTGGAATTAATAGGATTTCAATTAGAC-TTTTTACTAA
**
96002 TATGTTTTTCA
126 -ATGTTTTTTT
* *
96013 AATTAGACTTTTTATTTAATTGGAATTAATAGGATTTCAAATAGACTTTTTTTTTTTTTACTACA
1 AATTAGACTTTTTATTTAATTGAAATTAATAGGATTTCAATTAGAC--------TTTTTACTA-A
* *
96078 -ATGATTTTTTTAATTAGACT-TTTTACTCTTAATTGGAATTAATAGGATTTCAATTAGATTTTT
57 TATGATTTTTTTAATTAGA-TATTTTAAT-TTAATTGGAATTAATAGGATTTCAATTAGA--CTT
96141 TTTACTAAAATGATTTTTTT
118 TTTACT-AAATG-TTTTTTT
96161 TAGACCTTTA
Statistics
Matches: 349, Mismatches: 47, Indels: 54
0.78 0.10 0.12
Matches are distributed among these distances:
136 1 0.00
137 27 0.08
138 68 0.19
139 18 0.05
140 86 0.25
141 34 0.10
142 16 0.05
143 19 0.05
144 13 0.04
145 20 0.06
146 29 0.08
147 11 0.03
148 7 0.02
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (135 bp):
AATTAGACTTTTTATTTAATTGAAATTAATAGGATTTCAATTAGACTTTTTACTAATATGATTTT
TTTAATTAGATATTTTAATTTAATTGGAATTAATAGGATTTCAATTAGACTTTTTACTAAATGTT
TTTTT
Found at i:96064 original size:69 final size:70
Alignment explanation
Indices: 95593--96160 Score: 539
Period size: 69 Copynumber: 8.0 Consensus size: 70
95583 GTTTTCTTAA
* * * *
95593 AATTAGTCTTTTTACTTTAAATT--AATCAATAAGATTTCAATTAGATTTTTTTTTAACTAATAT
1 AATTAGACTTTTTACTTT-AATTGGAATTAATAGGATTTCAATTAGA--CTTTTTT-ACTAATAT
95656 GATTTTTTT
62 GATTTTTTT
** * * * * *
95665 GGTTAGATTTTTTTAATTTAATTGGAATTAATTA-AATTTCAATTAGACTTTGTTAGTAA-ACTG
1 AATTAGA-CTTTTTACTTTAATTGGAATTAA-TAGGATTTCAATTAGACTTTTTTACTAATA-TG
95728 -TTTTTTT
63 ATTTTTTT
* * *
95735 AATTAGACTTTTTACATTAATTGAAATTAATAGGATTTTAATTAGAC-TTTTTACTAATATGATT
1 AATTAGACTTTTTACTTTAATTGGAATTAATAGGATTTCAATTAGACTTTTTTACTAATATGA--
95799 TTTTTTT
64 TTTTTTT
* * * ** * *
95806 AATTAGA-TATTTTATTTTAACTGCAATTAATAGGATTTCAATTAGACTTTTCAACTGATAT-AA
1 AATTAGACT-TTTTACTTTAATTGGAATTAATAGGATTTCAATTAGACTTTTTTACTAATATGAT
95869 TTTTTT
65 TTTTTT
* * * ** * * *
95875 AATTAGAATTTTTATTTTAGTTATAGTTAATAGGATTTCAATTAAACCTTTTTACTAATATGA-T
1 AATTAGACTTTTTACTTTAATTGGAATTAATAGGATTTCAATTAGACTTTTTTACTAATATGATT
*
95939 ATTTT
66 TTTTT
* *
95944 AATTAGAATTTTTACTTTAATTGGAATTAATAGGATTTCAATTTGACTTTTTTACTAATATG-TT
1 AATTAGACTTTTTACTTTAATTGGAATTAATAGGATTTCAATTAGACTTTTTTACTAATATGATT
**
96008 TTTCA
66 TTTTT
*
96013 AATTAGACTTTTTA-TTTAATTGGAATTAATAGGATTTCAAATAGACTTTTTTTTTTTTTACTAC
1 AATTAGACTTTTTACTTTAATTGGAATTAATAGGATTTCAATTAGAC-------TTTTTTACTA-
96077 A-ATGATTTTTTT
58 ATATGATTTTTTT
* *
96089 AATTAGACTTTTTACTCTTAATTGGAATTAATAGGATTTCAATTAGATTTTTTTTACTAAAATGA
1 AATTAGACTTTTTACT-TTAATTGGAATTAATAGGATTTCAATTAGA-CTTTTTTACTAATATGA
96154 TTTTTTT
64 TTTTTTT
96161 TAGACCTTTA
Statistics
Matches: 410, Mismatches: 58, Indels: 56
0.78 0.11 0.11
Matches are distributed among these distances:
68 42 0.10
69 162 0.40
70 16 0.04
71 55 0.13
72 44 0.11
73 9 0.02
74 17 0.04
75 15 0.04
76 20 0.05
77 1 0.00
78 29 0.07
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (70 bp):
AATTAGACTTTTTACTTTAATTGGAATTAATAGGATTTCAATTAGACTTTTTTACTAATATGATT
TTTTT
Found at i:96093 original size:76 final size:76
Alignment explanation
Indices: 95991--96143 Score: 231
Period size: 78 Copynumber: 2.0 Consensus size: 76
95981 TCAATTTGAC
95991 TTTTTTACTAATATGTTTTTCAAATTAGACTTTTTA-T-TTAATTGGAATTAATAGGATTTCAAA
1 TTTTTTACTAATATGTTTTTCAAATTAGACTTTTTACTCTTAATTGGAATTAATAGGATTTCAAA
96054 TAGACTTTTTTT
66 TAGA-TTTTTTT
**
96066 TTTTTTACTACA-ATGATTTTTTTAATTAGACTTTTTACTCTTAATTGGAATTAATAGGATTTCA
1 TTTTTTACTA-ATATG-TTTTTCAAATTAGACTTTTTACTCTTAATTGGAATTAATAGGATTTCA
*
96130 ATTAGATTTTTTT
64 AATAGATTTTTTT
96143 T
1 T
96144 ACTAAAATGA
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
75 13 0.18
76 20 0.28
77 9 0.13
78 29 0.41
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.54
Consensus pattern (76 bp):
TTTTTTACTAATATGTTTTTCAAATTAGACTTTTTACTCTTAATTGGAATTAATAGGATTTCAAA
TAGATTTTTTT
Found at i:96218 original size:146 final size:138
Alignment explanation
Indices: 95923--96205 Score: 340
Period size: 146 Copynumber: 2.0 Consensus size: 138
95913 CAATTAAACC
*
95923 TTTTTACTAATATGATATTTTAATTAGAATTTTTACTTTAATTGGAATTAATAGGATTTCAATTT
1 TTTTTACTAATATGATATTTTAATTAGAATTTTTACTTTAATTGGAATTAATAGGATTTCAATTA
* * *
95988 GACTTTTTTACTAATATGTTTTTCAAATTAGACTTTTTATTTAATTGGAATTAATAGGATTTCAA
66 GACTTTTTTACTAAAATGTTTTT--AATTAGAC----TATTTAATTAGAATTAATAGAATTTCAA
96053 ATAGACTTTTTTTT
125 ATAGACTTTTTTTT
* *
96067 TTTTTACTACA-ATGATTTTTTTAATTAGACTTTTTACTCTTAATTGGAATTAATAGGATTTCAA
1 TTTTTACTA-ATATGA-TATTTTAATTAGAATTTTTACT-TTAATTGGAATTAATAGGATTTCAA
* * * *
96131 TTAGATTTTTTTTACTAAAATGATTTTT-TTTAGAC-CTTTAATTAGAATTAATAGAATTTCAAT
63 TTAGA-CTTTTTTACTAAAATG-TTTTTAATTAGACTATTTAATTAGAATTAATAGAATTTCAAA
*
96194 TAGA-TTTCTTTT
126 TAGACTTTTTTTT
96206 AATAAAATTT
Statistics
Matches: 123, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
139 7 0.06
140 28 0.23
144 13 0.11
145 27 0.22
146 29 0.24
147 14 0.11
148 5 0.04
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (138 bp):
TTTTTACTAATATGATATTTTAATTAGAATTTTTACTTTAATTGGAATTAATAGGATTTCAATTA
GACTTTTTTACTAAAATGTTTTTAATTAGACTATTTAATTAGAATTAATAGAATTTCAAATAGAC
TTTTTTTT
Found at i:98153 original size:2 final size:2
Alignment explanation
Indices: 98146--98192 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
98136 CAAAAAGATT
* * *
98146 TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
98188 TA TA T
1 TA TA T
98193 CCTTTTACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98233 original size:2 final size:2
Alignment explanation
Indices: 98226--98254 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
98216 TTAACTATTT
98226 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
98255 ACAAGTCTGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:98601 original size:23 final size:23
Alignment explanation
Indices: 98574--98626 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
98564 AAATTTTAAA
98574 ATATATATTCATACTATATCATAT-T
1 ATATAT-TTCATAC-ATATCAT-TCT
*
98599 ATATATTTTATACATATCATTCT
1 ATATATTTCATACATATCATTCT
98622 ATATA
1 ATATA
98627 ATCGTATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 13 0.50
24 6 0.23
25 6 0.23
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATTTCATACATATCATTCT
Found at i:98905 original size:16 final size:16
Alignment explanation
Indices: 98864--98911 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
98854 AGTTTATCGG
*
98864 ATTTTAAATA-ATATT
1 ATTTTAAATATATAAT
* *
98879 ACTTTATATATATAAT
1 ATTTTAAATATATAAT
*
98895 ATTTTAAATATAAAAT
1 ATTTTAAATATATAAT
98911 A
1 A
98912 AATAAAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTAAATATATAAT
Found at i:99090 original size:32 final size:32
Alignment explanation
Indices: 99054--99120 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
99044 ATTTTCGAAT
*
99054 AATTATATTTAATATTCATTAAATTTAAAATC
1 AATTATATTTAATATTCATCAAATTTAAAATC
*
99086 AATTATGTTTAATATTCATCAAATTTAAAATC
1 AATTATATTTAATATTCATCAAATTTAAAATC
99118 AAT
1 AAT
99121 ATCAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (32 bp):
AATTATATTTAATATTCATCAAATTTAAAATC
Found at i:99112 original size:16 final size:16
Alignment explanation
Indices: 99055--99113 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
99045 TTTTCGAATA
*
99055 ATTATATTTAATATTC
1 ATTAAATTTAATATTC
*
99071 ATTAAATTTAA-AATC
1 ATTAAATTTAATATTC
**
99086 AATTATGTTTAATATTC
1 -ATTAAATTTAATATTC
*
99103 ATCAAATTTAA
1 ATTAAATTTAA
99114 AATCAATATC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 3 0.09
16 27 0.82
17 3 0.09
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTAAATTTAATATTC
Found at i:101302 original size:2 final size:2
Alignment explanation
Indices: 101295--101325 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
101285 AACGGAGGCT
101295 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
101326 AGGCAGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:105514 original size:7 final size:7
Alignment explanation
Indices: 105484--105564 Score: 65
Period size: 7 Copynumber: 10.9 Consensus size: 7
105474 TTTTTTAAAA
105484 TTATAATT
1 TTAT-ATT
105492 TTAT-TT
1 TTATATT
105498 TTAAATATT
1 TT--ATATT
105507 TTATATT
1 TTATATT
* *
105514 TTTTAAT
1 TTATATT
*
105521 ATATATT
1 TTATATT
*
105528 AAATATATAT
1 --TTATAT-T
105538 TTATATT
1 TTATATT
105545 TTATATT
1 TTATATT
105552 TTATATT
1 TTATATT
105559 TTATAT
1 TTATAT
105565 ATTAAAATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
6 4 0.07
7 35 0.57
8 11 0.18
9 10 0.16
10 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTATATT
Found at i:105565 original size:31 final size:30
Alignment explanation
Indices: 105484--105567 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
105474 TTTTTTAAAA
*
105484 TTATAATTTTAT-TTTTAAATATTTTATATT
1 TTAT-ATTTTATATTTTATATATTTTATATT
* * * **
105514 TTTTAATATATATTAAATATATATTTATATT
1 TTATATTTTATATTTTATATAT-TTTATATT
105545 TTATATTTTATATTTTATATATT
1 TTATATTTTATATTTTATATATT
105568 AAAATTATAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
29 5 0.12
30 11 0.27
31 25 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATATTTTATATTTTATATATTTTATATT
Found at i:105585 original size:54 final size:53
Alignment explanation
Indices: 105484--105623 Score: 121
Period size: 52 Copynumber: 2.7 Consensus size: 53
105474 TTTTTTAAAA
* ** *
105484 TTATAATTTTATTTTTAAATATTTTATATTTTTTAATATATATTAAATATATAT
1 TTATAATTTTATTTTT-AATATTTTATATATTAAAATATATAATAAATATATAT
105538 TTAT-ATTTTATATTTT-ATATTTTATATATTAAAATTATATTAATAAATA-A-A-
1 TTATAATTTTAT-TTTTAATATTTTATATATTAAAA-TATA-TAATAAATATATAT
* * **
105589 TTATAA-TATATTTTTATTATAATATATAATTAAAA
1 TTATAATTTTATTTTTAATATTTTATAT-ATTAAAA
105624 ATAATATGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
50 4 0.06
51 16 0.22
52 24 0.33
53 12 0.17
54 16 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (53 bp):
TTATAATTTTATTTTTAATATTTTATATATTAAAATATATAATAAATATATAT
Found at i:105608 original size:33 final size:33
Alignment explanation
Indices: 105571--105635 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
105561 ATATATTAAA
* *
105571 ATTATATTA-ATAAATAAATTATAATATATTTTT
1 ATTATAATATATAAATAAA-AATAATATATTTTT
* *
105604 ATTATAATATATAATTAAAAATAATATGTTTT
1 ATTATAATATATAAATAAAAATAATATATTTT
105636 ACTCTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (33 bp):
ATTATAATATATAAATAAAAATAATATATTTTT
Found at i:107054 original size:10 final size:10
Alignment explanation
Indices: 107032--107077 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
107022 CGATATTAAT
107032 TTAATTAAA-A
1 TTAA-TAAATA
107042 TTAATAAATA
1 TTAATAAATA
*
107052 TTAATTAATA
1 TTAATAAATA
107062 TTAATATAATA
1 TTAATA-AATA
107073 TTAAT
1 TTAAT
107078 CATTATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
9 4 0.12
10 19 0.59
11 9 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TTAATAAATA
Found at i:107057 original size:20 final size:21
Alignment explanation
Indices: 107028--107077 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
107018 TTATCGATAT
107028 TAAT-TTAATTAAAATTAATA
1 TAATATTAATTAAAATTAATA
*
107048 -AATATTAATTAATATTAATA
1 TAATATTAATTAAAATTAATA
107068 TAATATTAAT
1 TAATATTAAT
107078 CATTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.11
20 15 0.56
21 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATATTAATTAAAATTAATA
Found at i:107626 original size:13 final size:14
Alignment explanation
Indices: 107608--107640 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
107598 AAGTTTAATC
107608 TAATTAT-TTTAAA
1 TAATTATGTTTAAA
107621 TAATTATGTTTAAA
1 TAATTATGTTTAAA
*
107635 AAATTA
1 TAATTA
107641 ATATTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TAATTATGTTTAAA
Found at i:108319 original size:18 final size:18
Alignment explanation
Indices: 108288--108325 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
108278 ATATGTTTTT
* *
108288 TAAAATATATTTAAAAAA
1 TAAAAAATAATTAAAAAA
108306 TAAAAAATAATTAAAAAA
1 TAAAAAATAATTAAAAAA
108324 TA
1 TA
108326 CAATATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAATAATTAAAAAA
Found at i:108596 original size:3 final size:3
Alignment explanation
Indices: 108588--108623 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
108578 ATATATTTAC
108588 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
108624 CAATAGGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:108812 original size:14 final size:14
Alignment explanation
Indices: 108793--108826 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
108783 TCCCCACATC
108793 AAATAACAATTTTA
1 AAATAACAATTTTA
108807 AAATAACAATTTTA
1 AAATAACAATTTTA
*
108821 AGATAA
1 AAATAA
108827 TTGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (14 bp):
AAATAACAATTTTA
Found at i:108931 original size:17 final size:18
Alignment explanation
Indices: 108911--108944 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
108901 ATAATATATT
108911 TATA-TTTAAAATTTTAA
1 TATATTTTAAAATTTTAA
*
108928 TATATTTTAATATTTTA
1 TATATTTTAAAATTTTA
108945 TATTTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTTAAAATTTTAA
Found at i:109381 original size:3 final size:3
Alignment explanation
Indices: 109373--109405 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
109363 GGTGTTTGGC
*
109373 GGA GGA GGA GGA GGA GGA GGA GGT GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
109406 TCGAAACTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.67, T:0.03
Consensus pattern (3 bp):
GGA
Found at i:109835 original size:18 final size:17
Alignment explanation
Indices: 109800--109846 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
109790 CACAATATCA
*
109800 AAAATAAT-TAAAATTT
1 AAAATAATATAAAAATT
*
109816 AATATAAATATAAAAATT
1 AAAAT-AATATAAAAATT
109834 AAAATAATATAAA
1 AAAATAATATAAA
109847 TATATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 11 0.42
18 11 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATATAAAAATT
Found at i:109841 original size:23 final size:24
Alignment explanation
Indices: 109805--109850 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
109795 TATCAAAAAT
109805 AATTAAAATTTAATATAAATATAAA
1 AATTAAAA-TTAATATAAATATAAA
109830 AATTAAAA-TAATATAAATATA
1 AATTAAAATTAATATAAATATA
109851 TTTATATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AATTAAAATTAATATAAATATAAA
Found at i:109903 original size:18 final size:17
Alignment explanation
Indices: 109863--109916 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
109853 TATATCTCAA
*
109863 AATTTATTTATAATACA-
1 AATTTATATA-AATACAT
109880 AA-TTAT-TAAAATAACAT
1 AATTTATAT-AAAT-ACAT
109897 AATTTATATAAATACAT
1 AATTTATATAAATACAT
109914 AAT
1 AAT
109917 AATTTTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 11 0.34
18 8 0.25
19 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTATATAAATACAT
Found at i:110232 original size:13 final size:13
Alignment explanation
Indices: 110214--110239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110204 TAAATATTTT
110214 TACTTAAATAAAA
1 TACTTAAATAAAA
110227 TACTTAAATAAAA
1 TACTTAAATAAAA
110240 CAACCCACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TACTTAAATAAAA
Found at i:110349 original size:19 final size:20
Alignment explanation
Indices: 110325--110369 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
110315 ATATTTTTAT
*
110325 TAATAAATA-AATATAATTA
1 TAATAAATATAATATAAATA
110344 TAAT-AATATAATATAAATA
1 TAATAAATATAATATAAATA
110363 TAATAAA
1 TAATAAA
110370 AATATACTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAAATATAATATAAATA
Found at i:110362 original size:11 final size:11
Alignment explanation
Indices: 110327--110375 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
110317 ATTTTTATTA
110327 ATAA-ATAAAT
1 ATAATATAAAT
110337 ATAATTATAATAAT
1 ATAA-TAT-A-AAT
110351 ATAATATAAAT
1 ATAATATAAAT
*
110362 ATAATAAAAAT
1 ATAATATAAAT
110373 ATA
1 ATA
110376 CTACCACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 4 0.12
11 16 0.47
12 3 0.09
13 4 0.12
14 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:110867 original size:18 final size:18
Alignment explanation
Indices: 110819--110870 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
110809 CAAAAGTTCA
110819 TTTTATAATTCAT-TATAT
1 TTTTATAATT-ATATATAT
* *
110837 TATTAAAATATTATATATAT
1 T-TTTATA-ATTATATATAT
110857 TTTTATAATTATAT
1 TTTTATAATTATAT
110871 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATAATTATATATAT
Found at i:116548 original size:18 final size:17
Alignment explanation
Indices: 116507--116541 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
116497 CCTTATTTAA
116507 AAATAAAAAAAAATATT
1 AAATAAAAAAAAATATT
*
116524 AATATAAAAATAAATATT
1 AA-ATAAAAAAAAATATT
116542 TTAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAAAAAAATATT
Found at i:121074 original size:2 final size:2
Alignment explanation
Indices: 121067--121099 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
121057 GCTAAGCTCT
121067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
121100 TAAGGTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123396 original size:3 final size:3
Alignment explanation
Indices: 123388--123430 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
123378 TTTGGTTTCA
123388 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
123431 GTGTATGGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:123777 original size:44 final size:44
Alignment explanation
Indices: 123714--123801 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
123704 AGAACTTGAG
*
123714 CAAGGGACATGAAAAAGATTAGCCATGGACACCTCTAGATTGGA
1 CAAGGGACATGAAAAAGATTAACCATGGACACCTCTAGATTGGA
*
123758 CAAGGGACATGAAAAAGATTAACCATGGACACCTTTAGATTGGA
1 CAAGGGACATGAAAAAGATTAACCATGGACACCTCTAGATTGGA
123802 GGTGGGGCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (44 bp):
CAAGGGACATGAAAAAGATTAACCATGGACACCTCTAGATTGGA
Found at i:125521 original size:26 final size:27
Alignment explanation
Indices: 125484--125550 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
125474 AATCACTCTT
* *
125484 TGTTTGT-CAAAATAGTGGTTACTTTG
1 TGTTTGTAAAAAATAGTAGTTACTTTG
* *
125510 TGTTTGTAAAAAATAGTAGTTTCTTTT
1 TGTTTGTAAAAAATAGTAGTTACTTTG
* *
125537 TATTTGTCAAAAAT
1 TGTTTGTAAAAAAT
125551 GGTGATATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 7 0.21
27 27 0.79
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (27 bp):
TGTTTGTAAAAAATAGTAGTTACTTTG
Found at i:130095 original size:24 final size:24
Alignment explanation
Indices: 130008--130097 Score: 74
Period size: 24 Copynumber: 3.6 Consensus size: 24
129998 AAAAGCCACC
* *
130008 TTTTGTTTGTCAAAAATGATGGTTA
1 TTTTGTTTGTCAAAAATGGTGG-CA
* *
130033 CTTTGTGTTTGTCAAAAATGGAT-TCT
1 -TTT-TGTTTGTCAAAAATGG-TGGCA
* *
130059 TTTTATTTATCAAAAATGGTGGCA
1 TTTTGTTTGTCAAAAATGGTGGCA
*
130083 TGTTGTTTGTCAAAA
1 TTTTGTTTGTCAAAA
130098 TTTATGGCTA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.02
24 27 0.54
25 3 0.06
26 3 0.06
27 15 0.30
28 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.46
Consensus pattern (24 bp):
TTTTGTTTGTCAAAAATGGTGGCA
Found at i:131299 original size:16 final size:16
Alignment explanation
Indices: 131269--131328 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
131259 TTGAATATCC
131269 ATAAAAACACCAAAAAA
1 ATAAAAA-ACCAAAAAA
*
131286 A-AGAAAATCCAAAATAA
1 ATA-AAAAACCAAAA-AA
131303 ATAAAAAACCAAAAAGA
1 ATAAAAAACCAAAAA-A
131320 ACTAAAAAA
1 A-TAAAAAA
131329 AATCCAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 8 0.22
17 20 0.56
18 8 0.22
ACGTcount: A:0.75, C:0.13, G:0.03, T:0.08
Consensus pattern (16 bp):
ATAAAAAACCAAAAAA
Found at i:132328 original size:18 final size:18
Alignment explanation
Indices: 132305--132343 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
132295 AAATATAAAA
*
132305 TTTAAAATTAAAGTTAAT
1 TTTAAAATTAAAGTCAAT
* *
132323 TTTAAATTTATAGTCAAT
1 TTTAAAATTAAAGTCAAT
132341 TTT
1 TTT
132344 TTTACAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTAAAATTAAAGTCAAT
Found at i:132493 original size:8 final size:8
Alignment explanation
Indices: 132482--132514 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
132472 AATTTGTCTA
132482 TTTATTTT
1 TTTATTTT
132490 TTTATTTT
1 TTTATTTT
*
132498 TTTATCTT
1 TTTATTTT
132506 TTTATTTT
1 TTTATTTT
132514 T
1 T
132515 ACAATAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTATTTT
Found at i:140649 original size:18 final size:18
Alignment explanation
Indices: 140626--140661 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
140616 TAAATTTTTA
* *
140626 TTTAAAATTTATATATTT
1 TTTAAAAATAATATATTT
140644 TTTAAAAATAATATATTT
1 TTTAAAAATAATATATTT
140662 ATATATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAAAATAATATATTT
Found at i:140728 original size:21 final size:22
Alignment explanation
Indices: 140704--140753 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
140694 TATTTACGAT
* * *
140704 ATTTTATATAAATTTTATT-TA
1 ATTTTATAAAAATATAATTCTA
140725 ATTTTA-AAAAATATAATTCTA
1 ATTTTATAAAAATATAATTCTA
140746 ATTTTATA
1 ATTTTATA
140754 GATAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.38
21 14 0.58
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTATAAAAATATAATTCTA
Found at i:140952 original size:3 final size:3
Alignment explanation
Indices: 140944--140976 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
140934 TTTGGTTTCA
140944 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
140977 GTATGGACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:141176 original size:14 final size:14
Alignment explanation
Indices: 141157--141184 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
141147 AATTATAAAA
141157 AATATAAAAATATT
1 AATATAAAAATATT
141171 AATATAAAAATATT
1 AATATAAAAATATT
141185 TTTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:143898 original size:45 final size:48
Alignment explanation
Indices: 143798--143906 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 48
143788 TTTTTAGGAT
*
143798 GAAATTCC-AAAAAATTTGAATATCCATAAAAACATAAAAAAAATAAA
1 GAAATTCCAAAAAAAATTGAATATCCATAAAAACATAAAAAAAATAAA
** *
143845 GAAATTCCAAAAAAAATTGAATAT-C-TGTAAACA-CAAAAAAATAAA
1 GAAATTCCAAAAAAAATTGAATATCCATAAAAACATAAAAAAAATAAA
143890 GAAATTCCAACAAAAAA
1 GAAATTCCAA-AAAAAA
143907 CCAAAAGGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 21 0.38
46 12 0.21
47 9 0.16
48 14 0.25
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (48 bp):
GAAATTCCAAAAAAAATTGAATATCCATAAAAACATAAAAAAAATAAA
Done.