Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006781.1 Hibiscus syriacus cultivar Beakdansim tig00017182_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: 63328
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3479 original size:18 final size:18
Alignment explanation
Indices: 3431--3473 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3421 ATTATATGGA
3431 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
3447 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
3465 TATTATTAT
1 TATTATTAT
3474 GTATGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:3749 original size:8 final size:8
Alignment explanation
Indices: 3701--3785 Score: 55
Period size: 8 Copynumber: 10.0 Consensus size: 8
3691 ATTTATTTGT
*
3701 TTATTTAA
1 TTATTTTA
*
3709 TATATCTTA
1 T-TATTTTA
*
3718 TAATTTTA
1 TTATTTTA
3726 TATATTTATA
1 T-TATTT-TA
3736 TT-TTTTA
1 TTATTTTA
3743 TTATTTTTA
1 TTA-TTTTA
*
3752 TTTTTTTA
1 TTATTTTA
3760 TTCATTATTA
1 TT-ATT-TTA
*
3770 TTATATTA
1 TTATTTTA
*
3778 TTTTTTTA
1 TTATTTTA
3786 AAAAAAACCT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
7 4 0.07
8 26 0.43
9 22 0.37
10 8 0.13
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:3757 original size:18 final size:18
Alignment explanation
Indices: 3721--3771 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
3711 TATCTTATAA
* *
3721 TTTTA-TATATTTATATT
1 TTTTATTATTTTTATTTT
3738 TTTTATTATTTTTA-TTT
1 TTTTATTATTTTTATTTT
*
3755 TTTTATTCATTATTATT
1 TTTTATT-ATTTTTATT
3772 ATATTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.50
18 13 0.46
19 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTATTTTTATTTT
Found at i:3759 original size:26 final size:25
Alignment explanation
Indices: 3715--3785 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
3705 TTAATATATC
* *
3715 TTATAATTTTATATATTTATATT-TT-
1 TTATTATTTTAT-T-TTTTTATTATTA
3740 TTATTATTTTTATTTTTTTATTCATTA
1 TTATTATTT-TATTTTTTTATT-ATTA
*
3767 TTATTATATTATTTTTTTA
1 TTATTATTTTATTTTTTTA
3786 AAAAAAACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 7 0.18
25 9 0.23
26 15 0.38
27 8 0.21
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (25 bp):
TTATTATTTTATTTTTTTATTATTA
Found at i:3759 original size:34 final size:34
Alignment explanation
Indices: 3663--3760 Score: 81
Period size: 34 Copynumber: 2.9 Consensus size: 34
3653 TTATTAAATA
* ** *
3663 TATATTTCTTAATTATTTTTATTTGATTATTTATT
1 TATATTT-TTTATTATTTTTATTTTTTTATATATT
* * * * **
3698 TGT-TTATTTAATATATCTTATAATTTTATATATT
1 TATATTTTTTATTAT-TTTTATTTTTTTATATATT
3732 TATATTTTTTATTATTTTTATTTTTTTAT
1 TATATTTTTTATTATTTTTATTTTTTTAT
3761 TCATTATTAT
Statistics
Matches: 45, Mismatches: 16, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
33 6 0.13
34 28 0.62
35 11 0.24
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (34 bp):
TATATTTTTTATTATTTTTATTTTTTTATATATT
Found at i:7752 original size:14 final size:15
Alignment explanation
Indices: 7735--7768 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7725 CAAAAAGGGC
7735 AAAAAG-AAAAAAAG
1 AAAAAGCAAAAAAAG
*
7749 AAAAAGCAAAAAAGG
1 AAAAAGCAAAAAAAG
7764 AAAAA
1 AAAAA
7769 ACAAGAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGCAAAAAAAG
Found at i:7799 original size:19 final size:20
Alignment explanation
Indices: 7734--7800 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 20
7724 ACAAAAAGGG
* *
7734 CAAAAAGAAAAAAAGAAAAA
1 CAAAAAGGAAAAAACAAAAA
*
7754 GCAAAAAAGGAAAAAACAAGAA
1 -C-AAAAAGGAAAAAACAAAAA
*
7776 CAAAAA-GAAAGAACAAAAA
1 CAAAAAGGAAAAAACAAAAA
*
7795 TAAAAA
1 CAAAAA
7801 AGGGAACAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.41
20 5 0.13
21 2 0.05
22 16 0.41
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.01
Consensus pattern (20 bp):
CAAAAAGGAAAAAACAAAAA
Found at i:9343 original size:36 final size:36
Alignment explanation
Indices: 9296--9400 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
9286 GTGCTCACCA
9296 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
9332 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
9369 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
9401 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:9390 original size:37 final size:37
Alignment explanation
Indices: 9296--9405 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
9286 GTGCTCACCA
9296 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
9332 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
9369 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
9406 ATTGAAACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:9550 original size:102 final size:102
Alignment explanation
Indices: 9314--9770 Score: 639
Period size: 102 Copynumber: 4.5 Consensus size: 102
9304 CTTGAGACAG
** * * *
9314 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
9379 TGAGACAGTTTCTCTTGAAACATAAACATT-GAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
* * *
9415 TTTCCCTTGAAATGAGTTTGGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
9480 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
9517 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
9582 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
* * *
9619 TTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
** * * * ***
9683 TGAGACAACTTCTCTTGAAACACAAACCTTTGAGATTG
66 TGAGACAGTTTCTCTTGAAACATAAACATTGGA-AACA
* ** * * * *
9721 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
9771 CAAAATCTTT
Statistics
Matches: 320, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
101 130 0.41
102 190 0.59
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
Found at i:9584 original size:37 final size:37
Alignment explanation
Indices: 9517--9603 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
9507 ATTGGAAACA
** * *
9517 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
9553 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
9590 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
9604 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:9673 original size:36 final size:36
Alignment explanation
Indices: 9618--9704 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
9608 CATTGAAAAC
* ** * *
9618 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
9654 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
9690 ACTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
9705 CAAACCTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:9674 original size:203 final size:204
Alignment explanation
Indices: 9314--9770 Score: 684
Period size: 203 Copynumber: 2.2 Consensus size: 204
9304 CTTGAGACAG
* *
9314 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * *
9379 TGAGACAGTTTCTCTTGAAACATAAACATTGAAACATTTCCCTTGAAATGAGTTTGGTCTCTCTT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAACATTTCCCTAGAAATGAATTTCGTCTCTCTT
* * ** *
9444 GAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
131 GAGATAATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAACAT
9509 TGGA-AACA
196 TGGAGAACA
** *
9517 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
9582 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTG-AAACATTTCCCTAGAAATGAATTTCGTCTCTCT
*
9647 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAACC
130 TGAGATAATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAACA
* ***
9711 TTTGAGATTG
195 TTGGAGAACA
* * * *
9721 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
9771 CAAAATCTTT
Statistics
Matches: 226, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
203 132 0.58
204 94 0.42
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (204 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAACATTTCCCTAGAAATGAATTTCGTCTCTCTT
GAGATAATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAACAT
TGGAGAACA
Found at i:9753 original size:66 final size:66
Alignment explanation
Indices: 9646--9774 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 66
9636 TTCGTCTCTC
* *
9646 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAACC
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAACC
9711 T
66 T
** **
9712 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAA
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAA
9775 ATCTTTGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (66 bp):
TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAACC
T
Found at i:11009 original size:105 final size:105
Alignment explanation
Indices: 10637--11609 Score: 1419
Period size: 105 Copynumber: 9.3 Consensus size: 105
10627 GCCATCCGCG
* * * * * *
10637 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
10702 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
10746 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
10811 ACCGCTGGTTGTCAATAAACAATTTTTCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAA-CAACAA-CTTCCCAATCTCAGAGCCA
*
10853 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
10918 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
10958 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
11023 ACCGCTGGTTGTCAACAACAACTTCCCAACCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
11063 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
11128 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
11168 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
11233 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
11268 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
11333 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* **
11373 ATTTCAACTTCACAATGAAATATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
11438 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* * *
11473 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
11538 ACGGCTGGTTGTCAACAAATAATTTCCCGGT-TCCAGAGCCA
66 ACCGCTGGTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCA
* *
11579 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
11610 TAGAACAATG
Statistics
Matches: 796, Mismatches: 55, Indels: 29
0.90 0.06 0.03
Matches are distributed among these distances:
100 168 0.21
101 8 0.01
102 6 0.01
103 7 0.01
104 7 0.01
105 387 0.49
106 93 0.12
107 98 0.12
109 22 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:11371 original size:205 final size:209
Alignment explanation
Indices: 10637--11609 Score: 1426
Period size: 205 Copynumber: 4.7 Consensus size: 209
10627 GCCATCCGCG
* * * * *
10637 ATTTCAACTCCAC-GACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
10701 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
62 AGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAG
* *
10766 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
126 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAAC
*
10831 AATTTTTCCAATTTCAGAGCCA
190 AA-TTTT-CAACTTCAGAGCCA
10853 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
10918 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
10983 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTT
* *
11048 CCAACCTCAGAGCCA
195 TCAACTTCAGAGCCA
* * *
11063 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
11128 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
11193 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTT
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTT
11256 C-A-TTCAGAGCCA
196 CAACTTCAGAGCCA
*
11268 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
11333 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAATGAAATATAT
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
11398 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTT
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTT
**
11461 C-A-TTCAGATTCA
196 CAACTTCAGAGCCA
* * * *
11473 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** * *
11538 ACGGCTGGTTGTCAACAAATAATTTCCCGGT-TCCAGAGCCAATTTCAACTTCACGACGGAGGAT
66 ACCGCTGGTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCAATTTCAACTTCACAACGAAGGAT
11602 ATTGGACT
129 ATTGGACT
11610 TAGAACAATG
Statistics
Matches: 704, Mismatches: 50, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
205 278 0.39
206 45 0.06
207 2 0.00
209 2 0.00
210 194 0.28
211 7 0.01
212 102 0.14
213 49 0.07
214 3 0.00
216 21 0.03
217 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (209 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTT
CAACTTCAGAGCCA
Found at i:12646 original size:18 final size:17
Alignment explanation
Indices: 12607--12649 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12597 ATTATATGGA
12607 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
12623 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
12641 TATTATTAT
1 TATTATTAT
12650 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:21907 original size:31 final size:31
Alignment explanation
Indices: 21871--21945 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
21861 TCAAAAAACA
*
21871 TAAGATATGATCACTTTCGTTTTTATTAAAT
1 TAAGATATGATCACTTTCATTTTTATTAAAT
*
21902 TAAGATATTG-TCACTTTCATTTTTATTTAAT
1 TAAGATA-TGATCACTTTCATTTTTATTAAAT
*
21933 TAAGATGTGATCA
1 TAAGATATGATCA
21946 TCACATGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 2 0.05
31 35 0.90
32 2 0.05
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (31 bp):
TAAGATATGATCACTTTCATTTTTATTAAAT
Found at i:22109 original size:21 final size:20
Alignment explanation
Indices: 22062--22116 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
22052 TTTTAAATAA
* *
22062 ATTTTAACATAAAATATATAT
1 ATTTTAA-ATAAAATAAAAAT
22083 -TTTTAAATGAAAATAAAAAT
1 ATTTTAAAT-AAAATAAAAAT
*
22103 ATTTTAAATTAAAT
1 ATTTTAAATAAAAT
22117 TATTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.07
20 19 0.66
21 8 0.28
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTTAAATAAAATAAAAAT
Found at i:22136 original size:22 final size:24
Alignment explanation
Indices: 22111--22159 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
22101 ATATTTTAAA
*
22111 TTAAATTA-TTAATA-AAATTTAT
1 TTAAATAAGTTAATATAAATTTAT
*
22133 TT-AATAAGTTAATATAAATTTTT
1 TTAAATAAGTTAATATAAATTTAT
22156 TTAA
1 TTAA
22160 CCAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 9 0.41
24 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTAAATAAGTTAATATAAATTTAT
Found at i:23026 original size:29 final size:29
Alignment explanation
Indices: 22931--23010 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
22921 ATTGTACAGT
22931 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAAGAGGTCGCCATGCACGCCCAAC
22960 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAAGAGGTCGCCATGCACGCCCAAC
*
22989 GACCAAGGAGGTCGCCATGCAC
1 GACCAAAGAGGTCGCCATGCAC
23011 TCGGGGCGAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.30, C:0.36, G:0.26, T:0.07
Consensus pattern (29 bp):
GACCAAAGAGGTCGCCATGCACGCCCAAC
Found at i:23054 original size:36 final size:36
Alignment explanation
Indices: 23007--23086 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
22997 AGGTCGCCAT
23007 GCACTCGGGGCGACCAAGGATCGGTTCATGCATGGG
1 GCACTCGGGGCGACCAAGGATCGGTTCATGCATGGG
23043 GCACTCGGGGCGACCAAGGATCGGTTCATGCATGGG
1 GCACTCGGGGCGACCAAGGATCGGTTCATGCATGGG
23079 GCACTCGG
1 GCACTCGG
23087 ATGCATGGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.19, C:0.26, G:0.39, T:0.16
Consensus pattern (36 bp):
GCACTCGGGGCGACCAAGGATCGGTTCATGCATGGG
Found at i:23128 original size:46 final size:46
Alignment explanation
Indices: 23061--23203 Score: 166
Period size: 46 Copynumber: 3.1 Consensus size: 46
23051 GGCGACCAAG
23061 GATCGGTTCATGCATGGGGCACTCGGATGCATGGGGAGATTGGGGA
1 GATCGGTTCATGCATGGGGCACTCGGATGCATGGGGAGATTGGGGA
* **** ***
23107 GATCGGTTCATGCATGGGGCACTCGG-GGCGACCAAG-GA-TGACCAA
1 GATCGGTTCATGCATGGGGCACTCGGATGC-ATGGGGAGATTG-GGGA
23152 GGATCGGTTCATGCATGGGGCACTCGGATGCATGGGGAGATTGGGGA
1 -GATCGGTTCATGCATGGGGCACTCGGATGCATGGGGAGATTGGGGA
23199 GATCG
1 GATCG
23204 TGCATGGGAG
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
44 2 0.03
45 5 0.07
46 61 0.81
47 5 0.07
48 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.41, T:0.20
Consensus pattern (46 bp):
GATCGGTTCATGCATGGGGCACTCGGATGCATGGGGAGATTGGGGA
Found at i:23142 original size:82 final size:86
Alignment explanation
Indices: 23025--23203 Score: 276
Period size: 92 Copynumber: 2.1 Consensus size: 86
23015 GGCGACCAAG
23025 GATCGGTTCATGCATGGGGCACTC-GGG-G-C-GACCAAGGATCGGTTCATGCATGGGGCACTCG
1 GATCGGTTCATGCATGGGGCACTCGGGGCGACAGACCAAGGATCGGTTCATGCATGGGGCACTCG
23086 GATGCATGGGGAGATTGGGGA
66 GATGCATGGGGAGATTGGGGA
23107 GATCGGTTCATGCATGGGGCACTCGGGGCGACCAAGGATGACCAAGGATCGGTTCATGCATGGGG
1 GATCGGTTCATGCATGGGGCACTCGGGGCGA-C----A-GACCAAGGATCGGTTCATGCATGGGG
23172 CACTCGGATGCATGGGGAGATTGGGGA
60 CACTCGGATGCATGGGGAGATTGGGGA
23199 GATCG
1 GATCG
23204 TGCATGGGAG
Statistics
Matches: 87, Mismatches: 0, Indels: 10
0.90 0.00 0.10
Matches are distributed among these distances:
82 24 0.28
83 3 0.03
84 1 0.01
86 1 0.01
92 58 0.67
ACGTcount: A:0.21, C:0.20, G:0.41, T:0.19
Consensus pattern (86 bp):
GATCGGTTCATGCATGGGGCACTCGGGGCGACAGACCAAGGATCGGTTCATGCATGGGGCACTCG
GATGCATGGGGAGATTGGGGA
Found at i:23858 original size:21 final size:21
Alignment explanation
Indices: 23833--23876 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
23823 AATCTAGTTA
23833 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
23854 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
23875 AT
1 AT
23877 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:23943 original size:38 final size:41
Alignment explanation
Indices: 23863--23944 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
23853 TATTAGTTTG
* *
23863 TTAGTTTAAGTTATATATTATATTATATAAAAAATTAGTTAA
1 TTAGTTTAAGTTATATA-TATATTATAAAAAAAATTAATTAA
23905 TTAGTTTAAGTTAT-TA-A-A-TATAAAAAAATATTAATTAA
1 TTAGTTTAAGTTATATATATATTATAAAAAAA-ATTAATTAA
23943 TT
1 TT
23945 TGTTAGTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 9 0.24
38 11 0.30
39 1 0.03
41 2 0.05
42 14 0.38
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTATATATATATTATAAAAAAAATTAATTAA
Found at i:24404 original size:17 final size:16
Alignment explanation
Indices: 24368--24397 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24358 AGATAATTTT
24368 TGTTTAAAAAATATTG
1 TGTTTAAAAAATATTG
24384 TGTTT-AAAAATATT
1 TGTTTAAAAAATATT
24398 TAGTGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
TGTTTAAAAAATATTG
Found at i:24610 original size:20 final size:21
Alignment explanation
Indices: 24571--24615 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
24561 AATCATGATT
* *
24571 ATTAGTAATAATTACTAAATG
1 ATTAGTAATAAATACTAAATC
*
24592 ATTAGTATTAAAT-CTAAATC
1 ATTAGTAATAAATACTAAATC
24612 ATTA
1 ATTA
24616 AATATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTAGTAATAAATACTAAATC
Found at i:24691 original size:26 final size:25
Alignment explanation
Indices: 24652--24726 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 25
24642 AATCATGACT
* * *
24652 ATATCATATTATTATTAAATCATTAA
1 ATATCAAATCATTATTAAAT-AATAA
24678 ATATCAAATCATTAGATT-AATAATAA
1 ATATCAAATCATT--ATTAAATAATAA
* *
24704 TTATTAAATCATTATT-AATAATA
1 ATATCAAATCATTATTAAATAATA
24727 TTAGTAATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 10 0.24
26 26 0.62
27 3 0.07
28 3 0.07
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (25 bp):
ATATCAAATCATTATTAAATAATAA
Found at i:27772 original size:17 final size:18
Alignment explanation
Indices: 27746--27780 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
27736 AATGATTAGT
27746 AATTATTAATAATAATGA
1 AATTATTAATAATAATGA
27764 AATTA-TAATAATAATGA
1 AATTATTAATAATAATGA
27781 TTTACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATTAATAATAATGA
Found at i:27997 original size:12 final size:12
Alignment explanation
Indices: 27976--28013 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
27966 AATAATCAAT
27976 ATAATG-ATTTA
1 ATAATGAATTTA
27987 ATAATGAATTTA
1 ATAATGAATTTA
*
27999 ATAATAAATTTA
1 ATAATGAATTTA
28011 ATA
1 ATA
28014 TTTAATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (12 bp):
ATAATGAATTTA
Found at i:28067 original size:37 final size:37
Alignment explanation
Indices: 28026--28227 Score: 137
Period size: 37 Copynumber: 5.4 Consensus size: 37
28016 TAATGATTTG
*
28026 ATGATTTAGTAATTAT-ATGATAATAATCATTATAATA
1 ATGATTTAGTAATAATCATGATAATAATCATT-TAATA
* *
28063 ATGATTTAGTAATAATCATTATAATAATGATTTAATA
1 ATGATTTAGTAATAATCATGATAATAATCATTTAATA
* * * * * *
28100 ATGATTTA--AATATTTAATGAT-TTGATGATTTAGTA
1 ATGATTTAGTAATA-ATCATGATAATAATCATTTAATA
* *
28135 ATGATTT-GATAATAATCATTATAATAATGATTTAATA
1 ATGATTTAG-TAATAATCATGATAATAATCATTTAATA
* * * *
28172 ATAATCATTA-TAATAATGATTTAATAATAATGATTTGATAGTA
1 ATGAT--TTAGTAATAATCA--TGATAATAATCATTT-A-A-TA
28215 ATGATTTAGTAAT
1 ATGATTTAGTAAT
28228 GATTAGTAAT
Statistics
Matches: 131, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
35 22 0.17
36 10 0.08
37 47 0.36
38 21 0.16
39 2 0.02
40 14 0.11
41 4 0.03
42 5 0.04
43 6 0.05
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (37 bp):
ATGATTTAGTAATAATCATGATAATAATCATTTAATA
Found at i:28075 original size:26 final size:26
Alignment explanation
Indices: 28045--28227 Score: 184
Period size: 26 Copynumber: 7.2 Consensus size: 26
28035 TAATTATATG
28045 ATAATAATCATTATAATAATGATTTA
1 ATAATAATCATTATAATAATGATTTA
*
28071 GTAATAATCATTATAATAATGA-TT-
1 ATAATAATCATTATAATAATGATTTA
*
28095 -TAATAATGATT-T-A-AAT-ATTTA
1 ATAATAATCATTATAATAATGATTTA
* * * * *
28116 ATGATTTGATGATT-TAGTAATGATTTG
1 AT-A-ATAATCATTATAATAATGATTTA
28143 ATAATAATCATTATAATAATGATTTA
1 ATAATAATCATTATAATAATGATTTA
28169 ATAATAATCATTATAATAATGATTTA
1 ATAATAATCATTATAATAATGATTTA
* *
28195 ATAATAATGATTTGATAGTAATGATTTA
1 ATAATAATCA-TT-ATAATAATGATTTA
*
28223 GTAAT
1 ATAAT
28228 GATTAGTAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 1 0.01
22 2 0.02
23 11 0.08
24 8 0.06
25 8 0.06
26 71 0.54
27 8 0.06
28 17 0.13
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (26 bp):
ATAATAATCATTATAATAATGATTTA
Found at i:28078 original size:98 final size:99
Alignment explanation
Indices: 28014--28201 Score: 333
Period size: 98 Copynumber: 1.9 Consensus size: 99
28004 AAATTTAATA
* *
28014 TTTAATGATTTGATGATTTAGTAATTATATGATAATAATCATTATAATAATGATTTAGTAATAAT
1 TTTAATGATTTGATGATTTAGTAATGATATGATAATAATCATTATAATAATGATTTAATAATAAT
*
28079 CATTATAATAATGATTTAATAAT-GATTTAAATA
66 CATTATAATAATGATTTAATAATAAATTTAAATA
*
28112 TTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAAT
1 TTTAATGATTTGATGATTTAGTAATGATATGATAATAATCATTATAATAATGATTTAATAATAAT
28177 CATTATAATAATGATTTAATAATAA
66 CATTATAATAATGATTTAATAATAA
28202 TGATTTGATA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
98 85 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (99 bp):
TTTAATGATTTGATGATTTAGTAATGATATGATAATAATCATTATAATAATGATTTAATAATAAT
CATTATAATAATGATTTAATAATAAATTTAAATA
Found at i:28253 original size:21 final size:21
Alignment explanation
Indices: 28229--28302 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
28219 TTTAGTAATG
28229 ATTAGTAATAATGAAATTATT
1 ATTAGTAATAATGAAATTATT
* * *
28250 ATTAATATTTAATGATTTGATATTAATG
1 ATTAGTA-ATAATGA----A-ATT-ATT
28278 ATTAGTAATAATGAAATTATT
1 ATTAGTAATAATGAAATTATT
28299 ATTA
1 ATTA
28303 ATATTTAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 12 0.30
22 9 0.22
23 1 0.03
26 1 0.03
27 9 0.22
28 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (21 bp):
ATTAGTAATAATGAAATTATT
Found at i:28281 original size:49 final size:49
Alignment explanation
Indices: 28224--28418 Score: 300
Period size: 49 Copynumber: 4.2 Consensus size: 49
28214 AATGATTTAG
28224 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
*
28273 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
* *
28322 TAATGATTAGTAATAAT-AATTTATTATTAATATTTAATAATTTG--A-
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
28367 T-A--A-TA-TAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
28411 TAATGATT
1 TAATGATT
28419 TGATATTAAT
Statistics
Matches: 133, Mismatches: 5, Indels: 17
0.86 0.03 0.11
Matches are distributed among these distances:
40 7 0.05
41 27 0.20
42 1 0.01
43 1 0.01
44 2 0.02
45 2 0.02
46 1 0.01
47 1 0.01
48 26 0.20
49 65 0.49
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (49 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:28415 original size:14 final size:14
Alignment explanation
Indices: 28396--28433 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
28386 TTATTAATAT
28396 TTAATGATTTGATA
1 TTAATGATTTGATA
28410 TTAATGATTTGATA
1 TTAATGATTTGATA
28424 TTAATGATTT
1 TTAATGATTT
28434 AGTAATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (14 bp):
TTAATGATTTGATA
Found at i:30726 original size:22 final size:22
Alignment explanation
Indices: 30701--30749 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
30691 ACAACTAATA
*
30701 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
30723 AACTATTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
30745 AACTA
1 AACTA
30750 ATAAACTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:30727 original size:30 final size:30
Alignment explanation
Indices: 30693--30819 Score: 94
Period size: 31 Copynumber: 4.4 Consensus size: 30
30683 TCCCTTAAAC
30693 AACTAATAAACTATTCTTTAATATAAC--T
1 AACTAATAAACTATTCTTTAATATAACTTT
*
30721 ---T--T-AACTATTCTTTAATATAACGTT
1 AACTAATAAACTATTCTTTAATATAACTTT
* * *
30745 AACTAATAAACTGTTTTTTTAATATAACTTA
1 AACTAATAAACT-ATTCTTTAATATAACTTT
*
30776 AACTAATAAATTATT-TTTAATTATAA-TTT
1 AACTAATAAACTATTCTTTAA-TATAACTTT
*
30805 ATTACTAAAAAACTA
1 A--ACTAATAAACTA
30820 ATTAACTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 21
0.72 0.08 0.19
Matches are distributed among these distances:
22 19 0.24
23 1 0.01
24 1 0.01
25 1 0.01
27 1 0.01
29 9 0.12
30 11 0.14
31 35 0.45
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTT
Found at i:30812 original size:31 final size:31
Alignment explanation
Indices: 30726--30801 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
30716 TAACTTTAAC
30726 TATTCTTTAATATAACGTT-AACTAATAAACTG
1 TATT-TTTAATATAAC-TTAAACTAATAAACTG
*
30758 TTTTTTTAATATAACTTAAACTAATAAA-T-
1 TATTTTTAATATAACTTAAACTAATAAACTG
30787 TATTTTTAATTATAA
1 TATTTTTAA-TATAA
30802 TTTATTACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
29 8 0.20
30 8 0.20
31 21 0.52
32 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (31 bp):
TATTTTTAATATAACTTAAACTAATAAACTG
Found at i:31099 original size:29 final size:29
Alignment explanation
Indices: 31066--31159 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 29
31056 TGTTTTACCC
31066 TAATTTATAATAATAAACTAATTAACTAA
1 TAATTTATAATAATAAACTAATTAACTAA
* *
31095 TAATTTATAACAATAAACTAATTTAAATAA
1 TAATTTATAATAATAAACTAA-TTAACTAA
* *
31125 TTATTCTTTTATATAACTTAAACTAATTAACTAA
1 -TAAT-TTATA-ATAA--TAAACTAATTAACTAA
31159 T
1 T
31160 TTTTTTTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 20 0.38
30 7 0.13
31 3 0.06
32 4 0.08
33 4 0.08
34 7 0.13
35 8 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATTTATAATAATAAACTAATTAACTAA
Found at i:31118 original size:18 final size:18
Alignment explanation
Indices: 31065--31119 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
31055 TTGTTTTACC
*
31065 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
31083 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
31095 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
31112 CTAATTTA
1 CTAATTTA
31120 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:31137 original size:34 final size:32
Alignment explanation
Indices: 31100--31178 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 32
31090 ACTAATAATT
31100 TATAACAATAAACTAATTTAAATAATTATTCTTTTA
1 TATAAC-ATAAACTAA-TTAAATAATT-TT-TTTTA
* *
31136 TATAACTTAAACTAATTAACTAATTTTTTTTA
1 TATAACATAAACTAATTAAATAATTTTTTTTA
*
31168 TATAATATAAA
1 TATAACATAAA
31179 TTCAACAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 14 0.36
33 2 0.05
34 9 0.23
35 8 0.21
36 6 0.15
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.46
Consensus pattern (32 bp):
TATAACATAAACTAATTAAATAATTTTTTTTA
Found at i:31533 original size:11 final size:11
Alignment explanation
Indices: 31514--31557 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
31504 TGAAGGACTG
31514 CAATAATGCAA
1 CAATAATGCAA
* *
31525 CACTAATGCAG
1 CAATAATGCAA
*
31536 CAATAAGTGCTA
1 CAATAA-TGCAA
31548 CAATAATGCA
1 CAATAATGCA
31558 GCTGAATTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (11 bp):
CAATAATGCAA
Found at i:31557 original size:23 final size:22
Alignment explanation
Indices: 31513--31559 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
31503 CTGAAGGACT
*
31513 GCAATAATGCAACACTAATGCA
1 GCAATAATGCAACAATAATGCA
*
31535 GCAATAAGTGCTACAATAATGCA
1 GCAATAA-TGCAACAATAATGCA
31558 GC
1 GC
31560 TGAATTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
GCAATAATGCAACAATAATGCA
Found at i:31685 original size:61 final size:61
Alignment explanation
Indices: 31610--31732 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
31600 GACCACGTGA
*
31610 ACAAAGCTCTTGGCGACCTATCCCATGCCCCGTGCATGGCCCATGCATAGCACCAAAGCAG
1 ACAAAGCTCTTGGCGACCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAG
*
31671 ACAAAGCTCTTGGCGACCTATCCCATACCCTGTGCATGGCCCATGCATAGCACCAAAGCAG
1 ACAAAGCTCTTGGCGACCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAG
31732 A
1 A
31733 GCATCAGCGG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (61 bp):
ACAAAGCTCTTGGCGACCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAG
Found at i:31754 original size:28 final size:28
Alignment explanation
Indices: 31722--31779 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
31712 CATGCATAGC
*
31722 ACCAAAGCAGAGCATCAGCGGGCAAAGA
1 ACCAAAGCAGAGCAGCAGCGGGCAAAGA
31750 ACCAAAGCAGAGCAGCAGCGGGCAAAGA
1 ACCAAAGCAGAGCAGCAGCGGGCAAAGA
31778 AC
1 AC
31780 GTTGGACGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.26, G:0.29, T:0.02
Consensus pattern (28 bp):
ACCAAAGCAGAGCAGCAGCGGGCAAAGA
Found at i:31896 original size:29 final size:29
Alignment explanation
Indices: 31783--31894 Score: 190
Period size: 29 Copynumber: 3.9 Consensus size: 29
31773 AAAGAACGTT
31783 GGACGCCGGGCGTGCATGGCGACCTTATA
1 GGACGCCGGGCGTGCATGGCGACCTTATA
*
31812 GGACGTCGGGCGTGCATGGCGACCTTATA
1 GGACGCCGGGCGTGCATGGCGACCTTATA
31841 GGACGCCGGGCGTGCATGGCGACC-TATAA
1 GGACGCCGGGCGTGCATGGCGACCTTAT-A
*
31870 GGACGTCGGGCGTGCATGGCGACCT
1 GGACGCCGGGCGTGCATGGCGACCT
31895 ATGCTGGTTG
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
28 3 0.04
29 75 0.96
ACGTcount: A:0.17, C:0.27, G:0.39, T:0.17
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTTATA
Found at i:33697 original size:49 final size:50
Alignment explanation
Indices: 33631--33742 Score: 174
Period size: 49 Copynumber: 2.3 Consensus size: 50
33621 TTTTTAAGAT
* **
33631 ATAATAA-ATATTAAATTTTAAATTTAAATTTAATTATATTA-TTTTATC
1 ATAATAACATAATAAATTTTAAATTTAAATCCAATTATATTATTTTTATC
*
33679 ATAATAACATAATAAATTTTAATTTTAAATCCAATTATATTATTTTTATC
1 ATAATAACATAATAAATTTTAAATTTAAATCCAATTATATTATTTTTATC
33729 ATAATAACATAATA
1 ATAATAACATAATA
33743 GTTTGAAGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 7 0.12
49 30 0.52
50 21 0.36
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (50 bp):
ATAATAACATAATAAATTTTAAATTTAAATCCAATTATATTATTTTTATC
Found at i:36247 original size:40 final size:40
Alignment explanation
Indices: 36192--36273 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
36182 CATAGCCCAA
36192 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
1 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
36232 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
1 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
36272 TG
1 TG
36274 AGCACAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (40 bp):
TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
Found at i:36535 original size:121 final size:121
Alignment explanation
Indices: 36300--36551 Score: 319
Period size: 121 Copynumber: 2.1 Consensus size: 121
36290 CAATGCTATC
* * * * *
36300 ATCATAATCAGAATATATAAGCACACACAGTGCTATCATATCAGAATCGTAATGTGCACACAAAG
1 ATCATAATCAGAACATATAAGCACACACAATACTATCATATCAGAATCGTAATCTGCACACAAAA
* * * *
36365 TGAAATAAGATCATAGTATATATATACTAGTGTACCCCACCGATTCACCACAGTAT
66 TGAAATAACATCAGAATATATATATACTAGTGTACCCCACCGATACACCACAGTAT
* * *
36421 ATCAGAATCGGAACATATAAGCACACACAATACTATCATATCAGAATTGTAATCTGCACACAAAA
1 ATCATAATCAGAACATATAAGCACACACAATACTATCATATCAGAATCGTAATCTGCACACAAAA
* * * * *
36486 TGCAATCACATCAGAATATATATATACTAGTGTACCTTCA--GGTAACACCACATTAT
66 TGAAATAACATCAGAATATATATATACTAGTGTACC-CCACCGAT-ACACCACAGTAT
36542 ATCATAATCA
1 ATCATAATCA
36552 CTCCACCTCA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
120 2 0.02
121 106 0.96
122 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.26
Consensus pattern (121 bp):
ATCATAATCAGAACATATAAGCACACACAATACTATCATATCAGAATCGTAATCTGCACACAAAA
TGAAATAACATCAGAATATATATATACTAGTGTACCCCACCGATACACCACAGTAT
Found at i:44142 original size:15 final size:15
Alignment explanation
Indices: 44124--44153 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44114 ACTAAAAAAA
44124 GTAAAAAGCTACTTT
1 GTAAAAAGCTACTTT
*
44139 GTAAAAAGGTACTTT
1 GTAAAAAGCTACTTT
44154 AATATGTTTC
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:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (15 bp):
GTAAAAAGCTACTTT
Found at i:45300 original size:54 final size:54
Alignment explanation
Indices: 45240--45417 Score: 157
Period size: 54 Copynumber: 3.3 Consensus size: 54
45230 GAAGTTTTAT
* *
45240 TTTATTTTAATAATTTAATATTAGTATCCTTAAAAATAATTTATTACTTAATAA
1 TTTATTTTAATAATTTAATATTAATATCCTTAAAAATAATTTATTATTTAATAA
* * ** * ** *
45294 TTTATTTTATTTATTTAA-A--AATAAACAT-AATTTAAATTATATATTTAATATAA
1 TTTATTTTAATAATTTAATATTAATATCCTTAAAAATAATTTAT-TATTT-A-ATAA
* * * *
45347 TTTATTACTTAATAATTTAATATTAACATCATTAAAAATAATGTATTATTTACTAA
1 TTTATT--TTAATAATTTAATATTAATATCCTTAAAAATAATTTATTATTTAATAA
45403 TTTATTTTAATAATT
1 TTTATTTTAATAATT
45418 ATTTTAAATA
Statistics
Matches: 93, Mismatches: 22, Indels: 18
0.70 0.17 0.14
Matches are distributed among these distances:
50 9 0.10
51 9 0.10
52 1 0.01
53 11 0.12
54 25 0.27
55 10 0.11
56 10 0.11
57 1 0.01
58 9 0.10
59 8 0.09
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (54 bp):
TTTATTTTAATAATTTAATATTAATATCCTTAAAAATAATTTATTATTTAATAA
Found at i:45363 original size:15 final size:14
Alignment explanation
Indices: 45343--45453 Score: 74
Period size: 15 Copynumber: 8.1 Consensus size: 14
45333 TATATTTAAT
45343 ATAATTTATTACTTA
1 ATAATTTATTA-TTA
*
45358 ATAATTTAATATTA
1 ATAATTTATTATTA
* * **
45372 A-CA-TCATTAAAA
1 ATAATTTATTATTA
*
45384 ATAATGTATTATTTA
1 ATAATTTATTA-TTA
*
45399 CTAATTTATT-TTA
1 ATAATTTATTATTA
45412 ATAA-TTATT-TTA
1 ATAATTTATTATTA
45424 A-ATATTTATTACTTA
1 ATA-ATTTATTA-TTA
45439 ATAATTTATT-TTA
1 ATAATTTATTATTA
45452 AT
1 AT
45454 TTATTATAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
11 1 0.01
12 16 0.22
13 18 0.24
14 8 0.11
15 30 0.41
16 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (14 bp):
ATAATTTATTATTA
Found at i:45416 original size:13 final size:13
Alignment explanation
Indices: 45395--45453 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
45385 TAATGTATTA
*
45395 TTTACTAATTTAT
1 TTTAATAATTTAT
45408 TTTAATAA-TTAT
1 TTTAATAATTTAT
45420 TTTAA-ATATTTAT
1 TTTAATA-ATTTAT
45433 TACTTAATAATTTAT
1 T--TTAATAATTTAT
45448 TTTAAT
1 TTTAAT
45454 TTATTATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 1 0.03
12 10 0.25
13 17 0.43
15 11 0.28
16 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAATAATTTAT
Found at i:45445 original size:40 final size:41
Alignment explanation
Indices: 45337--45453 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 41
45327 AAATTATATA
* *
45337 TTTAATATAATTTATTACTTAATAATTTAATATTAA-CATCAT
1 TTTAA-ATAATTTATTACTTAATAATTT-ATTTTAATAATCAT
** * * * *
45379 TAAAAATAATGTATTATTTACTAATTTATTTTAATAATTAT
1 TTTAAATAATTTATTACTTAATAATTTATTTTAATAATCAT
45420 TTTAAAT-ATTTATTACTTAATAATTTATTTTAAT
1 TTTAAATAATTTATTACTTAATAATTTATTTTAAT
45454 TTATTATAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 30 0.49
41 28 0.46
42 3 0.05
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (41 bp):
TTTAAATAATTTATTACTTAATAATTTATTTTAATAATCAT
Found at i:45452 original size:28 final size:25
Alignment explanation
Indices: 45402--45452 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 25
45392 TTATTTACTA
45402 ATTTATTTTAATAATTATTTTAAAT
1 ATTTATTTTAATAATTATTTTAAAT
45427 ATTTATTACTTAATAATTTATTTTAA
1 ATTTATT--TTAATAA-TTATTTTAA
45453 TTTATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTATTTTAATAATTATTTTAAAT
Found at i:45455 original size:25 final size:23
Alignment explanation
Indices: 45391--45460 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 23
45381 AAAATAATGT
45391 ATTATTTACTAATTTATT-TTAATA
1 ATTATTT--TAATTTATTATTAATA
45415 ATTATTTTAAATATTTATTACTTAATA
1 ATTATTTT--A-ATTTATTA-TTAATA
45442 ATTTATTTTAATTTATTAT
1 A-TTATTTTAATTTATTAT
45461 AATTTAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
22 1 0.03
24 9 0.22
25 15 0.38
26 1 0.03
27 7 0.17
28 7 0.17
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATTTTAATTTATTATTAATA
Found at i:45460 original size:41 final size:42
Alignment explanation
Indices: 45323--45469 Score: 133
Period size: 41 Copynumber: 3.5 Consensus size: 42
45313 AATAAACATA
*
45323 ATTTAAATTA-TATATTTAATATAATTTATTACTTAATAATTT
1 ATTTTAATTATTATATTTAA-ATAATTTATTACTTAATAATTT
* * * ** * * *
45365 AATATTAA-CATCAT-TAAAAATAATGTATTATTTACTAATTT
1 -ATTTTAATTATTATATTTAAATAATTTATTACTTAATAATTT
*
45406 ATTTTAATAATTAT-TTTAAAT-ATTTATTACTTAATAATTT
1 ATTTTAATTATTATATTTAAATAATTTATTACTTAATAATTT
45446 ATTTTAATTTATTATAATTTAAAT
1 ATTTTAA-TTATTAT-ATTTAAAT
45470 GATATATTTT
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
40 29 0.36
41 34 0.42
42 4 0.05
43 14 0.17
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (42 bp):
ATTTTAATTATTATATTTAAATAATTTATTACTTAATAATTT
Found at i:45467 original size:28 final size:27
Alignment explanation
Indices: 45408--45485 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
45398 ACTAATTTAT
*
45408 TTTAATAATTATTTTAAATATTTATTA
1 TTTAATAATTATTTTAAATATTTATAA
* *
45435 CTTAATAATTTATTTT-AATTTATTATAA
1 TTTAATAA-TTATTTTAAATAT-TTATAA
* *
45463 TTTAAATGATATATTTTATATAT
1 TTT-AATAAT-TATTTTAAATAT
45486 CATAATATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
27 11 0.28
28 15 0.38
29 10 0.26
30 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTAATAATTATTTTAAATATTTATAA
Found at i:46800 original size:81 final size:80
Alignment explanation
Indices: 46631--46800 Score: 182
Period size: 81 Copynumber: 2.1 Consensus size: 80
46621 AATTTGAAAC
* ** * * *
46631 ATATTTAATAGTTATATAACTCAACAAAATGTCACATTATACTCAAGAGACTATTTATATATTTT
1 ATATTTAATAATTATATAACTCAACAAAACCTCACAATATACTCAAGAGACTATTTATATACTTC
46696 ACGCTAAAATTTTGT
66 ACGCTAAAATTTTGT
* * * ** *
46711 AAATTTTAATAATTGATA-GACTCAACAAAACCTCACAATATAGTCAAGAGGTTATTTGTATACT
1 ATA-TTTAATAATT-ATATAACTCAACAAAACCTCACAATATACTCAAGAGACTATTTATATACT
46775 TCAC-CTAAAATTTATTGT
64 TCACGCTAAAA-TT-TTGT
46793 ATATTTAA
1 ATATTTAA
46801 ATGTTTTAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
80 8 0.11
81 56 0.77
82 9 0.12
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (80 bp):
ATATTTAATAATTATATAACTCAACAAAACCTCACAATATACTCAAGAGACTATTTATATACTTC
ACGCTAAAATTTTGT
Found at i:49057 original size:2 final size:2
Alignment explanation
Indices: 49050--49081 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49040 CTCTTTTTCC
49050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49082 GGGTAAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50790 original size:19 final size:19
Alignment explanation
Indices: 50766--50805 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
50756 GATTGGTTTT
50766 CTCAATCTCTATGCGTTGC
1 CTCAATCTCTATGCGTTGC
50785 CTCAATCTCTATGCGTTGC
1 CTCAATCTCTATGCGTTGC
50804 CT
1 CT
50806 ATATAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.38
Consensus pattern (19 bp):
CTCAATCTCTATGCGTTGC
Found at i:50924 original size:19 final size:20
Alignment explanation
Indices: 50888--50930 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
50878 TTTCGTTGTA
50888 TATTTTTTTAACGAAAAAAT
1 TATTTTTTTAACGAAAAAAT
50908 TATTTTTATTAA-G-AAAAAT
1 TATTTTT-TTAACGAAAAAAT
50927 TATT
1 TATT
50931 AGTACATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TATTTTTTTAACGAAAAAAT
Found at i:56248 original size:55 final size:55
Alignment explanation
Indices: 56175--56448 Score: 378
Period size: 55 Copynumber: 5.0 Consensus size: 55
56165 CATAGTACTA
* * * *
56175 TACGGTGA-TCATCAACTCATGATGAATTCTGTGGATTTGCACAC-AAGGTGTCTG
1 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAA-GTGCCTG
*
56229 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTT
1 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTG
* * *
56284 TATGGTGATTCATCAACTCATGATAAATTCCATGAATATGCACACGAAGTGCCTG
1 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTG
* *
56339 TACGGTGATTCATTAA--C-TGATGTATTCCGTGAATATGCACACGAAGTGCCTG
1 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTG
* * *
56391 TACGGTGATTCATAAAACTCATGATGAATTCCGTGAATATGCACATGAAGTGCTTG
1 TACGGTGATTCAT-CAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTG
56447 TA
1 TA
56449 GTACACATAT
Statistics
Matches: 196, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
52 45 0.23
53 3 0.02
54 8 0.04
55 104 0.53
56 36 0.18
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (55 bp):
TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTG
Found at i:56895 original size:20 final size:20
Alignment explanation
Indices: 56870--56921 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
56860 CGATGTTGGT
56870 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
56890 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
56910 TGGTATCGATAC
1 TGGTATCGATAC
56922 TACCCTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:56943 original size:22 final size:23
Alignment explanation
Indices: 56879--56936 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 23
56869 TTGGTATCGA
56879 TACCCTTACCATGGTATCG--A-
1 TACCCTTACCATGGTATCGATAC
56899 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTATCGATAC
*
56922 TACCCTT-CTATGGTA
1 TACCCTTACCATGGTA
56937 CTGATACCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 19 0.56
22 8 0.24
23 7 0.21
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (23 bp):
TACCCTTACCATGGTATCGATAC
Done.