Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 2 of 145
Found at i:580715 original size:12 final size:12
Alignment explanation
Indices: 580689--580764 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 12
580679 TATGCCTACT
**
580689 CCTATCTCTGCC
1 CCTATCTCTATC
580701 CCTATCTCTATC
1 CCTATCTCTATC
580713 CCTATGC-CTATC
1 CCTAT-CTCTATC
* *
580725 TCTGTCCCTCTTATC
1 CCTAT--CTC-TATC
*
580740 CCTATCCCTATC
1 CCTATCTCTATC
*
580752 CCTATCCCTATC
1 CCTATCTCTATC
580764 C
1 C
580765 TTGTCCTTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
12 40 0.77
13 4 0.08
14 1 0.02
15 7 0.13
ACGTcount: A:0.13, C:0.46, G:0.04, T:0.37
Consensus pattern (12 bp):
CCTATCTCTATC
Found at i:580747 original size:6 final size:6
Alignment explanation
Indices: 580700--580764 Score: 67
Period size: 6 Copynumber: 10.3 Consensus size: 6
580690 CTATCTCTGC
* * * *
580700 CCCTAT CTCTAT CCCTAT GCCTAT CTCTGT CCCTCTTAT CCCTAT CCCTAT
1 CCCTAT CCCTAT CCCTAT CCCTAT CCCTAT -CC-C-TAT CCCTAT CCCTAT
580751 CCCTAT CCCTAT CC
1 CCCTAT CCCTAT CC
580765 TTGTCCTTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 41 0.85
7 2 0.04
8 3 0.06
9 2 0.04
ACGTcount: A:0.14, C:0.46, G:0.03, T:0.37
Consensus pattern (6 bp):
CCCTAT
Found at i:588862 original size:1 final size:1
Alignment explanation
Indices: 588856--588905 Score: 64
Period size: 1 Copynumber: 50.0 Consensus size: 1
588846 TCCTTTCTTG
** **
588856 TTTTTTTTTTTTTTTTTTCCTTTAATTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
588906 CCATTAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.04, C:0.04, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:589554 original size:13 final size:12
Alignment explanation
Indices: 589538--589570 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
589528 TTATTTTAAA
589538 ATTTTAAAAAAGT
1 ATTTTAAAAAA-T
589551 ATTTT-AAAAAT
1 ATTTTAAAAAAT
589562 ATTTTAAAA
1 ATTTTAAAA
589571 TTAAAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 8 0.42
13 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
ATTTTAAAAAAT
Found at i:589564 original size:11 final size:11
Alignment explanation
Indices: 589529--589629 Score: 53
Period size: 11 Copynumber: 9.9 Consensus size: 11
589519 ACCAAAAATT
589529 TATTTT-AAAA
1 TATTTTAAAAA
*
589539 T-TTTAAAAAA
1 TATTTTAAAAA
589549 GTATTTTAAAAA
1 -TATTTTAAAAA
589561 TATTTT--AAA
1 TATTTTAAAAA
589570 -A--TTAAAAA
1 TATTTTAAAAA
589578 GTATTTT--AAA
1 -TATTTTAAAAA
*
589588 -A-TTAAAAAA
1 TATTTTAAAAA
* **
589597 TAATAAAAAAA
1 TATTTTAAAAA
589608 GTATTTTAAAAA
1 -TATTTTAAAAA
589620 TATTTTAAAA
1 TATTTTAAAA
589630 TTAAAAAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 27
0.67 0.07 0.26
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 5 0.07
9 9 0.13
10 10 0.14
11 24 0.34
12 18 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:589576 original size:17 final size:18
Alignment explanation
Indices: 589554--589595 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
589544 AAAAAGTATT
589554 TTAAAAA-TATTTTAAAA
1 TTAAAAAGTATTTTAAAA
589571 TTAAAAAGTATTTTAAAA
1 TTAAAAAGTATTTTAAAA
589589 TTAAAAA
1 TTAAAAA
589596 ATAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAAAAAGTATTTTAAAA
Found at i:589577 original size:30 final size:30
Alignment explanation
Indices: 589529--589637 Score: 132
Period size: 30 Copynumber: 3.6 Consensus size: 30
589519 ACCAAAAATT
589529 TATTTTAAAATTTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAA--TTAAAAAAGTATTTTAAAAA
*
589561 TATTTTAAAATT-AAAAAGTATTTTAAAAT
1 TATTTTAAAATTAAAAAAGTATTTTAAAAA
*** *
589590 TA-AAAAATAATAAAAAAAGTATTTTAAAAA
1 TATTTTAA-AATTAAAAAAGTATTTTAAAAA
589620 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
589638 ATTAAAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.03
29 21 0.33
30 29 0.45
31 2 0.03
32 10 0.16
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAGTATTTTAAAAA
Found at i:595209 original size:23 final size:23
Alignment explanation
Indices: 595184--595228 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
595174 TATAAATTAA
* *
595184 AAAAAAT-TGAATATATAAAAAT
1 AAAAAATATGAAAATAAAAAAAT
595206 AAAAAATATGAAAATAAAAAAAT
1 AAAAAATATGAAAATAAAAAAAT
595229 TACATTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAAATATGAAAATAAAAAAAT
Found at i:595214 original size:15 final size:15
Alignment explanation
Indices: 595196--595226 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
595186 AAAATTGAAT
595196 ATATAAAAATAAAAA
1 ATATAAAAATAAAAA
*
595211 ATATGAAAATAAAAA
1 ATATAAAAATAAAAA
595226 A
1 A
595227 ATTACATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
ATATAAAAATAAAAA
Found at i:595297 original size:18 final size:18
Alignment explanation
Indices: 595275--595320 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
595265 TGTTTAAAAT
*
595275 ATTTTTAAATTTTTTGT-
1 ATTTTTAAATTTCTTGTA
595292 ATTTTTACAATTTCTTGTA
1 ATTTTTA-AATTTCTTGTA
595311 ATTTTGTAAA
1 ATTTT-TAAA
595321 AAAAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 7 0.28
20 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (18 bp):
ATTTTTAAATTTCTTGTA
Found at i:599674 original size:13 final size:14
Alignment explanation
Indices: 599650--599683 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
599640 AAACAGCATT
*
599650 AGAAGGTTTATGGA
1 AGAAGATTTATGGA
599664 A-AAGATTTATGGA
1 AGAAGATTTATGGA
599677 AGAAGAT
1 AGAAGAT
599684 ATTCCACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
AGAAGATTTATGGA
Found at i:600954 original size:48 final size:48
Alignment explanation
Indices: 600897--600992 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
600887 GATCTAACTG
600897 GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
1 GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
* *
600945 GTTTGATTTTTACATCATTGAAAAATATGAACTAAATCTCTTTCCTTT
1 GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
600993 CAATTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (48 bp):
GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
Found at i:607782 original size:84 final size:83
Alignment explanation
Indices: 607671--608019 Score: 372
Period size: 84 Copynumber: 4.2 Consensus size: 83
607661 ACTTTGGCCC
607671 CTTCAACAGCCTTCTT-AT--TTTCTTCTGCAATCTTCCTTTGC-TCTTCTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTTTGCTTC-TCTGCTTTAGCCATCTC
** *
607732 AATATCAGCTTGTTTTCTTA
65 AA-ATCAGCACGTTTTCTTT
* *
607752 CTTCAACAGCCTTCTTCAT-GTTTTCTTCTGCAATCTTCCTTTGCTTCACTGCTTCAGCCATCTC
1 CTTCAACAGCCTTCTTCATAG-TTTCTTCTGCAATCTTCCTTTGCTTCTCTGCTTTAGCCATCTC
607816 TAAATCAGCACGTTTTCTTT
65 -AAATCAGCACGTTTTCTTT
* * *
607836 CTTCAACAGCCTTTTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCT-GCAATCTTCCTTTGCTTCTCTGCTTTAGCCATCT-
*
607900 CAAATCAGCACATTTTCTTT
64 CAAATCAGCACGTTTTCTTT
* * * * *** *
607920 CGTCAACAGCCTTTTTCTTAGTTTCTTCAGCAATCTTCCTCAAC-TCGCTTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTTTGCTTCTC-TGCTTTAGCCATCT-
***
607984 CAAATC-GACAAACTTTCTTT
64 CAAATCAG-CACGTTTTCTTT
*
608004 CTTCAACTGCCTTCTT
1 CTTCAACAGCCTTCTT
608020 TTTCTCTTCT
Statistics
Matches: 236, Mismatches: 21, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
81 16 0.07
82 2 0.01
83 5 0.02
84 207 0.88
85 6 0.03
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.43
Consensus pattern (83 bp):
CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTTTGCTTCTCTGCTTTAGCCATCTCA
AATCAGCACGTTTTCTTT
Found at i:613321 original size:25 final size:25
Alignment explanation
Indices: 613269--613323 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
613259 TTACATTTTT
* * *
613269 TTTTTGTTAATTTGATCATTATTAC
1 TTTTAGTTAATTTGACCATTAATAC
613294 TTTTAGTTAAATTTGACCATTAAT-C
1 TTTTAGTT-AATTTGACCATTAATAC
613319 TTTTA
1 TTTTA
613324 AAAAGAGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.56
Consensus pattern (25 bp):
TTTTAGTTAATTTGACCATTAATAC
Found at i:613471 original size:21 final size:18
Alignment explanation
Indices: 613440--613481 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
613430 CGAGTGCTAA
613440 TTTTTTGAATTTTTATGATT
1 TTTTTTGAATTTTT-T-ATT
613460 TTTTTTGTAATTTTTTATT
1 TTTTTTG-AATTTTTTATT
613479 TTT
1 TTT
613482 GAATATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTTTGAATTTTTTATT
Found at i:617995 original size:7 final size:7
Alignment explanation
Indices: 617983--618009 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
617973 TACCTTTATT
617983 AATTTTA
1 AATTTTA
617990 AATTTTA
1 AATTTTA
617997 AATTTTA
1 AATTTTA
618004 AATTTT
1 AATTTT
618010 CCAAAGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:638842 original size:33 final size:32
Alignment explanation
Indices: 638781--638843 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
638771 ATCATATAAT
*
638781 TAACTATGATTTTGTAATTTTTTTATAATTAAA
1 TAACTAT-ATTTTATAATTTTTTTATAATTAAA
638814 TAACTAT-TTTTATAATTTCTTTTCATAATT
1 TAACTATATTTTATAATTT-TTTT-ATAATT
638844 TGATGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 10 0.37
32 4 0.15
33 13 0.48
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (32 bp):
TAACTATATTTTATAATTTTTTTATAATTAAA
Found at i:642780 original size:31 final size:30
Alignment explanation
Indices: 642713--642785 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
642703 TAATTTACTG
* * * *
642713 TAATTATACATATGAAACTTTGATTTGGTT
1 TAATTGTACACATAAAACTTTGATTTGATT
* *
642743 CAATTGTACACATAAAATTTTGATCTTGATT
1 TAATTGTACACATAAAACTTTGAT-TTGATT
642774 TAATTGTACACA
1 TAATTGTACACA
642786 ATTTTTAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 19 0.54
31 16 0.46
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (30 bp):
TAATTGTACACATAAAACTTTGATTTGATT
Found at i:644669 original size:120 final size:122
Alignment explanation
Indices: 644453--644671 Score: 309
Period size: 120 Copynumber: 1.8 Consensus size: 122
644443 AGTGGAAACC
* * * *
644453 ATGCATGTTAAAAGGTATCATATTACCAACAATCCATGCTTAAAAGAACATGCTTTTTCTCTAAG
1 ATGCATGTTAAAAGCTAGCA-ATTACCAACAATCCATGCTTAAAAGAACATGCTATTTCTCAAAG
* *
644518 GAAAATCGATATCGGTTTGTTTACATACCCATCAATACGAAATTGAAATGGTGATCAT
65 GAAAATCAATATCAGTTTGTTTACATACCCATCAATACGAAATTGAAATGGTGATCAT
* *
644576 ATGCATGTTAAAAGCTAGC-ATTACCAACCATCCATGCTTAACA-AACA-GCCTATTTCTCAAAG
1 ATGCATGTTAAAAGCTAGCAATTACCAACAATCCATGCTTAAAAGAACATG-CTATTTCTCAAAG
* *
644638 GGAAATCAATATCAGTTTGTTTATATACCCATCA
65 GAAAATCAATATCAGTTTGTTTACATACCCATCA
644672 CTACAACAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
119 1 0.01
120 45 0.53
121 22 0.26
123 17 0.20
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (122 bp):
ATGCATGTTAAAAGCTAGCAATTACCAACAATCCATGCTTAAAAGAACATGCTATTTCTCAAAGG
AAAATCAATATCAGTTTGTTTACATACCCATCAATACGAAATTGAAATGGTGATCAT
Found at i:649420 original size:63 final size:63
Alignment explanation
Indices: 649287--649468 Score: 241
Period size: 63 Copynumber: 3.0 Consensus size: 63
649277 GTCGCCGGCG
* * * * * * *
649287 AAACCCAAGGAACCGGAGAAGAAACCCGACAAA-CC-AA-AAGAAGCTGAGAAGAAGCCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
649347 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
* *
649410 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAGCCCAAAG-A-C-GGTGAGAAGAAACCGGA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGA
649469 GAAGCCTAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
60 44 0.40
61 3 0.03
62 3 0.03
63 60 0.55
ACGTcount: A:0.51, C:0.21, G:0.25, T:0.03
Consensus pattern (63 bp):
AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
Found at i:649480 original size:30 final size:30
Alignment explanation
Indices: 649287--649468 Score: 247
Period size: 30 Copynumber: 6.0 Consensus size: 30
649277 GTCGCCGGCG
* * * * *
649287 AAACCCAAGGAACCGGAGAAGAAACCCGAC
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
* *
649317 AAACCAAAAGAAGCTGAGAAGAAGCCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
649347 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
649377 AAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
1 AAACCCAAAG-A--AGCTGAGAAGAAACCGGAA
649410 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
* * *
649440 AAGCCCAAAGACGGTGAGAAGAAACCGGA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGA
649469 GAAGCCTAAA
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
30 106 0.77
31 1 0.01
32 1 0.01
33 29 0.21
ACGTcount: A:0.51, C:0.21, G:0.25, T:0.03
Consensus pattern (30 bp):
AAACCCAAAGAAGCTGAGAAGAAACCGGAA
Found at i:649496 original size:93 final size:93
Alignment explanation
Indices: 649300--649468 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
649290 CCCAAGGAAC
* *
649300 CGGAGAAGAAACCCGACAAACCAAAAGAAGCTGAGAAGAAGCCGGAAAAACCCAAAGAAGCTGAG
1 CGGAGAAGAAACCCGAAAAACCAAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAG
649365 AAGAAACCGGAAAAACCCAAAGAAGCAG
66 AAGAAACCGGAAAAACCCAAAGAAGCAG
* * * * * *
649393 CTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAGAAGAAACCGGAAAAGCCCAAAGACGGTGAG
1 CGGAGAAGAAACCCGAAAAACCAAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAG
649458 AAGAAACCGGA
66 AAGAAACCGGA
649469 GAAGCCTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.50, C:0.21, G:0.26, T:0.03
Consensus pattern (93 bp):
CGGAGAAGAAACCCGAAAAACCAAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAG
AAGAAACCGGAAAAACCCAAAGAAGCAG
Found at i:667263 original size:57 final size:58
Alignment explanation
Indices: 667165--667291 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 58
667155 AAACGTTTGG
* * *
667165 CAAGTACCAAATCGAACACAAAAAAATTAGGTACCAAATTAGGAAAAAGA-GTTAAATT
1 CAAGTACCAAATCGAACACAAAAAAATTAAGTACCAAATTA-GAAAAAAATGTAAAATT
* ** *
667223 CAAGTACCAAATCGAATA-AAAAAGTTTAAGTACCAGATTAGAAAAAAATGTAAAATT
1 CAAGTACCAAATCGAACACAAAAAAATTAAGTACCAAATTAGAAAAAAATGTAAAATT
* *
667280 TATGTACCAAAT
1 CAAGTACCAAAT
667292 ATTATATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 7 0.12
57 35 0.59
58 17 0.29
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.22
Consensus pattern (58 bp):
CAAGTACCAAATCGAACACAAAAAAATTAAGTACCAAATTAGAAAAAAATGTAAAATT
Found at i:667517 original size:29 final size:28
Alignment explanation
Indices: 667476--667596 Score: 112
Period size: 29 Copynumber: 4.5 Consensus size: 28
667466 TAATAAACAC
667476 AAAAAAAATATTTTAAAAATAAAAAAAT
1 AAAAAAAATATTTTAAAAATAAAAAAAT
* ***
667504 AAAAAAATATATTTTAAAGTATTTTAAAAT
1 AAAAAAA-ATATTTTAAA-AATAAAAAAAT
* *
667534 --TAAAAA-A---TAAAAATAAAAATAT
1 AAAAAAAATATTTTAAAAATAAAAAAAT
667556 ACAAAAAAATATTTTAAAAATAAAAAAAT
1 A-AAAAAAATATTTTAAAAATAAAAAAAT
667585 AAAAAAAA-ATTT
1 AAAAAAAATATTT
667597 AAAGTATTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
22 6 0.08
23 4 0.06
25 5 0.07
26 2 0.03
27 5 0.07
28 18 0.25
29 25 0.35
30 7 0.10
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (28 bp):
AAAAAAAATATTTTAAAAATAAAAAAAT
Found at i:667592 original size:52 final size:52
Alignment explanation
Indices: 667489--667591 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
667479 AAAAATATTT
* *** *
667489 TAAAAATAAAAAAATAAAAAAATATATTTTAAAGTATTTTAAAATTAAAAAA
1 TAAAAATAAAAAAATAAAAAAATATATTTTAAAGAATAAAAAAATAAAAAAA
*
667541 TAAAAATAAAAATATACAAAAAA-ATATTTTAAA-AATAAAAAAATAAAAAAA
1 TAAAAATAAAAAAATA-AAAAAATATATTTTAAAGAATAAAAAAATAAAAAAA
667592 AATTTAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 13 0.30
52 25 0.57
53 6 0.14
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (52 bp):
TAAAAATAAAAAAATAAAAAAATATATTTTAAAGAATAAAAAAATAAAAAAA
Found at i:674631 original size:6 final size:6
Alignment explanation
Indices: 674622--674648 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
674612 CAGTCTCAAG
674622 CTCGGA CTCGGA CTCGGA CTCGGA CTC
1 CTCGGA CTCGGA CTCGGA CTCGGA CTC
674649 AGTCGTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.30, T:0.19
Consensus pattern (6 bp):
CTCGGA
Found at i:702387 original size:2 final size:2
Alignment explanation
Indices: 702380--702414 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
702370 CAATTAAAGG
*
702380 TA TA TA TA TA CA 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 TA T
702415 TCACACACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:702659 original size:137 final size:137
Alignment explanation
Indices: 702406--702675 Score: 339
Period size: 137 Copynumber: 2.0 Consensus size: 137
702396 TATATATATA
* * *
702406 TATATATATTCACACACCTTTAATTACTCTTTGATCTAATGTATAATGACTAATTTGAACATTTT
1 TATATATATTCACACACCTTTAATTACTCTTTGATCTAATGTACAAAGACTAATTTAAACATTTT
* * * *
702471 TTTGATAGATCGGCCACAATGCAATCCTACTCCTACTCTAAGGGCATCTATGGTACTTTTACCAA
66 TTTGATAGATCGGCCAAAATGCAATCATACTCCTACTCTAAGGACAGCTATGGTACTTTTACCAA
702536 TTAGAGG
131 TTAGAGG
* * * *
702543 TATATATATTCAGACACTTTTAATTGCTCTTTTG-TCTAA-GATACAAAGATTAATTTAAACATT
1 TATATATATTCACACACCTTTAATTACTC-TTTGATCTAATG-TACAAAGACTAATTTAAACATT
* * * * * *
702606 TTTTT-AGTAGATTGGCCAAAATGCAATCATGCTCTTAGTTTAAGGATAGCTATGGTACTTTTAC
64 TTTTTGA-TAGATCGGCCAAAATGCAATCATACTCCTACTCTAAGGACAGCTATGGTACTTTTAC
702670 CAATTA
128 CAATTA
702676 AACATGTGTG
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
136 2 0.02
137 107 0.95
138 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (137 bp):
TATATATATTCACACACCTTTAATTACTCTTTGATCTAATGTACAAAGACTAATTTAAACATTTT
TTTGATAGATCGGCCAAAATGCAATCATACTCCTACTCTAAGGACAGCTATGGTACTTTTACCAA
TTAGAGG
Found at i:712244 original size:182 final size:181
Alignment explanation
Indices: 711614--712325 Score: 789
Period size: 182 Copynumber: 3.9 Consensus size: 181
711604 TACTTTTATG
* * * * * * * *
711614 CTTTACTGACACAAACAAATACATAAATAGATTACTTTCATCAACTTAACCTGATTTTTAACACT
1 CTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTAACACT
* * *
711679 CCATTAAGCTTAATATTAGCTGCAATTCACAGCTTATTGATTAATTGCAGTTTGCTTCTAAAAAA
65 CCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAAGAAA
* * * *
711744 GAAACTTAACTGACTGAAGCCTGATTATAACATGTAATACTTCAACTTTCTC
130 GAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
* *
711796 CTTTTCTGAGACAAATATATACATGAATGGACTATTTTCATCAATTTAACCTGACA-TTTAACCC
1 C-TTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGA-ATTTTAACAC
* ** * * *
711860 TCCATTAAGCTTAATA-CAGCTGCAATTCACAGCTTCTTGATTAATAACAA-TTGGTCACT-GGA
64 TCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCT-TCTAAG-
* * * * *
711922 AAAGAAACTAAACTGACCCAAGCCTGGTTACAACATTTGATACTTGAA--TCCT-
127 AAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
* * *
711974 C-TTCTGAGACAAATACGA-ACATAAATGGACTATTTTCATCAATTTAATCTGAGTTTTAACACT
1 CTTTCTGAGACAAATA-TATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTAACACT
* * *
712037 CCATTAAGCTTAATATTAGCTGCAATTCGCAGCTTCTTGATTGATTGTAATTTGCTTCTAAGAAA
65 CCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAAGAAA
* *
712102 GAAACTAAACTGACTGAAGCCTGATTACAACATGTGATACATCAACTTTCTC
130 GAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
* * * ** * *
712154 CTTTCCTAAGACAAATATATACATAAACGGATTATTTTTGTCAATGTAA-CTCAATTTCTAACAC
1 CTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTT-TAACAC
* * ** * * * *
712218 TCCGTCAAGCTTAATATTAGCTGCAATTTGCATCTTCTTGATGAATTTCAAATTGCTTCCTAA-A
64 TCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTT-CTAAGA
* *
712282 AAGAAACTAAACTAACCGAAGCCTGATTACAACACGTGATACTT
128 AAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTT
712326 AATCCATAAT
Statistics
Matches: 442, Mismatches: 71, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
176 69 0.16
177 73 0.17
178 6 0.01
179 6 0.01
180 5 0.01
181 80 0.18
182 196 0.44
183 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (181 bp):
CTTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTAACACTC
CATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAAGAAAG
AAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
Found at i:718220 original size:4 final size:4
Alignment explanation
Indices: 718186--718250 Score: 66
Period size: 4 Copynumber: 16.5 Consensus size: 4
718176 TGAACTGAAA
*
718186 AACT AACT CAAC- AACT AATT CAACT --CT AACT AACT ATACT AAC- AACT
1 AACT AACT -AACT AACT AACT -AACT AACT AACT AACT A-ACT AACT AACT
718233 AACT AACT AACT AACT AA
1 AACT AACT AACT AACT AA
718251 AACAAATATG
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 2 0.04
3 6 0.12
4 34 0.65
5 10 0.19
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
AACT
Found at i:721418 original size:23 final size:24
Alignment explanation
Indices: 721380--721443 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
721370 CAATCTAATT
*
721380 AATTTTTTATTAAAAATTTCATCA
1 AATTTTTTGTTAAAAATTTCATCA
721404 AATTTTTTGTTAAAAATTTCATCA
1 AATTTTTTGTTAAAAATTTCATCA
* *
721428 ATTTTTTTGATAAAAA
1 AATTTTTTGTTAAAAA
721444 AACAGACACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTTTTTGTTAAAAATTTCATCA
Found at i:735727 original size:15 final size:15
Alignment explanation
Indices: 735704--735733 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
735694 AGTTTTGTAT
735704 TAAAAAATAATTAAA
1 TAAAAAATAATTAAA
*
735719 TAAATAATAATTAAA
1 TAAAAAATAATTAAA
735734 CCATAAAAAC
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAAATAATTAAA
Found at i:738769 original size:10 final size:12
Alignment explanation
Indices: 738743--738771 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
738733 AATAGTGTTT
738743 TATTTATAAATA
1 TATTTATAAATA
738755 TATTTATAAATA
1 TATTTATAAATA
738767 T-TTTA
1 TATTTA
738772 ATATTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTATAAATA
Found at i:739601 original size:20 final size:20
Alignment explanation
Indices: 739565--739604 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
739555 TTAATATATA
*
739565 TAATGAATTTAATTTTAAAT
1 TAATGAATTTAAGTTTAAAT
739585 TAATCGAATTT-AGTTTAAAT
1 TAAT-GAATTTAAGTTTAAAT
739605 AGTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
TAATGAATTTAAGTTTAAAT
Found at i:739631 original size:19 final size:19
Alignment explanation
Indices: 739553--739632 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
739543 TCATTGTTTC
*
739553 TTTTAATATATATAATGAA
1 TTTTAATATAAATAATGAA
*
739572 -TTTAATTTTAAATTAATCGAA
1 TTTTAA-TATAAA-TAAT-GAA
* * * *
739593 -TTTAGTTTAAATAGTTAA
1 TTTTAATATAAATAATGAA
*
739611 TTTTAATATATATAATGAA
1 TTTTAATATAAATAATGAA
739630 TTT
1 TTT
739633 CGGAATTTGG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
18 7 0.15
19 23 0.49
20 10 0.21
21 7 0.15
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAATATAAATAATGAA
Found at i:741574 original size:126 final size:124
Alignment explanation
Indices: 741292--741732 Score: 512
Period size: 124 Copynumber: 3.5 Consensus size: 124
741282 GATCAAATCA
* * * * * * *
741292 AAGCAGGATGATTTATTAGAAGGATTTTTTAAGTCGCGCCCACGTGTACG-GCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
741356 AGGTCCAGGAAAAATAATTTTGAGTTGACATTTATGAGCAAATAGTTTAAAAAACACTTC
66 AGGTCCTGGAAAAATAATTTTGAGTTGACATTTCTGAGCAAAAAG-TAAAAAAACGCTTC
* *
741416 AAGCAAGATGCTTTATGAGAAGAATATT-TGAAATCGCG-CCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAAT-TTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * * *
741479 TTGATTCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAAAAGTACAAAACAACGCTGC
65 TAGGTCCTGGAA-AAATAATTTTGAGTTGACATTTCTGAGCAAAAAGTA-AAAA-AACGCTTC
* * * *
741542 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGTGCTTTTGCTATAA
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * *
741606 TAGGTCCTGAAAAAATAATTTTGACTTGACATTTCTGAGCAAACAGTATAAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTTGAGTTGACATTTCTGAGCAAAAAGTAAAAAAACGCTTC
* * *
741666 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCTCACGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
741731 AG
66 AG
741733 CGTGTTTGGG
Statistics
Matches: 267, Mismatches: 41, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
123 11 0.04
124 114 0.43
125 41 0.15
126 69 0.26
127 32 0.12
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTTGAGTTGACATTTCTGAGCAAAAAGTAAAAAAACGCTTC
Found at i:742442 original size:21 final size:21
Alignment explanation
Indices: 742401--743034 Score: 282
Period size: 22 Copynumber: 26.9 Consensus size: 21
742391 CATCCAATTA
742401 AAGTTAAGGGTTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTTTTT
* * *
742423 AATTTAAGGGTTACGGTTTTA
1 AAGTTAAGGGTTAGGGTTTTT
* * * *
742444 AAGTGAATGGTTTATGTTTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
* * *
742466 AAGTTAAGGGTTACGGCTTTA
1 AAGTTAAGGGTTAGGGTTTTT
*
742487 AAGTTAACGGTTAGGGTTTTT
1 AAGTTAAGGGTTAGGGTTTTT
* *
742508 AGGTTAAGGGGTTAGGATTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
742530 AAGTTAAGGGTTAGGGTTAGTGTTTTT
1 AAGTTAAGGGTTA--G---G-GTTTTT
* *
742557 AGGTTAAGGGGTTAAGGTTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
742579 AAGTTAAGGGTTTAGGG-TTTT
1 AAGTTAAGGG-TTAGGGTTTTT
* *
742600 AGGTTAAGAGGCTAGGGTTTTT
1 AAGTTAAG-GGTTAGGGTTTTT
*
742622 AAGTTAACGGTTAGGGTTGGGGTTTTT
1 AAGTT-A-----AGGGTTAGGGTTTTT
*
742649 AGGTTAATGTGTTAGGGTTAGGGTTTTT
1 AAGTT-A------AGGGTTAGGGTTTTT
*
742677 AAGTTAATGGTTAGTGTTAAGGTTTTT
1 AAGTTAA--G---G-GTTAGGGTTTTT
*
742704 AGGTTAAGGGGTTAGGGTTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
742726 AAGTTAAGGGTTAGAGTTGGGGTTTTT
1 AAGTTAAGGGTT--A----GGGTTTTT
*
742753 ATGTTAATGGTTAGGGTTAGGGTTTTT
1 AAGTT-A-----AGGGTTAGGGTTTTT
742780 AAGTTAAGAGGTTAGGGTTTTT
1 AAGTTAAG-GGTTAGGGTTTTT
*
742802 AAGTTAACGGTTAGGGTTGGGGTTTTT
1 AAGTT-A-----AGGGTTAGGGTTTTT
* *
742829 AGGTTAAAGAGTTAGGG-TTTT
1 AAGTT-AAGGGTTAGGGTTTTT
742850 AAGTTAAAGGTTAGGGTTAGGGTTTTT
1 AAGTT--A----AGGGTTAGGGTTTTT
* *
742877 AGGTTAAGGTGTTAAGGTTTTT
1 AAGTTAAGG-GTTAGGGTTTTT
*
742899 AAGTTTAAGGTTTAAGGTTTAAGGTTTTT
1 AAG-TTAA-G-----GG-TTAGGGTTTTT
*
742928 AGGTTAAGGGGTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTTTTT
*
742950 AAGTTAAGGGTTAGAGTTTTT
1 AAGTTAAGGGTTAGGGTTTTT
* *
742971 AGGTTAAGGTGTTAGGATTTTT
1 AAGTTAAGG-GTTAGGGTTTTT
* * * *
742993 AGGTTAAGGATTTAAGATTTTT
1 AAGTTAAGG-GTTAGGGTTTTT
*
743015 AGGTTAAAGGGTTAGGGTTT
1 AAGTT-AAGGGTTAGGGTTT
743035 GTCAATTAAA
Statistics
Matches: 484, Mismatches: 67, Indels: 122
0.72 0.10 0.18
Matches are distributed among these distances:
21 108 0.22
22 190 0.39
23 15 0.03
24 1 0.00
25 1 0.00
26 14 0.03
27 97 0.20
28 37 0.08
29 14 0.03
31 1 0.00
33 6 0.01
ACGTcount: A:0.24, C:0.01, G:0.32, T:0.43
Consensus pattern (21 bp):
AAGTTAAGGGTTAGGGTTTTT
Found at i:742548 original size:49 final size:49
Alignment explanation
Indices: 742495--742798 Score: 341
Period size: 49 Copynumber: 6.1 Consensus size: 49
742485 TAAAGTTAAC
*
742495 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGATTTTTAAGTTAAGGGTTAG
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* *
742544 GGTTAGTGTTTTTAGGTTAAGGGGTTAAGGTTTTTAAGTTAAGGG-T--
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* * *
742590 --TTAGGG-TTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAACGGTTAG
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* *
742636 GGTTGGGGTTTTTAGGTTAATGTGTTAGGGTTAGGGTTTTTAAGTTAATGGTTAG
1 GGTTAGGGTTTTTAGGTTAA---G---GGGTTAGGGTTTTTAAGTTAAGGGTTAG
* *
742691 TGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* * *
742740 AGTTGGGGTTTTTATGTTAATGGTTAGGGTTAGGGTTTTTAAGTTAAGAGGTTAG
1 GGTTAGGGTTTTTAGGTTAA--G---GGGTTAGGGTTTTTAAGTTAAG-GGTTAG
742795 GGTT
1 GGTT
742799 TTTAAGTTAA
Statistics
Matches: 216, Mismatches: 21, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
43 32 0.15
44 6 0.03
48 6 0.03
49 96 0.44
51 1 0.00
52 2 0.01
54 22 0.10
55 51 0.24
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (49 bp):
GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
Found at i:742619 original size:43 final size:42
Alignment explanation
Indices: 742401--742639 Score: 196
Period size: 43 Copynumber: 5.5 Consensus size: 42
742391 CATCCAATTA
** *
742401 AAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTACGGTTTTA
1 AAGTTAAGGGTTTAGGG-TTTTAGGTTAAGGGTTACGGTTTTT
* * ** * * *
742444 AAGTGAATGGTTTATGTTTTTTAAGTTAAGGGTTACGGCTTTA
1 AAGTTAAGGGTTTA-GGGTTTTAGGTTAAGGGTTACGGTTTTT
*
742487 AAGTTAACGG-TTAGGGTTTTTAGGTTAAGGGGTTA-GGATTTTT
1 AAGTTAAGGGTTTAGGG-TTTTAGGTTAA-GGGTTACGG-TTTTT
* *
742530 AAGTTAAGGGTTAGGGTTAGTGTTTTTAGGTTAAGGGGTTAAGGTTTTT
1 AAGTTAAGGG-T----TTAG-GGTTTTAGGTTAA-GGGTTACGGTTTTT
* *
742579 AAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTAGGTTAAG-GGTTACGGTTTTT
*
742622 AAGTTAACGG-TTAGGGTT
1 AAGTTAAGGGTTTAGGGTT
742640 GGGGTTTTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 24 0.15
43 93 0.57
44 5 0.03
48 1 0.01
49 37 0.23
50 3 0.02
ACGTcount: A:0.24, C:0.03, G:0.31, T:0.42
Consensus pattern (42 bp):
AAGTTAAGGGTTTAGGGTTTTAGGTTAAGGGTTACGGTTTTT
Found at i:742711 original size:14 final size:14
Alignment explanation
Indices: 742642--742712 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
742632 TTAGGGTTGG
742642 GGTTTTTAGGTTAA
1 GGTTTTTAGGTTAA
* * *
742656 TG-TGTTAGGGTTAG
1 GGTTTTTA-GGTTAA
*
742670 GGTTTTTAAGTTAA
1 GGTTTTTAGGTTAA
742684 TGG---TTAGTGTTAA
1 -GGTTTTTAG-GTTAA
742697 GGTTTTTAGGTTAA
1 GGTTTTTAGGTTAA
742711 GG
1 GG
742713 GGTTAGGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
12 5 0.12
13 9 0.21
14 18 0.43
15 10 0.24
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (14 bp):
GGTTTTTAGGTTAA
Found at i:742729 original size:104 final size:97
Alignment explanation
Indices: 742472--742899 Score: 369
Period size: 92 Copynumber: 4.4 Consensus size: 97
742462 TTTTAAGTTA
* * * * * * *
742472 AGGGTTACGGCTTTAAAGTTAACGG-TTAGGGTTTTTAGGTTAAGGGGTTAGGATTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-TTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTA
* * * *
742536 AGGGTTAGGGTTAGTGTTTTTAGGTTAA--G--
65 ACGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
*
742565 -GGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAA
1 AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAA
*
742629 CGGTTAGGGTTGGGGTTTTTAGGTTAATGTGTT
66 CGGTTAGAGTTGGGGTTTTTAGGTTAATG-GTT
* * *
742662 AGGGTTAGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTA
1 AGGGTTAGGGTTTTTAAGTTAA-GG---GT-TT-AGGGTTTTAGGTTAAGAGGCTAGGGTTTTTA
* *
742727 AGTTAAGGGTTAGAGTTGGGGTTTTTATGTTAATGGTT
60 AGTTAACGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
* * *
742765 AGGGTTAGGGTTTTTAAGTTAAGAGG-TTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTT
1 AGGGTTAGGGTTTTTAAGTTAAG-GGTTTAGGG-TTTTAGGTTAA--G--A-GGCTAGGGTTTTT
* * * *
742829 AGGTTAA-----AGAGTTAGGG-TTTTAAGTTAAAGGTT
59 AAGTTAACGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
* * *
742862 AGGGTTAGGGTTTTTAGGTTAAGGTGTTAAGGTTTTTA
1 AGGGTTAGGGTTTTTAAGTTAAGG-GTTTAGGGTTTTA
742900 AGTTTAAGGT
Statistics
Matches: 285, Mismatches: 28, Indels: 40
0.81 0.08 0.11
Matches are distributed among these distances:
92 74 0.26
93 6 0.02
95 1 0.00
96 1 0.00
97 45 0.16
98 45 0.16
99 2 0.01
100 2 0.01
102 3 0.01
103 46 0.16
104 60 0.21
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.42
Consensus pattern (97 bp):
AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAA
CGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
Found at i:742760 original size:76 final size:76
Alignment explanation
Indices: 742635--742967 Score: 339
Period size: 76 Copynumber: 4.4 Consensus size: 76
742625 TTAACGGTTA
* * * * *
742635 GGGTTGGGGTTTTTAGGTTAATGTGTTAGGGTTAGGGTTTTTAAGTTAATGGTTAGTGTTAAGGT
1 GGGTTAGGGTTTTTAAGTTAA-GGGTTAGAGTTGGGGTTTTTAAGTTAATGGTTAGTGTTAAGGT
742700 TTTTAGGTTAAG
65 TTTTAGGTTAAG
* * *
742712 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTATGTTAATGGTTAGGGTTAGGGTT
1 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTT
*
742777 TTTAAGTTAAG
66 TTTAGGTTAAG
* * * * * *
742788 AGGTTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAAAGAGTTAGGGTTTTAA-
1 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTAAGTTAATG-GTTA--GTGTTAAG
**
742852 G-TTAAAGGTT-A-
63 GTTTTTAGGTTAAG
*
742863 GGGTTAGGGTTTTTAGGTTAAGGTGTTA-A-----GGTTTTTAAGTTTAA-GGTTTAAG-GTTTA
1 GGGTTAGGGTTTTTAAGTTAAGG-GTTAGAGTTGGGGTTTTTAAG-TTAATGG-TT-AGTG-TTA
742920 AGGTTTTTAGGTTAAG
61 AGGTTTTTAGGTTAAG
742936 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTT
1 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTT
742968 TTTAGGTTAA
Statistics
Matches: 211, Mismatches: 29, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
69 6 0.03
70 13 0.06
71 12 0.06
72 5 0.02
73 23 0.11
75 20 0.09
76 98 0.46
77 29 0.14
78 1 0.00
79 4 0.02
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.43
Consensus pattern (76 bp):
GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTT
TTTAGGTTAAG
Found at i:742799 original size:49 final size:49
Alignment explanation
Indices: 742612--742963 Score: 299
Period size: 49 Copynumber: 6.9 Consensus size: 49
742602 GTTAAGAGGC
* * *
742612 TAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAATGTGTTAGGGT
1 TAGGGTTTTTAAGTTAA--G--AGAGTTAGGGTTTTTAAGTTAA-G-GTTAGGGT
* * *
742667 TAGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTTTTTAGGTTAA-G---GGGT
1 TAGGGTTTTTAAGTTAA--G--AGAGTTAGGGTTTTTAAGTTAAGGTTAGGGT
* *
742716 TAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTATGTTAATGGTTAGGGT
1 TAGGGTTTTTAAGTTAA--G--AGAGTTAGGGTTTTTAAGTTAA-GGTTAGGGT
742770 TAGGGTTTTTAAGTTAAGAG-GTTAGGGTTTTTAAGTTAACGGTTAGGGT
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTTAA-GGTTAGGGT
* *
742819 TGGGGTTTTTAGGTTAA-AGAGTTAGGG-TTTTAAGTTAAAGGTTAGGGT
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTT-AAGGTTAGGGT
* * * *
742867 TAGGGTTTTTAGGTTAAG-GTGTTAAGGTTTTTAAGTTTAAGGTTTAAGGTT
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAG-TTAAGG-TT-AGGGT
* * *
742918 TAAGGTTTTTAGGTTAAG-GGGTTAGGGTTTTTAAGTTAAGGGTTAG
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTTAA-GGTTAG
742964 AGTTTTTAGG
Statistics
Matches: 263, Mismatches: 21, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
48 43 0.16
49 106 0.40
50 12 0.05
51 39 0.15
52 2 0.01
54 21 0.08
55 40 0.15
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.43
Consensus pattern (49 bp):
TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTTAAGGTTAGGGT
Found at i:742828 original size:28 final size:28
Alignment explanation
Indices: 742789--742883 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 28
742779 TAAGTTAAGA
*
742789 GGTTAGGGTTTTTAAGTTAACG-GTTAG
1 GGTTAGGGTTTTTAAGTTAAAGAGTTAG
* *
742816 GGTTGGGGTTTTTAGGTT-AA-AG--A-
1 GGTTAGGGTTTTTAAGTTAAAGAGTTAG
742839 -GTTAGGG-TTTTAAGTTAAAG-GTTAG
1 GGTTAGGGTTTTTAAGTTAAAGAGTTAG
*
742864 GGTTAGGGTTTTTAGGTTAA
1 GGTTAGGGTTTTTAAGTTAA
742884 GGTGTTAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
21 8 0.15
22 9 0.17
24 2 0.04
26 9 0.17
27 26 0.48
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.41
Consensus pattern (28 bp):
GGTTAGGGTTTTTAAGTTAAAGAGTTAG
Found at i:742864 original size:97 final size:100
Alignment explanation
Indices: 742738--742963 Score: 300
Period size: 97 Copynumber: 2.3 Consensus size: 100
742728 GTTAAGGGTT
* * * *
742738 AGAGTTGGGGTTTTTATGTTAATGGTTAGGGTTAGGGTTTTTAAGTTAAGAG-GTTAGGGTTTTT
1 AGAGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAAGTTAAG-GTGTTAAGGTTTTT
**
742802 AAG-TTAACGG-TT-AGGGTTGGGGTTTTTAGGTTAA
65 AAGTTTAA-GGTTTAAGGGTTAAGGTTTTTAGGTTAA
*
742836 AGAGTTAGGG-TTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAGGTTAAGGTGTTAAGGTTTTTA
1 AGAGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAAGTTAAGGTGTTAAGGTTTTTA
*
742900 AGTTTAAGGTTTAAGGTTTAAGGTTTTTAGGTTAA
66 AGTTTAAGGTTTAAGGGTTAAGGTTTTTAGGTTAA
* * *
742935 GGGGTTAGGGTTTTTAAGTTAAGGGTTAG
1 AGAGTTAGGGTTTTTAAGTTAAAGGTTAG
742964 AGTTTTTAGG
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
96 1 0.01
97 52 0.46
98 15 0.13
99 27 0.24
100 17 0.15
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.42
Consensus pattern (100 bp):
AGAGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAAGTTAAGGTGTTAAGGTTTTTA
AGTTTAAGGTTTAAGGGTTAAGGTTTTTAGGTTAA
Found at i:742913 original size:7 final size:7
Alignment explanation
Indices: 742880--742925 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
742870 GGTTTTTAGG
742880 TTAAGGT
1 TTAAGGT
742887 GTTAAGGTTT
1 -TTAAGG--T
742897 TTAA-GT
1 TTAAGGT
742903 TTAAGGT
1 TTAAGGT
742910 TTAAGGT
1 TTAAGGT
742917 TTAAGGT
1 TTAAGGT
742924 TT
1 TT
742926 TTAGGTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 5 0.14
7 18 0.51
8 7 0.20
9 4 0.11
10 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (7 bp):
TTAAGGT
Found at i:742946 original size:29 final size:29
Alignment explanation
Indices: 742878--742947 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
742868 AGGGTTTTTA
*
742878 GGTTAAGGTGTTAAGGTTTTTAAGTTTAAG
1 GGTTAAGGT-TTAAGGTTTTTAAGGTTAAG
*
742908 GTTTAAGGTTTAAGGTTTTT-AGGTTAAGG
1 GGTTAAGGTTTAAGGTTTTTAAGGTTAA-G
*
742937 GGTTAGGGTTT
1 GGTTAAGGTTT
742948 TTAAGTTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.17
29 21 0.60
30 8 0.23
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (29 bp):
GGTTAAGGTTTAAGGTTTTTAAGGTTAAG
Found at i:742957 original size:43 final size:43
Alignment explanation
Indices: 742910--743034 Score: 171
Period size: 43 Copynumber: 2.9 Consensus size: 43
742900 AGTTTAAGGT
742910 TTAAGGTTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
1 TTAAGGTTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
* * * *
742953 TTAAGGGTT-AGAGTTTTTAGGTTAAGGTGTTAGGATTTTTAGG
1 TTAAGGTTTAAG-GTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
* *
742996 TTAAGGATTTAAGATTTTTAGGTTAAAGGGTTAGGGTTT
1 TTAAGG-TTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTT
743035 GTCAATTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 42 0.60
44 24 0.34
45 2 0.03
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (43 bp):
TTAAGGTTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
Found at i:743312 original size:21 final size:21
Alignment explanation
Indices: 743288--743334 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
743278 GCGACGGTTG
*
743288 TGGTTCCTCCGGT-GGGGATTC
1 TGGTTCCTCCGGTAGGGCA-TC
*
743309 TGGTTCTTCCGGTAGGGCATC
1 TGGTTCCTCCGGTAGGGCATC
743330 TGGTT
1 TGGTT
743335 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.21, G:0.36, T:0.36
Consensus pattern (21 bp):
TGGTTCCTCCGGTAGGGCATC
Found at i:743610 original size:18 final size:18
Alignment explanation
Indices: 743587--743633 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
743577 TGAAATATAT
743587 AAGGGTTAGGATACATAA
1 AAGGGTTAGGATACATAA
743605 AAGGGTTAGGATACATAA
1 AAGGGTTAGGATACATAA
*
743623 AAGGGCTAGGA
1 AAGGGTTAGGA
743634 AACGCACCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.32, T:0.19
Consensus pattern (18 bp):
AAGGGTTAGGATACATAA
Found at i:744769 original size:39 final size:39
Alignment explanation
Indices: 744722--744801 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
744712 ATACCAATCG
744722 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
1 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
744761 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
1 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
744800 AC
1 AC
744802 ATGTGCTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (39 bp):
ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
Found at i:744960 original size:20 final size:20
Alignment explanation
Indices: 744923--744960 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
744913 TTTATTTTTA
*
744923 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
744943 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
744961 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:745910 original size:30 final size:30
Alignment explanation
Indices: 745854--745911 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
745844 ATTTTTACGG
*
745854 TTTAAAAAAATTTAAAAAAATTAAATTTTT
1 TTTAAAAAAATTTAAAAAAATGAAATTTTT
* *
745884 TTTAAAAATTATTTAAAAATA-GAAATTT
1 TTTAAAAA-AATTTAAAAAAATGAAATTT
745912 AAGAGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TTTAAAAAAATTTAAAAAAATGAAATTTTT
Found at i:745933 original size:12 final size:11
Alignment explanation
Indices: 745904--745933 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
745894 ATTTAAAAAT
745904 AGAAATTTAAG
1 AGAAATTTAAG
745915 AGAAATTTAAG
1 AGAAATTTAAG
745926 AGGAAATT
1 A-GAAATT
745934 GAGAGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (11 bp):
AGAAATTTAAG
Found at i:745938 original size:11 final size:11
Alignment explanation
Indices: 745924--746025 Score: 90
Period size: 11 Copynumber: 9.6 Consensus size: 11
745914 GAGAAATTTA
745924 AGAGGAAATTG
1 AGAGGAAATTG
*
745935 AGAGCAAATTG
1 AGAGGAAATTG
**
745946 AGATTAAA-T-
1 AGAGGAAATTG
* *
745955 A-TGG-ATTTG
1 AGAGGAAATTG
745964 AGA-GAAATTTG
1 AGAGGAAA-TTG
745975 -GAAGGAAATTG
1 AG-AGGAAATTG
745986 AGAGGAAATTG
1 AGAGGAAATTG
745997 AGAGGAAATTG
1 AGAGGAAATTG
*
746008 AAAGGAAATTG
1 AGAGGAAATTG
746019 AGAGGAA
1 AGAGGAA
746026 GTTTGAAAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 3 0.04
10 3 0.04
11 59 0.82
12 5 0.07
ACGTcount: A:0.46, C:0.01, G:0.31, T:0.22
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:745998 original size:33 final size:33
Alignment explanation
Indices: 745961--746025 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
745951 AAATATGGAT
*
745961 TTGAGA-GAAATTTGGAAGGAAATTGAGAGGAAA
1 TTGAGAGGAAA-TTGAAAGGAAATTGAGAGGAAA
745994 TTGAGAGGAAATTGAAAGGAAATTGAGAGGAA
1 TTGAGAGGAAATTGAAAGGAAATTGAGAGGAA
746026 GTTTGAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (33 bp):
TTGAGAGGAAATTGAAAGGAAATTGAGAGGAAA
Found at i:746040 original size:23 final size:22
Alignment explanation
Indices: 745977--746034 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
745967 GAAATTTGGA
*
745977 AGGAAATTGAGAGGAAATTGAG
1 AGGAAATTGAAAGGAAATTGAG
745999 AGGAAATTGAAAGGAAATTGAG
1 AGGAAATTGAAAGGAAATTGAG
*
746021 AGGAAGTTTGAAAG
1 AGGAA-ATTGAAAG
746035 AGAATTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (22 bp):
AGGAAATTGAAAGGAAATTGAG
Found at i:751440 original size:80 final size:79
Alignment explanation
Indices: 751278--751448 Score: 179
Period size: 80 Copynumber: 2.1 Consensus size: 79
751268 AATCCATTTA
* * * * *
751278 ATATATATATATATATAATGTATAAGCATAAATATGAAAATATGTATATATATTTAAATCCATTT
1 ATATATATATATATAAAATGTATAAGCATAAAAATGAAAATACGTATAAACATTTAAAT-CATTT
751343 AAAATATATATACAT
65 AAAATATATATACAT
*
751358 ATATATATATATATAAAATGTATAAGCGTATAAAAATTATAACATACG-A-AAACATTTAAAT-A
1 ATATATATATATATAAAATGTATAAGC--ATAAAAATGA-AA-ATACGTATAAACATTTAAATCA
**
751420 TTATAAAATATA-ATGTAT
62 TT-TAAAATATATATACAT
*
751438 ATATGTATATA
1 ATATATATATA
751449 CATATGTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
80 43 0.56
81 9 0.12
82 18 0.23
83 3 0.04
84 4 0.05
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (79 bp):
ATATATATATATATAAAATGTATAAGCATAAAAATGAAAATACGTATAAACATTTAAATCATTTA
AAATATATATACAT
Found at i:752466 original size:77 final size:77
Alignment explanation
Indices: 752339--752494 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 77
752329 TTCAGTTTTT
752339 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
1 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
752404 TGAGTCCGGGCC
66 TGAGTCCGGGCC
752416 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
1 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
**
752481 TGAGTTTGGGCC
66 TGAGTCCGGGCC
752493 TT
1 TT
752495 AGGCTTAGTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (77 bp):
TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
TGAGTCCGGGCC
Found at i:763886 original size:3 final size:3
Alignment explanation
Indices: 763878--763905 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
763868 CATCTTTTGA
763878 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
763906 TGTAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:769244 original size:36 final size:36
Alignment explanation
Indices: 769197--769271 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
769187 TATGATTTAC
* *
769197 GATTATAGTACTTCTTGTCAATGCATCATACCTTGT
1 GATTATAGTACTTATTGTCAATGCATCATACCATGT
769233 GATTATAGTACTTATTGTCAATGCATCATACCATGT
1 GATTATAGTACTTATTGTCAATGCATCATACCATGT
769269 GAT
1 GAT
769272 CTCTCATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (36 bp):
GATTATAGTACTTATTGTCAATGCATCATACCATGT
Found at i:771385 original size:23 final size:22
Alignment explanation
Indices: 771358--771407 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
771348 TTTTTTAATT
771358 ATATTCACTATTTTAAAT-ATAAA
1 ATATTCAC--TTTTAAATCATAAA
* *
771381 ATATTTACTTTTATATCATAAA
1 ATATTCACTTTTAAATCATAAA
771403 ATATT
1 ATATT
771408 AAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTCACTTTTAAATCATAAA
Found at i:775285 original size:14 final size:14
Alignment explanation
Indices: 775266--775299 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
775256 AAATTTAAAC
775266 ATTAACCATTAGAG
1 ATTAACCATTAGAG
775280 ATTAACCATTAGAG
1 ATTAACCATTAGAG
775294 ATTAAC
1 ATTAAC
775300 AAAATTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (14 bp):
ATTAACCATTAGAG
Found at i:775628 original size:13 final size:14
Alignment explanation
Indices: 775610--775656 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
775600 TTACTACTGG
*
775610 AAAAAGAAAAT-AC
1 AAAAAGAAAATAAA
*
775623 AAAAAGAAGATAAA
1 AAAAAGAAAATAAA
775637 AAAAAGAAAA-AGAA
1 AAAAAGAAAATA-AA
775651 AAAAAG
1 AAAAAG
775657 GAAACCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAATAAA
Found at i:776033 original size:36 final size:36
Alignment explanation
Indices: 775991--776066 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
775981 CAGGTTCAAG
* *
775991 GTTACTACTGCTAAATTTTTTTTGTTAAATTTGTTA
1 GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
776027 GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
1 GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
776063 GTTA
1 GTTA
776067 GGAATTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.54
Consensus pattern (36 bp):
GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
Found at i:788740 original size:2 final size:2
Alignment explanation
Indices: 788728--788766 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
788718 AGGCTGAAGA
*
788728 GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
788767 AGAGATATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
GT
Found at i:797099 original size:5 final size:5
Alignment explanation
Indices: 797091--797115 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
797081 TTTTTTTTCT
797091 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
797116 AATCTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:805834 original size:142 final size:142
Alignment explanation
Indices: 805573--805862 Score: 499
Period size: 142 Copynumber: 2.0 Consensus size: 142
805563 CCAGATAAAT
* * *
805573 TAATTATAACTAATAGCTAATTATTGTGGTTTGCTTGTATATGGAACCTAATGAACTTGGTTACG
1 TAATAATAACTAATAGCTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTGACG
* *
805638 CGGTTTAATGTTTGTTTGAATACTTAAGTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGCT
66 CGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
805703 CTTTGAGTTCCC
131 CTTTGAGTTCCC
* * *
805715 TAATAATAACTAATAGGTAATTATTGTGGTTTGATTGTATGTGGAACCTAATGAACTTGGTGATG
1 TAATAATAACTAATAGCTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTGACG
*
805780 TGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
66 CGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
805845 CTTTGAGTTCCC
131 CTTTGAGTTCCC
805857 TAATAA
1 TAATAA
805863 GTGTAGTTGA
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (142 bp):
TAATAATAACTAATAGCTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTGACG
CGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
CTTTGAGTTCCC
Found at i:813088 original size:18 final size:18
Alignment explanation
Indices: 813055--813127 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
813045 GAATTGATTT
*
813055 TATAATTTT-CTATTTTA
1 TATAATTTTAATATTTTA
813072 TATAATTTTAATATTTTA
1 TATAATTTTAATATTTTA
* * *
813090 TTTAATTTGAAT-TGGAGTTA
1 TATAATTTTAATAT---TTTA
813110 -ATAATTTTAATATTTTA
1 TATAATTTTAATATTTTA
813127 T
1 T
813128 TTACCCCAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
17 13 0.30
18 17 0.40
19 9 0.21
20 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (18 bp):
TATAATTTTAATATTTTA
Found at i:817992 original size:25 final size:25
Alignment explanation
Indices: 817953--818001 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
817943 ATTTTGGCTT
*
817953 TCAAAGACATAATTGGCTTACGTTG
1 TCAAAGACATAATTGGCTCACGTTG
817978 TCAAAGACA-AGATTGGCTCACGTT
1 TCAAAGACATA-ATTGGCTCACGTT
818002 TGCCTTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (25 bp):
TCAAAGACATAATTGGCTCACGTTG
Found at i:818131 original size:43 final size:42
Alignment explanation
Indices: 818075--818199 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 42
818065 CACTTGATTG
818075 TTTCATTTTAATTTAATCTCACTTTAAATATTCTCACTAATTC
1 TTTCATTTTAATTTAATCT-ACTTTAAATATTCTCACTAATTC
* *
818118 TTTCATTTTAATTTAATCAAACTTTAAATTTTCTCACTAATTC
1 TTTCATTTTAATTTAATC-TACTTTAAATATTCTCACTAATTC
*
818161 TTTCATTTTAATTTAATCTACTTTATAATATGCTCACTA
1 TTTCATTTTAATTTAATCTACTTTA-AATATTCTCACTA
818200 CTTTGTCTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
42 6 0.08
43 69 0.92
ACGTcount: A:0.31, C:0.17, G:0.01, T:0.51
Consensus pattern (42 bp):
TTTCATTTTAATTTAATCTACTTTAAATATTCTCACTAATTC
Found at i:819753 original size:16 final size:16
Alignment explanation
Indices: 819732--819768 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
819722 TAAGTTTCTT
819732 ATTTGAATTA-ATTTAA
1 ATTTGAATTAGA-TTAA
819748 ATTTGAATTAGATTAA
1 ATTTGAATTAGATTAA
819764 ATTTG
1 ATTTG
819769 TTTACGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
ATTTGAATTAGATTAA
Found at i:850074 original size:230 final size:231
Alignment explanation
Indices: 849658--850121 Score: 912
Period size: 230 Copynumber: 2.0 Consensus size: 231
849648 TTATTAATTT
849658 AAAATTTTATCAATTATAAATTATCTAAATAAAAAAATCATTTTAAGGGATGCGGAACGTTACCA
1 AAAATTTTATC-ATTATAAATTATCTAAATAAAAAAATCATTTTAAGGGATGCGGAACGTTACCA
849723 CACTCAGCTGGGAAAGTTGATTGTATGTATATCCATTATAATATACATTTGTCACTAACAAACAC
65 CACTCAGCTGGGAAAGTTGATTGTATGTATATCCATTATAATATACATTTGTCACTAACAAACAC
849788 TTTGCTTCGAATCTTCATATATTGCTTTAAATAAAATAGAGAGATAAAATAGATAATTTATGAGG
130 TTTGCTTCGAATCTTCATATATTGCTTTAAATAAAATAGAGAGATAAAATAGATAATTTATGAGG
849853 ATGAAGGATCAAGAGCCGAGTCATGCCGCACAAGTTG
195 ATGAAGGATCAAGAGCCGAGTCATGCCGCACAAGTTG
849890 AAAATTTTATC-TTATAAATTATCTAAATAAAAAAATCATTTTAAGGGATGCGGAACGTTACCAC
1 AAAATTTTATCATTATAAATTATCTAAATAAAAAAATCATTTTAAGGGATGCGGAACGTTACCAC
849954 ACTCAGCTGGGAAAGTTGATTGTATGTATATCCATTATAATATACATTTGTCACTAACAAACACT
66 ACTCAGCTGGGAAAGTTGATTGTATGTATATCCATTATAATATACATTTGTCACTAACAAACACT
850019 TTGCTTCGAATCTTCATATATTGCTTTAAATAAAATAGAGAGATAAAATAGATAATTTATGAGGA
131 TTGCTTCGAATCTTCATATATTGCTTTAAATAAAATAGAGAGATAAAATAGATAATTTATGAGGA
850084 TGAAGGATCAAGAGCCGAGTCATGCCGCACAAGTTG
196 TGAAGGATCAAGAGCCGAGTCATGCCGCACAAGTTG
850120 AA
1 AA
850122 TCCGTACAAG
Statistics
Matches: 232, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
230 221 0.95
232 11 0.05
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (231 bp):
AAAATTTTATCATTATAAATTATCTAAATAAAAAAATCATTTTAAGGGATGCGGAACGTTACCAC
ACTCAGCTGGGAAAGTTGATTGTATGTATATCCATTATAATATACATTTGTCACTAACAAACACT
TTGCTTCGAATCTTCATATATTGCTTTAAATAAAATAGAGAGATAAAATAGATAATTTATGAGGA
TGAAGGATCAAGAGCCGAGTCATGCCGCACAAGTTG
Found at i:854788 original size:20 final size:20
Alignment explanation
Indices: 854750--854793 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
854740 GTCATTTCGC
**
854750 TATTA-TATTGTTATTATAT
1 TATTATTATTGTTAGAATAT
854769 TATTATTATTGTTAGAATAT
1 TATTATTATTGTTAGAATAT
854789 T-TTAT
1 TATTAT
854794 AACTCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TATTATTATTGTTAGAATAT
Found at i:855761 original size:31 final size:31
Alignment explanation
Indices: 855723--855782 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
855713 TCATATTTTA
*
855723 ATTTGATCAAGTTTAGTCCTTGTACTTTTCT
1 ATTTGATCAAGTTTAGTCCATGTACTTTTCT
** *
855754 ATTTGATCATTTTTAGTTCATGTACTTTT
1 ATTTGATCAAGTTTAGTCCATGTACTTTT
855783 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.55
Consensus pattern (31 bp):
ATTTGATCAAGTTTAGTCCATGTACTTTTCT
Found at i:856243 original size:14 final size:14
Alignment explanation
Indices: 856224--856251 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
856214 ATATATTTAT
856224 TGTGAATTGTGAAA
1 TGTGAATTGTGAAA
856238 TGTGAATTGTGAAA
1 TGTGAATTGTGAAA
856252 CCAACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
TGTGAATTGTGAAA
Found at i:865426 original size:89 final size:90
Alignment explanation
Indices: 865314--865499 Score: 356
Period size: 89 Copynumber: 2.1 Consensus size: 90
865304 TTACATAATC
*
865314 ATTTTAATGGCAGCAACTAAAATTATTATTGTTTAATAATATTATAAAAGTAGAGAAATAATATT
1 ATTTAAATGGCAGCAACTAAAATTATTATTGTTTAATAATATTATAAAAGTAGAGAAATAATATT
865379 GTATTAAATTAATATAAAAAATTAA
66 GTATTAAATTAATATAAAAAATTAA
865404 ATTTAAATGGCAGCAA-TAAAATTATTATTGTTTAATAATATTATAAAAGTAGAGAAATAATATT
1 ATTTAAATGGCAGCAACTAAAATTATTATTGTTTAATAATATTATAAAAGTAGAGAAATAATATT
865468 GTATTAAATTAATATAAAAAATTAA
66 GTATTAAATTAATATAAAAAATTAA
865493 ATTTAAA
1 ATTTAAA
865500 ATAATAAATA
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
89 80 0.84
90 15 0.16
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (90 bp):
ATTTAAATGGCAGCAACTAAAATTATTATTGTTTAATAATATTATAAAAGTAGAGAAATAATATT
GTATTAAATTAATATAAAAAATTAA
Found at i:865498 original size:19 final size:18
Alignment explanation
Indices: 865470--865508 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
865460 ATAATATTGT
*
865470 ATTAAATTAATATAAAAA
1 ATTAAATTAAAATAAAAA
*
865488 ATTAAATTTAAAATAATAA
1 ATTAAA-TTAAAATAAAAA
865507 AT
1 AT
865509 AATAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAATTAAAATAAAAA
Found at i:882555 original size:34 final size:34
Alignment explanation
Indices: 882478--882548 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
882468 ACTATCGATA
* * *
882478 TTATATCAATCAAGTTTTTCTATTATTGAAACTG
1 TTATATTAATTAAGTTTTTCTATTATTGAAACCG
882512 TTATATTAATTAAGTCTTTT-TATTATTGAAACCG
1 TTATATTAATTAAGT-TTTTCTATTATTGAAACCG
882546 TTA
1 TTA
882549 ATTTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (34 bp):
TTATATTAATTAAGTTTTTCTATTATTGAAACCG
Found at i:884925 original size:109 final size:110
Alignment explanation
Indices: 884786--885005 Score: 433
Period size: 109 Copynumber: 2.0 Consensus size: 110
884776 ATATTATAAG
884786 TTTAAATCTTATCATAGATTATTTTATTAATTATATATATAAATATACATAAAAAAAAACACTCC
1 TTTAAATCTTATCATAGATTATTTTATTAATTATATATATAAATATACATAAAAAAAAACACTCC
884851 TAATTAAATAATAAAAATATATTTATTAAAAAAATTAATAGTATA
66 TAATTAAATAATAAAAATATATTTATTAAAAAAATTAATAGTATA
884896 TTTAAATCTT-TCATAGATTATTTTATTAATTATATATATAAATATACATAAAAAAAAACACTCC
1 TTTAAATCTTATCATAGATTATTTTATTAATTATATATATAAATATACATAAAAAAAAACACTCC
884960 TAATTAAATAATAAAAATATATTTATTAAAAAAATTAATAGTATA
66 TAATTAAATAATAAAAATATATTTATTAAAAAAATTAATAGTATA
885005 T
1 T
885006 ATAAGCACAC
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
109 100 0.91
110 10 0.09
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (110 bp):
TTTAAATCTTATCATAGATTATTTTATTAATTATATATATAAATATACATAAAAAAAAACACTCC
TAATTAAATAATAAAAATATATTTATTAAAAAAATTAATAGTATA
Found at i:886504 original size:39 final size:39
Alignment explanation
Indices: 886457--886563 Score: 187
Period size: 39 Copynumber: 2.7 Consensus size: 39
886447 TGATATGAAT
886457 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
1 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
886496 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
1 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
* * *
886535 GAAAGAAACCCTCAGGAGACTAAAAAGGA
1 GAAAGAAGCCCTCGGGAGACTAAGAAGGA
886564 AAATTGCAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.42, C:0.18, G:0.29, T:0.11
Consensus pattern (39 bp):
GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
Found at i:886519 original size:132 final size:130
Alignment explanation
Indices: 886139--886519 Score: 367
Period size: 132 Copynumber: 2.9 Consensus size: 130
886129 GGCTACTGTG
* * * * * *
886139 TTTATGAACATTAAAAAGCGGAGCAAACGTAGAAATTTGGACGGTGCGATGACTGAAAGAATCCC
1 TTTATGAACATTAAAGAGCAGAGCAAGCGCAGAAATTTGGACGGTGCGATGAATGAAAGAAGCCC
* *
886204 TCAGGAG-AATAAGGATGCAATGACTGAAAGAAGCCCT-GAAGAGACTAAGAAGGAAAACTGCGA
66 TCAGGAGTAAGAAGGATGCAATGACTGAAAGAAGCCCTCG-GGAGACT---AAGGAAAACTGCGA
886267 TCGT
127 TCGT
* * * **
886271 TTTATGAACGTTAAAGTGCAGAGCAAAG-GCAGAAACTTGGTTGGTGCGATGACA-GAAAGAAGC
1 TTTATGAACATTAAAGAGCAGAGC-AAGCGCAGAAATTTGGACGGTGCGATGA-ATGAAAGAAGC
* * * * * * * *
886334 CCTCAGGAGTGTGAGGAGAATGCGATGACTGAAAGTATCCCTCAGGAGACTAAGGAAAACTGTGA
64 CCTCAGGA--GTAAGAAGGATGCAATGACTGAAAGAAGCCCTCGGGAGACTAAGGAAAACTGCGA
*
886399 TCTT
127 TCGT
* * * * **
886403 TTTATGAACATTAAAGCGCAGAGCAAGCACAGGAATTTGGACAGTGATATGAATGAAAGAAGCCC
1 TTTATGAACATTAAAGAGCAGAGCAAGCGCAGAAATTTGGACGGTGCGATGAATGAAAGAAGCCC
*
886468 TCGGGAGACTAAGAAGGATGCAATGA-TCGAAAGAAGCCCTCGGGAGACTAAG
66 TCAGGAG--TAAGAAGGATGCAATGACT-GAAAGAAGCCCTCGGGAGACTAAG
886520 AAGGATGCAA
Statistics
Matches: 198, Mismatches: 40, Indels: 22
0.76 0.15 0.08
Matches are distributed among these distances:
130 1 0.01
131 5 0.03
132 160 0.81
133 2 0.01
134 1 0.01
135 29 0.15
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (130 bp):
TTTATGAACATTAAAGAGCAGAGCAAGCGCAGAAATTTGGACGGTGCGATGAATGAAAGAAGCCC
TCAGGAGTAAGAAGGATGCAATGACTGAAAGAAGCCCTCGGGAGACTAAGGAAAACTGCGATCGT
Found at i:886584 original size:39 final size:39
Alignment explanation
Indices: 886541--886619 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
886531 GATCGAAAGA
886541 AACCCTCAGGAGACTAAAAAGGAAAATTGCAATCTTTCT
1 AACCCTCAGGAGACTAAAAAGGAAAATTGCAATCTTTCT
886580 AACCCTCAGGAGACTAAAAAGGAAAATTGCAATCTTTCT
1 AACCCTCAGGAGACTAAAAAGGAAAATTGCAATCTTTCT
886619 A
1 A
886620 TGAATATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (39 bp):
AACCCTCAGGAGACTAAAAAGGAAAATTGCAATCTTTCT
Found at i:886852 original size:96 final size:96
Alignment explanation
Indices: 886634--886855 Score: 252
Period size: 96 Copynumber: 2.3 Consensus size: 96
886624 TATTAAAGCG
* * *
886634 AATTTGGACAGTGCTATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGCGATCTTTT
1 AATTTGGACAGTGCAATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGAAAAACTGCGATCTTTC
*
886699 TATGAACACTAAAGCACGGAGCAAACATAGA
66 TATAAACACTAAAGCACGGAGCAAACATAGA
* * * ** * ** *
886730 AATCTGGACAGTGCGATAACCAAAAGAAGTCCTTGGGAGACTAAGAAGAAAAACTGTGATCTTTC
1 AATTTGGACAGTGCAATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGAAAAACTGCGATCTTTC
* *
886795 TATAAACATTAAAGGGA-GGAGCAAAGGCA-A-A
66 TATAAACACTAAA-GCACGGAGCAAA--CATAGA
*
886826 AATTTGGACAGTGCAATGGCTGAAAGAAGC
1 AATTTGGACAGTGCAATGACTGAAAGAAGC
886856 GGCAATGATA
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
96 97 0.95
97 3 0.03
98 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (96 bp):
AATTTGGACAGTGCAATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGAAAAACTGCGATCTTTC
TATAAACACTAAAGCACGGAGCAAACATAGA
Found at i:900239 original size:26 final size:26
Alignment explanation
Indices: 900190--900239 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
900180 ATTAATACGA
*
900190 TTTGTATTTGATATACCTTTAAAAGT
1 TTTGTATTTGATATACCTTCAAAAGT
900216 TTTGTATTTGATATA-CTTCCAAAA
1 TTTGTATTTGATATACCTT-CAAAA
900240 TCATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (26 bp):
TTTGTATTTGATATACCTTCAAAAGT
Found at i:901367 original size:33 final size:30
Alignment explanation
Indices: 901292--901367 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
901282 TTTGAGGTTC
*
901292 TAATTAAAATTTTTAAAAATGTTAGGAGAT
1 TAATTAAATTTTTTAAAAATGTTAGGAGAT
* * *
901322 TAATGATAATTTTTTTAAAATTTTAGGAGAACT
1 TAATTA-AATTTTTTAAAAATGTTAGGAG-A-T
901355 TAATTAACATTTT
1 TAATTAA-ATTTT
901368 CGAAAAACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 5 0.14
31 19 0.51
32 2 0.05
33 11 0.30
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (30 bp):
TAATTAAATTTTTTAAAAATGTTAGGAGAT
Found at i:907028 original size:16 final size:16
Alignment explanation
Indices: 907007--907037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
906997 TATATTTTTA
907007 TTTTTTAAATTTTAAT
1 TTTTTTAAATTTTAAT
*
907023 TTTTTTAGATTTTAA
1 TTTTTTAAATTTTAA
907038 ATTTCAAATC
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTTAAATTTTAAT
Found at i:921049 original size:19 final size:18
Alignment explanation
Indices: 921022--921057 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
921012 TGTGTGTTAT
*
921022 AAATTACATAATATAAAAA
1 AAATAACATAATA-AAAAA
921041 AAATAACATAATAAAAA
1 AAATAACATAATAAAAA
921058 GTATTGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAACATAATAAAAAA
Found at i:922815 original size:45 final size:45
Alignment explanation
Indices: 922751--922838 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
922741 GAATCATTAG
* *
922751 CTTAAATATCGGGTTTGCTGAGTCGGACCGCACCGGGTCTAGGAA
1 CTTAAATATCGGGTTTGCTGAGTCGGACCCCACCGGATCTAGGAA
*
922796 CTTAAATATCGGGTTTGCTGAGTCGGACCCCATCGGATCTAGG
1 CTTAAATATCGGGTTTGCTGAGTCGGACCCCACCGGATCTAGG
922839 GATTTGACAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.26
Consensus pattern (45 bp):
CTTAAATATCGGGTTTGCTGAGTCGGACCCCACCGGATCTAGGAA
Found at i:936674 original size:51 final size:51
Alignment explanation
Indices: 936568--936679 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
936558 TACCCTTAAA
* * * *
936568 ATTTACACATTTTGTCAATTTTGTCCCGATTTAACAAATTTAGCTTGTAAC
1 ATTTACACATTTGGTCAATTTTGTCCCGATTTAACAAATTTAACCTGCAAC
* *
936619 ATTTACACATTTGGTCAATTTTAGT-CTGATTTAACAAATTTAACACT-CAAT
1 ATTTACACATTTGGTCAATTTT-GTCCCGATTTAACAAATTTAAC-CTGCAAC
*
936670 ATTTATACAT
1 ATTTACACAT
936680 ATCATGTCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 49 0.94
52 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (51 bp):
ATTTACACATTTGGTCAATTTTGTCCCGATTTAACAAATTTAACCTGCAAC
Found at i:938632 original size:19 final size:18
Alignment explanation
Indices: 938606--938648 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
938596 TTTAATAGAC
938606 AATAAAAACTTCACCGAAA
1 AATAAAAACTTCACC-AAA
* *
938625 ACTAAAAATTTCACCAAA
1 AATAAAAACTTCACCAAA
938643 AATAAA
1 AATAAA
938649 TTTTTGGCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAAAACTTCACCAAA
Found at i:941976 original size:17 final size:16
Alignment explanation
Indices: 941953--941996 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
941943 CTGTTTTATT
941953 TTTGAAATATTAATTA
1 TTTGAAATATTAATTA
941969 TATTGAAA-ATT-ATTA
1 T-TTGAAATATTAATTA
941984 TTT-AAATA-TAATT
1 TTTGAAATATTAATT
941997 TTATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.16
14 6 0.24
15 5 0.20
16 4 0.16
17 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTGAAATATTAATTA
Found at i:951914 original size:5 final size:5
Alignment explanation
Indices: 951906--951935 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
951896 AATTAAATTG
951906 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
951936 GAAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:952356 original size:59 final size:60
Alignment explanation
Indices: 952276--952395 Score: 224
Period size: 59 Copynumber: 2.0 Consensus size: 60
952266 CTTGTAATTT
952276 TGATGTTTCTGGAGTCCTAGAATTTAAGTTGAAATTTTGAAAATTAGTAGATTTTTTAGTA
1 TGATGTTTCT-GAGTCCTAGAATTTAAGTTGAAATTTTGAAAATTAGTAGATTTTTTAGTA
952337 TGATGTTTCT-AGTCCTAGAATTTAAGTTGAAATTTTGAAAATTAGTAGATTTTTTAGTA
1 TGATGTTTCTGAGTCCTAGAATTTAAGTTGAAATTTTGAAAATTAGTAGATTTTTTAGTA
952396 GGGTTCATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 49 0.83
61 10 0.17
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (60 bp):
TGATGTTTCTGAGTCCTAGAATTTAAGTTGAAATTTTGAAAATTAGTAGATTTTTTAGTA
Found at i:956298 original size:38 final size:38
Alignment explanation
Indices: 956176--956308 Score: 110
Period size: 38 Copynumber: 3.4 Consensus size: 38
956166 GACCTCGAGT
* * *
956176 CGATGAGACATTGGGTGTCACTATTTTACTTCGAA-TAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGAACT--ATC
* * * *
956217 CGATGAGATACTGGGTATC-ACTTTACTTCG-GCTAGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGAACTA-TC
* *
956254 CAATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGAACTATC
*
956292 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
956309 CCAATTTGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.01
37 16 0.22
38 37 0.51
39 3 0.04
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGAACTATC
Found at i:959778 original size:24 final size:24
Alignment explanation
Indices: 959745--959797 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
959735 AAAGTTCATC
959745 ATTAA-ACAATTGGAAATTTGATA
1 ATTAAGACAATTGGAAATTTGATA
959768 ATTAAGACAATTGGAAATTTGATA
1 ATTAAGACAATTGGAAATTTGATA
959792 ATTAAG
1 ATTAAG
959798 TGCCTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (24 bp):
ATTAAGACAATTGGAAATTTGATA
Found at i:962191 original size:2 final size:2
Alignment explanation
Indices: 962184--962213 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
962174 NNNNNNNNAA
962184 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
962214 GAAAATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:968623 original size:11 final size:11
Alignment explanation
Indices: 968607--968631 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
968597 GCGAGGATTC
968607 CATTCCTGTGT
1 CATTCCTGTGT
968618 CATTCCTGTGT
1 CATTCCTGTGT
968629 CAT
1 CAT
968632 CATCAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.44
Consensus pattern (11 bp):
CATTCCTGTGT
Found at i:972481 original size:51 final size:51
Alignment explanation
Indices: 972386--972647 Score: 396
Period size: 51 Copynumber: 5.3 Consensus size: 51
972376 ACTTCTAATC
972386 AGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
* *
972436 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTCATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
*
972487 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
* *
972538 AGTGACAAGTGATAAGTGATAGCCTTAGCTACACTTATCTGATC---G---
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
* * *
972583 -GTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
972633 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
972648 ATGTGATCCG
Statistics
Matches: 192, Mismatches: 12, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
44 39 0.20
47 1 0.01
48 1 0.01
50 21 0.11
51 130 0.68
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
Found at i:973160 original size:41 final size:41
Alignment explanation
Indices: 973102--973185 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
973092 AGTATGTATC
*
973102 GGGTCTCGTAGGCCCTATTTATTATGATTATAATATTTTGA
1 GGGTCTCGTAGGCCCTATTTATTATGAATATAATATTTTGA
* *
973143 GGGTCTTGTAGGTCCTATTTATTATGAATATAATATTTTGA
1 GGGTCTCGTAGGCCCTATTTATTATGAATATAATATTTTGA
973184 GG
1 GG
973186 ATATATTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (41 bp):
GGGTCTCGTAGGCCCTATTTATTATGAATATAATATTTTGA
Found at i:973570 original size:31 final size:31
Alignment explanation
Indices: 973513--973574 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
973503 CAAAAAAAAG
973513 TTCAAACCCCAATATGAAAAAAAATTATCTAA
1 TTCAAACCCCAATATGAAAAAAAATTA-CTAA
* *
973545 TTCAATCCCCAATAT-AAAAACAATTACTAA
1 TTCAAACCCCAATATGAAAAAAAATTACTAA
973575 ATTTAGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 10 0.36
32 14 0.50
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.26
Consensus pattern (31 bp):
TTCAAACCCCAATATGAAAAAAAATTACTAA
Found at i:979580 original size:20 final size:19
Alignment explanation
Indices: 979555--979603 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
979545 ATCTCTTTCT
979555 ATCAAAAAATTACAAAAAAA
1 ATCAAAAAATT-CAAAAAAA
* * *
979575 ATCAAAATATTTATAAAAA
1 ATCAAAAAATTCAAAAAAA
*
979594 TTCAAAAAAT
1 ATCAAAAAAT
979604 CTAGAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (19 bp):
ATCAAAAAATTCAAAAAAA
Found at i:984425 original size:14 final size:14
Alignment explanation
Indices: 984406--984460 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
984396 TTGAAAGATA
984406 AAATATTAATATAT
1 AAATATTAATATAT
*
984420 AAATATTAATTTACT
1 AAATATTAATATA-T
* *
984435 TATTGATTTAATATAT
1 AAAT-A-TTAATATAT
984451 AAATATTAAT
1 AAATATTAAT
984461 TTATTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 17 0.53
15 4 0.12
16 4 0.12
17 7 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATATTAATATAT
Found at i:984449 original size:31 final size:31
Alignment explanation
Indices: 984411--984469 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
984401 AGATAAAATA
984411 TTAATATATAAATATTAATTTACTTATTGAT
1 TTAATATATAAATATTAATTTACTTATTGAT
*
984442 TTAATATATAAATATTAATTTATTTATT
1 TTAATATATAAATATTAATTTACTTATT
984470 TNNNNNNNNN
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (31 bp):
TTAATATATAAATATTAATTTACTTATTGAT
Found at i:990957 original size:48 final size:48
Alignment explanation
Indices: 990899--990992 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
990889 TCTCTTAATG
* *
990899 TACTCACAGTGCCATTTTCCGAGCCTATTTCTTTCTTCTCCAACCCAA
1 TACTCACAGTGCCATTTTCCGAACCTATCTCTTTCTTCTCCAACCCAA
* *
990947 TACTCGCAGTGCCATTTTCCGAACTTATCTCTTTCTTCTCCAACCC
1 TACTCACAGTGCCATTTTCCGAACCTATCTCTTTCTTCTCCAACCC
990993 GACAACATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.36, G:0.09, T:0.36
Consensus pattern (48 bp):
TACTCACAGTGCCATTTTCCGAACCTATCTCTTTCTTCTCCAACCCAA
Found at i:994483 original size:14 final size:16
Alignment explanation
Indices: 994452--994483 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
994442 GTGACCAAAT
994452 TTATAGAAAATGTAAA
1 TTATAGAAAATGTAAA
994468 TTAT-GAAAAT-TAAA
1 TTATAGAAAATGTAAA
994482 TT
1 TT
994484 TATTGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
TTATAGAAAATGTAAA
Found at i:994486 original size:15 final size:17
Alignment explanation
Indices: 994448--994486 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
994438 AATCGTGACC
994448 AAATTTATAGAAAATGT
1 AAATTTATAGAAAATGT
994465 AAA-TTAT-GAAAAT-T
1 AAATTTATAGAAAATGT
994479 AAATTTAT
1 AAATTTAT
994487 TGTTATACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 4 0.19
17 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAATTTATAGAAAATGT
Found at i:1012685 original size:19 final size:18
Alignment explanation
Indices: 1012661--1012709 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
1012651 AATCATAAAA
*
1012661 AATTATAAAATGGTCATTT
1 AATTATAAAAT-GTCATAT
1012680 AATTATTAATAATGTCATAT
1 AATTA-TAA-AATGTCATAT
1012700 AATTATAAAA
1 AATTATAAAA
1012710 AATTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 14 0.52
21 3 0.11
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
AATTATAAAATGTCATAT
Found at i:1012726 original size:11 final size:11
Alignment explanation
Indices: 1012698--1012726 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1012688 ATAATGTCAT
1012698 ATAATTATAAA
1 ATAATTATAAA
1012709 A-AATTATAAA
1 ATAATTATAAA
1012719 ATAATTAT
1 ATAATTAT
1012727 TTAACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATTATAAA
Found at i:1012862 original size:106 final size:107
Alignment explanation
Indices: 1012741--1012959 Score: 424
Period size: 106 Copynumber: 2.1 Consensus size: 107
1012731 CTATTTAAAT
1012741 TTATTTTTTATCACTATTTGACTAACGTAGAAGTCAAAATGAAAAGACCTAAAAATCTAATATAA
1 TTATTTTTTATCACTATTTGACTAACGTAGAAGTCAAAATGAAAAGACCTAAAAATCTAATATAA
1012806 TTGGAAAATCAAAAAAATTTAAATTAAATAGTTAAGTGACCA
66 TTGGAAAATCAAAAAAATTTAAATTAAATAGTTAAGTGACCA
1012848 TTATTTTTTA-CACTATTTGACTAACGTAGAAGTCAAAATGAAAAGACCTAAAAATCTAATATAA
1 TTATTTTTTATCACTATTTGACTAACGTAGAAGTCAAAATGAAAAGACCTAAAAATCTAATATAA
1012912 TTGGAAAATCAAAAAAATTTAAATTAAATAGTTAAGTGACCA
66 TTGGAAAATCAAAAAAATTTAAATTAAATAGTTAAGTGACCA
1012954 TT-TTTT
1 TTATTTT
1012960 AACTTTTCAT
Statistics
Matches: 112, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 4 0.04
106 98 0.88
107 10 0.09
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (107 bp):
TTATTTTTTATCACTATTTGACTAACGTAGAAGTCAAAATGAAAAGACCTAAAAATCTAATATAA
TTGGAAAATCAAAAAAATTTAAATTAAATAGTTAAGTGACCA
Found at i:1020877 original size:42 final size:42
Alignment explanation
Indices: 1020830--1020915 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
1020820 GAATTTCGAC
1020830 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1020872 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1 TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
1020914 TT
1 TT
1020916 ATGGTGAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (42 bp):
TTCATTTTGTCTTTCATTTCATCTCCGACTTTACAATCAGAT
Found at i:1023886 original size:31 final size:31
Alignment explanation
Indices: 1023851--1023916 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1023841 AACAATCTAG
* *
1023851 TGACTTAAATAAAAACTTTCGAATAGTTCAA
1 TGACTTAAATAAAAAATTTCGAATAATTCAA
*
1023882 TGACTTAAATAAAAAATTTTGAATAATTCAA
1 TGACTTAAATAAAAAATTTCGAATAATTCAA
1023913 TGAC
1 TGAC
1023917 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTCGAATAATTCAA
Found at i:1042386 original size:13 final size:13
Alignment explanation
Indices: 1042368--1042413 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1042358 AAATTTTAAT
1042368 TAAATTGATGTCA
1 TAAATTGATGTCA
1042381 TAAATTGATGTC-
1 TAAATTGATGTCA
*
1042393 -AAA-TAATTGTCA
1 TAAATTGA-TGTCA
1042405 TAAATTGAT
1 TAAATTGAT
1042414 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 2 0.07
11 7 0.26
13 16 0.59
14 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (13 bp):
TAAATTGATGTCA
Found at i:1047240 original size:27 final size:27
Alignment explanation
Indices: 1047205--1047256 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1047195 TCATGTATGC
* *
1047205 ATATGAACCGCAATTTAAGTTTCATTT
1 ATATAAACCACAATTTAAGTTTCATTT
1047232 ATATAAACCACAATTTAAGTTTCAT
1 ATATAAACCACAATTTAAGTTTCAT
1047257 GTGTATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (27 bp):
ATATAAACCACAATTTAAGTTTCATTT
Found at i:1047263 original size:27 final size:27
Alignment explanation
Indices: 1047205--1047264 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1047195 TCATGTATGC
* * *
1047205 ATATGAACCGCAATTTAAGTTTCATTT
1 ATATAAACCACAATTTAAGTTTCATGT
1047232 ATATAAACCACAATTTAAGTTTCATGT
1 ATATAAACCACAATTTAAGTTTCATGT
*
1047259 GTATAA
1 ATATAA
1047265 TCGTACCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (27 bp):
ATATAAACCACAATTTAAGTTTCATGT
Found at i:1048364 original size:61 final size:61
Alignment explanation
Indices: 1048260--1048450 Score: 244
Period size: 60 Copynumber: 3.1 Consensus size: 61
1048250 ATAAATATAG
* * * * *
1048260 GTACTAAATTGAACCTAAAAAGAAGCTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAG
1 GTACCAAATTGAGCC-AAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
* * *
1048322 GTACCAAATTG-GGCACAAAAAAAGTTTAGGTATCAAATTAG-AAAAATGTGTCAAGTTCAA
1 GTACCAAATTGAGCCA-AAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
* *
1048382 GTACCAAATTGAGCCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAA-ATGTCAAATTTAA
1 GTACCAAATTGAGCCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
*
1048442 GTATCAAAT
1 GTACCAAAT
1048451 ATTATATTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
60 71 0.63
61 31 0.28
62 10 0.09
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (61 bp):
GTACCAAATTGAGCCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATATGTCAAGTTCAA
Found at i:1051664 original size:17 final size:17
Alignment explanation
Indices: 1051638--1051682 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1051628 CGAAATTTTA
*
1051638 AAATTAAAATTGATTAT
1 AAATTAAAATTAATTAT
*
1051655 AAATTTAAATTAATTATT
1 AAATTAAAATTAATTA-T
*
1051673 TAATTAAAAT
1 AAATTAAAAT
1051683 ATTCTACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATTAAAATTAATTAT
Found at i:1059228 original size:79 final size:79
Alignment explanation
Indices: 1059145--1059290 Score: 238
Period size: 79 Copynumber: 1.8 Consensus size: 79
1059135 CCGGGCCGGG
* * **
1059145 CCTGGGCAAAATTTCAGGCCCATATTTCGGGTCGGGCTGGGCCCGGGCCTAAGAGTCGGGCCAAA
1 CCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGAGCCAGGCCCGGGCCTAAGAGTCGGGCCAAA
1059210 AAAAATTGGCCAAA
66 AAAAATTGGCCAAA
* *
1059224 CCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGAGCCAGGCCCGGGCCTAAGAGTTGGGCCGAA
1 CCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGAGCCAGGCCCGGGCCTAAGAGTCGGGCCAAA
1059289 AA
66 AA
1059291 TTTTTTCTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (79 bp):
CCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGAGCCAGGCCCGGGCCTAAGAGTCGGGCCAAA
AAAAATTGGCCAAA
Found at i:1064769 original size:31 final size:31
Alignment explanation
Indices: 1064714--1064776 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1064704 GACAAAAAAA
* *
1064714 AATTCAAGCCCCATTGTGAAAACAATTGCCT
1 AATTCAAGCCCCATTATGAAAACAATTACCT
* **
1064745 AATTCAAGCCCTATTATGGGAACAATTACCT
1 AATTCAAGCCCCATTATGAAAACAATTACCT
1064776 A
1 A
1064777 GTTTGGGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (31 bp):
AATTCAAGCCCCATTATGAAAACAATTACCT
Found at i:1064769 original size:90 final size:90
Alignment explanation
Indices: 1064655--1064824 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 90
1064645 AAAACCCTAA
* *
1064655 AATTCAAACCCTAGTATGAGAACAATT-CTCAAGTTCAATGACTAGCTTGGACAAAAAAAAATTC
1 AATTCAAACCCTAGTATGAGAACAATTAC-CAAGTTCAAGGACTACCTTGGAC-AAAAAAAATTC
*
1064719 AAGCCCCATTGT-GAAAACAATTGCCT
64 AAGCCCCAATGTAGAAAACAATTGCCT
* * * * ***
1064745 AATTCAAGCCCTATTATGGGAACAATTACCTAGTTTGGGGACTACCTTGGACAAAAAAAATTCAA
1 AATTCAAACCCTAGTATGAGAACAATTACCAAGTTCAAGGACTACCTTGGACAAAAAAAATTCAA
1064810 GCCCCAATGTAGAAA
66 GCCCCAATGTAGAAA
1064825 TTGTTACCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 22 0.32
90 45 0.66
91 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (90 bp):
AATTCAAACCCTAGTATGAGAACAATTACCAAGTTCAAGGACTACCTTGGACAAAAAAAATTCAA
GCCCCAATGTAGAAAACAATTGCCT
Done.