Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 21 of 32
Found at i:3441770 original size:6 final size:6
Alignment explanation
Indices: 3441759--3441797 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3441749 AAATGTTAGA
* * *
3441759 TTTTAT TTTTAT TATTAT TATTAT TATTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
3441798 GGTTAGCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:3441775 original size:3 final size:3
Alignment explanation
Indices: 3441761--3441795 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3441751 ATGTTAGATT
* *
3441761 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3441796 TTGGTTAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:3442844 original size:3 final size:3
Alignment explanation
Indices: 3442836--3442860 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3442826 TTTCAAGTTG
3442836 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3442861 GTGTTATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3443396 original size:25 final size:25
Alignment explanation
Indices: 3443360--3443423 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
3443350 TTACTTTGTT
* * *
3443360 TTATATATATATATATATATATTTAAT
1 TTATAAATATATAT-TATA-ATATAAA
3443387 TTATAAATATA-ATTATAATATAAA
1 TTATAAATATATATTATAATATAAA
3443411 TTATTAAATATAT
1 TTA-TAAATATAT
3443424 TAAAATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 8 0.25
25 12 0.38
26 2 0.06
27 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATAAATATATATTATAATATAAA
Found at i:3443436 original size:22 final size:25
Alignment explanation
Indices: 3443383--3443438 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 25
3443373 TATATATATT
3443383 TAATTTA-TAAATATAATTATAATA
1 TAATTTATTAAATATAATTATAATA
*
3443407 TAAATTATTAAATAT-ATTA-AA-A
1 TAATTTATTAAATATAATTATAATA
3443429 TAATTTATTA
1 TAATTTATTA
3443439 TGTTAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 10 0.34
23 2 0.07
24 10 0.34
25 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTTATTAAATATAATTATAATA
Found at i:3443478 original size:18 final size:18
Alignment explanation
Indices: 3443449--3443503 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
3443439 TGTTAATTAA
3443449 ATTTAA-ATATATTTTAT
1 ATTTAATATATATTTTAT
* *
3443466 ATTTATTATATATATTAT
1 ATTTAATATATATTTTAT
3443484 A-TTAATATCATATTTT-T
1 ATTTAATAT-ATATTTTAT
3443501 ATT
1 ATT
3443504 GTGTTCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATATATATTTTAT
Found at i:3452029 original size:48 final size:49
Alignment explanation
Indices: 3451977--3452081 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 49
3451967 TTGGCACTAC
* *
3451977 CCCACCTTGGGTGAAACT-TATCCTTTGAGATTAGGCATTGATTCACGT
1 CCCACCTTGGATGAAACTCTATCCTTTGAAATTAGGCATTGATTCACGT
*
3452025 CCCACCTTGGATGAAGCTCTATCCTTTGAAATTAGGCATTGATTCACGT
1 CCCACCTTGGATGAAACTCTATCCTTTGAAATTAGGCATTGATTCACGT
*
3452074 CCAACCTT
1 CCCACCTT
3452082 CAAACAAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 16 0.31
49 36 0.69
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CCCACCTTGGATGAAACTCTATCCTTTGAAATTAGGCATTGATTCACGT
Found at i:3452643 original size:20 final size:20
Alignment explanation
Indices: 3452617--3452680 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
3452607 AAATATTAGC
3452617 ATAAAAAAATTTTAAAATTAA
1 ATAAAAAAATTTT-AAATTAA
*
3452638 ATAAAAATAATTTT-TATTAA
1 ATAAAAA-AATTTTAAATTAA
3452658 ATAAATAAAATTTTAAATTAA
1 ATAAA-AAAATTTTAAATTAA
3452679 AT
1 AT
3452681 TAATTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 16 0.42
21 16 0.42
22 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTTTAAATTAA
Found at i:3455623 original size:15 final size:17
Alignment explanation
Indices: 3455599--3455635 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3455589 AATTATTTAA
3455599 TTTT-TATTTAA-A-AT
1 TTTTATATTTAATATAT
3455613 TTTTATATTTAATATAT
1 TTTTATATTTAATATAT
3455630 TTTTAT
1 TTTTAT
3455636 TAAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 1 0.05
17 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATTTAATATAT
Found at i:3455636 original size:15 final size:15
Alignment explanation
Indices: 3455598--3455636 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3455588 AAATTATTTA
3455598 ATTTTTATTTAAAAT
1 ATTTTTATTTAAAAT
*
3455613 -TTTTATATTTAATAT
1 ATTTT-TATTTAAAAT
3455628 ATTTTTATT
1 ATTTTTATT
3455637 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTATTTAAAAT
Found at i:3458464 original size:27 final size:28
Alignment explanation
Indices: 3458430--3458482 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3458420 ATTATAAATA
*
3458430 ATTAAATAAA-AATTAAATATATTTTTT
1 ATTAAATAAATAAATAAATATATTTTTT
*
3458457 ATTAAATAAATAAATAAATTTATTTT
1 ATTAAATAAATAAATAAATATATTTT
3458483 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAAATAAATAAATAAATATATTTTTT
Found at i:3460426 original size:9 final size:9
Alignment explanation
Indices: 3460407--3460464 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 9
3460397 TTTTAATGAC
3460407 ATTTGTATTA
1 ATTT-TATTA
3460417 ATTTTATTA
1 ATTTTATTA
3460426 ATTTTTTATATA
1 A--TTTTAT-TA
*
3460438 ATTTTAATA
1 ATTTTATTA
3460447 ATTTTAATATA
1 ATTTT-AT-TA
3460458 ATTTTAT
1 ATTTTAT
3460465 AATAAAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 13 0.32
10 12 0.29
11 13 0.32
12 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTATTA
Found at i:3460463 original size:11 final size:10
Alignment explanation
Indices: 3460380--3460465 Score: 72
Period size: 11 Copynumber: 8.3 Consensus size: 10
3460370 GTAATCATTG
*
3460380 ATATAGTTTT
1 ATATAATTTT
3460390 ATAATAATTTT
1 AT-ATAATTTT
3460401 A-ATGACATTTGT
1 ATAT-A-ATTT-T
3460413 AT-TAATTTT
1 ATATAATTTT
3460422 AT-TAATTTTTT
1 ATATAA--TTTT
3460433 ATATAATTTT
1 ATATAATTTT
3460443 A-ATAATTTT
1 ATATAATTTT
3460452 AATATAATTTT
1 -ATATAATTTT
3460463 ATA
1 ATA
3460466 ATAAAAATGT
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
9 16 0.25
10 16 0.25
11 27 0.42
12 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (10 bp):
ATATAATTTT
Found at i:3460469 original size:11 final size:11
Alignment explanation
Indices: 3460386--3460469 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 11
3460376 ATTGATATAG
3460386 TTTTATAATAA
1 TTTTATAATAA
3460397 -TTT-TAATGACA
1 TTTTATAAT-A-A
3460408 TTTGTAT--TAA
1 TTT-TATAATAA
3460418 TTTTAT--TAA
1 TTTTATAATAA
*
3460427 TTTTTTATATAA
1 TTTTATA-ATAA
3460439 -TTT-TAATAA
1 TTTTATAATAA
3460448 TTTTA-ATATAA
1 TTTTATA-ATAA
3460459 TTTTATAATAA
1 TTTTATAATAA
3460470 AAATGTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 24
0.71 0.01 0.28
Matches are distributed among these distances:
9 19 0.32
10 14 0.23
11 18 0.30
12 7 0.12
13 1 0.02
14 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTATAATAA
Found at i:3460489 original size:28 final size:27
Alignment explanation
Indices: 3460453--3460508 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
3460443 AATAATTTTA
3460453 ATATAATTTTATAATAAAAATGT-TAAT
1 ATATAA-TTTATAATAAAAATGTCTAAT
*
3460480 ATATAGATTTATAATAAAAGTGTCTAAT
1 ATATA-ATTTATAATAAAAATGTCTAAT
3460508 A
1 A
3460509 AATTATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATAATTTATAATAAAAATGTCTAAT
Found at i:3462994 original size:26 final size:27
Alignment explanation
Indices: 3462921--3463009 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
3462911 TGAAAAGAAT
* *
3462921 TAATTCAAATTACAAGTTTTGAATATAAA
1 TAATT-AAATTA-AAATTTTAAATATAAA
*
3462950 TAATTAAATTAAAAATTTAAATATAAA
1 TAATTAAATTAAAATTTTAAATATAAA
* *
3462977 -AGTTAAATT-AAATTTT-TAT-TAAA
1 TAATTAAATTAAAATTTTAAATATAAA
3463000 TAATTGAAAT
1 TAATT-AAAT
3463010 AATTAAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
23 4 0.08
24 5 0.10
25 10 0.20
26 8 0.16
27 13 0.25
28 6 0.12
29 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (27 bp):
TAATTAAATTAAAATTTTAAATATAAA
Found at i:3464757 original size:142 final size:142
Alignment explanation
Indices: 3464501--3464918 Score: 793
Period size: 142 Copynumber: 3.0 Consensus size: 142
3464491 CATATATCTT
3464501 TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGAATAAACAATTGAAGGTGCT
1 TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGAATAAACAATTGAAGGTGCT
3464566 AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTTATTTTTAATAGATATTTGCCTTCT
66 AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTTATTTTTAATAGATATTTGCCTTCT
3464631 CATTTATGACTA
131 CATTTATGACTA
3464643 TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGAATAAACAATTGAAGGTGCT
1 TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGAATAAACAATTGAAGGTGCT
3464708 AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTTATTTTTAATAGATATTTGCCTTCT
66 AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTTATTTTTAATAGATATTTGCCTTCT
3464773 CATTTATGACTA
131 CATTTATGACTA
* *
3464785 TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGGATAAACAATTGAAGTTGCT
1 TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGAATAAACAATTGAAGGTGCT
* *
3464850 AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTT-TTTTTAATAGATATTTGCCCTCG
66 AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTTATTTTTAATAGATATTTGCCTTCT
3464914 CATTT
131 CATTT
3464919 GGATTTGAAC
Statistics
Matches: 272, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
141 26 0.10
142 246 0.90
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (142 bp):
TATTTTGCAAGTTTAATAACTTTGTCATCTTGTCTTCTCCATTCGAATAAACAATTGAAGGTGCT
AGAATGAAATCACAAGAGATCAAGAGATGTCATCACTCTTTATTTTTAATAGATATTTGCCTTCT
CATTTATGACTA
Found at i:3466070 original size:13 final size:13
Alignment explanation
Indices: 3466054--3466104 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3466044 TTCATTTAAG
*
3466054 AAAATATTTTATT
1 AAAATATTTAATT
**
3466067 AAAATAAATAATT
1 AAAATATTTAATT
*
3466080 AAATTTATTTAATT
1 AAA-ATATTTAATT
3466094 AAAATATTTAA
1 AAAATATTTAA
3466105 AATAAAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATATTTAATT
Found at i:3470452 original size:25 final size:24
Alignment explanation
Indices: 3470414--3470461 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3470404 TCAATCACTT
*
3470414 TTTATTAGTAAAGATTAGAAAAATA
1 TTTATTAGTAAAGAATA-AAAAATA
* *
3470439 TTTATTTGTTAAGAATAAAAAAT
1 TTTATTAGTAAAGAATAAAAAAT
3470462 CTTATTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (24 bp):
TTTATTAGTAAAGAATAAAAAATA
Found at i:3470752 original size:11 final size:10
Alignment explanation
Indices: 3470705--3470798 Score: 56
Period size: 10 Copynumber: 9.6 Consensus size: 10
3470695 ATATGACCTT
3470705 TTTTAAT-T-
1 TTTTAATATA
3470713 TTTT-ATATAA
1 TTTTAATAT-A
* *
3470723 TTTTGATAGA
1 TTTTAATATA
*
3470733 TTTTGATATTA
1 TTTTAATA-TA
3470744 TTTTAATAT-
1 TTTTAATATA
3470753 TTTT-ATATGA
1 TTTTAATAT-A
*
3470763 TTTTAA-ATC
1 TTTTAATATA
* *
3470772 TTTTGATAAA
1 TTTTAATATA
3470782 TTTTAATATAA
1 TTTTAATAT-A
3470793 TTTTAA
1 TTTTAA
3470799 AAGTATTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
7 2 0.03
8 9 0.13
9 9 0.13
10 28 0.42
11 19 0.28
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (10 bp):
TTTTAATATA
Found at i:3470760 original size:19 final size:19
Alignment explanation
Indices: 3470705--3470790 Score: 79
Period size: 19 Copynumber: 4.5 Consensus size: 19
3470695 ATATGACCTT
3470705 TTTTAAT-TTTTTATATAA
1 TTTTAATATTTTTATATAA
* * *
3470723 TTTTGATAGATTTTGATATTA
1 TTTT-A-ATATTTTTATATAA
*
3470744 TTTTAATATTTTTATATGA
1 TTTTAATATTTTTATATAA
3470763 TTTTAA-ATCTTTTGATA-AA
1 TTTTAATAT-TTTT-ATATAA
3470782 TTTTAATAT
1 TTTTAATAT
3470791 AATTTTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
18 6 0.11
19 29 0.53
20 7 0.13
21 13 0.24
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTTAATATTTTTATATAA
Found at i:3470792 original size:12 final size:11
Alignment explanation
Indices: 3470712--3470798 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 11
3470702 CTTTTTTAAT
*
3470712 TTTTTATATAA
1 TTTTAATATAA
* *
3470723 TTTTGATA-GA
1 TTTTAATATAA
* *
3470733 TTTTGATATTA
1 TTTTAATATAA
3470744 TTTTAATAT--
1 TTTTAATATAA
*
3470753 TTTT-ATATGA
1 TTTTAATATAA
*
3470763 TTTTAA-AT-C
1 TTTTAATATAA
*
3470772 TTTTGATA-AA
1 TTTTAATATAA
3470782 TTTTAATATAA
1 TTTTAATATAA
3470793 TTTTAA
1 TTTTAA
3470799 AAGTATTAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 4 0.07
9 9 0.15
10 23 0.38
11 25 0.41
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (11 bp):
TTTTAATATAA
Found at i:3470859 original size:21 final size:22
Alignment explanation
Indices: 3470835--3470885 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
3470825 CTAATAAAAT
3470835 TTTGATAATCTTT--ATATTAAG
1 TTTGATAATCTTTGAAT-TTAAG
*
3470856 TTTGATAA-CTTTGAATTTAAT
1 TTTGATAATCTTTGAATTTAAG
3470877 TTTGATAAT
1 TTTGATAAT
3470886 TCTTGGTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (22 bp):
TTTGATAATCTTTGAATTTAAG
Found at i:3474454 original size:2 final size:2
Alignment explanation
Indices: 3474447--3474480 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3474437 AAGATTTGTA
*
3474447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3474481 TTCATCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3480544 original size:34 final size:34
Alignment explanation
Indices: 3480477--3480692 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
3480467 CTTTGGTTTG
* * *
3480477 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
3480510 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3480544 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3480577 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
3480611 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
3480645 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
3480679 TGTTGATTAAATGG
1 TGTTGATTAAATGG
3480693 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:3480658 original size:68 final size:67
Alignment explanation
Indices: 3480477--3480694 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
3480467 CTTTGGTTTG
* * * * *
3480477 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
3480542 AT
66 AT
* * * *
3480544 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
3480609 AT
66 AT
* * *
3480611 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
3480676 CAT
65 CAT
3480679 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
3480695 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:3481017 original size:19 final size:19
Alignment explanation
Indices: 3480993--3481049 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
3480983 TTGGTTGTCG
*
3480993 AGGTACTATTCACGTATAT
1 AGGTACTATTCACGTATAC
*
3481012 AGGTACTATTCACATATAC
1 AGGTACTATTCACGTATAC
* *
3481031 GGGTACTATTCAAGTATAC
1 AGGTACTATTCACGTATAC
3481050 GGTTACTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
AGGTACTATTCACGTATAC
Found at i:3481050 original size:19 final size:19
Alignment explanation
Indices: 3480994--3481056 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
3480984 TGGTTGTCGA
* **
3480994 GGTACTATTCACGTATATA
1 GGTACTATTCAAGTATACG
3481013 GGTACTATTCACA-TATACG
1 GGTACTATTCA-AGTATACG
3481032 GGTACTATTCAAGTATACG
1 GGTACTATTCAAGTATACG
*
3481051 GTTACT
1 GGTACT
3481057 GTACACGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 1 0.03
19 37 0.97
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (19 bp):
GGTACTATTCAAGTATACG
Found at i:3485191 original size:34 final size:34
Alignment explanation
Indices: 3485122--3485339 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
3485112 AAGTGGGAGA
* * *
3485122 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3485155 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3485189 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3485222 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3485256 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3485290 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3485324 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3485340 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3485305 original size:68 final size:67
Alignment explanation
Indices: 3485122--3485341 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
3485112 AAGTGGGAGA
* * * * *
3485122 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
3485187 CC
66 CC
* * * *
3485189 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
3485254 CC
66 CC
* * *
3485256 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
3485321 GCC
65 GCC
3485324 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
3485342 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:3486676 original size:15 final size:17
Alignment explanation
Indices: 3486656--3486695 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3486646 CTAATAAATA
3486656 ATTAAATATT-ATTT-T
1 ATTAAATATTAATTTGT
*
3486671 ATTAAATTTTAATTTGT
1 ATTAAATATTAATTTGT
3486688 A-TAAATAT
1 ATTAAATAT
3486696 ATCATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 9 0.43
16 10 0.48
17 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTAAATATTAATTTGT
Found at i:3488022 original size:31 final size:30
Alignment explanation
Indices: 3487984--3488049 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
3487974 TTGTTTTGAG
*
3487984 TTTAAA-TTAAATTTAAAATAATTTTTTATAA
1 TTTAAATTTAAA-TTAAAATAATTATTTA-AA
* *
3488015 TTTAAATTTTAATTAAAATTATTATTTAAA
1 TTTAAATTTAAATTAAAATAATTATTTAAA
3488045 TTTAA
1 TTTAA
3488050 TTATAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 20 0.65
32 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTAAATTTAAATTAAAATAATTATTTAAA
Found at i:3488578 original size:18 final size:18
Alignment explanation
Indices: 3488551--3488595 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3488541 TTAAAAAATT
*
3488551 TAATTAATTAAT-ATAATA
1 TAATTTATTAATAAT-ATA
3488569 TAATTTATTAATAATATA
1 TAATTTATTAATAATATA
3488587 TAAATTTAT
1 T-AATTTAT
3488596 ATATTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTATTAATAATATA
Found at i:3489661 original size:12 final size:13
Alignment explanation
Indices: 3489636--3489664 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3489626 TAAGTAAATT
3489636 ATATTTATTATTA
1 ATATTTATTATTA
3489649 ATATTTATT-TTA
1 ATATTTATTATTA
3489661 ATAT
1 ATAT
3489665 ATAACTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTATTATTA
Found at i:3490094 original size:27 final size:27
Alignment explanation
Indices: 3490009--3490097 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
3489999 AGACATTAAG
* *
3490009 GCTTGAAGAGGTTTTTGGCGAGATGAT
1 GCTTGAAGAAGTTTTTGGCAAGATGAT
* * * **
3490036 GCCT-AAAAAGGCTTTTTGACAAGGCGAT
1 GCTTGAAGAA-G-TTTTTGGCAAGATGAT
*
3490064 GCTTGAAGAAGTTTTTGGCAAGATGAC
1 GCTTGAAGAAGTTTTTGGCAAGATGAT
3490091 GCTTGAA
1 GCTTGAA
3490098 AAGAAGTTGG
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
26 3 0.07
27 23 0.50
28 16 0.35
29 4 0.09
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.29
Consensus pattern (27 bp):
GCTTGAAGAAGTTTTTGGCAAGATGAT
Found at i:3493089 original size:30 final size:32
Alignment explanation
Indices: 3493055--3493115 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
3493045 ATTATGTTAG
* *
3493055 TAATTTGAATT-TTT-TAATTTTTAATTATTT
1 TAATTTGAATTATTTATAAGTTTAAATTATTT
*
3493085 TAATTTGATTTATTTATAAGTTTAAATTATT
1 TAATTTGAATTATTTATAAGTTTAAATTATT
3493116 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 10 0.38
31 3 0.12
32 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (32 bp):
TAATTTGAATTATTTATAAGTTTAAATTATTT
Found at i:3493097 original size:15 final size:15
Alignment explanation
Indices: 3493055--3493115 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
3493045 ATTATGTTAG
3493055 TAATTTGAATT-TTT
1 TAATTTGAATTATTT
*
3493069 TAATTTTTAATTATTT
1 TAA-TTTGAATTATTT
*
3493085 TAATTTGATTTATTT
1 TAATTTGAATTATTT
*
3493100 ATAAGTTTAAATTATT
1 -TAA-TTTGAATTATT
3493116 ATTTAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.08
15 17 0.45
16 9 0.24
17 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
TAATTTGAATTATTT
Found at i:3493863 original size:6 final size:6
Alignment explanation
Indices: 3493837--3493876 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
3493827 ATGCCATGCC
*
3493837 AGGGTG TGGGTG A-GGTCG AGGGTG AGGGTG AGGGTG AGGG
1 AGGGTG AGGGTG AGGGT-G AGGGTG AGGGTG AGGGTG AGGG
3493877 GTGTGCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.80
7 3 0.10
ACGTcount: A:0.15, C:0.03, G:0.65, T:0.17
Consensus pattern (6 bp):
AGGGTG
Found at i:3494405 original size:23 final size:24
Alignment explanation
Indices: 3494355--3494420 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
3494345 TTTAAAATAT
*
3494355 TATAAATTTATTTAATATTTTATACA
1 TATATATTT-TTT-ATATTTTATACA
3494381 TATATA-TTTTTATATTTGTAT-CA
1 TATATATTTTTTATATTT-TATACA
*
3494404 TATTTATTTTTTATATT
1 TATATATTTTTTATATT
3494421 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 13 0.36
24 16 0.44
25 2 0.06
26 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
TATATATTTTTTATATTTTATACA
Found at i:3494433 original size:23 final size:25
Alignment explanation
Indices: 3494407--3494452 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
3494397 TGTATCATAT
3494407 TTATTTTTTATAT-T-ATATTTTAA
1 TTATTTTTTATATATCATATTTTAA
3494430 TTATTTTTTATATATCATATTTT
1 TTATTTTTTATATATCATATTTT
3494453 TACTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTTTTTATATATCATATTTTAA
Found at i:3494438 original size:11 final size:12
Alignment explanation
Indices: 3494407--3494442 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
3494397 TGTATCATAT
3494407 TTATTTTTTATA
1 TTATTTTTTATA
*
3494419 TTATATTTTA-A
1 TTATTTTTTATA
3494430 TTATTTTTTATA
1 TTATTTTTTATA
3494442 T
1 T
3494443 ATCATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:3494642 original size:2 final size:2
Alignment explanation
Indices: 3494635--3494662 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3494625 AGATAAGAAC
3494635 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3494663 AAGAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3494667 original size:4 final size:4
Alignment explanation
Indices: 3494660--3494724 Score: 50
Period size: 4 Copynumber: 17.5 Consensus size: 4
3494650 AGAGAGAGAG
** * * *
3494660 AGAA AGAA A-AA AGTG AGAA AGAA AAAA ATAA A-AG AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
3494706 AGAA A-AA A-AA AG-A AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AG
3494725 GAAGGAGAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 14 0.29
4 35 0.71
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (4 bp):
AGAA
Found at i:3494692 original size:23 final size:22
Alignment explanation
Indices: 3494666--3494724 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
3494656 AGAGAGAAAG
**
3494666 AAAAAAGTGAGAAAGAAAAAAA
1 AAAAAAGAAAGAAAGAAAAAAA
* *
3494688 TAAAAGAGAAAGAAAGAAAGAAA
1 -AAAAAAGAAAGAAAGAAAAAAA
3494711 AAAAAAG-AAGAAAG
1 AAAAAAGAAAGAAAG
3494725 GAAGGAGAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 7 0.23
22 6 0.19
23 18 0.58
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (22 bp):
AAAAAAGAAAGAAAGAAAAAAA
Found at i:3494711 original size:19 final size:19
Alignment explanation
Indices: 3494654--3494724 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
3494644 AGAGAGAGAG
*
3494654 AGAGAGAGAAAGAAA-AAA
1 AGAGAAAGAAAGAAAGAAA
* * *
3494672 GTGAGAAAGAAAAAAATAAA
1 -AGAGAAAGAAAGAAAGAAA
3494692 AGAGAAAGAAAGAAAGAAA
1 AGAGAAAGAAAGAAAGAAA
*
3494711 A-AAAAAG-AAGAAAG
1 AGAGAAAGAAAGAAAG
3494725 GAAGGAGAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 7 0.16
18 5 0.11
19 29 0.66
20 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (19 bp):
AGAGAAAGAAAGAAAGAAA
Found at i:3495526 original size:9 final size:9
Alignment explanation
Indices: 3495514--3495550 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3495504 AAATAAAATT
3495514 ATTTTATTA
1 ATTTTATTA
3495523 ATTTTATTA
1 ATTTTATTA
*
3495532 ATTTTTTTA
1 ATTTTATTA
*
3495541 TTTTTATTA
1 ATTTTATTA
3495550 A
1 A
3495551 AGAATTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTTATTA
Found at i:3496397 original size:16 final size:18
Alignment explanation
Indices: 3496376--3496409 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3496366 CCAAACATTA
3496376 TTTCTTC-TA-AATTTTC
1 TTTCTTCTTATAATTTTC
3496392 TTTCTTCTTATAATTTTC
1 TTTCTTCTTATAATTTTC
3496410 ATTTATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTTCTTATAATTTTC
Found at i:3500644 original size:2 final size:2
Alignment explanation
Indices: 3500637--3500670 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3500627 TTAATTTAAC
3500637 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3500671 ACTAATGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3505826 original size:20 final size:21
Alignment explanation
Indices: 3505803--3505841 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3505793 GAGGTTTTTG
3505803 GTGAATTGT-ATGGTAAAGGA
1 GTGAATTGTGATGGTAAAGGA
* *
3505823 GTGATTTTTGATGGTAAAG
1 GTGAATTGTGATGGTAAAG
3505842 TTCTTACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (21 bp):
GTGAATTGTGATGGTAAAGGA
Found at i:3521648 original size:13 final size:13
Alignment explanation
Indices: 3521630--3521654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3521620 ATCTTTCTTC
3521630 TTTTTTTTTTTAA
1 TTTTTTTTTTTAA
3521643 TTTTTTTTTTTA
1 TTTTTTTTTTTA
3521655 CGTCTCCTCG
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTAA
Found at i:3527995 original size:22 final size:21
Alignment explanation
Indices: 3527965--3528005 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
3527955 GCCCCTTTTG
3527965 TTCATCTTTTTATGTAATTCT
1 TTCATCTTTTTATGTAATTCT
3527986 TTCATTCTTTTTATGTAATT
1 TTCA-TCTTTTTATGTAATT
3528006 GAATGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63
Consensus pattern (21 bp):
TTCATCTTTTTATGTAATTCT
Found at i:3529022 original size:21 final size:20
Alignment explanation
Indices: 3528978--3529022 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3528968 CTATAAGTTA
* * *
3528978 TTAATAAATATATTTTTATT
1 TTAATAAAAATATATTTATC
3528998 TTAATAAAAATCATATTTATC
1 TTAATAAAAAT-ATATTTATC
3529019 TTAA
1 TTAA
3529023 AATATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATAAAAATATATTTATC
Found at i:3530153 original size:4 final size:4
Alignment explanation
Indices: 3530136--3530166 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
3530126 TTATTTTAAA
3530136 AATT AATT ATATT AATT AATT AATT AATT AA
1 AATT AATT A-ATT AATT AATT AATT AATT AA
3530167 AACAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:3530971 original size:22 final size:22
Alignment explanation
Indices: 3530945--3530988 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3530935 AATTATTATT
3530945 TAAAT-TTAATTATAAAAATAAA
1 TAAATATTAA-TATAAAAATAAA
*
3530967 TAAATATTTATATAAAAATAAA
1 TAAATATTAATATAAAAATAAA
3530989 ATTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATATTAATATAAAAATAAA
Found at i:3538469 original size:29 final size:29
Alignment explanation
Indices: 3538437--3538492 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3538427 TATATTTTTA
* * *
3538437 TTAAATTTTAAAAAAATACGAACTTAAAC
1 TTAAATATAAAAAAAATACAAACTTAAAC
3538466 TTAAATATAAAAAAAATACAAACTTAA
1 TTAAATATAAAAAAAATACAAACTTAA
3538493 TAAAAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.29
Consensus pattern (29 bp):
TTAAATATAAAAAAAATACAAACTTAAAC
Found at i:3541338 original size:2 final size:2
Alignment explanation
Indices: 3541331--3541356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3541321 ATTTGTTATT
3541331 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3541357 CGAATCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3544726 original size:2 final size:2
Alignment explanation
Indices: 3544719--3544748 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3544709 AGCGTTTTTA
*
3544719 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3544749 TTTGAACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3545212 original size:2 final size:2
Alignment explanation
Indices: 3545205--3545234 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3545195 TGCTGCAGAG
*
3545205 AT AT AT AT GT 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
3545235 TTACATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3545592 original size:2 final size:2
Alignment explanation
Indices: 3545585--3545614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3545575 GGCAAACGAA
3545585 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
3545615 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3545702 original size:15 final size:15
Alignment explanation
Indices: 3545684--3545714 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3545674 TGATGAGTCT
3545684 ATCATATTTTAAGAC
1 ATCATATTTTAAGAC
3545699 ATCATATTTTAAGAC
1 ATCATATTTTAAGAC
3545714 A
1 A
3545715 GGCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
ATCATATTTTAAGAC
Found at i:3546150 original size:50 final size:50
Alignment explanation
Indices: 3546075--3546334 Score: 319
Period size: 50 Copynumber: 5.2 Consensus size: 50
3546065 AGGTATTGTT
* * * * *
3546075 ATTGTTGACTATTCTTCACAAACCTTTGATAATCAAGAGAGATGTCTATG
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGTGTCCATA
* * * *
3546125 ATTGTTGATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGTGTCCATA
* * * *
3546175 ATTGTTGACTATTCTTTACCAATCTTTGACAATCAAGAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGTGTCCATA
* *
3546225 ATTGTTGACTATTTTTCACCAACCTTTGACAATCAAGAGAGGTAGT-CGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGT-GTCCATA
* *
3546275 ATTGTTGACTATTCTTCACCAATCTTTGACAAT-AGAGAGAGGTGGT-CGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCA-AGAGAGGT-GTCCATA
3546325 ATTGTTGACT
1 ATTGTTGACT
3546335 CCAAGCAACT
Statistics
Matches: 187, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 185 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCAAGAGAGGTGTCCATA
Found at i:3546248 original size:100 final size:100
Alignment explanation
Indices: 3546075--3546334 Score: 362
Period size: 100 Copynumber: 2.6 Consensus size: 100
3546065 AGGTATTGTT
* * * * * ** * *
3546075 ATTGTTGACTATTCTTCACAAACCTTTGATAATCAAGAGAGATGTCTATGATTGTTGATTATTCT
1 ATTGTTGACTATTCTTCACCAATCTTTGACAATCAAGAGAGGTGGCCGTAATTGTTGACTATTCT
*
3546140 TCACCAACCTTTGACAATCGAGAGAGGT-GACCGTA
66 TCACCAACCTTTGACAATCAAGAGAGGTAG-CCGTA
* *
3546175 ATTGTTGACTATTCTTTACCAATCTTTGACAATCAAGAGAGGTGGCCGTAATTGTTGACTATTTT
1 ATTGTTGACTATTCTTCACCAATCTTTGACAATCAAGAGAGGTGGCCGTAATTGTTGACTATTCT
*
3546240 TCACCAACCTTTGACAATCAAGAGAGGTAGTCGTA
66 TCACCAACCTTTGACAATCAAGAGAGGTAGCCGTA
*
3546275 ATTGTTGACTATTCTTCACCAATCTTTGACAAT-AGAGAGAGGTGGTCGTAATTGTTGACT
1 ATTGTTGACTATTCTTCACCAATCTTTGACAATCA-AGAGAGGTGGCCGTAATTGTTGACT
3546335 CCAAGCAACT
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
99 1 0.01
100 141 0.99
101 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (100 bp):
ATTGTTGACTATTCTTCACCAATCTTTGACAATCAAGAGAGGTGGCCGTAATTGTTGACTATTCT
TCACCAACCTTTGACAATCAAGAGAGGTAGCCGTA
Found at i:3551975 original size:19 final size:19
Alignment explanation
Indices: 3551947--3551994 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3551937 AAGTGTATTG
*
3551947 ATAAATTATTTATATATTTTA
1 ATAAA-TATTTA-AAATTTTA
3551968 AT-AATATTTAAAATTTTA
1 ATAAATATTTAAAATTTTA
3551986 ATAAATATT
1 ATAAATATT
3551995 ATTTATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 12 0.48
20 2 0.08
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAAATATTTAAAATTTTA
Found at i:3568101 original size:72 final size:72
Alignment explanation
Indices: 3567982--3568298 Score: 399
Period size: 72 Copynumber: 4.4 Consensus size: 72
3567972 CTGTCTCCAG
* *
3567982 TTGAGGTGGTTGGGAATTTGGGTTTTGGGGTGGAGTTTGAGGTTGTTGAGGGTTTGGTGTCTGGG
1 TTGAGGTGGTTGAGAATTTGGGTTTTGGGGTGGAGTTTGAGGCTGTTGAGGGTTTGGTGTCTGGG
3568047 GAGGACT
66 GAGGACT
3568054 TTGAGGTGGTTGAGAATTTGGGTTTTGGGGTGGAGTTTGAGGCTGTTGAGGGTTTGGTGTCTGGG
1 TTGAGGTGGTTGAGAATTTGGGTTTTGGGGTGGAGTTTGAGGCTGTTGAGGGTTTGGTGTCTGGG
*
3568119 GTGGACT
66 GAGGACT
* * **
3568126 TTGAGGTGGTTGAGAATTTGGGTGTTGGGGTGGAGTTTGAGGCTGTTGAGGGTTTAGCATCTGGG
1 TTGAGGTGGTTGAGAATTTGGGTTTTGGGGTGGAGTTTGAGGCTGTTGAGGGTTTGGTGTCTGGG
*
3568191 GTGGACT
66 GAGGACT
* * * * * *
3568198 TTGAGGGGGTTGAGAGTTT-GGATTCGAGGGT-GATTTTAGAGGTTGTTGAGGGTATTGGT-T-T
1 TTGAGGTGGTTGAGAATTTGGGTTTTG-GGGTGGAGTTT-GAGGCTGTTGAGGGT-TTGGTGTCT
* *
3568259 TGGGATGGGCT
63 GGGGA-GGACT
* * *
3568270 TTGAGGTGGTTCAGAGTTTGGGTTCTGGG
1 TTGAGGTGGTTGAGAATTTGGGTTTTGGG
3568299 ATGAAATTTG
Statistics
Matches: 216, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
71 13 0.06
72 196 0.91
73 7 0.03
ACGTcount: A:0.13, C:0.04, G:0.46, T:0.37
Consensus pattern (72 bp):
TTGAGGTGGTTGAGAATTTGGGTTTTGGGGTGGAGTTTGAGGCTGTTGAGGGTTTGGTGTCTGGG
GAGGACT
Found at i:3568299 original size:36 final size:36
Alignment explanation
Indices: 3567982--3568622 Score: 291
Period size: 36 Copynumber: 17.8 Consensus size: 36
3567972 CTGTCTCCAG
* * * *
3567982 TTGAGGTGGTTGGGAATTTGGGTTTTGGGGTGGAGT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* * *
3568018 TTGAGGTTGTTGAGGGTTT-GGTGTCTGGGGAGGACT
1 TTGAGGTGGTTGAGAGTTTGGGT-TCTGGGGTGGACT
* * *
3568054 TTGAGGTGGTTGAGAATTTGGGTTTTGGGGTGGAGT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
*
3568090 TTGAGGCT-GTTGAGGGTTT-GGTGTCTGGGGTGGACT
1 TTGAGG-TGGTTGAGAGTTTGGGT-TCTGGGGTGGACT
* *
3568126 TTGAGGTGGTTGAGAATTTGGGTGT-TGGGGTGGAGT
1 TTGAGGTGGTTGAGAGTTTGGGT-TCTGGGGTGGACT
* * **
3568162 TTGAGGCT-GTTGAGGGTTTAGCATCTGGGGTGGACT
1 TTGAGG-TGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* * *
3568198 TTGAGGGGGTTGAGAGTTTGGATTC-GAGGGT-GATT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTG-GGGTGGACT
* * * * *
3568233 TTAGAGGTTGTTGAGGGTATT-GGTTTTGGGATGGGCT
1 TT-GAGGTGGTTGAGAGT-TTGGGTTCTGGGGTGGACT
* * * *
3568270 TTGAGGTGGTTCAGAGTTTGGGTTCTGGGATGAAAT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* * ** * * * *
3568306 TTGCGTTTCTCGAGAGTTTGGGTTCTGGGATGAAGT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* ** ** * * * * *
3568342 TTTAATTTCTTCAGAGTGT-GGTATCTGTGATGGATT
1 TTGAGGTGGTTGAGAGTTTGGGT-TCTGGGGTGGACT
** ** * * *
3568378 TTGATATTCTTGAGAGTTT-GGTATCTGGGCTAGATT
1 TTGAGGTGGTTGAGAGTTTGGGT-TCTGGGGTGGACT
* * * * * **
3568414 TTGAGATTGTTGAGAGTTTGGATTCTGGAGTTGTTT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* * * * * * * *
3568450 TTGAGGTTGTTGGGAGCTTGAGTTTTGGGATGAATT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* ** * *
3568486 TTGAGGTTGTTGAGAGTTT-GGTATCTGGAATAGATT
1 TTGAGGTGGTTGAGAGTTTGGGT-TCTGGGGTGGACT
* * * * * *
3568522 TTGAGGTTGCTGAGAGTTTGGGTCCTGGGATGAAGT
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
* * * *
3568558 TTGAGGCT-CTTGAGAGTTTGGTTTCTGGGGT-AAGTT
1 TTGAGG-TGGTTGAGAGTTTGGGTTCTGGGGTGGA-CT
* * *
3568594 TTGAAGTTGTTGAGAGTTTGGGTTTTGGG
1 TTGAGGTGGTTGAGAGTTTGGGTTCTGGG
3568623 ACAAAGTTTG
Statistics
Matches: 471, Mismatches: 112, Indels: 44
0.75 0.18 0.07
Matches are distributed among these distances:
35 24 0.05
36 424 0.90
37 23 0.05
ACGTcount: A:0.15, C:0.05, G:0.40, T:0.39
Consensus pattern (36 bp):
TTGAGGTGGTTGAGAGTTTGGGTTCTGGGGTGGACT
Found at i:3568681 original size:36 final size:36
Alignment explanation
Indices: 3568641--3568710 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
3568631 TGAGGCTCTA
* * * *
3568641 TCTGAGGTGGATTTTGAGGTTGTTGAGAGTTTGGCT
1 TCTGAAGTGGATTTTGAGATTCTTGAGAATTTGGCT
* *
3568677 TCTGAATTTGATTTTGAGATTCTTGAGAATTTGG
1 TCTGAAGTGGATTTTGAGATTCTTGAGAATTTGG
3568711 GTCCGGAGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (36 bp):
TCTGAAGTGGATTTTGAGATTCTTGAGAATTTGGCT
Found at i:3568780 original size:36 final size:36
Alignment explanation
Indices: 3568723--3568821 Score: 144
Period size: 36 Copynumber: 2.8 Consensus size: 36
3568713 CCGGAGACGG
* * * *
3568723 ATTTCGAGATTGCTGAGGGTTTGGTATTTGGAGTGA
1 ATTTCGAGGTTGTTGAAGGTTTGGTATTTGCAGTGA
*
3568759 ATTTTGAGGTTGTTGAAGGTTTGGTATTTGCAGTGA
1 ATTTCGAGGTTGTTGAAGGTTTGGTATTTGCAGTGA
*
3568795 ATTTCGAGGTTGTTGAAGTTTTGGTAT
1 ATTTCGAGGTTGTTGAAGGTTTGGTAT
3568822 CTCGGGTGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.19, C:0.04, G:0.33, T:0.43
Consensus pattern (36 bp):
ATTTCGAGGTTGTTGAAGGTTTGGTATTTGCAGTGA
Found at i:3572203 original size:13 final size:13
Alignment explanation
Indices: 3572164--3572205 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3572154 TGTACATAAT
3572164 TAATATAAATAAAA
1 TAAT-TAAATAAAA
*
3572178 T-ATAAAATAAAA
1 TAATTAAATAAAA
*
3572190 TAATTAAATTAAA
1 TAATTAAATAAAA
3572203 TAA
1 TAA
3572206 ATATAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.38
13 14 0.58
14 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATTAAATAAAA
Found at i:3574774 original size:3 final size:3
Alignment explanation
Indices: 3574766--3574808 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
3574756 AGTACTCTTT
3574766 ATA ATA ATA ATA ATA ATA A-A ATAA ATAA ATAA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA ATA AT
3574809 TTTATTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 25 0.66
4 11 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3574963 original size:27 final size:26
Alignment explanation
Indices: 3574929--3574980 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
3574919 TATTTTTTAT
3574929 ATCATATATAAGATA-AATTAATATAA
1 ATCATATATAA-ATATAATTAATATAA
*
3574955 ATCAGTATATAAATATATTTAATATA
1 ATCA-TATATAAATATAATTAATATA
3574981 TATAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
ATCATATATAAATATAATTAATATAA
Found at i:3578905 original size:2 final size:2
Alignment explanation
Indices: 3578900--3578952 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3578890 TTTACTTCAG
3578900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3578942 TA TA TA TA TA T
1 TA TA TA TA TA T
3578953 TCCTTCCATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3579508 original size:42 final size:42
Alignment explanation
Indices: 3579414--3579542 Score: 163
Period size: 42 Copynumber: 3.1 Consensus size: 42
3579404 GTCACTGCAA
* * *
3579414 AGCATTGCCACAATTCAAT-CTCGCCATTACCTT-CTGCCATC
1 AGCATTGCAAAAATTC-ATCCTTGCCATTACCTTACTGCCATC
**
3579455 AGCATCACAAAAATTCATCCTTGCCATTACCTTACTGCCATC
1 AGCATTGCAAAAATTCATCCTTGCCATTACCTTACTGCCATC
* * *
3579497 AGCATTGCAAAAATTCAACCTTGCCATTAACTCACTGCCATC
1 AGCATTGCAAAAATTCATCCTTGCCATTACCTTACTGCCATC
3579539 AGCA
1 AGCA
3579543 GTGTTACTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
40 2 0.03
41 25 0.33
42 49 0.64
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.27
Consensus pattern (42 bp):
AGCATTGCAAAAATTCATCCTTGCCATTACCTTACTGCCATC
Found at i:3583687 original size:48 final size:48
Alignment explanation
Indices: 3583612--3583708 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
3583602 CACCATCAAC
*
3583612 AAGACAATTTCACCATTTCCGTGCTCTTCATTATCGAATATTATATTA
1 AAGACAATTTCACCATTTCCGTACTCTTCATTATCGAATATTATATTA
*
3583660 AAGACAATTTCACCATTTCCGTACTCTTCATTATTGAATATTATATTA
1 AAGACAATTTCACCATTTCCGTACTCTTCATTATCGAATATTATATTA
3583708 A
1 A
3583709 CTTTTACGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (48 bp):
AAGACAATTTCACCATTTCCGTACTCTTCATTATCGAATATTATATTA
Found at i:3585029 original size:28 final size:28
Alignment explanation
Indices: 3584998--3585057 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
3584988 CAAGATTAAA
* *
3584998 CAAAGATACAAGTAAAAAAAAGAATTTG
1 CAAAGATACAAATAAAAAAAAGAACTTG
*
3585026 CAAAGATACAAATAAATAAAAGAACTTG
1 CAAAGATACAAATAAAAAAAAGAACTTG
3585054 CAAA
1 CAAA
3585058 AAATTAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.17
Consensus pattern (28 bp):
CAAAGATACAAATAAAAAAAAGAACTTG
Found at i:3586074 original size:3 final size:3
Alignment explanation
Indices: 3586066--3586092 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3586056 AAACGAGAGA
3586066 AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG
3586093 GAGGGCACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:3586466 original size:11 final size:11
Alignment explanation
Indices: 3586450--3586500 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
3586440 ATTATATGTT
3586450 ATATAAATATA
1 ATATAAATATA
*
3586461 ATATAAAAAATA
1 ATAT-AAATATA
3586473 AT-TAAAATATA
1 ATAT-AAATATA
3586484 AT-TAAATATAA
1 ATATAAATAT-A
3586495 ATATAA
1 ATATAA
3586501 TTTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 6 0.17
11 18 0.51
12 11 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:3586473 original size:18 final size:20
Alignment explanation
Indices: 3586450--3586501 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
3586440 ATTATATGTT
3586450 ATATAAATATAATATAA-AA
1 ATATAAATATAATATAATAA
* *
3586469 A-ATAATTAAAATATAATTAA
1 ATATAAATATAATATAA-TAA
3586489 ATATAAATATAAT
1 ATATAAATATAAT
3586502 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 3 0.12
21 9 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAATATAATATAATAA
Found at i:3586533 original size:17 final size:18
Alignment explanation
Indices: 3586513--3586576 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
3586503 TTTTTTTAAA
3586513 ATTAAT-TAATAAAAATT
1 ATTAATATAATAAAAATT
* *
3586530 ATTAATATATTAAAATTT
1 ATTAATATAATAAAAATT
3586548 ATATAA-AT-ATAAAATATT
1 AT-TAATATAATAAAA-ATT
3586566 -TTAAATATAAT
1 ATT-AATATAAT
3586577 TTTAATATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
16 1 0.03
17 14 0.38
18 17 0.46
19 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAATATAATAAAAATT
Found at i:3586572 original size:16 final size:17
Alignment explanation
Indices: 3586521--3586575 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
3586511 AAATTAATTA
3586521 ATAAAA-ATTATTAATAT
1 ATAAAATATTATTAA-AT
3586538 ATTAAAAT-TTATATAAAT
1 A-TAAAATATTAT-TAAAT
3586556 ATAAAATATT-TTAAAT
1 ATAAAATATTATTAAAT
3586572 ATAA
1 ATAA
3586576 TTTTAATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.26
17 8 0.24
18 14 0.41
19 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATATTATTAAAT
Found at i:3595198 original size:2 final size:2
Alignment explanation
Indices: 3595191--3595224 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3595181 TCGAATAGTG
*
3595191 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3595225 GTATCTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3597390 original size:26 final size:25
Alignment explanation
Indices: 3597338--3597395 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
3597328 ATTATAAATA
3597338 TTAAAATAAAATTAATATTTTATTT
1 TTAAAATAAAATTAATATTTTATTT
3597363 TTAAAATAATAATTTAA-ATTATTATTT
1 TTAAAATAA-AA-TTAATATT-TTATTT
*
3597390 TAAAAA
1 TTAAAA
3597396 ATTTAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 9 0.31
26 5 0.17
27 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAAAATAAAATTAATATTTTATTT
Found at i:3597692 original size:2 final size:2
Alignment explanation
Indices: 3597685--3597713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3597675 TTCCATTACT
3597685 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 T
3597714 TTGCATAAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3600180 original size:13 final size:14
Alignment explanation
Indices: 3600155--3600246 Score: 73
Period size: 13 Copynumber: 6.5 Consensus size: 14
3600145 GTAGATTTAA
*
3600155 ATAATAATTATAAT
1 ATAATATTTATAAT
3600169 ATAAT-TTTATAATT
1 ATAATATTTATAA-T
* * *
3600183 TTAATTTTTATTAT
1 ATAATATTTATAAT
3600197 CATAAATATTTATAAT
1 -AT-AATATTTATAAT
*
3600213 -TAATATTTATTAT
1 ATAATATTTATAAT
*
3600226 ATTCATATTTATAAT
1 A-TAATATTTATAAT
3600241 A-AATAT
1 ATAATAT
3600247 AATATAATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
13 21 0.34
14 12 0.19
15 19 0.31
16 10 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATATTTATAAT
Found at i:3600237 original size:44 final size:40
Alignment explanation
Indices: 3600149--3600257 Score: 96
Period size: 44 Copynumber: 2.6 Consensus size: 40
3600139 CACTATGTAG
* *
3600149 ATTTA-AAT-AATAATTATAATATAATTTTATAATTTTAAT
1 ATTTATAATAAATATTTATAAT-TAATTTTATAATATTAAT
* * *
3600188 TTTTATTATCATAAATATTTATAATTAATATTTATTATATTCAT
1 ATTTA-TA--ATAAATATTTATAATTAAT-TTTATAATATTAAT
*
3600232 ATTTATAATAAATATAATATAATTAA
1 ATTTATAATAAATAT-TTATAATTAA
3600258 AAATACATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
39 4 0.07
41 9 0.16
42 9 0.16
43 8 0.14
44 26 0.46
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (40 bp):
ATTTATAATAAATATTTATAATTAATTTTATAATATTAAT
Found at i:3602350 original size:7 final size:7
Alignment explanation
Indices: 3602340--3602384 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
3602330 TGTCACGTGT
3602340 CCAAGTG
1 CCAAGTG
3602347 CCAAGTG
1 CCAAGTG
3602354 CCAAGTG
1 CCAAGTG
3602361 CCAAGTG
1 CCAAGTG
3602368 CCAAGTG
1 CCAAGTG
3602375 CCAAGTG
1 CCAAGTG
3602382 CCA
1 CCA
3602385 TATAATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (7 bp):
CCAAGTG
Found at i:3608013 original size:41 final size:41
Alignment explanation
Indices: 3607956--3608034 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
3607946 GTTCTTAAAT
*
3607956 CTTCCCTTCCCTTGCCAAAAGAAATGGTACTAATAATGAAA
1 CTTCCCTTCCCTTGCCAAAAGAAAAGGTACTAATAATGAAA
3607997 CTTCCCTTCCCTTGCCAAAAGAAAAGGTACTAATAATG
1 CTTCCCTTCCCTTGCCAAAAGAAAAGGTACTAATAATG
3608035 GATTTAAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (41 bp):
CTTCCCTTCCCTTGCCAAAAGAAAAGGTACTAATAATGAAA
Found at i:3610572 original size:2 final size:2
Alignment explanation
Indices: 3610538--3610564 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3610528 AATGCACATC
3610538 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 T
3610565 GGATATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3612193 original size:64 final size:64
Alignment explanation
Indices: 3612089--3612220 Score: 237
Period size: 64 Copynumber: 2.1 Consensus size: 64
3612079 GCCCAATCGA
*
3612089 CTGAGAAATCTAAGCACTAGTTGAAAAGTGGTTGTATTATATTCGGATCAACTTACTTTACCAG
1 CTGAGAAATCTAAACACTAGTTGAAAAGTGGTTGTATTATATTCGGATCAACTTACTTTACCAG
* *
3612153 CTGAGAAATCTAAACGCTAGTTGAAAAGTGGTTGTTTTATATTCGGATCAACTTACTTTACCAG
1 CTGAGAAATCTAAACACTAGTTGAAAAGTGGTTGTATTATATTCGGATCAACTTACTTTACCAG
3612217 CTGA
1 CTGA
3612221 AGGATAATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (64 bp):
CTGAGAAATCTAAACACTAGTTGAAAAGTGGTTGTATTATATTCGGATCAACTTACTTTACCAG
Found at i:3620290 original size:42 final size:43
Alignment explanation
Indices: 3620217--3620302 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 43
3620207 GAGATAAAAT
3620217 AATTAATATATATATGAAATATTAAATAATA-TAATAATTTTAA
1 AATTAATATATATATGAAATATTAAATAATATTAAT-ATTTTAA
*
3620260 AATTTATATA-ATAT-AAATTATT-AATAAATATTAATATTTTAA
1 AATTAATATATATATGAAA-TATTAAAT-AATATTAATATTTTAA
3620302 A
1 A
3620303 TATAATTACT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
41 6 0.15
42 20 0.51
43 13 0.33
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (43 bp):
AATTAATATATATATGAAATATTAAATAATATTAATATTTTAA
Found at i:3621248 original size:2 final size:2
Alignment explanation
Indices: 3621237--3621268 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3621227 AGTCATGTAT
3621237 TA TA -A 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
3621269 TTTACTGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3627746 original size:2 final size:2
Alignment explanation
Indices: 3627739--3627781 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
3627729 GAATACCCAA
*
3627739 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
3627782 TTACGAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3627934 original size:19 final size:20
Alignment explanation
Indices: 3627910--3627947 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3627900 CTGGTACTTG
*
3627910 TAAT-AATTTTAGTAATTTA
1 TAATAAATTTAAGTAATTTA
3627929 TAATAAATTTAAGTAATTT
1 TAATAAATTTAAGTAATTT
3627948 GAGAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATAAATTTAAGTAATTTA
Found at i:3627956 original size:21 final size:20
Alignment explanation
Indices: 3627914--3627956 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3627904 TACTTGTAAT
* *
3627914 AATTTTAGTAATTTATAATA
1 AATTTAAGTAATTTAGAATA
3627934 AATTTAAGTAATTTGAGAATA
1 AATTTAAGTAATTT-AGAATA
3627955 AA
1 AA
3627957 AGTTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (20 bp):
AATTTAAGTAATTTAGAATA
Found at i:3629068 original size:6 final size:6
Alignment explanation
Indices: 3629046--3629085 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3629036 CTATAATTAA
* * *
3629046 GATCAT GATAAT GATCAT AATCAT GATCAT GATCAA GATC
1 GATCAT GATCAT GATCAT GATCAT GATCAT GATCAT GATC
3629086 GTGGTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (6 bp):
GATCAT
Found at i:3629570 original size:2 final size:2
Alignment explanation
Indices: 3629563--3629587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3629553 CAACAAAGGA
3629563 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3629588 GATAGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3631176 original size:25 final size:25
Alignment explanation
Indices: 3631148--3631197 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3631138 ATGTATTTTT
*
3631148 TAAAATTATT-ATATATAATAATAAA
1 TAAAATAATTAAT-TATAATAATAAA
*
3631173 TAAAATAATTAATTATTATAATAAA
1 TAAAATAATTAATTATAATAATAAA
3631198 ATTTTATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAAATAATTAATTATAATAATAAA
Found at i:3635736 original size:20 final size:19
Alignment explanation
Indices: 3635711--3635756 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3635701 TTTATAATTA
3635711 AATTTAAATAAAAATATATT
1 AATTTAAATAAAAAT-TATT
*
3635731 AATTT-AATTAAAATTATT
1 AATTTAAATAAAAATTATT
*
3635749 ATTTTAAA
1 AATTTAAA
3635757 CATATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTAAATAAAAATTATT
Found at i:3638119 original size:19 final size:20
Alignment explanation
Indices: 3638097--3638138 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
3638087 ATAAATATTT
*
3638097 AAATTATTTTA-AATAAATA
1 AAATTAATTTATAATAAATA
*
3638116 AAA-TAATTTATTATAAATA
1 AAATTAATTTATAATAAATA
3638135 AAAT
1 AAAT
3638139 CATGAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTAATTTATAATAAATA
Found at i:3644440 original size:2 final size:2
Alignment explanation
Indices: 3644433--3644458 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3644423 TAAAAATTCT
3644433 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3644459 CACAAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3645719 original size:11 final size:11
Alignment explanation
Indices: 3645703--3645738 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3645693 TTATAAAAAG
3645703 TTAAAAATTAA
1 TTAAAAATTAA
3645714 TTAAAAATTAA
1 TTAAAAATTAA
*
3645725 ATAAAAATTTAA
1 TTAAAAA-TTAA
3645737 TT
1 TT
3645739 TAATTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAAAATTAA
Found at i:3645892 original size:2 final size:2
Alignment explanation
Indices: 3645885--3645932 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3645875 GAAGAGGAAG
* * *
3645885 AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3645927 GT AT AT
1 AT AT AT
3645933 GTATGTATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3645911 original size:14 final size:14
Alignment explanation
Indices: 3645888--3645945 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
3645878 GAGGAAGATA
*
3645888 TATATATATATATG
1 TATATATATGTATG
* *
3645902 TATGTATA--TATA
1 TATATATATGTATG
3645914 TATATATATGTATG
1 TATATATATGTATG
*
3645928 TATATGTATGTATG
1 TATATATATGTATG
3645942 TATA
1 TATA
3645946 ACAACCACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.27
14 27 0.73
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:3645911 original size:18 final size:18
Alignment explanation
Indices: 3645888--3645945 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
3645878 GAGGAAGATA
3645888 TATATATATATATGTATG
1 TATATATATATATGTATG
*
3645906 TATATATATATATATATG
1 TATATATATATATGTATG
* *
3645924 TATGTATATGTATGTATG
1 TATATATATATATGTATG
3645942 TATA
1 TATA
3645946 ACAACCACGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (18 bp):
TATATATATATATGTATG
Found at i:3645913 original size:22 final size:22
Alignment explanation
Indices: 3645885--3645932 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3645875 GAAGAGGAAG
3645885 ATATATATATATATATGTATGT
1 ATATATATATATATATGTATGT
3645907 ATATATATATATATATGTATGT
1 ATATATATATATATATGTATGT
3645929 ATAT
1 ATAT
3645933 GTATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (22 bp):
ATATATATATATATATGTATGT
Found at i:3645933 original size:10 final size:10
Alignment explanation
Indices: 3645886--3645940 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
3645876 AAGAGGAAGA
* *
3645886 TATATATATA
1 TATATGTATG
3645896 TATATGTATG
1 TATATGTATG
* *
3645906 TATATATATATA
1 --TATATGTATG
3645918 TATATGTATG
1 TATATGTATG
3645928 TATATGTATG
1 TATATGTATG
3645938 TAT
1 TAT
3645941 GTATAACAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
10 29 0.78
12 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (10 bp):
TATATGTATG
Found at i:3646231 original size:3 final size:3
Alignment explanation
Indices: 3646223--3646257 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3646213 TTTATTGTTA
3646223 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3646258 CTAGCATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3647767 original size:1 final size:1
Alignment explanation
Indices: 3647761--3647837 Score: 154
Period size: 1 Copynumber: 77.0 Consensus size: 1
3647751 TTTACTTGTA
3647761 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3647826 GGGGGGGGGGGG
1 GGGGGGGGGGGG
3647838 AAGATAGCGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3648946 original size:13 final size:13
Alignment explanation
Indices: 3648928--3648953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3648918 TTAAGCTTAA
3648928 ATTTGGTAAATCT
1 ATTTGGTAAATCT
3648941 ATTTGGTAAATCT
1 ATTTGGTAAATCT
3648954 TGTCTACTCA
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:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTTGGTAAATCT
Found at i:3653050 original size:3 final size:3
Alignment explanation
Indices: 3653042--3653088 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3653032 CTTTAAAAGA
3653042 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3653089 ACTAGGGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3654728 original size:4 final size:4
Alignment explanation
Indices: 3654687--3654740 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
3654677 TCATATATGT
* * * * * *
3654687 TATA TATA CATA TACA TACA TACA TACA TATA TGTA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
3654735 TATA TA
1 TATA TA
3654741 GAGAGAGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:3654730 original size:6 final size:6
Alignment explanation
Indices: 3654687--3654740 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
3654677 TCATATATGT
* * * * * *
3654687 TATATA TACATA TACATA CATACA TACATA TATGTA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
3654735 TATATA
1 TATATA
3654741 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (6 bp):
TATATA
Found at i:3654745 original size:2 final size:2
Alignment explanation
Indices: 3654740--3654766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3654730 ATATATATAT
3654740 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 A
3654767 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3655193 original size:9 final size:9
Alignment explanation
Indices: 3655173--3655221 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
3655163 TTTTATACGT
3655173 TATA-ATTA
1 TATATATTA
3655181 -ATATATTA
1 TATATATTA
3655189 TATAT-TTA
1 TATATATTA
3655197 TAT-TATTTA
1 TATATA-TTA
3655206 TATATATTA
1 TATATATTA
3655215 TAT-TATT
1 TATATATT
3655222 TTTAAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 4 0.11
8 14 0.39
9 16 0.44
10 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATTA
Found at i:3655200 original size:13 final size:13
Alignment explanation
Indices: 3655182--3655222 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3655172 TTATAATTAA
3655182 TATATTATATATT
1 TATATTATATATT
* *
3655195 TATATTATTTATA
1 TATATTATATATT
3655208 TATATTATATTATT
1 TATATTATA-TATT
3655222 T
1 T
3655223 TTAAATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTATATATT
Found at i:3655217 original size:18 final size:18
Alignment explanation
Indices: 3655186--3655234 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
3655176 AATTAATATA
3655186 TTATATAT-TTATATTAT
1 TTATATATATTATATTAT
3655203 TTATATATATTATATTAT
1 TTATATATATTATATTAT
*
3655221 TT-T-TAAATTATATT
1 TTATATATATTATATT
3655235 TAATGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 10 0.33
17 9 0.30
18 11 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATATATTATATTAT
Found at i:3655221 original size:21 final size:18
Alignment explanation
Indices: 3655187--3655250 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
3655177 ATTAATATAT
3655187 TATATATTTATATTATTTA
1 TATATATTTATATT-TTTA
3655206 TATATATTATATTATTTTTA
1 TATATATT-TA-TATTTTTA
* *
3655226 AATTATATTTA-ATGTATTA
1 TA-TATATTTATAT-TTTTA
3655245 TATATA
1 TATATA
3655251 AATTTTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.16
19 13 0.34
20 9 0.24
21 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATATATTTATATTTTTA
Found at i:3655243 original size:25 final size:25
Alignment explanation
Indices: 3655215--3655263 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3655205 ATATATATTA
* * *
3655215 TATTATTTTTAAATTATATTTAATG
1 TATTATATATAAATTATAATTAATG
*
3655240 TATTATATATAAATTTTAATTAAT
1 TATTATATATAAATTATAATTAAT
3655264 TAATAATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTATATATAAATTATAATTAATG
Found at i:3655257 original size:32 final size:31
Alignment explanation
Indices: 3655200--3655298 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 31
3655190 ATATTTATAT
*
3655200 TATTTATATATATTATAT-T-ATTTTTAAATTA
1 TATTTA-ATATATTATATATAAATTTT-AATTA
*
3655231 TATTTAATGTATTATATATAAATTTTAATTA
1 TATTTAATATATTATATATAAATTTTAATTA
*
3655262 -A-TTAATAATTTATATTATATAAATTTTAA-TA
1 TATTTAAT-ATAT-TA-TATATAAATTTTAATTA
3655293 TATTTA
1 TATTTA
3655299 TAAATTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
29 5 0.09
30 13 0.23
31 16 0.28
32 20 0.35
33 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TATTTAATATATTATATATAAATTTTAATTA
Found at i:3655293 original size:17 final size:17
Alignment explanation
Indices: 3655245--3655306 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 17
3655235 TAATGTATTA
3655245 TATATAAATTTTAATTAAT
1 TATATAAATTTTAA-T-AT
3655264 TA-AT-AA-TTT-ATAT
1 TATATAAATTTTAATAT
3655277 TATATAAATTTTAATAT
1 TATATAAATTTTAATAT
*
3655294 ATTTATAAATTTT
1 -TATATAAATTTT
3655307 TATTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.11
14 3 0.08
15 3 0.08
16 6 0.16
17 6 0.16
18 13 0.35
19 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATAAATTTTAATAT
Found at i:3655318 original size:20 final size:21
Alignment explanation
Indices: 3655279--3655338 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3655269 ATTTATATTA
*
3655279 TATAA-ATTTTA-ATA-TATT
1 TATAATATTTTATATATTTTT
3655297 TATAA-ATTTT-TATTATTTTT
1 TATAATATTTTATA-TATTTTT
3655317 TATAATATTTTATATATTTTT
1 TATAATATTTTATATATTTTT
3655338 T
1 T
3655339 TTCATGTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 11 0.31
19 2 0.06
20 8 0.22
21 13 0.36
22 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATAATATTTTATATATTTTT
Done.