Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008286.1 Hibiscus syriacus cultivar Beakdansim tig00110949_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 504059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:10826 original size:29 final size:32
Alignment explanation
Indices: 10758--10833 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 32
10748 CTTTTTAATA
**
10758 TTATAATTTTAGTC-CCTAAACTTTTACAAAGT
1 TTAT-ATTTTAGTCACCTAAACTTTTACAAAAC
10790 TTATATTTTAGTCACC-AAAC-TTT-CAAAAC
1 TTATATTTTAGTCACCTAAACTTTTACAAAAC
*
10819 TTATATTTTAATCAC
1 TTATATTTTAGTCAC
10834 TAACCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 18 0.45
30 3 0.08
31 13 0.32
32 6 0.15
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (32 bp):
TTATATTTTAGTCACCTAAACTTTTACAAAAC
Found at i:11351 original size:27 final size:26
Alignment explanation
Indices: 11308--11369 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
11298 TTCGTGCAAA
11308 TAATTTAAAGTTTTAATTCATTTGTTAT-T
1 TAATTTAAA--TTTAATT-A-TTGTTATCT
*
11337 TATTTTAAATTTAATTATTGTTATCT
1 TAATTTAAATTTAATTATTGTTATCT
11363 TAATTTA
1 TAATTTA
11370 TATCCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.23
26 8 0.27
27 7 0.23
29 8 0.27
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (26 bp):
TAATTTAAATTTAATTATTGTTATCT
Found at i:14621 original size:20 final size:20
Alignment explanation
Indices: 14598--14696 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 20
14588 CTTAATCTCT
*
14598 GGTATGGATACTAGTCCTTC
1 GGTATGGAGACTAGTCCTTC
* * *
14618 GGTATGGAGACCAATTCTTC
1 GGTATGGAGACTAGTCCTTC
14638 GGTATGGAGACTAGTCCTTC
1 GGTATGGAGACTAGTCCTTC
* **
14658 AGTATAAAGACTAGTCCTTC
1 GGTATGGAGACTAGTCCTTC
**
14678 AATA-GGAAGACTAGTCCTT
1 GGTATGG-AGACTAGTCCTT
14697 AAGTATAAAG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (20 bp):
GGTATGGAGACTAGTCCTTC
Found at i:14707 original size:20 final size:20
Alignment explanation
Indices: 14645--14710 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
14635 TTCGGTATGG
*
14645 AGACTAGTCCTTCAGTATAA
1 AGACTAGTCCTTAAGTATAA
**
14665 AGACTAGTCCTTCAA-TAGGA
1 AGACTAGTCCTT-AAGTATAA
14685 AGACTAGTCCTTAAGTATAA
1 AGACTAGTCCTTAAGTATAA
14705 AGACTA
1 AGACTA
14711 ATCGCTCTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (20 bp):
AGACTAGTCCTTAAGTATAA
Found at i:14781 original size:19 final size:20
Alignment explanation
Indices: 14738--14781 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
14728 GCAGCCAACC
*
14738 TCGATACCAAGCATCCAATA
1 TCGATACCAAACATCCAATA
* *
14758 CCGATACCAAACCT-CAATA
1 TCGATACCAAACATCCAATA
14777 TCGAT
1 TCGAT
14782 TCTAAGGGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.20
Consensus pattern (20 bp):
TCGATACCAAACATCCAATA
Found at i:18126 original size:2 final size:2
Alignment explanation
Indices: 18121--18154 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
18111 ACCGTAAAAA
18121 AT AT 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 AT AT A
18155 AAGTTTATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18414 original size:18 final size:18
Alignment explanation
Indices: 18391--18442 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
18381 CATTTTTGTA
18391 TCAGTACTATGTGTACTT
1 TCAGTACTATGTGTACTT
18409 TCAGTACTATGTGTACTT
1 TCAGTACTATGTGTACTT
*
18427 TCAGCACTATGTGTAC
1 TCAGTACTATGTGTAC
18443 ACCCATGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (18 bp):
TCAGTACTATGTGTACTT
Found at i:26954 original size:29 final size:29
Alignment explanation
Indices: 26912--26996 Score: 129
Period size: 29 Copynumber: 2.9 Consensus size: 29
26902 GTGATGGCCA
26912 TAGGACGCCATGCAATCCAGACGATC-TTG
1 TAGGACGCCATGCAATCCAGACGA-CATTG
*
26941 TAGGACGCCATGCAATCCAGGCGACATTG
1 TAGGACGCCATGCAATCCAGACGACATTG
26970 TAGGACGCCATGCAATCCATG-CGACAT
1 TAGGACGCCATGCAATCCA-GACGACAT
26997 ACGGGGTGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
28 1 0.02
29 51 0.96
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (29 bp):
TAGGACGCCATGCAATCCAGACGACATTG
Found at i:27032 original size:20 final size:20
Alignment explanation
Indices: 27007--27045 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
26997 ACGGGGTGAC
27007 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
27027 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
27046 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:27039 original size:9 final size:9
Alignment explanation
Indices: 27006--27045 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
26996 TACGGGGTGA
27006 CATACGAGC
1 CATACGAGC
*
27015 CATACAAGC
1 CATACGAGC
27024 CATATACGAGC
1 C--ATACGAGC
27035 CATACGAGC
1 CATACGAGC
27044 CA
1 CA
27046 ATGGAGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (9 bp):
CATACGAGC
Found at i:27172 original size:29 final size:29
Alignment explanation
Indices: 27125--27200 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
27115 GCCAATGGAG
* * **
27125 AGGTCGCCATGCAGCCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCAAGT
27154 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCAAGT
27183 AGGTCGCCATGTAGTCCC
1 AGGTCGCCATGTAGTCCC
27201 ATGTAGTCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.17, C:0.34, G:0.30, T:0.18
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCAAGT
Found at i:27561 original size:25 final size:26
Alignment explanation
Indices: 27511--27561 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
27501 CTTGGTCGCC
**
27511 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
27537 GAGATTGCAGCCG-AGAAAGAAAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
27562 AGGGAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.08
Consensus pattern (26 bp):
GAGATTGCAGCCGAAGAAAGAAAGAA
Found at i:27596 original size:14 final size:13
Alignment explanation
Indices: 27556--27599 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
27546 GCCGAGAAAG
27556 AAAGAAAGGGAGA
1 AAAGAAAGGGAGA
**
27569 AAAGAAAGTAAGA
1 AAAGAAAGGGAGA
27582 AGAAGAAAGGGAGA
1 A-AAGAAAGGGAGA
27596 AAAG
1 AAAG
27600 GTAAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (13 bp):
AAAGAAAGGGAGA
Found at i:27848 original size:45 final size:44
Alignment explanation
Indices: 27745--27874 Score: 128
Period size: 45 Copynumber: 3.0 Consensus size: 44
27735 TACATAAATT
*
27745 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTATATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTATATAGTAA
*
27787 AAAAATCA-TTAATTAGTTTGTTTTGTTAATAGTTAGTTATA-TAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTA--TATAGTAA
* *
27831 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAATAGT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTTATATAGT
27875 TAAGTTATAT
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 9 0.12
42 7 0.10
43 7 0.10
44 9 0.12
45 20 0.27
46 6 0.08
47 8 0.11
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (44 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTATATAGTAA
Found at i:28079 original size:16 final size:16
Alignment explanation
Indices: 28047--28093 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
28037 TTTAAAAAGT
*
28047 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
28063 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
28079 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
28094 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:28088 original size:15 final size:14
Alignment explanation
Indices: 28068--28098 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
28058 GTTTATTAGT
28068 TTATTATATTATAAG
1 TTATTATATTA-AAG
28083 TTATTATATTAAAG
1 TTATTATATTAAAG
28097 TT
1 TT
28099 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:30267 original size:17 final size:17
Alignment explanation
Indices: 30245--30277 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30235 CAATGATTTT
*
30245 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
30262 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
30278 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:30294 original size:24 final size:22
Alignment explanation
Indices: 30262--30330 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
30252 AAATCATTAC
30262 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
30284 TAGTAAATCAATTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
30309 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
30331 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:30550 original size:35 final size:37
Alignment explanation
Indices: 30469--30555 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
30459 TTAGTATTCT
* * *
30469 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
30507 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
30542 ATAATTATTATAAA
1 ATAATTATTATAAA
30556 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:30576 original size:12 final size:13
Alignment explanation
Indices: 30485--30715 Score: 126
Period size: 14 Copynumber: 17.3 Consensus size: 13
30475 ATTAGTAATA
30485 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
30499 AGTATTAAATCATT
1 ATTA-TAAATCATT
30513 ATTATAAAT-A--
1 ATTATAAATCATT
30523 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
30534 ATAACTAAATAATT
1 ATTA-TAAATCATT
30548 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
30562 ATTAT-AATGATT
1 ATTATAAATCATT
30574 ATTATCAAATCATT
1 ATTAT-AAATCATT
30588 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
30607 AAATATTTAAATCATT
1 --AT-TATAAATCATT
30623 A-T-TAAATCATT
1 ATTATAAATCATT
* *
30634 TTTAT-AATGATT
1 ATTATAAATCATT
30646 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
30660 ATTAT-AATGATT
1 ATTATAAATCATT
30672 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
30686 ACTAT-AATGATT
1 ATTATAAATCATT
30698 ATTATCAAATCATT
1 ATTAT-AAATCATT
30712 ATTA
1 ATTA
30716 AATCATCAAA
Statistics
Matches: 177, Mismatches: 18, Indels: 44
0.74 0.08 0.18
Matches are distributed among these distances:
10 4 0.02
11 24 0.14
12 45 0.25
13 9 0.05
14 69 0.39
15 1 0.01
16 8 0.05
17 1 0.01
18 3 0.02
19 11 0.06
20 1 0.01
21 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:30583 original size:26 final size:26
Alignment explanation
Indices: 30485--30715 Score: 180
Period size: 26 Copynumber: 9.3 Consensus size: 26
30475 ATTAGTAATA
* * *
30485 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
30510 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
30534 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
30559 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
30585 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
30608 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
30631 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
30657 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
30683 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
30709 ATTATTA
1 ATTATTA
30716 AATCATCAAA
Statistics
Matches: 160, Mismatches: 32, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.03
22 2 0.01
23 16 0.10
24 20 0.12
25 28 0.17
26 89 0.56
27 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:30709 original size:124 final size:123
Alignment explanation
Indices: 30501--30770 Score: 427
Period size: 124 Copynumber: 2.2 Consensus size: 123
30491 AAATCATTAG
* * *
30501 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
30564 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* * * * *
30622 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
*
30687 CTATAATGATTATTATCAAATCATTATTAAATCATCAAATCATTAAATATTTAAATCAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
30746 TATTAAATTATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
30771 ATAAATACAT
Statistics
Matches: 136, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 101 0.74
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (123 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:30713 original size:37 final size:37
Alignment explanation
Indices: 30646--30721 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
30636 TATAATGATT
* *
30646 ATTACTAAATCATTATTATAATGATTATTATCAAATC
1 ATTACTAAATCATTATTATAATAATCATTATCAAATC
* * *
30683 ATTACTATAATGATTATTATCA-AATCATTATTAAATC
1 ATTACTA-AATCATTATTATAATAATCATTATCAAATC
30720 AT
1 AT
30722 CAAATCATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (37 bp):
ATTACTAAATCATTATTATAATAATCATTATCAAATC
Found at i:30753 original size:11 final size:11
Alignment explanation
Indices: 30485--30721 Score: 75
Period size: 11 Copynumber: 19.2 Consensus size: 11
30475 ATTAGTAATA
30485 ATTATTAAATC
1 ATTATTAAATC
30496 ATTAGTATTAAATC
1 A-T--TATTAAATC
*
30510 ATTATTATAAATA
1 ATTA-T-TAAATC
* *
30523 ATTACTAAATA
1 ATTATTAAATC
* * *
30534 ATAACTAAATA
1 ATTATTAAATC
30545 ATTATTATAAAATC
1 ATTA-T-T-AAATC
*
30559 ATTATTATAATG
1 ATTATTA-AATC
30571 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
30585 ATTACTAAATC
1 ATTATTAAATC
30596 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
30611 A-T-TTAAATC
1 ATTATTAAATC
30620 ATTATTAAATC
1 ATTATTAAATC
* *
30631 ATTTTTATAATG
1 ATTATTA-AATC
30643 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
30657 ATTATTATAATG
1 ATTATTA-AATC
30669 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
30683 ATTACTATAATGATT
1 ATTA-T-TAA--ATC
*
30698 ATTATCAAATC
1 ATTATTAAATC
30709 ATTATTAAATC
1 ATTATTAAATC
30720 AT
1 AT
30722 CAAATCATTA
Statistics
Matches: 175, Mismatches: 21, Indels: 60
0.68 0.08 0.23
Matches are distributed among these distances:
8 6 0.03
9 1 0.01
10 2 0.01
11 59 0.34
12 24 0.14
13 20 0.11
14 45 0.26
15 12 0.07
16 6 0.03
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:33653 original size:26 final size:24
Alignment explanation
Indices: 33595--33653 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
33585 CTAATAAACC
*
33595 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
33619 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
33647 TAATAAT
1 TAATAAT
33654 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:34443 original size:42 final size:47
Alignment explanation
Indices: 34387--34499 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 47
34377 GTTTAAAGAC
*
34387 ACTAAAAAATTAATTAATATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAAAAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
*
34429 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAAAAAACTAATTAA-T-ATTTTTTATATAATAT-ATATATAACTTAA
*
34479 ACTAATAAACTAATATAATAT
1 ACTAAAAAACTAAT-TAATAT
34500 AACTTAAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
42 15 0.25
43 1 0.02
44 7 0.12
45 3 0.05
46 2 0.03
47 1 0.02
49 4 0.07
50 23 0.39
51 3 0.05
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (47 bp):
ACTAAAAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
Found at i:34499 original size:28 final size:30
Alignment explanation
Indices: 34459--34521 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
34449 ATTTTTTATA
*
34459 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
34489 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
34517 TAATA
1 TAATA
34522 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:34528 original size:28 final size:28
Alignment explanation
Indices: 34463--34528 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
34453 TTTATATAAT
*
34463 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
34491 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
34519 ATAATTTATA
1 ATAATATATA
34529 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:34531 original size:21 final size:21
Alignment explanation
Indices: 34498--34546 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34488 CTAATATAAT
34498 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
34519 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
34540 ATTAACT
1 A-TAACT
34547 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:35119 original size:20 final size:20
Alignment explanation
Indices: 35094--35166 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
35084 CCAAGCACAG
35094 CATGCATCCCACAACTCCCC
1 CATGCATCCCACAACTCCCC
**
35114 CATGCATTCCCACGTC-CCATGCAC
1 CATGCA-TCCCACAACTCC---C-C
35138 AGCATGCATCCCACAACTCCCC
1 --CATGCATCCCACAACTCCCC
35160 CATGCAT
1 CATGCAT
35167 GCTCCAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 15 0.37
21 7 0.17
22 1 0.02
23 2 0.05
24 1 0.02
25 7 0.17
26 8 0.20
ACGTcount: A:0.25, C:0.48, G:0.10, T:0.18
Consensus pattern (20 bp):
CATGCATCCCACAACTCCCC
Found at i:35138 original size:46 final size:46
Alignment explanation
Indices: 35074--35166 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
35064 CCATGCACAG
35074 TTCCCACGTCCCAAGCACAGCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCAAGCACAGCATGCATCCCACAACTCCCCCATGCA
*
35120 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCAAGCACAGCATGCATCCCACAACTCCCCCATGCA
35166 T
1 T
35167 GCTCCAATAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.25, C:0.47, G:0.11, T:0.17
Consensus pattern (46 bp):
TTCCCACGTCCCAAGCACAGCATGCATCCCACAACTCCCCCATGCA
Found at i:35259 original size:29 final size:29
Alignment explanation
Indices: 35226--35345 Score: 213
Period size: 29 Copynumber: 4.1 Consensus size: 29
35216 AACACCACAC
*
35226 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
35255 AGGTCGCCTGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
35284 AGGTCGCCCGGATGCCATGACGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
35313 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
35342 AGGT
1 AGGT
35346 TGCTGTAGAA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:40487 original size:12 final size:12
Alignment explanation
Indices: 40466--40508 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
40456 CATTTTAGTT
*
40466 GGATTGGGAGGA
1 GGATTAGGAGGA
*
40478 GGATTTGGAGGA
1 GGATTAGGAGGA
* *
40490 GGGTTAGGAGGT
1 GGATTAGGAGGA
40502 GGATTAG
1 GGATTAG
40509 CTTGGGAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.53, T:0.23
Consensus pattern (12 bp):
GGATTAGGAGGA
Found at i:52609 original size:46 final size:46
Alignment explanation
Indices: 52539--52795 Score: 243
Period size: 46 Copynumber: 5.6 Consensus size: 46
52529 TGAACACTAT
* * * * *
52539 TTAGAGAAGATGAACATACGAAGAAAAAGAAGGGGAAGAGTCTCAG
1 TTAGAGAAGAGGAACAAAAGAAGAAGAAGAAGGGGAAGAGTCTCGG
* * * * *
52585 TTAGAGAAGAGGAACAAAATAAGAAGAAGTA---GAAGAATCTTGA
1 TTAGAGAAGAGGAACAAAAGAAGAAGAAGAAGGGGAAGAGTCTCGG
* *
52628 TTAGAGAAGATGAACAGAAGAAGAAGAAGAAGAAGGGGAAGAGTCTCGA
1 TTAGAGAAGAGGAAC--AA-AAGAAGAAGAAGAAGGGGAAGAGTCTCGG
* * * *
52677 TTAGAGAAGAGGGACAGAAGAAGAAGAAGAATGGGAAGAGTATCGG
1 TTAGAGAAGAGGAACAAAAGAAGAAGAAGAAGGGGAAGAGTCTCGG
* * * * *
52723 TTAGAGAAGAGGGACATAAA-AAGAATAATAATGGAAAGAGTCTCGG
1 TTAGAGAAGAGGAACA-AAAGAAGAAGAAGAAGGGGAAGAGTCTCGG
* *
52769 TTAGCGAAGAAGAACAAAAGAAGAAGA
1 TTAGAGAAGAGGAACAAAAGAAGAAGA
52796 GTCTCAATTA
Statistics
Matches: 173, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
43 22 0.13
45 5 0.03
46 120 0.69
47 3 0.02
49 23 0.13
ACGTcount: A:0.50, C:0.06, G:0.31, T:0.13
Consensus pattern (46 bp):
TTAGAGAAGAGGAACAAAAGAAGAAGAAGAAGGGGAAGAGTCTCGG
Found at i:52658 original size:49 final size:49
Alignment explanation
Indices: 52558--52795 Score: 153
Period size: 49 Copynumber: 5.1 Consensus size: 49
52548 ATGAACATAC
* * *
52558 GAAGAAAAAGAAGGGGAAGAGTCTC-AGTTAGAGAAGAGGAAC-----AA
1 GAAGAAGAAGAAGGAGAAGAATCTCGA-TTAGAGAAGAGGAACAGAAGAA
* * * *
52602 -AATAAGAAGAAGTAGAAGAATCTTGATTAGAGAAGATGAACAGAAGAA
1 GAAGAAGAAGAAGGAGAAGAATCTCGATTAGAGAAGAGGAACAGAAGAA
* * *
52650 GAAGAAGAAGAAGGGGAAGAGTCTCGATTAGAGAAGAGGGACAGAAGAA
1 GAAGAAGAAGAAGGAGAAGAATCTCGATTAGAGAAGAGGAACAGAAGAA
* * * * * *
52699 GAAGAAG-A-ATGG-GAAGAGTATCGGTTAGAGAAGAGGGACA-TA-AA
1 GAAGAAGAAGAAGGAGAAGAATCTCGATTAGAGAAGAGGAACAGAAGAA
* * * * * * *
52743 -AAGAATAATAATGGA-AAGAGTCTCGGTTAGCGAAGAAGAACAAAAGAA
1 GAAGAAGAAGAA-GGAGAAGAATCTCGATTAGAGAAGAGGAACAGAAGAA
52791 GAAGA
1 GAAGA
52796 GTCTCAATTA
Statistics
Matches: 155, Mismatches: 25, Indels: 23
0.76 0.12 0.11
Matches are distributed among these distances:
43 37 0.24
44 4 0.03
45 2 0.01
46 51 0.33
47 4 0.03
48 5 0.03
49 52 0.34
ACGTcount: A:0.50, C:0.06, G:0.32, T:0.12
Consensus pattern (49 bp):
GAAGAAGAAGAAGGAGAAGAATCTCGATTAGAGAAGAGGAACAGAAGAA
Found at i:52696 original size:43 final size:43
Alignment explanation
Indices: 52558--52747 Score: 159
Period size: 43 Copynumber: 4.2 Consensus size: 43
52548 ATGAACATAC
* *
52558 GAAGAAAAAGAAGGGGAAGAGTCTC-AGTTAGAGAAGAGGAACA
1 GAAGAAGAAGAAGGGGAAGAGTCTCGA-TTAGAGAAGAGGGACA
* * ** * *
52601 AAATAAGAAGAAGTAGAAGAATCTTGATTAGAGAAGATGAACAGAAGA-A
1 GAAGAAGAAGAAGGGGAAGAGTCTCGATTAGAGAAGA-G----G--GACA
52650 GAAGAAGAAGAAGGGGAAGAGTCTCGATTAGAGAAGAGGGACA
1 GAAGAAGAAGAAGGGGAAGAGTCTCGATTAGAGAAGAGGGACA
* *
52693 GAAGAAGAAGAAGAATGGGAAGAGTATCGGTTAGAGAAGAGGGACA
1 GAAGAAGAAGAAG---GGGAAGAGTCTCGATTAGAGAAGAGGGACA
* *
52739 TAAAAAGAA
1 GAAGAAGAA
52748 TAATAATGGA
Statistics
Matches: 117, Mismatches: 18, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 42 0.36
44 3 0.03
46 35 0.30
48 2 0.02
49 32 0.27
50 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.33, T:0.12
Consensus pattern (43 bp):
GAAGAAGAAGAAGGGGAAGAGTCTCGATTAGAGAAGAGGGACA
Found at i:53078 original size:101 final size:101
Alignment explanation
Indices: 52885--53087 Score: 232
Period size: 101 Copynumber: 2.0 Consensus size: 101
52875 AATTTTTATT
* * * * *
52885 GTGTTTGTAAGGATCAAACGGGGGTTTAGGGGTGAACTAAGATGAATAGTGTTTGAGGCTTGAGT
1 GTGTTTGAAAGGATCAAACGAGGGTTTAGAGATGAACTAAGATGAATAGTGTTTGAGGCTTGAGA
* *
52950 TTTGATATAAAAAGACATGTTATGTCTTAGGTTTTG
66 TTTAATATAAAAAGACAGGTTATGTCTTAGGTTTTG
* * * *
52986 GTGTTTGAAAGGATCAAACGAGGGTTTTGAAGATGAACTCAGATGAATAGTTTTTG-GGTTTTGA
1 GTGTTTGAAAGGATCAAACGAGGGTTTAG-AGATGAACTAAGATGAATAGTGTTTGAGG-CTTGA
* * *
53050 GATTTAATCTAAAAA-ATAGGTTGA-GTCTTGGGTTTTG
64 GATTTAATATAAAAAGACAGGTT-ATGTCTTAGGTTTTG
53087 G
1 G
53088 GGGATGAATA
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
101 46 0.54
102 39 0.46
ACGTcount: A:0.29, C:0.06, G:0.30, T:0.36
Consensus pattern (101 bp):
GTGTTTGAAAGGATCAAACGAGGGTTTAGAGATGAACTAAGATGAATAGTGTTTGAGGCTTGAGA
TTTAATATAAAAAGACAGGTTATGTCTTAGGTTTTG
Found at i:53449 original size:2 final size:2
Alignment explanation
Indices: 53442--53491 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
53432 ATTTATCCAA
*
53442 AT AT AT AT AT AT -T TT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53482 AT AT AT AT AT
1 AT AT AT AT AT
53492 GTGTGTGTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:65617 original size:3 final size:3
Alignment explanation
Indices: 65609--65653 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
65599 AATTATTTTT
*
65609 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
65654 AATGAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:66206 original size:113 final size:113
Alignment explanation
Indices: 65900--66784 Score: 1104
Period size: 113 Copynumber: 7.8 Consensus size: 113
65890 TTGAATAAGC
* * * * ****
65900 TCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
* * * * * * ***
65965 AAAGGTTGATGCTAACAT-ATATGTGATAAAATT-ATGTAAAAGGTTGAACATGC
66 AAAAGCTGAT-C---CATCA-A-GTGATGAATTTGA-GCAAAAGGTTAAACAAAT
* * * ****
66018 TCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTTATTATGAACTTTCTCTG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCATTATGAACTCGAACTG
* * **
66081 GAAATGTTGATCCATCAAGTGATGAATTTGAATAAAAGGTTAAACAAAT
65 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
66130 TCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTG
1 TCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTG
66194 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
65 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
66243 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
*
66308 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAAT
66 AAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
66356 TCTTCTCATTATGAA-----T-TT-CTTCTTCAGATGAATTCTTCTCA-T-T----TCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
66408 AAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
66 AAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
66456 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
* *
66521 AAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAAT
66 AAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
* * * *
66569 TCTTATTATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTCATTATGAACTCGAAT
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTC--A-GATGAATTCTTCTCATTATGAACTCGAAC
* *
66634 TGGAAAATGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAAT
63 TGGAAAA-GCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
* * *
66686 TCTTCTTATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTCATTATGAACTCGAAT
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTC--A-GATGAATTCTTCTCATTATGAACTCGAAC
* * *
66751 TGGAAAATGCTAATCCATCAAATGATGGATTTGA
63 TGGAAAA-GCTGATCCATCAAGTGATGAATTTGA
66785 ATCTTTGCTA
Statistics
Matches: 707, Mismatches: 36, Indels: 49
0.89 0.05 0.06
Matches are distributed among these distances:
100 71 0.10
104 1 0.00
105 2 0.00
106 25 0.04
107 25 0.04
108 2 0.00
109 1 0.00
112 46 0.07
113 289 0.41
114 3 0.00
115 1 0.00
116 36 0.05
117 181 0.26
118 24 0.03
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (113 bp):
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
AAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
Found at i:66377 original size:17 final size:16
Alignment explanation
Indices: 66353--66398 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
66343 AGGTTAAACA
66353 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
*
66369 AATTTCTTCTTCA-GATG
1 AA-TTCTTC-TCATTATG
66386 AATTCTTCTCATT
1 AATTCTTCTCATT
66399 TCGAACTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 8 0.32
17 11 0.44
18 3 0.12
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.50
Consensus pattern (16 bp):
AATTCTTCTCATTATG
Found at i:66439 original size:213 final size:219
Alignment explanation
Indices: 66018--66785 Score: 1048
Period size: 213 Copynumber: 3.4 Consensus size: 219
66008 TTGAACATGC
* * * ****
66018 TCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAGAT-AAGTTCTTCTTATTATGAACTTTCTCTG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTCATTATGAACTCGAACTG
* * *
66081 GAAATGTTGATCCATCAAGTGATGAATTTGAATAAAAGGTTAAACAAATTCTTCTCATTATGAAC
65 GAAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATGAA-
66146 TTTTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCA
129 ---TTCTTCCTTCTTCAGATGAATTCTTCTCATTAT--A-TCGAACTGGAAAAGCTGATCCATCA
66211 AGTGATGAATTTGAGCAAAAGGTTAAACAAAT
188 AGTGATGAATTTGAGCAAAAGGTTAAACAAAT
66243 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
66308 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATGAA-T
66 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATGAATT
66372 -TT-CTTCTTCAGATGAATTCTTCTCA-T-T-TCGAACTGGAAAAGCTGATCCATCAAGTGATGA
131 CTTCCTTCTTCAGATGAATTCTTCTCATTATATCGAACTGGAAAAGCTGATCCATCAAGTGATGA
66432 ATTTGAGCAAAAGGTTAAACAAAT
196 ATTTGAGCAAAAGGTTAAACAAAT
66456 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
* * * * *
66521 AAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAATTCTTATTATTATGAATT
66 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATGAA--
* * *
66586 TCTTCTTCCTTCTTCAAATGATGAGTTCTTCTCATTATGAACTCGAATTGGAAAATGCTAATCCA
129 --TTCTTCCTTCTTC--A-GATGAATTCTTCTCATTAT--A-TCGAACTGGAAAA-GCTGATCCA
*
66651 TCAAGTGATGGATTTGAGCAAAAGGTTAAACAAAT
185 TCAAGTGATGAATTTGAGCAAAAGGTTAAACAAAT
* * *
66686 TCTTCTTATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTTCTCATTATGAACTCGAAT
1 TCTTCTCATTATGAATTTCTTCTTCCTTCTTC--A-GATGAATTCTTCTCATTATGAACTCGAAC
* * *
66751 TGGAAAATGCTAATCCATCAAATGATGGATTTGAA
63 TGGAAAA-GCTGATCCATCAAGTGATGAATTTGAA
66786 TCTTTGCTAA
Statistics
Matches: 494, Mismatches: 26, Indels: 37
0.89 0.05 0.07
Matches are distributed among these distances:
213 180 0.36
217 1 0.00
218 2 0.00
219 25 0.05
220 9 0.02
221 1 0.00
222 1 0.00
223 14 0.03
224 1 0.00
225 25 0.05
226 90 0.18
227 2 0.00
229 12 0.02
230 73 0.15
232 1 0.00
233 34 0.07
234 23 0.05
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (219 bp):
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGG
AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATGAATT
CTTCCTTCTTCAGATGAATTCTTCTCATTATATCGAACTGGAAAAGCTGATCCATCAAGTGATGA
ATTTGAGCAAAAGGTTAAACAAAT
Found at i:66509 original size:326 final size:329
Alignment explanation
Indices: 66078--66710 Score: 1094
Period size: 326 Copynumber: 1.9 Consensus size: 329
66068 TGAACTTTCT
* * *
66078 CTGGAAATGTTGATCCATCAAGTGATGAATTTGAATAAAAGGTTAAACAAATTCTTCTCATTATG
1 CTGGAAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATG
*
66143 AACTTTTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCA
66 AACTTTTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAACTGATCCA
*
66208 TCAAGTGATGAATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCT
131 TCAAGTGATGAATTTGAGCAAAAGGTTAAACAAATTCTTATCATTATGAATTTCTTCTTCCTTCT
*
66273 TC-A-GATGAATTCTTCTCATTATGAACTCGAACTGGAAAA-GCTGATCCATCAAGTGATGAATT
196 TCAATGATGAATTCTTCTCATTATGAACTCGAACTGGAAAATGCTAATCCATCAAGTGATGAATT
66335 TGAACAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCAGATGAATTCTTCTCATTT
261 TGAACAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCAGATGAATTCTTCTCATTT
66400 CGAA
326 CGAA
*
66404 CTGGAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATG
1 CTGGAAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATG
66469 AA-TTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAACTGATCC
66 AACTTT-TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAACTGATCC
* *
66533 ATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAATTCTTATTATTATGAATTTCTTCTTCCTTC
130 ATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAATTCTTATCATTATGAATTTCTTCTTCCTTC
* * *
66598 TTCAAATGATGAGTTCTTCTCATTATGAACTCGAATTGGAAAATGCTAATCCATCAAGTGATGGA
195 TTC-AATGATGAATTCTTCTCATTATGAACTCGAACTGGAAAATGCTAATCCATCAAGTGATGAA
* *
66663 TTTGAGCAAAAGGTTAAACAAATTCTTCTTATTATGAATTTCTTCTTC
259 TTTGAACAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTC
66711 CTTCTTCAAA
Statistics
Matches: 288, Mismatches: 14, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
325 3 0.01
326 185 0.64
328 1 0.00
329 34 0.12
330 65 0.23
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (329 bp):
CTGGAAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAATTCTTCTCATTATG
AACTTTTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAAAAACTGATCCA
TCAAGTGATGAATTTGAGCAAAAGGTTAAACAAATTCTTATCATTATGAATTTCTTCTTCCTTCT
TCAATGATGAATTCTTCTCATTATGAACTCGAACTGGAAAATGCTAATCCATCAAGTGATGAATT
TGAACAAAAGGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCAGATGAATTCTTCTCATTT
CGAA
Found at i:67593 original size:92 final size:92
Alignment explanation
Indices: 67477--68275 Score: 1274
Period size: 92 Copynumber: 8.7 Consensus size: 92
67467 TTCCAATGAT
* * * * *
67477 TGGTTATGTGGTTCCTACCGAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
67542 GCACATTCCTCTTCCAAATTCAATAAC
66 GCACATTCATCTTCCAAATTCAATAAC
*
67569 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
67634 GCACATTCCTCTTCCAAATTCAATAAC
66 GCACATTCATCTTCCAAATTCAATAAC
* *
67661 TGGTTCTGTGGTTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * * *
67726 GAACATTTATCTTCCAAATTCAATGAT
66 GCACATTCATCTTCCAAATTCAATAAC
* * *
67753 TGGTTCCGTGGTTCATACCAAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
67818 GCATATTCCTCTTCCAAATTCAATAAC
66 GCACATTCATCTTCCAAATTCAATAAC
* **
67845 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATATTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
67910 GCACATTTATCTTCCAAATTCAATGAC
66 GCACATTCATCTTCCAAATTCAATAAC
* *
67937 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAATATACTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * * *
68002 GCATATTTATCTTCCAAATTCAATGAT
66 GCACATTCATCTTCCAAATTCAATAAC
*
68029 TGGTTCTATGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
68094 GCACATTCATCTTCCAAATTCAATGAT
66 GCACATTCATCTTCCAAATTCAATAAC
68121 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
68186 GCACATTCCTCTTCCAAATTCAATAAC
66 GCACATTCATCTTCCAAATTCAATAAC
* *
68213 TGGTTCTGTGGTTCATACAAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTAT
1 TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
68276 TAGGTCTTCT
Statistics
Matches: 658, Mismatches: 49, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 658 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (92 bp):
TGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTCCAAATTCAATAAC
Found at i:69553 original size:11 final size:10
Alignment explanation
Indices: 69534--69573 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
69524 CTTAACCCCC
69534 TTTTTTCTTT
1 TTTTTTCTTT
69544 TTTCTTTC-TT
1 TTT-TTTCTTT
69554 TTTTTTCTTT
1 TTTTTTCTTT
69564 TCTTTTTCTT
1 T-TTTTTCTT
69574 CTCTTCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 11 0.41
11 12 0.44
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:69556 original size:18 final size:18
Alignment explanation
Indices: 69533--69568 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
69523 CCTTAACCCC
69533 CTTTTTTCTT-TTTTCTTT
1 CTTTTTT-TTCTTTTCTTT
69551 CTTTTTTTTCTTTTCTTT
1 CTTTTTTTTCTTTTCTTT
69569 TTCTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTTTTTTCTTTTCTTT
Found at i:69558 original size:14 final size:14
Alignment explanation
Indices: 69541--69575 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
69531 CCCTTTTTTC
69541 TTTTTTC-TTTCTT
1 TTTTTTCTTTTCTT
69554 TTTTTTCTTTTCTT
1 TTTTTTCTTTTCTT
*
69568 TTTCTTCT
1 TTTTTTCT
69576 CTTCAAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTTCTT
Found at i:69559 original size:20 final size:20
Alignment explanation
Indices: 69534--69573 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
69524 CTTAACCCCC
69534 TTTTTTCTTTT-TTCTTTCTT
1 TTTTTTCTTTTCTT-TTTCTT
69554 TTTTTTCTTTTCTTTTTCTT
1 TTTTTTCTTTTCTTTTTCTT
69574 CTCTTCAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTCTTTTCTTTTTCTT
Found at i:76895 original size:18 final size:18
Alignment explanation
Indices: 76872--76941 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
76862 ACCGGTCACA
76872 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
76890 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
76907 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
76921 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
76939 ACC
1 ACC
76942 GTTGACCCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
18 33 0.73
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:76915 original size:31 final size:31
Alignment explanation
Indices: 76876--76956 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 31
76866 GTCACAACCC
76876 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
76907 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
76938 GACCGTTGACCCGTTGACC
1 GACC--CGACCCGTTGACC
76957 GGAGTTGACC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 33 0.73
33 12 0.27
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:76941 original size:13 final size:13
Alignment explanation
Indices: 76894--76930 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
76884 CCGTTGACCC
76894 GACCCGACCCGTT
1 GACCCGACCCGTT
*
76907 TACCCGACCCGTT
1 GACCCGACCCGTT
76920 GACCCGACCCG
1 GACCCGACCCG
76931 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:78293 original size:18 final size:18
Alignment explanation
Indices: 78267--78302 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
78257 TCGAAAGGAC
*
78267 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
78285 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
78303 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:79528 original size:24 final size:24
Alignment explanation
Indices: 79436--79528 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
79426 ATCTGATTTA
* *
79436 TGATTTGAATTATGTTTTGACATC
1 TGATCTGAATTATGTTTTGATATC
* * *
79460 TGATCTGAAATCTGTTCTGAT-TCC
1 TGATCTGAATTATGTTTTGATAT-C
* * * * *
79484 TAACCTGGATTCTGTTATGATATC
1 TGATCTGAATTATGTTTTGATATC
79508 TGATCTGAATTATGTTTTGAT
1 TGATCTGAATTATGTTTTGAT
79529 TTTTGATATC
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (24 bp):
TGATCTGAATTATGTTTTGATATC
Found at i:79535 original size:24 final size:24
Alignment explanation
Indices: 79429--79535 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 24
79419 ATATTTTATC
* *
79429 TGATTTATGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
79453 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
79477 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
79501 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
79525 TGATTTTTGAT
1 TGATTTCTGAT
79536 ATCTCCGTTT
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:86449 original size:3 final size:3
Alignment explanation
Indices: 86441--86491 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
86431 AATTATTTTT
* *
86441 TAA TAA TAA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
86489 TAA
1 TAA
86492 AATGAGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:86461 original size:15 final size:15
Alignment explanation
Indices: 86441--86491 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
86431 AATTATTTTT
86441 TAATAATAATAATTA
1 TAATAATAATAATTA
86456 TAATAATAATAATTA
1 TAATAATAATAATTA
*
86471 TAATAATAATAATAA
1 TAATAATAATAATTA
86486 TAATAA
1 TAATAA
86492 AATGAGTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:91505 original size:19 final size:19
Alignment explanation
Indices: 91481--91532 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
91471 AAATGCAGTT
*
91481 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGA
91500 AGTGCATCGATGCATAAGA
1 AGTGCATCGATGCATAAGA
91519 AGTGCATCGATGCA
1 AGTGCATCGATGCA
91533 CCCCCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGA
Found at i:91573 original size:83 final size:83
Alignment explanation
Indices: 91434--91596 Score: 208
Period size: 83 Copynumber: 2.0 Consensus size: 83
91424 CTATGCACAG
*
91434 GAAGTGCATCGATGCACCCATTAAAAATGGAAACATCAAATGCAGTTAGTGCATCGATGCATAAG
1 GAAGTGCATCGATGCACCCATTAAAAATGAAAACATCAAATGCAGTTAGTGCATCGATGCAT-AG
91499 G-AGTGCATCGATGCATAA
65 GTAGTGCATCGATGCATAA
* * * *
91517 GAAGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTG-A-TTGGTGTATCGATGCAT
1 GAAGTGCATCGATGCA-CCCATTAAAAATGAAAACATC-AA-ATGCAGTTAGTGCATCGATGCAT
*
91579 GGGTAGTGCATCGATGCA
63 AGGTAGTGCATCGATGCA
91597 CATGTTAAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
82 2 0.03
83 58 0.83
84 8 0.11
85 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (83 bp):
GAAGTGCATCGATGCACCCATTAAAAATGAAAACATCAAATGCAGTTAGTGCATCGATGCATAGG
TAGTGCATCGATGCATAA
Found at i:91630 original size:20 final size:22
Alignment explanation
Indices: 91585--91642 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
91575 GCATGGGTAG
91585 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
91609 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
91629 TGTATCGATGCACT
1 TGCATCGATGCACT
91643 TCAAGAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:93379 original size:21 final size:20
Alignment explanation
Indices: 93353--93391 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
93343 CAAGAGATTT
93353 CATCTCCAAACGGCTAGAAAA
1 CATCT-CAAACGGCTAGAAAA
*
93374 CATCTCTAACGGCTAGAA
1 CATCTCAAACGGCTAGAA
93392 CCGGCCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (20 bp):
CATCTCAAACGGCTAGAAAA
Found at i:94645 original size:15 final size:15
Alignment explanation
Indices: 94613--94652 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
94603 GAAGATGATG
* *
94613 AAGAA-AAGAAAGAC
1 AAGAAGAAGGAAGAA
94627 AAGAAGAAGGAAGAA
1 AAGAAGAAGGAAGAA
94642 AAGAAGAAGGA
1 AAGAAGAAGGA
94653 GGTAGGCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGGAAGAA
Found at i:100250 original size:176 final size:176
Alignment explanation
Indices: 99956--100312 Score: 669
Period size: 176 Copynumber: 2.0 Consensus size: 176
99946 AGGAAGATAT
* *
99956 TTATTGGCAGCAGTCCACATATGATACCTTGTCAGTTGTGCCCCACACGTGAAGGGTATATTCCC
1 TTATTGGCAGCAGTCAACATATGATACCTTGTCAGTTGTACCCCACACGTGAAGGGTATATTCCC
100021 TCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTAT
66 TCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTAT
*
100086 AGGAGGATGGAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
131 AGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
100132 TTATTGGCAGCAGTCAACATATGATACCTTGTCAGTTGTACCCCACACGTGAAGGGTATATTCCC
1 TTATTGGCAGCAGTCAACATATGATACCTTGTCAGTTGTACCCCACACGTGAAGGGTATATTCCC
*
100197 TCAAGAATTAGGGCACAAAACCCTAGGAGCCCCCACTATATAAAGAAAAAGAACACCACATTTAT
66 TCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTAT
*
100262 AGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAGCTAGAAGTGG
131 AGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
100308 TTATT
1 TTATT
100313 CTTCTTTCTT
Statistics
Matches: 176, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 176 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (176 bp):
TTATTGGCAGCAGTCAACATATGATACCTTGTCAGTTGTACCCCACACGTGAAGGGTATATTCCC
TCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTAT
AGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
Found at i:102355 original size:20 final size:20
Alignment explanation
Indices: 102332--102382 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
102322 CTATGCTAGA
102332 AGTATCGATACTATCTCTAT
1 AGTATCGATACTATCTCTAT
102352 AGTATCGATACTATCTCTAT
1 AGTATCGATACTATCTCTAT
*
102372 AGTATCAATAC
1 AGTATCGATAC
102383 CACATGAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATCTCTAT
Found at i:103329 original size:17 final size:16
Alignment explanation
Indices: 103288--103317 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
103278 AATACCTTTT
103288 AAAAATAA-TTTTAAG
1 AAAAATAATTTTTAAG
103303 AAAAATAATTTTTAA
1 AAAAATAATTTTTAA
103318 AGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AAAAATAATTTTTAAG
Found at i:104432 original size:21 final size:20
Alignment explanation
Indices: 104408--104447 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
104398 TGTAGAGATT
104408 TCATCCCCAAACGGCTAGAAA
1 TCAT-CCCAAACGGCTAGAAA
*
104429 TCATCCCTAACGGCTAGAA
1 TCATCCCAAACGGCTAGAA
104448 CCACAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (20 bp):
TCATCCCAAACGGCTAGAAA
Found at i:111211 original size:15 final size:16
Alignment explanation
Indices: 111191--111222 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
111181 ATATTATCCG
111191 ATCCG-AAATTTGGAT
1 ATCCGAAAATTTGGAT
111206 ATCCGAAAATTTGGAT
1 ATCCGAAAATTTGGAT
111222 A
1 A
111223 CTTAAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
ATCCGAAAATTTGGAT
Found at i:111280 original size:16 final size:16
Alignment explanation
Indices: 111246--111294 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
111236 TCCGTATCCG
*
111246 ATCCGAAAAATTCGGAT
1 ATCCG-AAATTTCGGAT
*
111263 ATCCGAAATTTTGGAT
1 ATCCGAAATTTCGGAT
*
111279 ATCCTAAATTTCGGAT
1 ATCCGAAATTTCGGAT
111295 CGGATATCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (16 bp):
ATCCGAAATTTCGGAT
Found at i:117112 original size:51 final size:51
Alignment explanation
Indices: 117013--117147 Score: 148
Period size: 51 Copynumber: 2.6 Consensus size: 51
117003 CACCCGTAGA
* * * * *
117013 AGTAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGGCACCACGTGG
1 AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACTGGGCACCACGTGG
** *
117064 AGTATAGCTTGCCCCCTGTACCGCGCTATACGCTGACTGGGTTA-CACGTGG
1 AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACTGGG-CACCACGTGG
* *
117115 GGTATAGCGCGCCCCCTGCT-CCGGGCTATACGC
1 AGTATAGCGCGCCCCCTG-TACCGCGCTATACGC
117148 CACGTAGGGG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
51 68 0.97
52 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACTGGGCACCACGTGG
Found at i:117852 original size:16 final size:16
Alignment explanation
Indices: 117833--117866 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
117823 CAATATACGA
117833 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
117849 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
117865 AT
1 AT
117867 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:118600 original size:130 final size:130
Alignment explanation
Indices: 118398--118642 Score: 436
Period size: 130 Copynumber: 1.9 Consensus size: 130
118388 AATTTTCTTC
* *
118398 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTGACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
118463 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* **
118528 TAATTAGGTGGTGACATGTGTCACCAATGACATGTATCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
118593 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACTAAATT
66 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATT
118643 TAATATTAGG
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:121420 original size:35 final size:34
Alignment explanation
Indices: 121335--121421 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
121325 ATTTGTTATT
*
121335 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
*
121369 TAAATGATAATC-AAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAA-CAAAATTACAATAA--GA-ATTAAATGG
121407 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
121422 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:121658 original size:9 final size:9
Alignment explanation
Indices: 121644--121684 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
121634 GTCATCATCG
121644 TCGTCGTCA
1 TCGTCGTCA
121653 TCGTCGTCA
1 TCGTCGTCA
* *
121662 CCATCGTCA
1 TCGTCGTCA
121671 TCGTCGTCA
1 TCGTCGTCA
121680 TCGTC
1 TCGTC
121685 ATTTCGTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.12, C:0.37, G:0.20, T:0.32
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:123691 original size:111 final size:111
Alignment explanation
Indices: 123551--123883 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
123541 ATTACAAAAA
*
123551 TTAATTATTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
123616 AATTAAAAAGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
123662 TTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
123727 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
123773 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
123838 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
123884 ATGATTTCCA
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:126751 original size:28 final size:30
Alignment explanation
Indices: 126696--126753 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
126686 TGACGTTATT
* *
126696 AGTGTCTTAGGAATAACTGATTTAGATTAAC
1 AGTGTATTAGGAATAACTGA-TAAGATTAAC
126727 AGTGTATTAGGAATAACT-A-AAGATTAA
1 AGTGTATTAGGAATAACTGATAAGATTAA
126754 AGGATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
30 1 0.04
31 17 0.68
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (30 bp):
AGTGTATTAGGAATAACTGATAAGATTAAC
Found at i:127538 original size:13 final size:13
Alignment explanation
Indices: 127520--127545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127510 TACAGACGCT
127520 CATATGAAGACTG
1 CATATGAAGACTG
127533 CATATGAAGACTG
1 CATATGAAGACTG
127546 TTCAACTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CATATGAAGACTG
Found at i:130690 original size:28 final size:28
Alignment explanation
Indices: 130644--130716 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
130634 AACTAAAAGT
* * *
130644 TTATGAAATTATAGAAATTAAGGATCCTAG
1 TTAT-AAA-TATAAAAATTAAGGATACTAA
*
130674 TTATAAATATAAAAATTGAGGATACTAA
1 TTATAAATATAAAAATTAAGGATACTAA
130702 TTATAAATATAAAAA
1 TTATAAATATAAAAA
130717 ATTGAAGGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 32 0.82
29 3 0.08
30 4 0.10
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (28 bp):
TTATAAATATAAAAATTAAGGATACTAA
Found at i:131578 original size:2 final size:2
Alignment explanation
Indices: 131571--131595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
131561 ACCAAAATTA
131571 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
131596 ATTGAGAAAA
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:146986 original size:21 final size:22
Alignment explanation
Indices: 146962--147007 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
146952 AACACACATG
146962 TATCATGT-AAACATATGCTCA
1 TATCATGTCAAACATATGCTCA
* *
146983 TATCATGTCATACGTATGCTCA
1 TATCATGTCAAACATATGCTCA
147005 TAT
1 TAT
147008 TAATGAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (22 bp):
TATCATGTCAAACATATGCTCA
Found at i:147413 original size:20 final size:20
Alignment explanation
Indices: 147385--147435 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
147375 TTCAAATAAT
* *
147385 GTATTGATAGCTTCCTTAAG
1 GTATCGATACCTTCCTTAAG
147405 GTATCGATACCTTCCTTAAG
1 GTATCGATACCTTCCTTAAG
*
147425 GTATCGGTACC
1 GTATCGATACC
147436 CTGGGTATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (20 bp):
GTATCGATACCTTCCTTAAG
Found at i:149707 original size:23 final size:23
Alignment explanation
Indices: 149681--149739 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
149671 CGCCAGCCTT
*
149681 CAATATGCCACCTTCGTCACTTC
1 CAATCTGCCACCTTCGTCACTTC
*
149704 CAATCTGCCACCTTTGTCACTTC
1 CAATCTGCCACCTTCGTCACTTC
*
149727 CAATCTACCACCT
1 CAATCTGCCACCT
149740 CAGTCGAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.41, G:0.07, T:0.31
Consensus pattern (23 bp):
CAATCTGCCACCTTCGTCACTTC
Found at i:151114 original size:18 final size:19
Alignment explanation
Indices: 151093--151131 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
151083 TGAAATTGAG
*
151093 ATAAATTAATCA-ATTTTA
1 ATAAAATAATCATATTTTA
*
151111 ATAAAATGATCATATTTTA
1 ATAAAATAATCATATTTTA
151130 AT
1 AT
151132 TTTGATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAAAATAATCATATTTTA
Found at i:160298 original size:42 final size:42
Alignment explanation
Indices: 160228--160312 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
160218 CGCCACAAAA
* * * * ** *
160228 TGATACTTTAGCGGCGTTTGTTGGAAAAATGCCGCAATAGAG
1 TGATAATTTAGCGGCGTTTATAGCAAAAACACCGAAATAGAG
*
160270 TGATAATTTAGTGGCGTTTATAGCAAAAACACCGAAATAGAG
1 TGATAATTTAGCGGCGTTTATAGCAAAAACACCGAAATAGAG
160312 T
1 T
160313 TCTTTATAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (42 bp):
TGATAATTTAGCGGCGTTTATAGCAAAAACACCGAAATAGAG
Found at i:160568 original size:40 final size:40
Alignment explanation
Indices: 160521--160614 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
160511 AGGTGTTCAT
*
160521 CAATAGTGGCATTTGTTAAAAAACACCACAAAAACATGTA
1 CAATAGTGGCATTTGTTAAAAAACACCACAAAAACATGCA
* *
160561 CAATAGTGGCGTTTGTTAAAAAACACCGCAAAAACATGCA
1 CAATAGTGGCATTTGTTAAAAAACACCACAAAAACATGCA
*
160601 CTATAGTGGCATTT
1 CAATAGTGGCATTT
160615 TTATTAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (40 bp):
CAATAGTGGCATTTGTTAAAAAACACCACAAAAACATGCA
Found at i:161022 original size:22 final size:22
Alignment explanation
Indices: 160994--161035 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
160984 GTTTTTCTTC
160994 TTTCGAATAGAAAAATAATATT
1 TTTCGAATAGAAAAATAATATT
*
161016 TTTCGAATAGGAAAATAATA
1 TTTCGAATAGAAAAATAATA
161036 GCTTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (22 bp):
TTTCGAATAGAAAAATAATATT
Found at i:161471 original size:43 final size:44
Alignment explanation
Indices: 161413--161549 Score: 116
Period size: 43 Copynumber: 3.1 Consensus size: 44
161403 CGTTTGTAAC
* * * *
161413 AAAAAACGCCACTATATACCATACATTT-GCGACGTTTGTATCC-
1 AAAAAACGTCGCTATATACCAGACATTTAACGA-GTTTGTATCCA
* * *
161456 TAAAAACGTCGCTATATACTAGACCTTTAACGAGTTTGTATCCA
1 AAAAAACGTCGCTATATACCAGACATTTAACGAGTTTGTATCCA
** ** * * *
161500 AAAAAATATCGCTATATACCAGATGTTTTACGACATTTGTATCCG
1 AAAAAACGTCGCTATATACCAGACATTTAACGA-GTTTGTATCCA
161545 AAAAA
1 AAAAA
161550 TGTCGTAAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
43 32 0.43
44 29 0.39
45 14 0.19
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.30
Consensus pattern (44 bp):
AAAAAACGTCGCTATATACCAGACATTTAACGAGTTTGTATCCA
Found at i:161549 original size:44 final size:44
Alignment explanation
Indices: 161424--161550 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 44
161414 AAAAACGCCA
* * * * **
161424 CTATATACCATACATTT-GCGACGTTTGTATCCTAAAAACGTCG
1 CTATATACCAGACCTTTAACGACGTTTGTATCCAAAAAATATCG
*
161467 CTATATACTAGACCTTTAACGA-GTTTGTATCCAAAAAAATATCG
1 CTATATACCAGACCTTTAACGACGTTTGTATCC-AAAAAATATCG
** * * *
161511 CTATATACCAGATGTTTTACGACATTTGTATCCGAAAAAT
1 CTATATACCAGACCTTTAACGACGTTTGTATCCAAAAAAT
161551 GTCGTAAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
43 24 0.35
44 35 0.51
45 9 0.13
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (44 bp):
CTATATACCAGACCTTTAACGACGTTTGTATCCAAAAAATATCG
Found at i:161674 original size:43 final size:41
Alignment explanation
Indices: 161612--161741 Score: 118
Period size: 43 Copynumber: 3.0 Consensus size: 41
161602 CATACGTATT
* *
161612 TTACGGTGTTGTGTGGAAAAATGCCGCTAAATCTCAACACATA
1 TTACGGTGTT-TGTGGAAAAACG-AGCTAAATCTCAACACATA
* *
161655 TTACGGTGTTTGTGAGAAAAACGAGCTTAATCTCAACACCTA
1 TTACGGTGTTTGTG-GAAAAACGAGCTAAATCTCAACACATA
* * * * *
161697 TTGCGGCGTTTGTAGGACAAAAAC-TGCTAAATATCAACACCTA
1 TTACGGTGTTTGT-GG--AAAAACGAGCTAAATCTCAACACATA
161740 TT
1 TT
161742 GCGGCATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
42 32 0.43
43 36 0.49
44 6 0.08
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TTACGGTGTTTGTGGAAAAACGAGCTAAATCTCAACACATA
Found at i:161708 original size:42 final size:42
Alignment explanation
Indices: 161637--161746 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
161627 GAAAAATGCC
* * * *
161637 GCTAAATCTCAACACATATTACGGTGTTTGT-GAGAAAAACGA
1 GCTAAATCTCAACACCTATTGCGGCGTTTGTAGACAAAAAC-A
* *
161679 GCTTAATCTCAACACCTATTGCGGCGTTTGTAGGACAAAAACT
1 GCTAAATCTCAACACCTATTGCGGCGTTTGTA-GACAAAAACA
*
161722 GCTAAATATCAACACCTATTGCGGC
1 GCTAAATCTCAACACCTATTGCGGC
161747 ATTTTTTGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 27 0.47
43 23 0.40
44 8 0.14
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (42 bp):
GCTAAATCTCAACACCTATTGCGGCGTTTGTAGACAAAAACA
Found at i:161742 original size:43 final size:43
Alignment explanation
Indices: 161637--161760 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
161627 GAAAAATGCC
* * * *
161637 GCTAAATCTCAACACATATTACGGTGTTTGT-GAGAAAAACGA
1 GCTAAATCTCAACACCTATTGCGGCGTTTGTGGACAAAAACGA
* *
161679 GCTTAATCTCAACACCTATTGCGGCGTTTGTAGGACAAAAAC-T
1 GCTAAATCTCAACACCTATTGCGGCGTTTGT-GGACAAAAACGA
* * *
161722 GCTAAATATCAACACCTATTGCGGCATTTTTTGGACAAA
1 GCTAAATCTCAACACCTATTGCGGC-GTTTGTGGACAAA
161761 CGCCGTGAAC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 27 0.39
43 30 0.43
44 12 0.17
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (43 bp):
GCTAAATCTCAACACCTATTGCGGCGTTTGTGGACAAAAACGA
Found at i:162663 original size:62 final size:62
Alignment explanation
Indices: 162574--162698 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
162564 GACCATTTGT
162574 ATACTTTATCCTAATTGTAATTGATTTTATGAAAAACATTTTCTTTAATATTTTATTTGTAG
1 ATACTTTATCCTAATTGTAATTGATTTTATGAAAAACATTTTCTTTAATATTTTATTTGTAG
162636 ATACTTTATCCTAATTGTAATTGATTTTATGAAAAACATTTTCTTTAATATTTTATTTGTAG
1 ATACTTTATCCTAATTGTAATTGATTTTATGAAAAACATTTTCTTTAATATTTTATTTGTAG
162698 A
1 A
162699 CACCCATTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (62 bp):
ATACTTTATCCTAATTGTAATTGATTTTATGAAAAACATTTTCTTTAATATTTTATTTGTAG
Found at i:163315 original size:18 final size:17
Alignment explanation
Indices: 163292--163325 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
163282 TAAAAAACCC
163292 CAAATAAAAAATAGAGAA
1 CAAAT-AAAAATAGAGAA
*
163310 CAAATATAAATAGAGA
1 CAAATAAAAATAGAGA
163326 TCTCGAGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.06, G:0.12, T:0.15
Consensus pattern (17 bp):
CAAATAAAAATAGAGAA
Found at i:164615 original size:2 final size:2
Alignment explanation
Indices: 164608--164637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
164598 GGCGTGAAAA
164608 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
164638 TACTTAATAG
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:164933 original size:6 final size:5
Alignment explanation
Indices: 164897--164939 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
164887 ATACTATATT
* * *
164897 TTTTA CTTTA CTTTA CTTTA TTTTA TTTTA TTTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TT
164940 ATGTTTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:165690 original size:13 final size:13
Alignment explanation
Indices: 165672--165697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
165662 ATATTTAATA
165672 TTAATAAAATATT
1 TTAATAAAATATT
165685 TTAATAAAATATT
1 TTAATAAAATATT
165698 AATTATTAAG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATAAAATATT
Found at i:166959 original size:83 final size:83
Alignment explanation
Indices: 166868--167115 Score: 351
Period size: 83 Copynumber: 3.0 Consensus size: 83
166858 GAAATTTCGA
*
166868 GAGAGTTTTACTCCAACTAAAACTCTTTTAATATCTAAATTTAAACAGATAATATTATCTTTTAA
1 GAGAGTTTTACTCCAACTAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAA
166933 ATTTAAAATATAAAA-ATT
66 ATTTAAAATATAAAACA-T
* *
166951 GAGAGTTTTACTCCAACT-AAACAACTTTTAATATCTAAATTTAAAAAGATAATAATATCTTTTA
1 GAGAGTTTTACTCCAACTAAAAC-TCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTA
167015 AATTTAAAATATTAAAACAT
65 AATTTAAAATA-TAAAACAT
* * * *
167035 -AGAGTTTTACTTCAACTAAATA-TCTTTTAATATCTAAATTTAAACATATAATAATATCATCTA
1 GAGAGTTTTACTCCAACTAAA-ACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTA
* *
167098 AATATAAAATATTAAACA
65 AATTTAAAATATAAAACA
167116 AATATACACT
Statistics
Matches: 149, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
82 10 0.07
83 129 0.87
84 8 0.05
85 2 0.01
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (83 bp):
GAGAGTTTTACTCCAACTAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAA
ATTTAAAATATAAAACAT
Found at i:170611 original size:21 final size:23
Alignment explanation
Indices: 170587--170632 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
170577 GTTGCTAAGA
*
170587 AAGCTAAGGTT-A-ATGAAGGAG
1 AAGCTAAGGTTGAGAAGAAGGAG
*
170608 AAGCTGAGGTTGAGAAGAAGGAG
1 AAGCTAAGGTTGAGAAGAAGGAG
170631 AA
1 AA
170633 AAGAAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.43, C:0.04, G:0.37, T:0.15
Consensus pattern (23 bp):
AAGCTAAGGTTGAGAAGAAGGAG
Found at i:173132 original size:3 final size:3
Alignment explanation
Indices: 173116--173176 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
173106 TTTGGGCTTG
* * * **
173116 TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TTT
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
173162 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
173177 AAACAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:174542 original size:16 final size:16
Alignment explanation
Indices: 174521--174583 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 16
174511 TAAAGTAAAA
174521 ATAAAAATATATACAT
1 ATAAAAATATATACAT
*
174537 AT-AAAATAT-TAGAT
1 ATAAAAATATATACAT
*
174551 AGAAAAA-ATAATA-AT
1 ATAAAAATAT-ATACAT
*
174566 AAAATAAATATATACAT
1 ATAA-AAATATATACAT
174583 A
1 A
174584 CTAACTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.18
15 16 0.42
16 10 0.26
17 5 0.13
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAAAAATATATACAT
Found at i:174739 original size:16 final size:16
Alignment explanation
Indices: 174711--174753 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
174701 AAGTAACAAT
174711 AATAACAAATAATAAAA
1 AATAA-AAATAATAAAA
* *
174728 AATAAGAATAATAAAT
1 AATAAAAATAATAAAA
174744 AATAAAAATA
1 AATAAAAATA
174754 TATGGTTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AATAAAAATAATAAAA
Found at i:182124 original size:37 final size:39
Alignment explanation
Indices: 182054--182127 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
182044 GCAGGTGCAA
* *
182054 CTTTCGCTTTGGTAACGAATGAGTCCCCGGGTAATACAG
1 CTTTCCCTTTAGTAACGAATGAGTCCCCGGGTAATACAG
*
182093 CTTTCCCTTTAGTAGCG-ATGAGT-CCCGGGTAATAC
1 CTTTCCCTTTAGTAACGAATGAGTCCCCGGGTAATAC
182128 TCCGGGAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 12 0.38
38 6 0.19
39 14 0.44
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (39 bp):
CTTTCCCTTTAGTAACGAATGAGTCCCCGGGTAATACAG
Found at i:182511 original size:23 final size:25
Alignment explanation
Indices: 182456--182504 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
182446 AGTTAATACG
*
182456 AATGTAAAAACATGGAAAATAAAAA
1 AATGAAAAAACATGGAAAATAAAAA
182481 AAT-AAAAAACAT-GAAATATAAAAA
1 AATGAAAAAACATGGAAA-ATAAAAA
182505 TGCAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 15 0.68
25 3 0.14
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.16
Consensus pattern (25 bp):
AATGAAAAAACATGGAAAATAAAAA
Found at i:185920 original size:16 final size:16
Alignment explanation
Indices: 185892--185934 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
185882 AAGTAACAAT
185892 AATAACAAATAATAAAA
1 AATAA-AAATAATAAAA
* *
185909 AATAAGAATAATAAAT
1 AATAAAAATAATAAAA
185925 AATAAAAATA
1 AATAAAAATA
185935 TATGGTTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AATAAAAATAATAAAA
Found at i:191482 original size:70 final size:70
Alignment explanation
Indices: 191400--191579 Score: 344
Period size: 70 Copynumber: 2.6 Consensus size: 70
191390 TGGTCATATG
191400 TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAAGACTAAAATATTT-AAAATATAAAA
1 TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAAGACTAAAATATTTAAAAATAT-AAA
191464 CATTTT
65 CATTTT
191470 TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAAGACTAAAATATTTAAAAATATAAAC
1 TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAAGACTAAAATATTTAAAAATATAAAC
191535 ATTTT
66 ATTTT
191540 TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAA
1 TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAA
191580 CCCTGCTTCT
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
70 102 0.94
71 7 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (70 bp):
TCATAAATTTTATATTTAATTATATAATTGTTTAATTAAAGACTAAAATATTTAAAAATATAAAC
ATTTT
Found at i:191565 original size:34 final size:34
Alignment explanation
Indices: 191447--191566 Score: 95
Period size: 34 Copynumber: 3.5 Consensus size: 34
191437 AAAGACTAAA
191447 ATATTTAA-AATATAAAACATTTTTCATAAATTTT
1 ATATTTAATAATAT-AAACATTTTTCATAAATTTT
* * ***
191481 ATATTTAAT--TATATA-ATTGTTTAATTAAAGACTAAA
1 ATATTTAATAATATAAACATT-TTTCA-T-AA-A-TTTT
*
191517 ATATTTAAAAATATAAACATTTTTCATAAATTTT
1 ATATTTAATAATATAAACATTTTTCATAAATTTT
*
191551 ATATTTAATTATATAA
1 ATATTTAATAATATAA
191567 TTGTTTAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
31 3 0.05
32 6 0.09
33 4 0.06
34 25 0.39
35 2 0.03
36 11 0.17
37 1 0.02
38 9 0.14
39 3 0.05
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (34 bp):
ATATTTAATAATATAAACATTTTTCATAAATTTT
Found at i:192355 original size:142 final size:137
Alignment explanation
Indices: 192136--192407 Score: 343
Period size: 142 Copynumber: 1.9 Consensus size: 137
192126 TTTATAAAAC
* * * * * *
192136 TAAATAGAGTATTTATTTATTTAAAAATATTTAGAAAATGACATCTAGTTACTTTAAGACTGCCC
1 TAAATAGAATATTTATTTATTTAAAAATATTCAGAAAAGGACATCCAATTACTTTAAGACCGCCC
* *
192201 GTTTCTTTAATATTAATAAATAAATAAATAAATATTAATGATAATTT-CTAAAAAAATATAATTT
66 GTTTCTTCAATATGAATAAAT--ATAAA-AAATATT-AT-A-AATTTCCTAAAAAAA-ATAATTT
192265 AAATAAAACTAAAT
124 AAATAAAACTAAAT
*
192279 TAAATATAATATTTATTTATTTAAAAATA-TCAGAAAAGGACATCCAATTACTTTAAGACCGTCC
1 TAAATAGAATATTTATTTATTTAAAAATATTCAGAAAAGGACATCCAATTACTTTAAGACCG-CC
* * *
192343 C-TTTCTTCAATATGAATGAATATAAAAAATATTATAATTTTCCTAAGAAAAATAATTTAAATAA
65 CGTTTCTTCAATATGAATAAATATAAAAAATATTATAAATTTCCTAAAAAAAATAATTTAAATAA
192407 A
130 A
192408 TATATTATTT
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
136 18 0.16
137 9 0.08
138 2 0.02
139 7 0.06
140 5 0.04
142 44 0.38
143 30 0.26
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (137 bp):
TAAATAGAATATTTATTTATTTAAAAATATTCAGAAAAGGACATCCAATTACTTTAAGACCGCCC
GTTTCTTCAATATGAATAAATATAAAAAATATTATAAATTTCCTAAAAAAAATAATTTAAATAAA
ACTAAAT
Found at i:192539 original size:2 final size:2
Alignment explanation
Indices: 192532--192557 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
192522 CAAATCTTTC
192532 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
192558 TAATATGACT
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):
AT
Found at i:193919 original size:3 final size:3
Alignment explanation
Indices: 193913--193975 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
193903 TATTTATTAT
* * *
193913 TAA TAA TAA -AA T-A TAA TAG TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
193959 TAA -AA AAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
193976 AACGAGATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 6 0.12
3 44 0.88
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:193950 original size:21 final size:21
Alignment explanation
Indices: 193893--193961 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 21
193883 GGCCTGAAAT
193893 GTAATAA-AATTATTTAT--TA
1 GTAATAATAA-TATTTATAATA
* *
193912 TTAATAATAA-A-ATATAATA
1 GTAATAATAATATTTATAATA
193931 GTAATAATAATATTTATAATA
1 GTAATAATAATATTTATAATA
*
193952 ATAATAATAA
1 GTAATAATAA
193962 AAAAAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 17 0.43
20 3 0.08
21 16 0.40
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
GTAATAATAATATTTATAATA
Found at i:194333 original size:17 final size:17
Alignment explanation
Indices: 194311--194369 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
194301 GTTGAACAAG
194311 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
194328 TTCTTCTTCCTATTAAGATGAG
1 TTCTTC-T-C-ATTATGA--AC
194350 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
194367 TTC
1 TTC
194370 CTCTGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 10 0.30
18 1 0.03
19 7 0.21
20 7 0.21
21 1 0.03
22 7 0.21
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:194464 original size:139 final size:137
Alignment explanation
Indices: 194211--194518 Score: 386
Period size: 139 Copynumber: 2.2 Consensus size: 137
194201 AGGTTAAATA
* * * *
194211 AGTTGTTCTCATTATGAAC-TCCTTCTGGAAATGTTGATCCTTAAGAAAGGTGTCGTTGATTCAA
1 AGTTCTTCTCATTATGAACTTCC-TCTGAAAATGTTGATCCTCAAGAAAGGTGTCGTTCATTCAA
* * * * * *
194275 CTTCATATGTGATGAATTATGGCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTA
65 CTCCACAGGTGATGAATCATAGCAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTA
194340 TTAAGATG
130 TTAAGATG
* ** * *
194348 AGTTCTTCTCATTATGAACTTCCTCTGAAAATGTTGATCCTCACGTGAGGTTCTTCTTTCATTCA
1 AGTTCTTCTCATTATGAACTTCCTCTGAAAATGTTGATCCTCAAGAAAGG-T-GTCGTTCATTCA
194413 ACTCCACAGGTGATGAATCA-AGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
64 ACTCCACAGGTGATGAATCATAGC-AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* *
194477 TCTTCAGATG
128 TATTAAGATG
* *
194487 AATTCTTCTCATTATGAACTTTCTCTGGAAAA
1 AGTTCTTCTCATTATGAACTTCCTCT-GAAAA
194519 ATTGATGCTG
Statistics
Matches: 147, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
137 40 0.27
138 6 0.04
139 96 0.65
140 5 0.03
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (137 bp):
AGTTCTTCTCATTATGAACTTCCTCTGAAAATGTTGATCCTCAAGAAAGGTGTCGTTCATTCAAC
TCCACAGGTGATGAATCATAGCAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTAT
TAAGATG
Found at i:194769 original size:123 final size:123
Alignment explanation
Indices: 194443--194770 Score: 498
Period size: 123 Copynumber: 2.7 Consensus size: 123
194433 AGCTAAGGTC
* *
194443 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
194508 TCTCTGGAAAAATTGATGCTGATCTATCTCATTCTATGATAGAGTCATGCAAAAGGTT
66 TCTCTGGAAAAGTTGATGCTGATCTATCTCATTCTATGATAGAGTCATGCAAAAAGTT
* *
194566 GAACAAATTCTTCTCATTATGAACTTCTTT-TTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTT-TTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * *
194630 TTTTCTTGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGA-GCAAAAAGTT
65 TTCTCTGGAAAAGTTGATGCTGATCTATCTCATTCTATGATAGAGTC-ATGCAAAAAGTT
*
194689 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAACTT
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
194754 CCTCTGGAAATGTTGAT
66 TCTCTGGAAAAGTTGAT
194771 CCATCGAGTG
Statistics
Matches: 184, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
122 3 0.02
123 178 0.97
124 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (123 bp):
GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
TCTCTGGAAAAGTTGATGCTGATCTATCTCATTCTATGATAGAGTCATGCAAAAAGTT
Found at i:194849 original size:36 final size:36
Alignment explanation
Indices: 194809--194933 Score: 92
Period size: 36 Copynumber: 3.5 Consensus size: 36
194799 AGTGAAACTG
* *
194809 TCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATATTGTTTTAAGAAAAACAA
* * * ** **
194845 TCTCAAGTGAGA-TAA-ATTGTTTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAATATTG-TTTT-AAGAAAAACAA
* *
194881 TCTCAAGCGTGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATATTGTTTTAAGAAAAACAA
* * *
194917 TCTTAAGTGAGATAAAT
1 TCTCAAGCGAGACAAAT
194934 TACTATTTGA
Statistics
Matches: 64, Mismatches: 21, Indels: 8
0.69 0.23 0.09
Matches are distributed among these distances:
34 3 0.05
35 6 0.09
36 46 0.72
37 6 0.09
38 3 0.05
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATATTGTTTTAAGAAAAACAA
Found at i:194880 original size:72 final size:72
Alignment explanation
Indices: 194794--194934 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 72
194784 GAAATTTCTG
* *
194794 TTTCTAGTGAAACTGTCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
194859 AATTGTT
66 AATTGTT
* * *
194866 TTTCGAGTGAAACTGTCTCAAGCGTGACAAATTTTGTTTTAAGAAAAACAATCTTAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
194931 AATT
66 AATT
194935 ACTATTTGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (72 bp):
TTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
AATTGTT
Found at i:195689 original size:22 final size:22
Alignment explanation
Indices: 195632--195689 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
195622 AATAAAGCTT
*
195632 ATCTTTGAAAAGA-GAATCTATC
1 ATCTTTGAAAA-ATGAATATATC
195654 ATCTTT-AAAGAATGAATATATC
1 ATCTTTGAAA-AATGAATATATC
*
195676 ATTTTTGAAAAATG
1 ATCTTTGAAAAATG
195690 TAGATATACC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 4 0.13
22 24 0.77
23 3 0.10
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
ATCTTTGAAAAATGAATATATC
Found at i:197140 original size:75 final size:75
Alignment explanation
Indices: 197038--197211 Score: 215
Period size: 75 Copynumber: 2.3 Consensus size: 75
197028 ATGATGTGGG
** ** * * * *
197038 CTTTCAGCATG-CCCAGTATTTGCTGATATGAACGTTCAAAATACATCAATATTCCTGATTCTGT
1 CTTTCAGCATGCCCCAACATTTGCTGATACAAACATTCAAAATACATCAAAATTCCTGATTATGA
197102 TTGAAATGGC
66 TTGAAATGGC
* * *
197112 CTTTCAGCATGCCCCAACATTTGTTGATACAAACATTCAAAATGCATCAAAATTCTTGATTATGA
1 CTTTCAGCATGCCCCAACATTTGCTGATACAAACATTCAAAATACATCAAAATTCCTGATTATGA
*
197177 TTGAAATGGG
66 TTGAAATGGC
* *
197187 TTTTCAGCATACCCCAACATTTGCT
1 CTTTCAGCATGCCCCAACATTTGCT
197212 TTTTTGTTGA
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
74 11 0.13
75 73 0.87
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (75 bp):
CTTTCAGCATGCCCCAACATTTGCTGATACAAACATTCAAAATACATCAAAATTCCTGATTATGA
TTGAAATGGC
Found at i:201439 original size:14 final size:14
Alignment explanation
Indices: 201420--201450 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
201410 AAATGTAATT
201420 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
201434 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
201448 ATG
1 ATG
201451 TAAATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGCAAAAATGAAA
Found at i:201450 original size:20 final size:20
Alignment explanation
Indices: 201424--201483 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
201414 GTAATTATGC
201424 AAAAATGAAAATGCAAAAAT
1 AAAAATGAAAATGCAAAAAT
* * * **
201444 GAAAATGTAAATACAAACGT
1 AAAAATGAAAATGCAAAAAT
201464 AAAAATGCAAAGATGCAAAA
1 AAAAATG-AAA-ATGCAAAA
201484 TGCAAATGCA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 21 0.72
21 2 0.07
22 6 0.21
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAATGCAAAAAT
Found at i:201632 original size:43 final size:44
Alignment explanation
Indices: 201568--201654 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 44
201558 CGGTGCATCA
* *
201568 AACAAAACTTTTACATGTAGGGGATAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
*
201612 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
201655 TCTAAAGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 32 0.80
44 8 0.20
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
Found at i:202158 original size:36 final size:36
Alignment explanation
Indices: 202106--202177 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
202096 TCTTACCATA
* *
202106 GAATGCTTTTGGTATCAATCTAACATGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACATGATCTTTGTG
*
202142 GAATACTTTTGGTATCAATATAACATGATGTTTGTG
1 GAATACTTTTGGTATCAATATAACATGATCTTTGTG
202178 TGCATAGCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACATGATCTTTGTG
Found at i:203728 original size:140 final size:135
Alignment explanation
Indices: 203529--203796 Score: 353
Period size: 140 Copynumber: 1.9 Consensus size: 135
203519 TTTATAAAAC
* * *
203529 TAAATAGAGTATTTATTTATTTAAAAATATTTAGAAAAGGACATCTAGTTACTTTAAGACTG-CT
1 TAAATAGAATATTTATTTATTTAAAAATATTCAGAAAAGGACATCCAGTTACTTTAAGACTGTC-
* * * *
203593 CGTTTCTTTAATATTAATAAATAAATAAATAAATATTAATGATAATTT-CTAAAAATATAATTTA
65 CCTTTCTTCAATATGAAT-AA-AAA-AAA-AAATATT-AT-A-AATTTCCTAAAAAAATAATTTA
203657 AATAAAACTAAAT
123 AATAAAACTAAAT
*
203670 TAAATATAATATTTATTTATTTAAAAATA-TCAGAAAAGGACATCCAGTTACTTTAAGACTGTCC
1 TAAATAGAATATTTATTTATTTAAAAATATTCAGAAAAGGACATCCAGTTACTTTAAGACTGTCC
* *
203734 CTTTCTTCAATATGAATAAAAACAAAAATATTATAATTTTCCTAAAAAAATAATTTAAATAAA
66 CTTTCTTCAATATGAATAAAAAAAAAAATATTATAAATTTCCTAAAAAAATAATTTAAATAAA
203797 TATATTATTT
Statistics
Matches: 115, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
133 4 0.03
134 22 0.19
135 2 0.02
136 7 0.06
137 2 0.02
138 3 0.03
139 2 0.02
140 45 0.39
141 28 0.24
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (135 bp):
TAAATAGAATATTTATTTATTTAAAAATATTCAGAAAAGGACATCCAGTTACTTTAAGACTGTCC
CTTTCTTCAATATGAATAAAAAAAAAAATATTATAAATTTCCTAAAAAAATAATTTAAATAAAAC
TAAAT
Done.