Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168022.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_276, 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: 40149
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
File 1 of 2
Found at i:596 original size:182 final size:182
Alignment explanation
Indices: 295--1513 Score: 601
Period size: 177 Copynumber: 6.8 Consensus size: 182
285 TTTAAAACTT
* * *
295 TTACTTATTAAGTTTTGGAACATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAA
1 TTACTTATTAAATTTTGGAACATTAATAAATTTATATTATTTTATTTCAAATAAGCTTAAATGAA
* * ** *
360 TAGAACCAATTGTTTTATGACAAAACAAAGGGTTGTAATGTTTTGAAATAGATAATTATT-AAGA
66 TAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAATAGATAATTATTCAA-A
424 TAGTCATAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTTAATTTTC
130 TAGTCATAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTTAATTTTC
* **
477 TTACTTTTTAAATTTTGGAATGTTAATAAA-TTAGTATTATTTTATTTCAAATAAGC-TAACATG
1 TTACTTATTAAATTTTGGAACATTAATAAATTTA-TATTATTTTATTTCAAATAAGCTTAA-ATG
* * * * * *
540 AATTGAAATAATTGTTTTATTACGAAACAAAATGTTACAATGATTTGAAGTAGATAATTATTCAA
64 AATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAATAGATAATTATTCAA
* * *** *
605 ATAGTCATGACTATTTGAACTTGTTTGGTAAAC----TTATTTTTATAAATCTTT-
129 ATAGTCATAACTATTTGAACTTATTCAATAAACAGATTTATTTTT-TTAAT-TTTC
* * ** * * * * *
656 TAACTTATT-AATTGTT-GAATATTAATAAATCAATATTA-TTTAATCCGAATTAAGCTCATATT
1 TTACTTATTAAATT-TTGGAACATTAATAAATTTATATTATTTTATTTC-AAATAAGCTTA-AAT
* * * * * *
718 G-AT-GGAACAATTATTTTATGACAAAACAAAAAGTCATAA-GAATTTGAAATAAAT-ATGTATT
63 GAATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATG-ATTTGAAATAGATAAT-TA-T
* * * * * *
779 TCAAATAGTCATAAC-ATTTAAATTTGTTCGATAAATAGATTTA-TTTTTTAATCTT-
125 TCAAATAGTCATAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTTAATTTTC
** * * * * * *
834 TTACTTATT-AATTGTTTAAATATTAATAAATTTGTATT-TTTCTTTTTGGAAGTAAGCTTATAT
1 TTACTTATTAAATT-TTGGAACATTAATAAATTTATATTATTT-TATTT-CAAATAAGCTTAAAT
* * ** * * * * * ** *
897 GAACA-ATA-AATCATTATATGA-AAACCAAAAGGTTATAGGCTAATTCCAAATCA-ATAATTGT
63 GAATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACA--ATGATTTGAAAT-AGATAATTAT
* * * * ** * * * *
958 TCAAAT-GGCTATAATTATTTAAACTTGTTCGGTAAATAGATTCA-TTTTTTAAATCTC
125 TCAAATAGTC-ATAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTTAATTTTC
* * * * ** * * **
1015 TTAATTATTAATTTTTAGAATATTAATAACA-TGGTATTATTTTATTTCCAATAACCTTTTATGA
1 TTACTTATTAAATTTTGGAACATTAATAA-ATTTATATTATTTTATTTCAAATAAGCTTAAATGA
* * * * * *
1079 ACT-GAAATAAGTT-TTTTATGACAAAACAAAAGGTCATAACGATTTGAAACAGATAACTATTCA
65 A-TAGAAACAA-TTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAATAGATAATTATTCA
* ** * * **
1142 AATAGTCATGAC--TTT---C-TA---GGTAAACATATTTATTTCTAAAATTTT-
128 AATAGTCATAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTTAATTTTC
* *** * * * * * **
1187 TAACTTATT-AATTGTCAAAATATTAATAAAATTAGTATGATTTTAATCCAAATAAGCTTGTATG
1 TTACTTATTAAATT-TTGGAACATTAATAAATTTA-TATTATTTTATTTCAAATAAGCTTAAATG
* * * * * * **
1251 AATAGAAACAATTGTTTTATAACAAAACAAAATGTCATAAAGATTTGAAATAAATAATTGCTCAA
64 AATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAATAGATAATTATTCAA
* * ** * *
1316 ACAGTCATAACTATTTGAAC-AAGTTTGATAAATAGATTTA-TTTTTTAA--ATC
129 ATAGTCATAACTATTTGAACTTA-TTCAATAAACAGATTTATTTTTTTAATTTTC
* * * * * * * * * *
1367 --ACTTTTTAATTTTTGAAATATTAATAGA-TTAGTATTACTTTATTCCTAATAAACTTATATGA
1 TTACTTATTAAATTTTGGAACATTAATAAATTTA-TATTATTTTATTTCAAATAAGCTTAAATGA
* * * * *
1429 ACA-AAACCATTTGTTTTATGACAAAACAAAAAGTAATAATGATTTGAAATATG-TAATTATTCA
65 ATAGAAA-CAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAATA-GATAATTATTCA
* *
1492 AATAGTCATAATTATTTAAACT
128 AATAGTCATAACTATTTGAACT
1514 GATTAGGTAA
Statistics
Matches: 799, Mismatches: 177, Indels: 126
0.73 0.16 0.11
Matches are distributed among these distances:
171 4 0.01
172 35 0.04
173 90 0.11
175 4 0.01
176 7 0.01
177 158 0.20
178 106 0.13
179 71 0.09
180 79 0.10
181 70 0.09
182 158 0.20
183 17 0.02
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (182 bp):
TTACTTATTAAATTTTGGAACATTAATAAATTTATATTATTTTATTTCAAATAAGCTTAAATGAA
TAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAATAGATAATTATTCAAAT
AGTCATAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTTAATTTTC
Found at i:1566 original size:20 final size:20
Alignment explanation
Indices: 1541--1628 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
1531 AATTAATGTT
*
1541 ATAATAATATATTTTAATTA
1 ATAATAATATATATTAATTA
*
1561 ATAATAATAAATATTAATTA
1 ATAATAATATATATTAATTA
** *
1581 ATAA-AATAT-TAAAAAATTT
1 ATAATAATATAT-ATTAATTA
*
1600 ATAATAATATAAATTAAATTA
1 ATAATAATATATATT-AATTA
1621 AT-ATAATA
1 ATAATAATA
1629 ATAATAGAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.02
19 13 0.24
20 34 0.63
21 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATAATATATATTAATTA
Found at i:1568 original size:10 final size:10
Alignment explanation
Indices: 1555--1634 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
1545 TAATATATTT
1555 TAATTAATAA
1 TAATTAATAA
* *
1565 TAATAAATAT
1 TAATTAATAA
1575 TAATTAATAA
1 TAATTAATAA
*
1585 AATATTAA-AA
1 TA-ATTAATAA
*
1595 -AATTTATAA
1 TAATTAATAA
*
1604 TAATATAA-AT
1 TAAT-TAATAA
1614 TAAATTAAT-A
1 T-AATTAATAA
1624 TAA-TAATAA
1 TAATTAATAA
1633 TA
1 TA
1635 GAGATAGTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
8 8 0.15
9 8 0.15
10 28 0.52
11 10 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATTAATAA
Found at i:2799 original size:177 final size:177
Alignment explanation
Indices: 2141--3425 Score: 855
Period size: 177 Copynumber: 7.2 Consensus size: 177
2131 TATTAACATA
* * * * * *
2141 ACAAAACCAAAA-TCATAA-CATGTT-AAATAAATAACTGCTCAAATAGCCATAA-TGATTAGAA
1 ACAAAACAAAAAGTCATAATGAT-TTGAAATAAATAATTGTTCAAATAGTCATAACT-ATTTGAA
* *
2202 CTTGTTT-AGTAAACAGATTGTA-TTTTTAAATCTTTTACTTATTAATTGTCTT--AATATTAAT
64 CTGGTTTGA-TAAACAAATT-TATTTTTTAAATC----ACTTATTAATT-T-TTGAAATATTAAT
* * *
2263 AAATTTGTATTATTTT-TATTCGAAATAAGCTTAG-ATGAATAGAAAAAATTCTTTTTATGG
121 AAATTAGTATTATTTTAT-TTCG-AATAAGCTT-GTATGAATAGAAACAATT-GTTTTAT-G
* * * * * * * * *
2323 ACAAAACAAAAGGTTATAGCT-ATTTCAAATAGATAATTATTCAAACT-GTCCTAATTATTTAAA
1 ACAAAACAAAAAGTCATA-ATGATTTGAAATAAATAATTGTTCAAA-TAGTCATAACTATTTGAA
* * * * * * *
2386 TTTGTTT-AGTAAACAAAGTCATTTTTTAAATCTCTTTATCATTAATTTTTTGGGATTATTAATA
64 CTGGTTTGA-TAAACAAATTTATTTTTTAAATCAC--T-T-ATTAA-TTTTT-GAAATATTAATA
* *
2450 AATTAGTATTATTTTATTTTGAATAAG-TTATATGAACT-GAAACAACTCT-TTTTATG
122 AATTAGTATTATTTTATTTCGAATAAGCTTGTATGAA-TAGAAACAA-T-TGTTTTATG
* * * * * * * * * *
2506 ACAAATCAAAAGGTCATAACGATTTGAAATAGATAATTATTCAAATTGTCATGATTATATGATCT
1 ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
* * * * * * * **
2571 AGTGTGGTAAAC--A--TATTTTTAAAAATTTTTACTTACTAATTGTCAAAATATTAATAAATTA
66 GGTTTGATAAACAAATTTATTTTT-TAAA---TCACTTATTAATTTTTGAAATATTAATAAATTA
* * * **
2632 GTATTATTTTAATGCAAATAAGCTTGTATGAATAGAAACAATTGTTTTACA
127 GTATTATTTTATTTCGAATAAGCTTGTATGAATAGAAACAATTGTTTTATG
2683 ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
1 ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
* * * * * * * *
2748 AGTTTGATACATAGATTTATTGTCTAAATCACTTTTTAATTTTTGAAATATTAATAGATTAGTAT
66 GGTTTGATAAACAAATTTATTTTTTAAATCACTTATTAATTTTTGAAATATTAATAAATTAGTAT
* * * * * * * *
2813 TACTTTATTCCGAATAAACTTATATGAACAAAAACATTTGTTGTATG
131 TATTTTATTTCGAATAAGCTTGTATGAATAGAAACAATTGTTTTATG
* * * *
2860 ACAAAACAAAAAGTAATAATGATTTGAAATATATAATTGTTC---TAGT-ATAATTTTTTGAACT
1 ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
* * * *
2921 GGTTAGGTAAA-AAAATTATTTTTTAAATCTCTTACTTATTATTTTTTGAAATATTAATAAATTC
66 GGTTTGATAAACAAATTTATTTTTTAAA--TC--ACTTATTAATTTTTGAAATATTAATAAATT-
* * * *
2985 A-TTTTATTTTATTTTGAATAAGCTAGTATGAATTGAGAA-AATTGTTTTATG
126 AGTATTATTTTATTTCGAATAAGCTTGTATGAATAGA-AACAATTGTTTTATG
* * * * * * * * ** * *
3036 GCAAGATAAAAGGTCATAACGATTTGAAATAGATAATTTTTCATATAGTTTTAAATATTTGAATT
1 ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
** * * * * *
3101 GGTTCAACAAACAAATTTATTTTTTAAATCCCTTGGTTATTAATTTTTGGAATATTATTAGATTA
66 GGTTTGATAAACAAATTTATTTTTTAAATCAC----TTATTAATTTTTGAAATATTAATAAATTA
* * **
3166 GTATTGTTTTATTTTGAATAAGCTTGTATGAATAGAAGTAATTGTTTTATG
127 GTATTATTTTATTTCGAATAAGCTTGTATGAATAGAAACAATTGTTTTATG
* * * * * *
3217 ACATAACAAAATGTTATAATGATTTGAAGTATAGAATTGTTCAAATAGTCATAACTATTTGAAC-
1 ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
* * * * * * *
3281 GGATTCAGTAAACATATTCATTTTTTAAATCTCTTATTAATTTTTGAAAGATTAATAAATTATTA
66 GGTTTGA-TAAACAAATTTATTTTTTAAATCACTTATTAATTTTTGAAATATTAATAAATTAGTA
* * * *
3346 TTATTTTATTTCAAATAAGCATGTATG-ATAAAAAACAATTGTTATATG
130 TTATTTTATTTCGAATAAGCTTGTATGAAT-AGAAACAATTGTTTTATG
* * * *
3394 ACCAAACAAAAGGTGATAACGATTTGAAATAA
1 ACAAAACAAAAAGTCATAATGATTTGAAATAA
3426 TATCTTATTA
Statistics
Matches: 864, Mismatches: 186, Indels: 111
0.74 0.16 0.10
Matches are distributed among these distances:
172 12 0.01
173 20 0.02
174 6 0.01
176 99 0.11
177 300 0.35
178 18 0.02
179 17 0.02
180 32 0.04
181 158 0.18
182 12 0.01
183 72 0.08
184 78 0.09
185 12 0.01
186 27 0.03
187 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (177 bp):
ACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTGTTCAAATAGTCATAACTATTTGAACT
GGTTTGATAAACAAATTTATTTTTTAAATCACTTATTAATTTTTGAAATATTAATAAATTAGTAT
TATTTTATTTCGAATAAGCTTGTATGAATAGAAACAATTGTTTTATG
Found at i:3576 original size:18 final size:19
Alignment explanation
Indices: 3546--3582 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3536 TTCAATATGT
3546 TTAATTAATAATATGATTA
1 TTAATTAATAATATGATTA
*
3565 TTAATT-ATAATATTATTA
1 TTAATTAATAATATGATTA
3583 GTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAATTAATAATATGATTA
Found at i:3879 original size:14 final size:13
Alignment explanation
Indices: 3860--3919 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
3850 AATATTTTGA
3860 ATAATTAAGTAATT
1 ATAATTAA-TAATT
3874 ATAATTAATAATT
1 ATAATTAATAATT
* *
3887 AATATTTAACAATT
1 -ATAATTAATAATT
3901 AT-A-TATATAATT
1 ATAATTA-ATAATT
3913 A-AATTAA
1 ATAATTAA
3920 ATTCTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 9 0.24
14 19 0.50
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:3886 original size:7 final size:7
Alignment explanation
Indices: 3859--3901 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
3849 AAATATTTTG
3859 AATAATT
1 AATAATT
3866 AAGTAATT
1 AA-TAATT
3874 -ATAATT
1 AATAATT
3880 AATAATT
1 AATAATT
*
3887 AATATTT
1 AATAATT
*
3894 AACAATT
1 AATAATT
3901 A
1 A
3902 TATATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
6 5 0.16
7 21 0.68
8 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (7 bp):
AATAATT
Found at i:4019 original size:21 final size:22
Alignment explanation
Indices: 3975--4020 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3965 AAATTGATTA
*
3975 TTAAAATAAAATAAAATAATAT
1 TTAAAATAAAATAAAATAAGAT
* *
3997 TTAAAAT-AAATACAATTAGAT
1 TTAAAATAAAATAAAATAAGAT
4018 TTA
1 TTA
4021 TAACTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAAATAAAATAAAATAAGAT
Found at i:4755 original size:10 final size:10
Alignment explanation
Indices: 4736--4774 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
4726 CATGTTATTC
4736 ATTA-TAATA
1 ATTATTAATA
4745 ATTATTAATA
1 ATTATTAATA
4755 ATTAATTAATA
1 ATT-ATTAATA
*
4766 ATAATTAAT
1 ATTATTAAT
4775 TAACCATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 4 0.15
10 14 0.52
11 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTATTAATA
Found at i:4762 original size:14 final size:14
Alignment explanation
Indices: 4739--4777 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
4729 GTTATTCATT
*
4739 ATAA-TAATTATTA
1 ATAATTAATTAATA
4752 ATAATTAATTAATA
1 ATAATTAATTAATA
4766 ATAATTAATTAA
1 ATAATTAATTAA
4778 CCATCGACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATTAATTAATA
Found at i:5260 original size:11 final size:11
Alignment explanation
Indices: 5235--5274 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5225 ATTATTTTTG
*
5235 TTTATATAATTA
1 TTTAT-TAATAA
5247 TTTATTAATAA
1 TTTATTAATAA
5258 TTTATTAATAA
1 TTTATTAATAA
5269 -TTATTA
1 TTTATTA
5275 TAAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 6 0.22
11 16 0.59
12 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTATTAATAA
Found at i:5296 original size:23 final size:24
Alignment explanation
Indices: 5248--5297 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
5238 ATATAATTAT
* *
5248 TTATTAATAATTTATTAATAATTA
1 TTATAAATAATTTATTAATAAATA
5272 TTATAAAT-ATTTA-TAATCAAATA
1 TTATAAATAATTTATTAAT-AAATA
5295 TTA
1 TTA
5298 ATAATAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATAAATAATTTATTAATAAATA
Found at i:5303 original size:23 final size:23
Alignment explanation
Indices: 5249--5303 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
5239 TATAATTATT
*
5249 TATTAAT-A-ATTTATTAATAAT
1 TATTAATAATATTTATTAATAAA
5270 TATT-ATAAATATTTA-TAATCAAA
1 TATTAAT-AATATTTATTAAT-AAA
5293 TATTAATAATA
1 TATTAATAATA
5304 ACTATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 2 0.07
21 4 0.14
22 5 0.18
23 15 0.54
24 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTAATAATATTTATTAATAAA
Found at i:5403 original size:28 final size:25
Alignment explanation
Indices: 5352--5403 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 25
5342 AGTATTATTA
5352 ATTAATTATGAATATTATAATTAAT
1 ATTAATTATGAATATTATAATTAAT
*
5377 ATTAATTATTTAATAGTATATAATTAA
1 ATTAATTA-TGAATA-T-TATAATTAA
5404 GTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 5 0.22
27 1 0.04
28 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
ATTAATTATGAATATTATAATTAAT
Found at i:5409 original size:32 final size:29
Alignment explanation
Indices: 5338--5413 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
5328 CTTCTATTTA
*
5338 AATAAGTATTATTAATTAATTATGAATAT
1 AATAAGTAATATTAATTAATTATGAATAT
* * * *
5367 TATAATTAATATTAATTATTTAATAGTATAT
1 AATAAGTAATATTAATTAATT-AT-GAATAT
5398 AATTAAGTAATATTAA
1 AA-TAAGTAATATTAA
5414 AATTATTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 17 0.46
30 2 0.05
31 6 0.16
32 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
AATAAGTAATATTAATTAATTATGAATAT
Found at i:5544 original size:17 final size:15
Alignment explanation
Indices: 5522--5556 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
5512 TTTATTTTTA
5522 ATTTAAACAAATAATAT
1 ATTTAAAC-AAT-ATAT
5539 ATTTAAACAATATAT
1 ATTTAAACAATATAT
5554 ATT
1 ATT
5557 AGTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAACAATATAT
Found at i:6139 original size:25 final size:22
Alignment explanation
Indices: 6110--6175 Score: 62
Period size: 26 Copynumber: 2.9 Consensus size: 22
6100 TAATCTTATA
6110 ATATATAAATATTTTTATTTATT
1 ATATATAAATATTTTTATTT-TT
* *
6133 ATGTATATAAAATAGTTTAATTTTT
1 A--TATAT-AAATATTTTTATTTTT
*
6158 A-ATATAAATATATTTATT
1 ATATATAAATATTTTTATT
6176 AATAGTAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
21 10 0.29
22 4 0.11
23 1 0.03
25 8 0.23
26 12 0.34
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
ATATATAAATATTTTTATTTTT
Found at i:6209 original size:16 final size:16
Alignment explanation
Indices: 6190--6220 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6180 GTAAGTAAAA
*
6190 ATAATTTATTAATATT
1 ATAATTTATAAATATT
6206 ATAATTTATAAATAT
1 ATAATTTATAAATAT
6221 ATATTATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATTTATAAATATT
Found at i:6309 original size:15 final size:14
Alignment explanation
Indices: 6254--6430 Score: 74
Period size: 13 Copynumber: 12.6 Consensus size: 14
6244 ATTATATATG
*
6254 ATATTATTATTAA-
1 ATATTATAATTAAT
*
6267 ATATT-TAACTAAT
1 ATATTATAATTAAT
*
6280 ATTTGCTATTAATTAAT
1 ATAT--TA-TAATTAAT
6297 AATATTATAATT-AT
1 -ATATTATAATTAAT
6311 AT-TTATATTATTAAT
1 ATATTATA--ATTAAT
*
6326 A-ATTATAGTTAAT
1 ATATTATAATTAAT
6339 ATATTAT--TTGAAT
1 ATATTATAATT-AAT
*
6352 AT-TTA-ATTTAAT
1 ATATTATAATTAAT
6364 ATAATTTATAA-TAAT
1 AT-A-TTATAATTAAT
*
6379 ATAATATAA-TAAT
1 ATATTATAATTAAT
6392 -TATTA-ATATATAATT
1 ATATTATA-AT-TAA-T
**
6407 ATATTTATAATTGGT
1 ATA-TTATAATTAAT
6422 ATATTATAA
1 ATATTATAA
6431 ATAGTATCTA
Statistics
Matches: 128, Mismatches: 11, Indels: 49
0.68 0.06 0.26
Matches are distributed among these distances:
11 1 0.01
12 25 0.20
13 32 0.25
14 20 0.16
15 28 0.22
16 6 0.05
17 12 0.09
18 4 0.03
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATTATAATTAAT
Found at i:6328 original size:21 final size:22
Alignment explanation
Indices: 6299--6346 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
6289 TAATTAATAA
6299 TATTATAATTATA-TT-TATAT
1 TATTATAATTATAGTTATATAT
6319 TATTAATAATTATAGTTAATATAT
1 TATT-ATAATTATAGTT-ATATAT
6343 TATT
1 TATT
6347 TGAATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 2 0.08
24 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATAATTATAGTTATATAT
Found at i:6383 original size:20 final size:20
Alignment explanation
Indices: 6355--6417 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
6345 TTTGAATATT
*
6355 TAATTTAATATAATTTATAA
1 TAATATAATATAATTTATAA
6375 TAATATAATATAATAATTATTAA
1 TAATATAATATAAT--TTA-TAA
6398 T-ATATAAT-TATATTTATAA
1 TAATATAATATA-ATTTATAA
6417 T
1 T
6418 TGGTATATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 4 0.11
20 16 0.42
21 2 0.05
22 12 0.32
23 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATAATATAATTTATAA
Found at i:6390 original size:23 final size:20
Alignment explanation
Indices: 6203--6417 Score: 66
Period size: 20 Copynumber: 10.8 Consensus size: 20
6193 ATTTATTAAT
6203 ATTATAATTTATAA-ATATA
1 ATTATAATTTATAATATATA
6222 TATTATAA--TATCAAT-TATA
1 -ATTATAATTTAT-AATATATA
* * * *
6241 ATTATTATATATGATATTATT
1 ATTATAATTTATAATA-TATA
* *
6262 ATTAAATATTTAACTAATAT-TT
1 ATTATA-ATTT-A-TAATATATA
** *
6284 GCTATTAATTAATAATATTATA
1 ATTA-TAATTTATAATA-TATA
*
6306 ATTAT-ATTTATATTATTAATA
1 ATTATAATTTATAATA-T-ATA
* *
6327 ATTAT-A-GT-TAATATATT
1 ATTATAATTTATAATATATA
6344 ATT-TGAATATT-TAAT-T-TA
1 ATTAT-AAT-TTATAATATATA
6362 A-TATAATTTATAATAATATA
1 ATTATAATTTATAAT-ATATA
6382 A-TATAATAATTATTAATATATA
1 ATTATAAT--TTA-TAATATATA
6404 ATTAT-ATTTATAAT
1 ATTATAATTTATAAT
6418 TGGTATATTA
Statistics
Matches: 148, Mismatches: 21, Indels: 53
0.67 0.09 0.24
Matches are distributed among these distances:
16 3 0.02
17 13 0.09
18 14 0.09
19 18 0.12
20 43 0.29
21 19 0.13
22 24 0.16
23 10 0.07
24 4 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTATAATTTATAATATATA
Found at i:7082 original size:24 final size:25
Alignment explanation
Indices: 7052--7107 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
7042 GTTTATTTTA
7052 AATAATTAAAT-AATTTCAAT-ATAAT
1 AATAATT-AATGAATTT-AATGATAAT
7077 -ATAATTAATGAATTTAATGATAAT
1 AATAATTAATGAATTTAATGATAAT
7101 AATAATT
1 AATAATT
7108 GATATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.21
24 16 0.57
25 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (25 bp):
AATAATTAATGAATTTAATGATAAT
Found at i:7103 original size:18 final size:16
Alignment explanation
Indices: 7073--7122 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
7063 AATTTCAATA
7073 TAATATAATTAATGAATT
1 TAATATAA-TAAT-AATT
7091 TAATGATAATAATAA-T
1 TAAT-ATAATAATAATT
*
7107 TGATATAATAATAATT
1 TAATATAATAATAATT
7123 GTTATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 10 0.34
16 5 0.17
17 2 0.07
18 8 0.28
19 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TAATATAATAATAATT
Found at i:7161 original size:21 final size:22
Alignment explanation
Indices: 7137--7200 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 22
7127 TTTAATTATT
*
7137 TATAAATTAATAATATTTA-AA
1 TATAAATTAATAAGATTTATAA
*
7158 TAT-AATCTAATTAGATTTATAA
1 TATAAAT-TAATAAGATTTATAA
*
7180 TATATATT-ATAA-ATTATATAA
1 TATAAATTAATAAGATT-TATAA
7201 GAAGTGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.17
21 21 0.60
22 6 0.17
23 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATAAATTAATAAGATTTATAA
Found at i:7386 original size:23 final size:23
Alignment explanation
Indices: 7341--7394 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
7331 TATTGATATC
7341 ATATATAATAATTATAAACAATT
1 ATATATAATAATTATAAACAATT
* *
7364 ATATATTATAATTTATATA-AATT
1 ATATATAATAA-TTATAAACAATT
7387 AT-TATAAT
1 ATATATAAT
7395 TTAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 16 0.59
24 6 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATATAATAATTATAAACAATT
Found at i:7929 original size:30 final size:31
Alignment explanation
Indices: 7893--7956 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
7883 TAAAATATAT
*
7893 ATTAAATTATTTAATGATTAT-TAATTAACA
1 ATTAAATTAATTAATGATTATATAATTAACA
* * *
7923 ATTAAATTAATTGATTATTATATACTTAACA
1 ATTAAATTAATTAATGATTATATAATTAACA
7954 ATT
1 ATT
7957 GTCTTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTAAATTAATTAATGATTATATAATTAACA
Found at i:8115 original size:40 final size:43
Alignment explanation
Indices: 8071--8175 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 43
8061 TATTAAGTCT
* *
8071 AATTATGATA-TATAAAT-TTCATATTAAAT-TTAATTATAAC
1 AATTATAATATTATAAATATTAATATTAAATATTAATTATAAC
*
8111 AATTATAATATTTTAAATACTTAATATTAAATATTAATTAT--C
1 AATTATAATATTATAAATA-TTAATATTAAATATTAATTATAAC
*
8153 -ATTATAA-ATTATAAATTTTAATA
1 AATTATAATATTATAAATATTAATA
8176 AATTATAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 6 0.11
40 17 0.30
41 13 0.23
42 1 0.02
43 11 0.20
44 8 0.14
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (43 bp):
AATTATAATATTATAAATATTAATATTAAATATTAATTATAAC
Found at i:8195 original size:17 final size:17
Alignment explanation
Indices: 8153--8200 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
8143 ATTAATTATC
* *
8153 ATTATAAATTATAAATT
1 ATTAAAAATTATAATTT
8170 -TTAATAAATTATAATTT
1 ATTAA-AAATTATAATTT
8187 ATTAAAAA-TATAAT
1 ATTAAAAATTATAAT
8201 GATATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 14 0.52
18 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAAAAATTATAATTT
Found at i:8613 original size:18 final size:18
Alignment explanation
Indices: 8579--8627 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
8569 GATTAAATAA
8579 TAATTTAATATAA-ATTAGT
1 TAATTT-ATATAATATTA-T
*
8598 T-ATTTGTATAATATTAT
1 TAATTTATATAATATTAT
8615 TAATTTATATAAT
1 TAATTTATATAAT
8628 TAATTATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 18 0.69
19 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TAATTTATATAATATTAT
Found at i:8757 original size:19 final size:20
Alignment explanation
Indices: 8716--8760 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
8706 TTAAAAACTA
*
8716 ATTAATTAAGTGATTATTAT
1 ATTAAATAAGTGATTATTAT
8736 ATTAAATAAGT-ATTA-TATT
1 ATTAAATAAGTGATTATTA-T
8755 ATTAAA
1 ATTAAA
8761 ACAATTATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTAAATAAGTGATTATTAT
Found at i:8793 original size:27 final size:27
Alignment explanation
Indices: 8763--8832 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 27
8753 TTATTAAAAC
8763 AATTATAGTAATAATATATATTAT-TTT
1 AATTATA-TAATAATATATATTATATTT
* *
8790 AATTATA-ATTAAAATATATTATATTT
1 AATTATATAATAATATATATTATATTT
*
8816 AAATATA-ATATAATATA
1 AATTATATA-ATAATATA
8833 ATATACATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.36
26 10 0.28
27 13 0.36
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
AATTATATAATAATATATATTATATTT
Found at i:8810 original size:16 final size:16
Alignment explanation
Indices: 8791--8829 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
8781 TATTATTTTA
8791 ATTATAATTAAAATAT
1 ATTATAATTAAAATAT
*
8807 ATTAT-ATTTAAATAT
1 ATTATAATTAAAATAT
*
8822 AATATAAT
1 ATTATAAT
8830 ATAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATAATTAAAATAT
Found at i:8830 original size:25 final size:26
Alignment explanation
Indices: 8778--8837 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
8768 TAGTAATAAT
*
8778 ATATATTAT-TTTAATTATAATTAAA
1 ATATATTATATTTAAATATAATTAAA
*
8803 ATATATTATATTTAAATATAA-TATA
1 ATATATTATATTTAAATATAATTAAA
*
8828 ATATAATATA
1 ATATATTATA
8838 CATGTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATATTATATTTAAATATAATTAAA
Found at i:8946 original size:21 final size:21
Alignment explanation
Indices: 8922--8998 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
8912 TTTATATAAC
8922 AATTATATTAATAATAATATT
1 AATTATATTAATAATAATATT
8943 AATTAT-TT-AT-AT--TA-T
1 AATTATATTAATAATAATATT
8958 AATTATA-TAATATTATAATATT
1 AATTATATTAATA--ATAATATT
* * *
8980 TACTATATTAATTATAATA
1 AATTATATTAATAATAATA
8999 AAGTATTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 18
0.68 0.05 0.28
Matches are distributed among these distances:
15 8 0.18
16 4 0.09
18 2 0.05
19 4 0.09
20 2 0.05
21 14 0.32
22 6 0.14
23 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTATATTAATAATAATATT
Found at i:8952 original size:36 final size:36
Alignment explanation
Indices: 8909--8979 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
8899 TCATAGTCAT
8909 TTATTTATATAACAATTATATTAATA-ATAATATTAA
1 TTATTTATATAACAATTATA-TAATATATAATATTAA
* *
8945 TTATTTATATTATAATTATATAATATTATAATATT
1 TTATTTATATAACAATTATATAATA-TATAATATT
8980 TACTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 5 0.16
36 18 0.58
37 8 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (36 bp):
TTATTTATATAACAATTATATAATATATAATATTAA
Found at i:8962 original size:15 final size:15
Alignment explanation
Indices: 8942--8994 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
8932 ATAATAATAT
8942 TAATTATTTATATTA
1 TAATTATTTATATTA
*
8957 TAATTATATAATATTA
1 TAATTAT-TTATATTA
8973 TAA-TATTTACTA-TA
1 TAATTATTTA-TATTA
8987 TTAATTAT
1 -TAATTAT
8995 AATAAAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 4 0.12
15 15 0.47
16 13 0.41
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATTTATATTA
Found at i:8972 original size:16 final size:16
Alignment explanation
Indices: 8913--8976 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
8903 AGTCATTTAT
*
8913 TTATATAACAATTAT-A
1 TTATATAA-TATTATAA
*
8929 TTA-ATAATAATATTAA
1 TTATATAATATTA-TAA
*
8945 TTAT-TTATATTATAA
1 TTATATAATATTATAA
8960 TTATATAATATTATAA
1 TTATATAATATTATAA
8976 T
1 T
8977 ATTTACTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.08
15 12 0.31
16 24 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATATAATATTATAA
Found at i:8972 original size:25 final size:25
Alignment explanation
Indices: 8924--8973 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
8914 TATATAACAA
*
8924 TTATATTAATAATAATATTAATTAT
1 TTATATTAATAATAATATAAATTAT
*
8949 TTATATT-ATAATTATATAATATTAT
1 TTATATTAATAATAATATAA-ATTAT
8974 AATATTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATATTAATAATAATATAAATTAT
Found at i:8995 original size:31 final size:29
Alignment explanation
Indices: 8925--8995 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
8915 ATATAACAAT
*
8925 TATATTAA-TA-ATAATATTAATTATTTA
1 TATATTAATTATATAATATTAAATATTTA
8952 TAT-TATAATTATATAATATTATAATATTTA
1 TATAT-TAATTATATAATATTA-AATATTTA
8982 CTATATTAATTATA
1 -TATATTAATTATA
8996 ATAAAGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 1 0.03
27 6 0.16
28 2 0.05
29 9 0.24
30 7 0.19
31 11 0.30
32 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
TATATTAATTATATAATATTAAATATTTA
Found at i:9154 original size:21 final size:22
Alignment explanation
Indices: 9123--9164 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9113 AATAATTTAA
9123 TTATTATATTTAATAAT-AATTG
1 TTATTATATTTAA-AATGAATTG
9145 TTATTA-ATTTAAAATGAATT
1 TTATTATATTTAAAATGAATT
9165 AGATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 10 0.53
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTATTATATTTAAAATGAATTG
Found at i:9957 original size:26 final size:30
Alignment explanation
Indices: 9886--9959 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 30
9876 TTATATTATA
*
9886 TATATGTAATA-TACTTATAATTATACATAT
1 TATAAGTAATAGTA-TTATAATTATACATAT
*
9916 TATAAGTAAAAG-ATTATAATT-TA-A-AT
1 TATAAGTAATAGTATTATAATTATACATAT
9942 TATAA-TAATAGTATTATA
1 TATAAGTAATAGTATTATA
9960 TAATATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 5 0.13
26 13 0.33
27 1 0.03
28 2 0.05
29 8 0.21
30 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (30 bp):
TATAAGTAATAGTATTATAATTATACATAT
Found at i:10142 original size:63 final size:63
Alignment explanation
Indices: 9884--10142 Score: 140
Period size: 66 Copynumber: 4.0 Consensus size: 63
9874 GTTTATATTA
*
9884 TATATATGTAATATACTTATAATTATACATATTATAAGTAAAAGATTATAATTTAAATTATAAT
1 TATATATGTAATATACTTATAATTATAAATATTATAAGTAAAAGATTATAATTTAAATTAT-AT
* * * * *
9948 AATAGTATTATATAATATA-TTA-ACTTAAAAATATTATAACT---TGATTACT-ATATT-AATT
1 --TA-TA-TATGTAATATACTTATAATTATAAATATTATAAGTAAAAGATTA-TAAT-TTAAATT
10006 A-AT
60 ATAT
* * * * * * * * * *
10009 TGTTTCTTGTTAT-TATTTATAACTAAGTTAAATAATATAATTAACATTAAAATATAATTGTACA
1 TATAT-ATGTAATATACTTATAA-TTA--TAAATATTATAAGTAA-A--AGATTATAATT-TA-A
*
10073 GTTTATAT
57 -ATTATAT
*
10081 TATATATGTAATATACTTATAATTATACATATTATAAGTAAAAGATTATAATTTAAATTATA
1 TATATATGTAATATACTTATAATTATAAATATTATAAGTAAAAGATTATAATTTAAATTATA
10143 ATAATACTAT
Statistics
Matches: 138, Mismatches: 32, Indels: 49
0.63 0.15 0.22
Matches are distributed among these distances:
57 3 0.02
58 8 0.06
59 2 0.01
60 2 0.01
61 2 0.01
62 11 0.08
63 17 0.12
64 4 0.03
65 2 0.01
66 26 0.19
67 7 0.05
68 17 0.12
69 13 0.09
70 1 0.01
71 10 0.07
72 13 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (63 bp):
TATATATGTAATATACTTATAATTATAAATATTATAAGTAAAAGATTATAATTTAAATTATAT
Found at i:10167 original size:197 final size:198
Alignment explanation
Indices: 9785--10179 Score: 724
Period size: 197 Copynumber: 2.0 Consensus size: 198
9775 AGCTTAATTA
9785 ATAATTGATTAATATATTAATTAATTGTTTCTTGTTATTATTTTATAACTAAGTTAATAATATAA
1 ATAATTGATTAATATATTAATTAATTGTTTCTTGTTATTATTTTATAACTAAGTTAATAATATAA
*
9850 TTAACATTAAAATATAATTGTATAGTTTATATTATATATATGTAATATACTTATAATTATACATA
66 TTAACATTAAAATATAATTGTACAGTTTATATTATATATATGTAATATACTTATAATTATACATA
*
9915 TTATAAGTAAAAGATTATAATTTAAATTATAATAATAGTATTATATAATATATTAACTTAAAAAT
131 TTATAAGTAAAAGATTATAATTTAAATTATAATAATACTATTATATAATATATTAACTTAAAAAT
9980 ATT
196 ATT
*
9983 ATAACTTGATTACTATATTAATTAATTGTTTCTTGTTATTA-TTTATAACTAAGTTAAATAATAT
1 ATAA-TTGATTAATATATTAATTAATTGTTTCTTGTTATTATTTTATAACTAAGTT-AATAATAT
10047 AATTAACATTAAAATATAATTGTACAGTTTATA-T-TATATATGTAATATACTTATAATTATACA
64 AATTAACATTAAAATATAATTGTACAGTTTATATTATATATATGTAATATACTTATAATTATACA
10110 TATTATAAGTAAAAGATTATAATTTAAATTATAATAATACTATTATATAATATATTAACTTAAAA
129 TATTATAAGTAAAAGATTATAATTTAAATTATAATAATACTATTATATAATATATTAACTTAAAA
10175 ATATT
194 ATATT
10180 TATTATAAAA
Statistics
Matches: 192, Mismatches: 3, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
197 98 0.51
198 19 0.10
199 75 0.39
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (198 bp):
ATAATTGATTAATATATTAATTAATTGTTTCTTGTTATTATTTTATAACTAAGTTAATAATATAA
TTAACATTAAAATATAATTGTACAGTTTATATTATATATATGTAATATACTTATAATTATACATA
TTATAAGTAAAAGATTATAATTTAAATTATAATAATACTATTATATAATATATTAACTTAAAAAT
ATT
Found at i:10211 original size:17 final size:17
Alignment explanation
Indices: 10162--10212 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
10152 TTATATAATA
*
10162 TATTAACTTAAAAATATT
1 TATTAA-TTAAATATATT
*
10180 TATT-ATAAAACTATATT
1 TATTAATTAAA-TATATT
10197 TATTAATTAAATATAT
1 TATTAATTAAATATAT
10213 ATTGATTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 15 0.54
18 9 0.32
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAATTAAATATATT
Found at i:10319 original size:16 final size:15
Alignment explanation
Indices: 10278--10315 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
10268 AGCCTTTTGT
10278 TTAATAATTAAATTTA
1 TTAATAATT-AATTTA
*
10294 TTATTAATTAATTTA
1 TTAATAATTAATTTA
10309 TTAATAA
1 TTAATAA
10316 ATTATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATAATTAATTTA
Found at i:10320 original size:11 final size:11
Alignment explanation
Indices: 10293--10326 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
10283 AATTAAATTT
10293 ATTATTAATTAA
1 ATTATTAA-TAA
*
10305 TTTATTAATAA
1 ATTATTAATAA
10316 ATTATTAATAA
1 ATTATTAATAA
10327 TTTAATATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTATTAATAA
Found at i:10793 original size:14 final size:16
Alignment explanation
Indices: 10776--10808 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10766 AATGAAATTA
10776 ATTAT-ATT-AAATAT
1 ATTATAATTAAAATAT
10790 ATTATAATTAAAATAT
1 ATTATAATTAAAATAT
10806 ATT
1 ATT
10809 TTCTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 3 0.18
16 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATAATTAAAATAT
Found at i:11019 original size:27 final size:27
Alignment explanation
Indices: 10982--11033 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
10972 AATAATTTAT
10982 TTAATTATTATATA-TATAACAAATTCA
1 TTAATTATTATA-ACTATAACAAATTCA
* *
11009 TTAATTGTTATAACTATTACAAATT
1 TTAATTATTATAACTATAACAAATT
11034 AAAGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATTATTATAACTATAACAAATTCA
Found at i:11368 original size:23 final size:23
Alignment explanation
Indices: 11323--11368 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11313 TTACAATAAC
*
11323 TAATATTATAATCAATTAGGTTA
1 TAATATTATAATCAATTAAGTTA
*
11346 TAATA-TATAATTCATTTAAGTTA
1 TAATATTATAA-TCAATTAAGTTA
11369 ATTCATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (23 bp):
TAATATTATAATCAATTAAGTTA
Found at i:11587 original size:54 final size:51
Alignment explanation
Indices: 11512--11617 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 51
11502 GGTTTTTATT
* *
11512 TATATTATGATAATAAAAACCCTAATTTATACATATAATTATTA-AATTATTAA
1 TATAATATGATAATAAAAACCCTAATTTATAC-TAT-ATTAATATAA-TATTAA
11565 TATAATATGTATAATAAAAACCCTAATTTATACTATATTAATATAATATTAA
1 TATAATATG-ATAATAAAAACCCTAATTTATACTATATTAATATAATATTAA
11617 T
1 T
11618 CAATATACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
52 13 0.27
53 13 0.27
54 23 0.47
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (51 bp):
TATAATATGATAATAAAAACCCTAATTTATACTATATTAATATAATATTAA
Found at i:11677 original size:9 final size:9
Alignment explanation
Indices: 11663--11756 Score: 54
Period size: 9 Copynumber: 10.2 Consensus size: 9
11653 AAAAGCACAT
11663 ATTAATATA
1 ATTAATATA
11672 ATTAAT-T-
1 ATTAATATA
*
11679 A-TATTATA
1 ATTAATATA
11687 ATTAATATA
1 ATTAATATA
* *
11696 ATAAATCTA
1 ATTAATATA
11705 ATTGTTAAT-TA
1 A---TTAATATA
11716 A-TAATATTA
1 ATTAATA-TA
11725 ATTATATTATA
1 ATTA-A-TATA
*
11736 ATTAATTTA
1 ATTAATATA
11745 ATTTAATATA
1 A-TTAATATA
11755 AT
1 AT
11757 AATTATATCA
Statistics
Matches: 66, Mismatches: 7, Indels: 24
0.68 0.07 0.25
Matches are distributed among these distances:
6 3 0.05
7 6 0.09
8 2 0.03
9 28 0.42
10 11 0.17
11 10 0.15
12 6 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (9 bp):
ATTAATATA
Found at i:11736 original size:40 final size:38
Alignment explanation
Indices: 11665--11759 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 38
11655 AAGCACATAT
* *
11665 TAATATAATTAATTATATTATAATTAATATAATAAATC
1 TAATTTAATTAATAATATTATAATTAATATAATAAATC
* *
11703 TAATTGTTAATTAATAATA-T-TAATTATATTATAATTAATT
1 TAA-T-TTAATTAATAATATTATAATTA-A-TATAATAAATC
11743 TAATTTAATATAATAAT
1 TAATTTAAT-TAATAAT
11760 TATATCAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
38 14 0.29
39 11 0.23
40 23 0.48
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (38 bp):
TAATTTAATTAATAATATTATAATTAATATAATAAATC
Found at i:12145 original size:22 final size:22
Alignment explanation
Indices: 12095--12138 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12085 TATTACAATT
*
12095 AATAAATTAATTAAATATATTA
1 AATATATTAATTAAATATATTA
*
12117 AATATATTAATTAACTA-ATTA
1 AATATATTAATTAAATATATTA
12138 A
1 A
12139 CTTATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATTAATTAAATATATTA
Found at i:15021 original size:30 final size:32
Alignment explanation
Indices: 14969--15034 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
14959 TAATGAATTG
*
14969 ATATTATATTATGGATTATAATAAATGGTTATT
1 ATATTATATTAT-GATTATAATAAATGCTTATT
*
15002 ATATTATATTAT-A-TATAATAATTGCTTATT
1 ATATTATATTATGATTATAATAAATGCTTATT
15032 ATA
1 ATA
15035 ATGTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 18 0.58
31 1 0.03
33 12 0.39
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (32 bp):
ATATTATATTATGATTATAATAAATGCTTATT
Found at i:15081 original size:9 final size:9
Alignment explanation
Indices: 15027--15102 Score: 59
Period size: 9 Copynumber: 8.3 Consensus size: 9
15017 TAATAATTGC
15027 TTATTATAA
1 TTATTATAA
*
15036 TGTATTTTAA
1 T-TATTATAA
*
15046 -TATTTTAA
1 TTATTATAA
15054 -TATTA-AA
1 TTATTATAA
15061 TTATATTATAA
1 -T-TATTATAA
*
15072 TTAGTATAA
1 TTATTATAA
*
15081 TTATTAAAA
1 TTATTATAA
15090 TTATTAGTAA
1 TTATTA-TAA
15100 TTA
1 TTA
15103 ACAACAATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 2 0.04
8 12 0.22
9 21 0.38
10 18 0.33
11 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (9 bp):
TTATTATAA
Found at i:15253 original size:26 final size:26
Alignment explanation
Indices: 15206--15255 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
15196 TATAATATAA
* *
15206 TAATTGTCATAATTTATTATTATTTT
1 TAATTGTCACAATATATTATTATTTT
15232 TAATTGT-ACAATATATTAATTATT
1 TAATTGTCACAATATATT-ATTATT
15256 ATTATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TAATTGTCACAATATATTATTATTTT
Found at i:15300 original size:22 final size:21
Alignment explanation
Indices: 15274--15326 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 21
15264 TTATAATAAG
15274 TTTAATAAAACCTTCATAAT-TA
1 TTTAATAAAACCTT-A-AATCTA
15296 TTTAATAAAACCTTAAATCTA
1 TTTAATAAAACCTTAAATCTA
15317 TGTTAATAAA
1 T-TTAATAAA
15327 TATAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 22 0.76
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTAATAAAACCTTAAATCTA
Found at i:15880 original size:27 final size:24
Alignment explanation
Indices: 15850--15917 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 24
15840 GCAAATACAT
15850 TTATTAATAATTTATAATTATTAAATA
1 TTATTAATAA-TTATAATTA-T-AATA
15877 TTATT-A-AATTATAATTATAATA
1 TTATTAATAATTATAATTATAATA
15899 TTAAATTAATAAATTATAA
1 TT--ATTAAT-AATTATAA
15918 AAATATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
22 6 0.17
23 1 0.03
24 12 0.33
25 3 0.08
26 1 0.03
27 13 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTAATAATTATAATTATAATA
Found at i:15902 original size:19 final size:21
Alignment explanation
Indices: 15878--15917 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
15868 TATTAAATAT
15878 TATTAAATT-AT-AATTATAA
1 TATTAAATTAATAAATTATAA
15897 TATTAAATTAATAAATTATAA
1 TATTAAATTAATAAATTATAA
15918 AAATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTAAATTAATAAATTATAA
Found at i:15907 original size:24 final size:24
Alignment explanation
Indices: 15851--15901 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
15841 CAAATACATT
* *
15851 TATTAATAATTTATAATTATTAAA
1 TATTATTAAATTATAATTATTAAA
15875 TATTATTAAATTATAATTA-T-AA
1 TATTATTAAATTATAATTATTAAA
15897 TATTA
1 TATTA
15902 AATTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
23 1 0.04
24 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTATTAAATTATAATTATTAAA
Found at i:15927 original size:27 final size:29
Alignment explanation
Indices: 15866--15927 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
15856 ATAATTTATA
* **
15866 ATTATTAAATATTATTAAATTATAATTAT
1 ATTATTAAATATTAATAAATTATAAAAAT
*
15895 AATATT-AA-ATTAATAAATTATAAAAAT
1 ATTATTAAATATTAATAAATTATAAAAAT
15922 ATTATT
1 ATTATT
15928 TATCTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.75
28 2 0.07
29 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTATTAAATATTAATAAATTATAAAAAT
Found at i:16049 original size:23 final size:23
Alignment explanation
Indices: 15979--16056 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
15969 AATATAAATT
* *
15979 ATTT-AATTATTATAACTATATTA
1 ATTTAAATTATTATAA-TTTATCA
* * **
16002 A--TAAATTATTTTAGTTTATGT
1 ATTTAAATTATTATAATTTATCA
16023 ATTTAAATTATTATAATTTATCA
1 ATTTAAATTATTATAATTTATCA
16046 ATTTAATATTA
1 ATTTAA-ATTA
16057 AACAATATAC
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
21 6 0.14
22 9 0.21
23 23 0.55
24 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (23 bp):
ATTTAAATTATTATAATTTATCA
Found at i:16103 original size:16 final size:16
Alignment explanation
Indices: 16078--16111 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16068 TATAATTTTA
* *
16078 TAATTTATTATTAAAT
1 TAATTAATTATAAAAT
16094 TAATTAATTATAAAAT
1 TAATTAATTATAAAAT
16110 TA
1 TA
16112 GTATATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTAATTATAAAAT
Found at i:16105 original size:34 final size:33
Alignment explanation
Indices: 16028--16106 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
16018 TATGTATTTA
16028 AATT-ATTATAATTTATCAATTTAATATTAAAC
1 AATTAATTATAATTTATCAATTTAATATTAAAC
* * *
16060 AATATACTTATAATTTTAT-AATTTATTATTAAATT
1 AAT-TAATTATAA-TTTATCAATTTAATATTAAA-C
16095 AATTAATTATAA
1 AATTAATTATAA
16107 AATTAGTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 3 0.08
33 1 0.03
34 27 0.69
35 8 0.21
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (33 bp):
AATTAATTATAATTTATCAATTTAATATTAAAC
Found at i:16942 original size:180 final size:180
Alignment explanation
Indices: 16471--17116 Score: 693
Period size: 180 Copynumber: 3.6 Consensus size: 180
16461 TTAATTTAAA
* * *
16471 TTATTTTTTAAATCTTTTACTTATT-AATTATTGGAATATGATTAAA-TTAGTATTATTTTATTT
1 TTATTTTTTAAATCTTTTACTTATTAAATT-TTAGAATATTAATAAATTTA--ATTATTTTATTT
* * *
16534 TGAATAAGCTTATAT-AGATAGAAACAATTGA-TTCATCACAAAACAAAAGGTCATAACTATTCG
63 CGAATAAGCTTATATGA-ATAGAAACAATT-ATTTTATCACAAAACAAAAGGTCATAACTATTTG
* * *
16597 AAATAGATAATTGTTCAAATAGT-TGATCTATTTGAACATGTTCAAAAAATAAAT
126 AAATAGATAATTGTTCAAATAGTCAGAACTATTTGAACATGTTCAAAAAACAAAT
* * * *
16651 TTATTTTTTTAAT-TTTCATTTATTAAATTTTAGAATATTAATAAATTTAATTATTTTA-TTCAA
1 TTATTTTTTAAATCTTTTACTTATTAAATTTTAGAATATTAATAAATTTAATTATTTTATTTC-G
* * * ** *
16714 AATAAGCTTGTATGGACAGAAACAATTGGTTTATCACAAAATAAAAGGTCATAACTATTTGAAAT
65 AATAAGCTTATATGAATAGAAACAATTATTTTATCACAAAACAAAAGGTCATAACTATTTGAAAT
* * * *
16779 AAATAATTATTCAAATAATCAGAACTATTCGAACATGTTCAAAAAAACAAAT
130 AGATAATTGTTCAAATAGTCAGAACTATTTGAACATGTTC-AAAAAACAAAT
* *
16831 TTATTTTTTAAAT-TTTTACTTATTAAATTTTGGAATATTAATTAATTTAATTATTTTA-TTCGA
1 TTATTTTTTAAATCTTTTACTTATTAAATTTTAGAATATTAATAAATTTAATTATTTTATTTCG-
* * * *
16894 AATAAAGCTTGTATGAATGGAAACAATTATTTTATGAC-AAACAAAAGGTCATAACGATTTGAAA
65 AAT-AAGCTTATATGAATAGAAACAATTATTTTATCACAAAACAAAAGGTCATAACTATTTGAAA
** * * * **
16958 TAGATAATTGTTCAAATAGTCATCACTATTTAAACTTGTTTAGTAAACAAAT
129 TAGATAATTGTTCAAATAGTCAGAACTATTTGAACATGTTCAAAAAACAAAT
* * * *
17010 TCATTTTTTTAAATCTCTTACTCATTAATTTTTAGAATATTAATAAATTAGTAA-TATTTTATTT
1 TTA-TTTTTTAAATCTTTTACTTATTAAATTTTAGAATATTAATAAATT--TAATTATTTTATTT
* * * * * *
17074 CGAATAAGCCTATCTGAATTGATACAATTGTTTTATGACAAAA
63 CGAATAAGCTTATATGAATAGAAACAATTATTTTATCACAAAA
17117 TAATTAAATA
Statistics
Matches: 392, Mismatches: 59, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
177 2 0.01
178 81 0.21
179 50 0.13
180 154 0.39
181 85 0.22
182 13 0.03
183 7 0.02
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (180 bp):
TTATTTTTTAAATCTTTTACTTATTAAATTTTAGAATATTAATAAATTTAATTATTTTATTTCGA
ATAAGCTTATATGAATAGAAACAATTATTTTATCACAAAACAAAAGGTCATAACTATTTGAAATA
GATAATTGTTCAAATAGTCAGAACTATTTGAACATGTTCAAAAAACAAAT
Found at i:17501 original size:16 final size:16
Alignment explanation
Indices: 17480--17510 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17470 GTTTAATGTT
*
17480 ATATTAATATTAATTA
1 ATATTAAGATTAATTA
17496 ATATTAAGATTAATT
1 ATATTAAGATTAATT
17511 TAGTATAATA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTAAGATTAATTA
Found at i:17757 original size:20 final size:20
Alignment explanation
Indices: 17706--17763 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
17696 ATTCAATTAT
17706 TAAT-ATTAATCATATATATA
1 TAATAATTAAT-ATATATATA
*
17726 TAATTAATTTAATATATATTTA
1 TAA-TAA-TTAATATATATATA
17748 TAATAATTAACTATAT
1 TAATAATTAA-TATAT
17764 TTCATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 7 0.21
21 9 0.27
22 12 0.36
23 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAATTAATATATATATA
Found at i:18213 original size:36 final size:36
Alignment explanation
Indices: 18173--18242 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
18163 AACTATATCT
18173 TAATAACA-CATTTATTATA-TAATATATAAATATATA
1 TAATAA-ATCATTTATTATACTAAT-TATAAATATATA
* *
18209 TAATAAATTATTTATTATACTAATTATAATTATA
1 TAATAAATCATTTATTATACTAATTATAAATATA
18243 GAAAAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 1 0.03
36 25 0.83
37 4 0.13
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (36 bp):
TAATAAATCATTTATTATACTAATTATAAATATATA
Found at i:18827 original size:18 final size:18
Alignment explanation
Indices: 18732--18827 Score: 54
Period size: 18 Copynumber: 5.1 Consensus size: 18
18722 AAGTATAAAT
*
18732 TTATAAATTATTAATATT
1 TTATAAATTATTAATATA
*
18750 TTATAATTTATATAACTA-A
1 TTATAAATTAT-TAA-TATA
* *
18769 TATATAATACTATTTAA-AAA
1 T-TATAA-ATTA-TTAATATA
* *
18789 TTAAATAACTATTAA-ATTA
1 TTATA-AATTATTAATA-TA
18808 TTATAAATTATTAATATA
1 TTATAAATTATTAATATA
18826 TT
1 TT
18828 TTTTAATAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
18 27 0.44
19 18 0.30
20 10 0.16
21 5 0.08
22 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATAAATTATTAATATA
Found at i:19162 original size:19 final size:17
Alignment explanation
Indices: 19138--19197 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
19128 TAGTATACTT
19138 ATTATAATTTAATGTATTA
1 ATTATAATTTAATG-A-TA
*
19157 ATTATATTATTATATGATA
1 ATTATAAT-TTA-ATGATA
* *
19176 ATTATAATATAATAATA
1 ATTATAATTTAATGATA
19193 ATTAT
1 ATTAT
19198 TATATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 10 0.29
18 2 0.06
19 16 0.46
20 4 0.11
21 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTATAATTTAATGATA
Found at i:19573 original size:181 final size:179
Alignment explanation
Indices: 19209--20739 Score: 1071
Period size: 181 Copynumber: 8.5 Consensus size: 179
19199 ATATATAAAT
* * * * * *
19209 ATAA-GATTTGAAATAGATAATTCTTCAAATAGTCATAACTATTTGAAATTGCTTAGAAAATATA
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTAAACATA
* * *
19273 TTTATTTTTTAAAGT-T-TTACTTATTAATTTTTGGAATATTAATAAATTTA-AATTACTTTATT
66 -TTATTTTTTAAA-TCTCTTACTTATTAATTTTTAGAATATTAATAAA-TTAGTATTATTTTATT
* ** * * * *
19335 TGAAATAAGCTTGCATGAACAGAATCAATTGTTTAATGAC-AAAGCAAAAGATC
128 CG-AATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAG-AAAAGGTC
* * * *
19388 ATAATGTTTTGAAATAGATAATTGTTCAGATAGTCATAACTATTTGAACTTATTTGGTAAACATA
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTAAACATA
* * * *
19453 TTCTTTTTTAAATTCTCTTACTCATTAATTTTTAGAATATTAATGAATTAGTATTATCTTACTTC
66 TTATTTTTTAAA-TCTCTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTATTTTA-TTC
* * * *
19518 AAATAAGCTTATATGAATTGAAACAAGTGTTTTATTACAAAAGAAAAGGTC
129 GAATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAGAAAAGGTC
* * * * *
19569 ATAATGATTTCAAATAGATAATTATTCAAATATTCATGACTATTTGAACTTGTTTAGTAAATATA
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTAAACATA
* * * * * * *
19634 TTTATTTTTTAAATCTTTTACTTATTAATTGTCAAAATATTTATAAAATTAATATTATTTTAATC
66 -TTATTTTTTAAATCTCTTACTTATTAATTTTTAGAATATTAAT-AAATTAGTATTATTTTATTC
* * * * *
19699 TGAATAAACTTGTATGAATAGAAATAATTGTTTTATGACAAAACAAAAGGTT
129 -GAATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAGAAAAGGTC
* * * * * * * * * * * *
19751 ATAGCT-ATTTCAAATAGATAATTATTTAAACAGTCCTAATTATTTAAATTTGTTTAGAAAATAG
1 ATA-ATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTAAACAT
* * * * * *
19815 AGTCATTTTTTAAATCTGTTTA-TTATAAATTTTTGGATTATTAATATATTAGTATTATTTTATT
65 A-TTATTTTTTAAATCT-CTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTATTTTA-T
* * * *
19879 TTGAATAAGTTTATATGAATTGAAACAATTCTTTTATGAC-AAAGCAAAAGGTC
127 TCGAATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAG-AAAAGGTC
* * * * * * * *
19932 ------A-TTGAAATTGATAATTATTCAAATTGTCGTGATTATTTGATCTAGTGTGGTAAACATA
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTAAACATA
* * * * * * * *
19990 TTTATTTTTAAAAT-TTTGTACTTATTAATTGTCAAAATATTAACAAATTAGTAATATTTTAATC
66 -TTATTTTTTAAATCTCT-TACTTATTAATTTTTAGAATATTAATAAATTAGTATTATTTTATTC
* * * * * * * * *
20054 TAAATAAGCTTGTATAAATAGAAACAATTGTTTTATAATAGAACAAAAAGTT
129 -GAATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAGAAAAGGTC
* * * * * * * *
20106 ATAACGGTTTGAAATAAATAATTACTCAAATAGTCATAACTTTTTGAACTAGTTTGATACATAGA
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTA-A-ACA
* *
20171 T-TTATTTTTTAAA--TC--ACTTATTAATTTTT-GAAATATTAATAGATTAGTATTACTTTATT
64 TATTATTTTTTAAATCTCTTACTTATTAATTTTTAG-AATATTAATAAATTAGTATTATTTTATT
* * * * * * *
20230 CTGAATAA-ATTATATGAACAAAAACATTTGTTTTATGACGAAACAAAA-GTA
128 C-GAATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAGAAAAGGTC
* * * * *
20281 ATAATGATTTGAAATATATAATTGTTCAAATAGT-ATAATTTTTTGAA-TTGGTTAGGTAAACAG
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTT-GTTTGGTAAACA-
* * * * *
20344 AATTATTTTTTAAATCTCTTATTTATTAATTTTT-GAAATATTAACAAATTTGTTTTATTTTATT
64 TATTATTTTTTAAATCTCTTACTTATTAATTTTTAG-AATATTAATAAATTAGTATTATTTTA-T
*
20408 TCGAATAAGC-TAGTATGAATTCAG-AA-AATTGTTTTAT-A-ACAAGACAAAGGTC
127 TCGAATAAGCTTA-TATGAA-T-AGAAACAATTGTTTTATGACAAAAGA-AAAGGTC
* * * * * * *
20460 ATAACGATTTGAATTAGATAATTGTTCATATAGTCTTAACTATTTGAA-TTGGTTTGGCAAACAA
1 ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTT-GTTTGGTAAACAT
* * * *** * ** * * *
20524 ATTTATTTTTCAAATCCCTTAATTATTAATTTTT-TTCTAATGTTAGATTTGTATTGTTTTATTT
65 A-TTATTTTTTAAATCTCTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTATTTTA-TT
* * * * * *
20588 TGAATAAGCTTGTATGAACAGAAATAATTGTTTTATGACAAAACAAAAGGTT
128 CGAATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAGAAAAGGTC
* * * * * * * * *
20640 ATAATGATATGAAGTATAGAATTGGTTTCAAATACGTCATAACTATTTAAACTAGTTTCGTAAAT
1 ATAATGATTTGAAATAGATAATT--ATTCAAATA-GTCATAACTATTTGAACTTGTTTGGTAAAC
* * *
20705 AGATTCATTTTTTAAA-CTCTTATTTATTAAATTTT
63 ATATT-ATTTTTTAAATCTCTTACTTATTAATTTTT
20740 GAAATTGTTA
Statistics
Matches: 1062, Mismatches: 237, Indels: 103
0.76 0.17 0.07
Matches are distributed among these distances:
172 4 0.00
173 6 0.01
174 149 0.14
175 34 0.03
176 32 0.03
177 47 0.04
178 50 0.05
179 114 0.11
180 139 0.13
181 263 0.25
182 182 0.17
183 41 0.04
184 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (179 bp):
ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAACTTGTTTGGTAAACATA
TTATTTTTTAAATCTCTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTATTTTATTCGA
ATAAGCTTATATGAATAGAAACAATTGTTTTATGACAAAAGAAAAGGTC
Found at i:20341 original size:355 final size:351
Alignment explanation
Indices: 19208--20687 Score: 1063
Period size: 355 Copynumber: 4.1 Consensus size: 351
19198 TATATATAAA
* * * *
19208 TATAA-GATTTGAAATAGATAATTCTTCAAATAGTCATAACTATTTGAAATTGCTTAGAAAATAT
1 TATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTG-AATTGGTTAGTAAACAT
* * *** * *
19272 ATTTATTTTTTAAA-GTTTTACTTATTAATTTTTGGAATATTAATAAATT-TAA-ATTACTTTAT
65 ATTTATTTTTTAAATCTTTTACTTATTAATTGTCAAAATATTAACAAATTATAATATT--TTAAT
* * * * * * * *
19334 TTGAAATAAGCTTGCATGAACAGAATCAATTGTTTAATGACAAAGC-AAAAGATCATAATGTTTT
128 CT-AAATAAGCTTGTATGAATAGAAACAATTGTTTTATGACAAA-CAAAAAG-TTATAACGATTT
* * * * * *
19398 GAAATAGATAATTGTTCAGATAGTCATAACTATTTGAACTTA-TTTGGTAA-ACATATTCTTTTT
190 GAAATAGATAATTATTCAAATAGTCATAACTTTTTGAAC-TAGTTTGATAATAGAT-TTATTTTT
* *
19461 TAAATTCTCTTACTCATTAATTTTT-AGAATATTAAT-GAATTAGTATTATCTTACTTC-AAATA
253 TAAA---TC-TACTTATTAATTTTTGA-AATATTAATAG-ATTAGTATTAT-TTA-TTCTGAATA
* * * *
19523 AGCTTATATGAATTGAAACAAGTGTTTTATTACAAAAGAAAAGG
310 AGATTATATGAATTGAAACAATTGTTTTATGAC-AAACAAAA-G
* * * * *
19567 TCATAATGATTTCAAATAGATAATTATTCAAATATTCATGACTATTTGAACTTGTTTAGTAAATA
1 T-ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAA-TTGGTTAGTAAACA
*
19632 TATTTATTTTTTAAATCTTTTACTTATTAATTGTCAAAATATTTATA-AAATTAATATTATTTTA
64 TATTTATTTTTTAAATCTTTTACTTATTAATTGTCAAAATA-TTA-ACAAATT-ATAATATTTTA
* * * * * *
19696 ATCTGAATAAACTTGTATGAATAGAAATAATTGTTTTATGACAAAACAAAAGGTTATAGCTATTT
126 ATCTAAATAAGCTTGTATGAATAGAAACAATTGTTTTATGAC-AAACAAAAAGTTATAACGATTT
* * * * * * * * * *
19761 CAAATAGATAATTATTTAAACAGTCCTAA-TTATTTAAATTTGTTTAGAAAATAGAGTCATTTTT
190 GAAATAGATAATTATTCAAATAGTCATAACTT-TTTGAACTAGTTT-GATAATAGATTTATTTTT
** * * * * *
19825 TAAATCTGTTTATTATAAATTTTTGGATTATTAATATATTAGTATTATTTTATTTTGAATAAGTT
253 TAAATCTACTTA-T-T-AATTTTTGAAATATTAATAGATTAGTATTA-TTTATTCTGAATAAGAT
*
19890 TATATGAATTGAAACAATTCTTTTATGACAAAGCAAAAG
314 TATATGAATTGAAACAATTGTTTTATGACAAA-CAAAAG
* * * * * * * * *
19929 ----GTCA-TTGAAATTGATAATTATTCAAATTGTCGTGATTATTTG-ATCTAGTGTGGTAAACA
1 TATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAAT-TGGT-TAGTAAACA
*
19988 TATTTATTTTTAAAAT-TTTGTACTTATTAATTGTCAAAATATTAACAAATTAGTAATATTTTAA
64 TATTTATTTTTTAAATCTTT-TACTTATTAATTGTCAAAATATTAACAAATTA-TAATATTTTAA
* * * *
20052 TCTAAATAAGCTTGTATAAATAGAAACAATTGTTTTATAATAGAACAAAAAGTTATAACGGTTTG
127 TCTAAATAAGCTTGTATGAATAGAAACAATTGTTTTATGACA-AACAAAAAGTTATAACGATTTG
* *
20117 AAATAAATAATTACTCAAATAGTCATAACTTTTTGAACTAGTTTGATACATAGATTTATTTTTTA
191 AAATAGATAATTATTCAAATAGTCATAACTTTTTGAACTAGTTTGATA-ATAGATTTATTTTTTA
20182 AATC-ACTTATTAATTTTTGAAATATTAATAGATTAGTATTACTTTATTCTGAATAA-ATTATAT
255 AATCTACTTATTAATTTTTGAAATATTAATAGATTAGTATTA-TTTATTCTGAATAAGATTATAT
*** *
20245 GAACAAAAACATTTGTTTTATGACGAAACAAAAG
319 GAATTGAAACAATTGTTTTATGAC-AAACAAAAG
* * * *
20279 TAATAATGATTTGAAATATATAATTGTTCAAATAGT-ATAATTTTTTGAATTGGTTAGGTAAACA
1 T-ATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAATTGGTTA-GTAAACA
* * * * * ** * **
20343 GAATTATTTTTTAAATCTCTTATTTATTAATTTTTGAAATATTAACAAATTTGTTTTATTTT-AT
64 TATTTATTTTTTAAATCTTTTACTTATTAATTGTCAAAATATTAACAAA-TTATAATATTTTAAT
* * * * * *
20407 TTCGAATAAGCTAGTATGAATTCAG-AA-AATTGTTTTATAACAAGAC-AAAGGTCATAACGATT
128 CT-AAATAAGCTTGTATGAA-T-AGAAACAATTGTTTTATGACAA-ACAAAAAGTTATAACGATT
* * * * * * * * *
20469 TGAATTAGATAATTGTTCATATAGTCTTAACTATTTGAATTGGTTTGGCA-AACAAATTTATTTT
189 TGAAATAGATAATTATTCAAATAGTCATAACTTTTTGAACTAGTTT-G-ATAATAGATTTATTTT
* * *** * ** * * * *
20533 TCAAATCCCTTAATTATTAATTTTT-TTCTAATGTTAGATTTGTATTGTTTTATTTTGAATAAGC
252 TTAAAT--C-TACTTATTAATTTTTGAAATATTAATAGATTAGTATT-ATTTATTCTGAATAAGA
* ** *
20597 TTGTATGAACAGAAATAATTGTTTTATGACAAAACAAAAGG
313 TTATATGAATTGAAACAATTGTTTTATGAC-AAACAAAA-G
* * * * *
20638 TTATAATGATATGAAGTATAGAATTGGTTTCAAATACGTCATAACTATTT
1 -TATAATGATTTGAAATAGATAATT--ATTCAAATA-GTCATAACTATTT
20688 AAACTAGTTT
Statistics
Matches: 892, Mismatches: 169, Indels: 116
0.76 0.14 0.10
Matches are distributed among these distances:
350 31 0.03
351 43 0.05
352 1 0.00
353 1 0.00
354 81 0.09
355 224 0.25
356 110 0.12
357 31 0.03
358 47 0.05
359 22 0.02
360 10 0.01
361 75 0.08
362 31 0.03
363 151 0.17
364 27 0.03
365 4 0.00
366 3 0.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (351 bp):
TATAATGATTTGAAATAGATAATTATTCAAATAGTCATAACTATTTGAATTGGTTAGTAAACATA
TTTATTTTTTAAATCTTTTACTTATTAATTGTCAAAATATTAACAAATTATAATATTTTAATCTA
AATAAGCTTGTATGAATAGAAACAATTGTTTTATGACAAACAAAAAGTTATAACGATTTGAAATA
GATAATTATTCAAATAGTCATAACTTTTTGAACTAGTTTGATAATAGATTTATTTTTTAAATCTA
CTTATTAATTTTTGAAATATTAATAGATTAGTATTATTTATTCTGAATAAGATTATATGAATTGA
AACAATTGTTTTATGACAAACAAAAG
Found at i:20944 original size:17 final size:17
Alignment explanation
Indices: 20900--20945 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
20890 TTTATATTAA
20900 ATTATAA-AT-ATAAAT
1 ATTATAATATAATAAAT
*
20915 -TTATATTATTAATAAAT
1 ATTATAATA-TAATAAAT
20932 ATTATAATATAATA
1 ATTATAATATAATA
20946 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 1 0.04
17 11 0.44
18 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTATAATATAATAAAT
Found at i:21099 original size:11 final size:11
Alignment explanation
Indices: 21083--21125 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
21073 TACTTGTCAA
21083 ATAATATTAAT
1 ATAATATTAAT
21094 ATAATATT-AT
1 ATAATATTAAT
*
21104 A-AATCATTACT
1 ATAAT-ATTAAT
21115 ATAATATTAAT
1 ATAATATTAAT
21126 TTTAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.11
10 6 0.22
11 15 0.56
12 3 0.11
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:21138 original size:21 final size:21
Alignment explanation
Indices: 21092--21164 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
21082 AATAATATTA
* * *
21092 ATATAATATT-ATAAATCATT
1 ATATAATATTAATTATTAATT
21112 ACTATAATATTAATT-TTAAATT
1 A-TATAATATTAATTATT-AATT
* *
21134 ATATATTATTTATTATTAATT
1 ATATAATATTAATTATTAATT
21155 ATA-AATATTA
1 ATATAATATTA
21165 GGTATCTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 6 0.14
21 28 0.67
22 8 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATAATATTAATTATTAATT
Found at i:21319 original size:15 final size:15
Alignment explanation
Indices: 21299--21328 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21289 ACAATTATTA
21299 AATTAATTAAATAAT
1 AATTAATTAAATAAT
*
21314 AATTAATTAATTAAT
1 AATTAATTAAATAAT
21329 TTATAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAATTAAATAAT
Found at i:21323 original size:19 final size:19
Alignment explanation
Indices: 21299--21346 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
21289 ACAATTATTA
*
21299 AATTAATTAAATAATAATT
1 AATTAATTAAATAATAAAT
* *
21318 AATTAATTAATTTATAAAT
1 AATTAATTAAATAATAAAT
21337 AATT-ATTAAA
1 AATTAATTAAA
21347 ATTACTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTAATTAAATAATAAAT
Found at i:21325 original size:23 final size:22
Alignment explanation
Indices: 21291--21345 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
21281 TAATTTATAC
21291 AATTATTAAATTAATTAA-ATAAT
1 AATTATT-AATTAATTAATA-AAT
*
21314 AATTAATTAATTAATTTATAAAT
1 AATT-ATTAATTAATTAATAAAT
21337 AATTATTAA
1 AATTATTAA
21346 AATTACTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 20 0.69
24 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATTAATTAATTAATAAAT
Found at i:21523 original size:19 final size:19
Alignment explanation
Indices: 21499--21536 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21489 TTGCTCATCT
21499 TATAATATTACAA-ATATTA
1 TATAAT-TTACAATATATTA
*
21518 TATAATTTATAATATATTA
1 TATAATTTACAATATATTA
21537 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAATTTACAATATATTA
Found at i:21564 original size:18 final size:18
Alignment explanation
Indices: 21541--21578 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21531 ATATTAATTA
*
21541 AATTAATTATTAAATATT
1 AATTAATTAATAAATATT
21559 AATTAATTAATAAATATT
1 AATTAATTAATAAATATT
21577 AA
1 AA
21579 GAATCTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAATTAATAAATATT
Found at i:21578 original size:14 final size:14
Alignment explanation
Indices: 21511--21570 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
21501 TAATATTACA
21511 AATATT-ATATAATT
1 AATATTAAT-TAATT
* *
21525 TATAATATATTAATT
1 AATATTA-ATTAATT
21540 AA-ATTAATT-ATT
1 AATATTAATTAATT
21552 AAATATTAATTAATT
1 -AATATTAATTAATT
21567 AATA
1 AATA
21571 AATATTAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
12 3 0.08
13 5 0.14
14 18 0.49
15 9 0.24
16 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTAATTAATT
Found at i:21638 original size:25 final size:26
Alignment explanation
Indices: 21595--21644 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
21585 TATAATACAT
* *
21595 AAATAGTTTTATTTATTATATATATC
1 AAATAGTTTAATTTATTATACATATC
21621 AAATAGTTTAATTT-TTATACATAT
1 AAATAGTTTAATTTATTATACATAT
21645 TAATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (26 bp):
AAATAGTTTAATTTATTATACATATC
Found at i:22135 original size:17 final size:18
Alignment explanation
Indices: 22108--22141 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
22098 TTAATGTTAC
22108 ATTATTTATTATATTATA
1 ATTATTTATTATATTATA
22126 ATTA-TTATTATATTAT
1 ATTATTTATTATATTAT
22142 TTATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTTATTATATTATA
Found at i:22275 original size:27 final size:28
Alignment explanation
Indices: 22230--22296 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
22220 CTAATAATAA
* * * *
22230 TATTTAATTATTAATTAGTATTA-TAGT
1 TATTTAATAAATAAATAGTATAATTAGT
22257 TATTTAATAAATAAATAGTATAATTAGT
1 TATTTAATAAATAAATAGTATAATTAGT
*
22285 AATTT-ATAAATA
1 TATTTAATAAATA
22297 TTTTTATGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 26 0.76
28 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (28 bp):
TATTTAATAAATAAATAGTATAATTAGT
Found at i:22558 original size:20 final size:21
Alignment explanation
Indices: 22521--22564 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
22511 CGTTGATTAT
*
22521 TTATAATTTATTATTATAA-A
1 TTATAATTAATTATTATAAGA
22541 TTATAATTAA-TATATATAAGA
1 TTATAATTAATTAT-TATAAGA
22562 TTA
1 TTA
22565 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATAATTAATTATTATAAGA
Found at i:22628 original size:21 final size:22
Alignment explanation
Indices: 22602--22654 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
22592 ACATGTTAGC
22602 TAATTATTATAATAT-AT-ATAA
1 TAATTATT-TAATATAATCATAA
22623 TAATTA-TTAATATAATCATAA
1 TAATTATTTAATATAATCATAA
22644 TAATATATTTA
1 TAAT-TATTTA
22655 TTATGTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.21
20 3 0.11
21 14 0.50
22 2 0.07
23 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTATTTAATATAATCATAA
Found at i:23121 original size:28 final size:29
Alignment explanation
Indices: 23090--23147 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
23080 ATATCAATAA
23090 TTAAATA-ATAAAAATT-AAATATTTTAAT
1 TTAAATATATAAAAATTAAAAT-TTTTAAT
* *
23118 TTAAATATTTAAAATTTAAAATTTTTAAT
1 TTAAATATATAAAAATTAAAATTTTTAAT
23147 T
1 T
23148 ATTAACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 15 0.58
30 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTAAATATATAAAAATTAAAATTTTTAAT
Found at i:23128 original size:13 final size:14
Alignment explanation
Indices: 23104--23147 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
23094 ATAATAAAAA
23104 TTAAATATTTTAAT
1 TTAAATATTTTAAT
*
23118 TTAAATATTTAAAAT
1 TTAAATATTT-TAAT
23133 TTAAA-ATTTTTAAT
1 TTAAATA-TTTTAAT
23147 T
1 T
23148 ATTAACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATATTTTAAT
Found at i:23152 original size:23 final size:24
Alignment explanation
Indices: 23117--23161 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
23107 AATATTTTAA
*
23117 TTTAAATATTTAAAATTTAAAATT
1 TTTAAATATTTAAAATTAAAAATT
* *
23141 TTTAATTA-TTAACATTAAAAA
1 TTTAAATATTTAAAATTAAAAA
23162 AATTAATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATATTTAAAATTAAAAATT
Found at i:23396 original size:18 final size:19
Alignment explanation
Indices: 23375--23433 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
23365 TATTATTATA
23375 ATAATATTAG-TAATTAAT
1 ATAATATTAGTTAATTAAT
*
23393 ATAA-AATAGTTAATTAAT
1 ATAATATTAGTTAATTAAT
* *
23411 GATATTTATTAGTTAAATAAT
1 -ATA-ATATTAGTTAATTAAT
23432 AT
1 AT
23434 CAACAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.12
18 12 0.36
19 3 0.09
20 2 0.06
21 12 0.36
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
ATAATATTAGTTAATTAAT
Found at i:23607 original size:22 final size:22
Alignment explanation
Indices: 23575--23617 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23565 TATAAACAAT
*
23575 TATTATTGTATTAATTT-AATAA
1 TATTATAGTATT-ATTTGAATAA
23597 TATTATAGTATTATTTGAATA
1 TATTATAGTATTATTTGAATA
23618 TAACTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
TATTATAGTATTATTTGAATAA
Found at i:24199 original size:14 final size:13
Alignment explanation
Indices: 24173--24437 Score: 67
Period size: 12 Copynumber: 21.2 Consensus size: 13
24163 TTAATTTGAT
24173 TTAATATTATATA
1 TTAATATTATATA
*
24186 TTAACTATTGTATA
1 TTAA-TATTATATA
24200 TGT-AT-TTATA-A
1 T-TAATATTATATA
*
24211 TATAATAAT-TATA
1 T-TAATATTATATA
*
24224 TTAATA--ATTTA
1 TTAATATTATATA
*
24235 -TAATATTATTAAA
1 TTAATATTA-TATA
*
24248 TT-ATATAAATATTA
1 TTAATAT-TATA-TA
*
24262 TTTATATTATTATA
1 TTAATATTA-TATA
24276 TT-ATATTATATA
1 TTAATATTATATA
*
24288 TT-A-ATT-TA-G
1 TTAATATTATATA
*
24297 TTAAT-TTATAAA
1 TTAATATTATATA
*
24309 TT-ATATTAAATA
1 TTAATATTATATA
*
24321 TT-ATAATATAT-
1 TTAATATTATATA
*
24332 TTAATATATTAATTTCA
1 TT-A-ATATT-ATAT-A
*
24349 TTAATCTTATA-A
1 TTAATATTATATA
*
24361 ATAAT-TTA-ATA
1 TTAATATTATATA
*
24372 TTTAAAATTA-ATTA
1 -TTAATATTATA-TA
24386 TTAATA-TA-ATA
1 TTAATATTATATA
24397 TTAATTATTAT-TA
1 TTAA-TATTATATA
* *
24410 TTATTATTATTTA
1 TTAATATTATATA
* *
24423 TAAATGTTATA-A
1 TTAATATTATATA
24435 TTA
1 TTA
24438 TAATAAATAA
Statistics
Matches: 189, Mismatches: 30, Indels: 67
0.66 0.10 0.23
Matches are distributed among these distances:
9 2 0.01
10 11 0.06
11 25 0.13
12 59 0.31
13 47 0.25
14 28 0.15
15 14 0.07
16 1 0.01
17 2 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (13 bp):
TTAATATTATATA
Found at i:24226 original size:5 final size:5
Alignment explanation
Indices: 24196--24286 Score: 52
Period size: 5 Copynumber: 19.0 Consensus size: 5
24186 TTAACTATTG
* * * *
24196 TATAT GTAT-T TATAA TATAA TA-AT TATAT TA-AT AAT-T TATAA TATTAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT
* *
24244 TAAAT TATAT AAATAT TAT-T TATA- T-TAT TATAT TATAT TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT
24287 ATTAATTTAG
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
3 2 0.03
4 18 0.27
5 35 0.53
6 11 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:24228 original size:9 final size:9
Alignment explanation
Indices: 24211--24345 Score: 65
Period size: 9 Copynumber: 15.1 Consensus size: 9
24201 GTATTTATAA
*
24211 TATAATAAT
1 TATATTAAT
24220 TATATTAAT
1 TATATTAAT
* *
24229 AAT-TTATAA
1 TATATTA-AT
24238 TATTATTAAAT
1 TA-TATT-AAT
24249 TATA-TAA-
1 TATATTAAT
*
24256 -ATATTATT
1 TATATTAAT
24264 TATATT-AT
1 TATATTAAT
24272 TATATTATATT
1 TATATTA-A-T
24283 ATATATTAAT
1 -TATATTAAT
24293 T-TAGTTAAT
1 TATA-TTAAT
*
24302 T-TATAAAT
1 TATATTAAT
24310 TATATTAA-
1 TATATTAAT
*
24318 -ATATTATAA
1 TATATTA-AT
24327 TATATTTAA-
1 TATA-TTAAT
24336 TATATTAAT
1 TATATTAAT
24345 T
1 T
24346 TCATTAATCT
Statistics
Matches: 99, Mismatches: 9, Indels: 36
0.69 0.06 0.25
Matches are distributed among these distances:
6 3 0.03
7 8 0.08
8 24 0.24
9 37 0.37
10 9 0.09
11 10 0.10
12 8 0.08
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (9 bp):
TATATTAAT
Found at i:24278 original size:17 final size:17
Alignment explanation
Indices: 24176--24342 Score: 84
Period size: 17 Copynumber: 9.8 Consensus size: 17
24166 ATTTGATTTA
24176 ATATTATATATTAACTATT
1 ATATTATATATT-A-TATT
* * *
24195 GTA-TATGTATT-TATA
1 ATATTATATATTATATT
*
24210 ATATAATA-ATTATATT
1 ATATTATATATTATATT
*
24226 AATAATT-TATAATATTATT
1 -AT-ATTATATATTA-TATT
* *
24245 AAATTATATA-AATATT
1 ATATTATATATTATATT
24261 AT-TTATATTATTATATT
1 ATATTATA-TATTATATT
24278 ATATTATATATTA-ATT
1 ATATTATATATTATATT
24294 -TAGTTA-AT-TTATAAATT
1 ATA-TTATATATTAT--ATT
* *
24311 ATATTAAATATTATAAT
1 ATATTATATATTATATT
24328 ATATTTAATATATTA
1 ATA-TT-ATATATTA
24343 ATTTCATTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
14 3 0.03
15 17 0.15
16 18 0.16
17 31 0.27
18 28 0.25
19 17 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
ATATTATATATTATATT
Found at i:24344 original size:17 final size:17
Alignment explanation
Indices: 24208--24406 Score: 64
Period size: 17 Copynumber: 11.6 Consensus size: 17
24198 TATGTATTTA
*
24208 TAATATAATAAT-TATAT
1 TAATATATTAATATAT-T
*
24225 TAATAATTTATAATATTATT
1 TAAT-ATAT-TAATA-TATT
* *
24245 AAATTATATAAATATTATT
1 TAA-TATATTAATA-TATT
24264 T-ATATTATT-ATATTATAT
1 TAATA-TATTAATA-TAT-T
* *
24282 T-ATATATTAATTTAGT
1 TAATATATTAATATATT
* *
24298 TAATTTATAAATTATATT
1 TAATATATTAA-TATATT
*
24316 AAATAT-TATAATATATT
1 TAATATAT-TAATATATT
*
24333 TAATATATTAATTTCA-T
1 TAATATATTAATAT-ATT
* *
24350 TAATCTTATAAATA-ATT
1 TAAT-ATATTAATATATT
24367 TAATAT-TTAA-A-A-T
1 TAATATATTAATATATT
24380 TAAT-TATTAATATAATAT
1 TAATATATTAATAT-AT-T
24398 TAAT-TATTA
1 TAATATATTA
24407 TTATTATTAT
Statistics
Matches: 138, Mismatches: 23, Indels: 41
0.68 0.11 0.20
Matches are distributed among these distances:
12 1 0.01
13 9 0.07
14 3 0.02
15 3 0.02
16 5 0.04
17 53 0.38
18 41 0.30
19 13 0.09
20 6 0.04
21 4 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
TAATATATTAATATATT
Found at i:24353 original size:26 final size:24
Alignment explanation
Indices: 24235--24363 Score: 73
Period size: 26 Copynumber: 4.9 Consensus size: 24
24225 TAATAATTTA
24235 TAATATTATTAAATTATATAAATATTAT
1 TAAT-TTATT-AA-TATATAAATA-TAT
* *
24263 TTATATTATT-ATATTATATTATATAT
1 TAAT-TTATTAATA-TATA-AATATAT
*
24289 TAATTTAGTTAATTTATAAATTATAT
1 TAATTTA-TTAATATATAAA-TATAT
*
24315 TAAATATTA-TAATATATTTAATATAT
1 T-AAT-TTATTAATATA-TAAATATAT
*
24341 TAATTTCATTAATCTTATAAATA
1 TAATTT-ATTAAT-ATATAAATA
24364 ATTTAATATT
Statistics
Matches: 81, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
24 2 0.02
25 10 0.12
26 44 0.54
27 13 0.16
28 12 0.15
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (24 bp):
TAATTTATTAATATATAAATATAT
Found at i:24486 original size:25 final size:24
Alignment explanation
Indices: 24430--24488 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
24420 TTATAAATGT
24430 TATAATTATAATAAATAAGTATTA
1 TATAATTATAATAAATAAGTATTA
* *
24454 TCTCAATT-TAATAATATAATTATTA
1 TAT-AATTATAATAA-ATAAGTATTA
24479 TAATAATTAT
1 T-ATAATTAT
24489 TTTATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 8 0.29
25 18 0.64
26 2 0.07
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (24 bp):
TATAATTATAATAAATAAGTATTA
Found at i:24539 original size:13 final size:12
Alignment explanation
Indices: 24521--24563 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
24511 ATTATCTATA
24521 ATATATTACAATT
1 ATATATTA-AATT
24534 ATATATTAAATT
1 ATATATTAAATT
24546 ATATAATT-AA-T
1 ATAT-ATTAAATT
24557 ATATATT
1 ATATATT
24564 CTAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.10
11 5 0.17
12 10 0.34
13 11 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATTAAATT
Found at i:26610 original size:6 final size:6
Alignment explanation
Indices: 26599--26637 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
26589 AATAAAAAGC
* *
26599 TTAATA TTAATA TCAATA TTAA-A TTAGTA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
26638 ACAATATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (6 bp):
TTAATA
Found at i:26633 original size:17 final size:17
Alignment explanation
Indices: 26599--26638 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
26589 AATAAAAAGC
26599 TTAATATTAATATCAATA
1 TTAA-ATTAATATCAATA
* *
26617 TTAAATTAGTATTAATA
1 TTAAATTAATATCAATA
26634 TTAAA
1 TTAAA
26639 CAATATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAATTAATATCAATA
Found at i:26776 original size:22 final size:24
Alignment explanation
Indices: 26728--26786 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
26718 TATTAATCTA
*
26728 ATTAATTATAATATTAATATTGAT
1 ATTAATTATAATATAAATATTGAT
26752 ATTAA-TA-AATATAAATATTTG-T
1 ATTAATTATAATATAAATA-TTGAT
*
26774 ATT-ATTTTAATAT
1 ATTAATTATAATAT
26787 TATATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 14 0.47
23 10 0.33
24 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
ATTAATTATAATATAAATATTGAT
Found at i:26828 original size:15 final size:15
Alignment explanation
Indices: 26799--26840 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
26789 TATTAATAAC
*
26799 TTAA-TAATAAAATA
1 TTAATTAATAATATA
*
26813 TTAATTTATAATATA
1 TTAATTAATAATATA
26828 TTAATTAATAATA
1 TTAATTAATAATA
26841 ATTTATACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATTAATAATATA
Found at i:27016 original size:26 final size:26
Alignment explanation
Indices: 26979--27047 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
26969 GTATTATAAT
26979 ATAAATAT-AATATTAATAATCATTA
1 ATAAATATAAATATTAATAATCATTA
* *
27004 TTAAA-ATCAAATAATT-ATAATTATTA
1 ATAAATAT-AAAT-ATTAATAATCATTA
27030 ATAAATATAATATATTAA
1 ATAAATATAA-ATATTAA
27048 ATTATATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
24 2 0.06
25 4 0.11
26 21 0.60
27 8 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAATATAAATATTAATAATCATTA
Found at i:27038 original size:16 final size:17
Alignment explanation
Indices: 27013--27047 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
27003 ATTAAAATCA
*
27013 AATAATTATAAT-TATT
1 AATAAATATAATATATT
27029 AATAAATATAATATATT
1 AATAAATATAATATATT
27046 AA
1 AA
27048 ATTATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAATATAATATATT
Found at i:27050 original size:25 final size:25
Alignment explanation
Indices: 26979--27088 Score: 66
Period size: 26 Copynumber: 4.1 Consensus size: 25
26969 GTATTATAAT
*
26979 ATAAATATAATATTAATAATCATTATT-
1 ATAAATATAATA-TATTAA--ATTATTA
27006 A-AAATCA-AATA-ATTATAATTATTA
1 ATAAAT-ATAATATATTA-AATTATTA
27030 ATAAATATAATATATTAAATTATATA
1 ATAAATATAATATATTAAATTAT-TA
*
27056 TTAATATAGTTATATTATATATAAATTATTA
1 ATAA-ATA--TA-A-TATAT-TAAATTATTA
27087 AT
1 AT
27089 TTTATAATGA
Statistics
Matches: 67, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
23 6 0.09
24 5 0.07
25 15 0.22
26 17 0.25
27 5 0.07
29 2 0.03
30 1 0.01
31 8 0.12
32 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (25 bp):
ATAAATATAATATATTAAATTATTA
Found at i:27052 original size:31 final size:34
Alignment explanation
Indices: 27016--27089 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 34
27006 AAAATCAAAT
27016 AATTATAATTATTAATA-A-ATATAATATAT-TA
1 AATTATAATTATTAATATAGATATAATATATATA
* *
27047 AATTAT-A-TATTAATATAGTTATATTATATATA
1 AATTATAATTATTAATATAGATATAATATATATA
27079 AATTATTAATT
1 AATTA-TAATT
27090 TTATAATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
29 8 0.23
30 2 0.06
31 15 0.43
32 7 0.20
33 1 0.03
34 1 0.03
35 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
AATTATAATTATTAATATAGATATAATATATATA
Found at i:27074 original size:21 final size:20
Alignment explanation
Indices: 27037--27087 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
27027 TTAATAAATA
27037 TAATATATTAAATTATATAT
1 TAATATATTAAATTATATAT
*
27057 TAATATAGTTATATTATATAT
1 TAATATA-TTAAATTATATAT
*
27078 AAAT-TATTAA
1 TAATATATTAA
27088 TTTTATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 9 0.33
21 15 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATATATTAAATTATATAT
Found at i:27407 original size:18 final size:16
Alignment explanation
Indices: 27365--27417 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
27355 TTAAAGATTG
27365 TAGTATGAATAATTAACT
1 TAGTAT-AATAATTAA-T
*
27383 TAATATAATTAATCTAAT
1 TAGTATAA-TAAT-TAAT
27401 TAGTATAAATAATTAAT
1 TAGTAT-AATAATTAAT
27418 ATATCCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 6 0.20
18 19 0.63
19 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (16 bp):
TAGTATAATAATTAAT
Found at i:27989 original size:17 final size:16
Alignment explanation
Indices: 27939--27991 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
27929 AGTAATAATC
* *
27939 ATAATTTATATTTTAA
1 ATAATTTATATATTAT
27955 ATAATCTTATATTATTAT
1 ATAAT-TTATA-TATTAT
27973 ATAATTATATATATTAT
1 ATAATT-TATATATTAT
27990 AT
1 AT
27992 CTTAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 14 0.44
18 13 0.41
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAATTTATATATTAT
Found at i:27995 original size:32 final size:31
Alignment explanation
Indices: 27958--28070 Score: 110
Period size: 32 Copynumber: 3.6 Consensus size: 31
27948 ATTTTAAATA
27958 ATCTT-ATATTATTATATAATTATATATATTAT
1 ATCTTAATATTATTATAT-ATTA-ATATATTAT
*
27990 ATCTTAATAATTATTA-ATATTAAATAGATTTAAT
1 ATCTTAAT-ATTATTATATATT-AATATA-TT-AT
28024 AT-TTAATATTATTATAT-TTAA-ATATTAT
1 ATCTTAATATTATTATATATTAATATATTAT
* *
28052 AACTTAATATTATAATATA
1 ATCTTAATATTATTATATA
28071 ACTTAGTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
28 3 0.04
29 16 0.23
30 2 0.03
31 2 0.03
32 21 0.30
33 14 0.20
34 11 0.16
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (31 bp):
ATCTTAATATTATTATATATTAATATATTAT
Found at i:28047 original size:16 final size:17
Alignment explanation
Indices: 27963--28051 Score: 73
Period size: 16 Copynumber: 5.4 Consensus size: 17
27953 AAATAATCTT
*
27963 ATATTATTATATAATTAT
1 ATATTATTATAT-ATTAA
*
27981 ATA-TATTATATCTT-A
1 ATATTATTATATATTAA
27996 ATAATTATTA-ATATTAA
1 AT-ATTATTATATATTAA
* *
28013 ATA-GATT-TAATATTTA
1 ATATTATTAT-ATATTAA
28029 ATATTATTATAT-TTAA
1 ATATTATTATATATTAA
28045 ATATTAT
1 ATATTAT
28052 AACTTAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
15 5 0.09
16 27 0.47
17 21 0.37
18 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
ATATTATTATATATTAA
Found at i:28047 original size:23 final size:23
Alignment explanation
Indices: 28003--28216 Score: 79
Period size: 23 Copynumber: 9.6 Consensus size: 23
27993 TTAATAATTA
28003 TTAATATTAAATAGATTTAATAT
1 TTAATATTAAATAGATTTAATAT
* *
28026 TTAATATT-ATTATATTTAAATAT
1 TTAATATTAAATAGATTT-AATAT
*
28049 TATAA-CTT-AAT--ATTATAATA-
1 T-TAATATTAAATAGATT-TAATAT
*
28069 -TAACTTAGTAAATAGATTTAATATT
1 TTAA--TATTAAATAGATTTAATA-T
*
28094 AAATTAATATTAAA-A-TTTATAATAT
1 ---TTAATATTAAATAGATT-TAATAT
*
28119 TATAATATT--A-AGTTTATAATAT
1 T-TAATATTAAATAGATT-TAATAT
*
28141 TAAATA-T-AAT--A-TTAATAT
1 TTAATATTAAATAGATTTAATAT
* **
28159 TAAATATTAAATCTATTTAATA-
1 TTAATATTAAATAGATTTAATAT
28181 TTAATATTAAATAGATTATAA-AT
1 TTAATATTAAATAGATT-TAATAT
*
28204 TAAATATTAAATA
1 TTAATATTAAATA
28217 TTATAATGTT
Statistics
Matches: 150, Mismatches: 14, Indels: 54
0.69 0.06 0.25
Matches are distributed among these distances:
18 15 0.10
19 2 0.01
20 4 0.03
21 15 0.10
22 39 0.26
23 51 0.34
24 6 0.04
25 3 0.02
26 6 0.04
27 6 0.04
29 3 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAATATTAAATAGATTTAATAT
Found at i:28105 original size:6 final size:6
Alignment explanation
Indices: 28086--28190 Score: 78
Period size: 6 Copynumber: 17.7 Consensus size: 6
28076 GTAAATAGAT
* * * * *
28086 TTAATA TTAA-A TTAATA TTAAAA TTTATA ATATTA -TAATA TTAAGTT
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA-TA
28133 TATAATA TTAA-A TATAATA TTAATA TTAAATA TTAA-A TCT-AT- TTAATA
1 T-TAATA TTAATA T-TAATA TTAATA TT-AATA TTAATA T-TAATA TTAATA
28181 TTAATA TTAA
1 TTAATA TTAA
28191 ATAGATTATA
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
4 1 0.01
5 17 0.22
6 46 0.58
7 12 0.15
8 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (6 bp):
TTAATA
Found at i:28117 original size:26 final size:26
Alignment explanation
Indices: 28087--28170 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
28077 TAAATAGATT
28087 TAATATTAAATTAATATTAAAATTTA
1 TAATATTAAATTAATATTAAAATTTA
*
28113 TAATATT--A-TAATATT-AAGTTTA
1 TAATATTAAATTAATATTAAAATTTA
*
28135 TAATATTAAATATAATATTAATA-TTA
1 TAATATTAAAT-TAATATTAAAATTTA
28161 -AATATTAAAT
1 TAATATTAAAT
28171 CTATTTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 13 0.26
23 7 0.14
24 2 0.04
25 10 0.20
26 17 0.34
27 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
TAATATTAAATTAATATTAAAATTTA
Found at i:28125 original size:34 final size:38
Alignment explanation
Indices: 28119--28259 Score: 70
Period size: 38 Copynumber: 3.7 Consensus size: 38
28109 TTTATAATAT
28119 TATAATATTAAGT-TTATAATATTAAATATAATATT-AA
1 TATAATATTAA-TATTATAATATTAAATATAATATTAAA
*
28156 TAT--TA--AATATTA-AATCTATTTAATATTAATATTAAA
1 TATAATATTAATATTATAA--TATTAAATA-TAATATTAAA
* * *
28192 TAGATTA-TAA-ATTA-AATATTAAATATTATAATGTTTAAA
1 TATAATATTAATATTATAATATT-AA-A-TATAAT-ATTAAA
28231 CT-TAATATTATAATATTATAATATTAAAT
1 -TATAATA-T-TAATATTATAATATTAAAT
28260 CTATTTACTT
Statistics
Matches: 80, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
32 3 0.04
33 5 0.06
34 8 0.10
35 9 0.11
36 8 0.10
37 4 0.05
38 13 0.16
39 12 0.15
40 1 0.01
41 1 0.01
42 4 0.05
43 6 0.08
44 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (38 bp):
TATAATATTAATATTATAATATTAAATATAATATTAAA
Found at i:28137 original size:14 final size:13
Alignment explanation
Indices: 28113--28168 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
28103 TTAAAATTTA
28113 TAATATTATAATAT
1 TAAT-TTATAATAT
28127 TAAGTTTATAATAT
1 TAA-TTTATAATAT
*
28141 TAA-ATATAATAT
1 TAATTTATAATAT
28153 TAATATTA-AATAT
1 TAAT-TTATAATAT
28166 TAA
1 TAA
28169 ATCTATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
12 11 0.30
13 8 0.22
14 17 0.46
15 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
TAATTTATAATAT
Found at i:28139 original size:71 final size:67
Alignment explanation
Indices: 28010--28140 Score: 174
Period size: 67 Copynumber: 1.9 Consensus size: 67
28000 TTATTAATAT
* * * *
28010 TAAATAGATTTAATATTTAATATTATTATATTTAAATATTATAACTTAATATTATAATATAACTT
1 TAAATAGATTTAATATTAAATAATATTAAATTTAAATATTATAAATTAATATTATAATATAACTT
28075 AG
66 AG
28077 TAAATAGATTTAATATTAAATTAATATTAAAATTTATAATATTATAATATTAAGT-TTATAATAT
1 TAAATAGATTTAATATTAAA-TAATATT-AAATTTA-AATATTATAA-ATTAA-TATTATAATAT
28141 TAAATATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 19 0.35
68 6 0.11
69 6 0.11
70 10 0.18
71 13 0.24
72 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (67 bp):
TAAATAGATTTAATATTAAATAATATTAAATTTAAATATTATAAATTAATATTATAATATAACTT
AG
Found at i:28146 original size:29 final size:28
Alignment explanation
Indices: 28096--28258 Score: 119
Period size: 29 Copynumber: 5.7 Consensus size: 28
28086 TTAATATTAA
*
28096 ATTAATATTAAAAT-TTATAATATTATAAT
1 ATTAATATTATAATATTA-AA-ATTATAAT
28125 ATTAAGT-TTATAATATT-AAA-TATAAT
1 ATTAA-TATTATAATATTAAAATTATAAT
28151 ATTAATATTA-AATATT-AAATCTATTTAAT
1 ATTAATATTATAATATTAAAAT-TA--TAAT
28180 ATTAATATTA-AATAGATTATAAATTA-AAT
1 ATTAATATTATAAT--ATTA-AAATTATAAT
* * *
28209 ATTAAATATTATAATGTTTAAACT-TAAT
1 ATT-AATATTATAATATTAAAATTATAAT
28237 ATTATAATATTATAATATTAAA
1 A-T-TAATATTATAATATTAAA
28259 TCTATTTACT
Statistics
Matches: 112, Mismatches: 6, Indels: 32
0.75 0.04 0.21
Matches are distributed among these distances:
25 10 0.09
26 14 0.12
27 3 0.03
28 10 0.09
29 52 0.46
30 11 0.10
31 6 0.05
32 2 0.02
33 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTAATATTATAATATTAAAATTATAAT
Done.