Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005159.1 Hibiscus syriacus cultivar Beakdansim tig00011632_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: 51299
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:5284 original size:15 final size:16
Alignment explanation
Indices: 5254--5286 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5244 ATTTTTCTTA
*
5254 ATAAAATATGTTATTT
1 ATAAAATATATTATTT
5270 ATAAAA-ATATTATTT
1 ATAAAATATATTATTT
5285 AT
1 AT
5287 GAGTTACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATAAAATATATTATTT
Found at i:5743 original size:16 final size:18
Alignment explanation
Indices: 5722--5767 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
5712 TATAATTGCT
5722 TAATTTTATTT-AAAA-A
1 TAATTTTATTTAAAAATA
5738 TAATTTTATTCTAAAAATA
1 TAATTTTATT-TAAAAATA
5757 TAATTTTATTT
1 TAATTTTATTT
5768 TATTTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.37
17 1 0.04
18 5 0.19
19 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTTTATTTAAAAATA
Found at i:5775 original size:40 final size:43
Alignment explanation
Indices: 5700--5787 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 43
5690 TATACATATA
5700 TATTCTAAAAAATATAATTGCTTAATTTTATTTAAAAATAATTT
1 TATTCTAAAAAATATAATT-CTTAATTTTATTTAAAAATAATTT
* *
5744 TATTCT-AAAAATATAATT-TT-ATTTTATTTAAATATGATTT
1 TATTCTAAAAAATATAATTCTTAATTTTATTTAAAAATAATTT
5784 TATT
1 TATT
5788 TTATTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 22 0.52
41 2 0.05
43 12 0.29
44 6 0.14
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (43 bp):
TATTCTAAAAAATATAATTCTTAATTTTATTTAAAAATAATTT
Found at i:5792 original size:26 final size:26
Alignment explanation
Indices: 5759--5812 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
5749 TAAAAATATA
*
5759 ATTTTATTTTATTTAAATATGATTTT
1 ATTTTATTTTATTTAAATATAATTTT
5785 ATTTTATTTTATTTAAATATAATTTT
1 ATTTTATTTTATTTAAATATAATTTT
5811 AT
1 AT
5813 CTAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTTATTTTATTTAAATATAATTTT
Found at i:5811 original size:16 final size:16
Alignment explanation
Indices: 5722--5825 Score: 68
Period size: 16 Copynumber: 6.3 Consensus size: 16
5712 TATAATTGCT
*
5722 TAATTTTATTTAAAAA
1 TAATTTTATTTAAATA
5738 TAATTTTATTCTAAAAATA
1 TAATTTTATT-T--AAATA
* *
5757 TAATTTTATTT-TATT
1 TAATTTTATTTAAATA
* * * *
5772 TAAATATGATTT-TATT
1 T-AATTTTATTTAAATA
*
5788 TTATTTTATTTAAATA
1 TAATTTTATTTAAATA
*
5804 TAATTTTATCTAAAATA
1 TAATTTTAT-TTAAATA
5821 TAATT
1 TAATT
5826 AAACTTAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
15 10 0.14
16 33 0.47
17 12 0.17
18 1 0.01
19 14 0.20
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (16 bp):
TAATTTTATTTAAATA
Found at i:5821 original size:17 final size:16
Alignment explanation
Indices: 5790--5825 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5780 ATTTTATTTT
*
5790 ATTTTATTTAAATATA
1 ATTTTATTAAAATATA
5806 ATTTTATCTAAAATATA
1 ATTTTAT-TAAAATATA
5823 ATT
1 ATT
5826 AAACTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTATTAAAATATA
Found at i:7103 original size:14 final size:14
Alignment explanation
Indices: 7084--7123 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
7074 ACAGACTTGT
7084 TGTTTTCTACATTC
1 TGTTTTCTACATTC
* *
7098 TGTTTTATACAGTC
1 TGTTTTCTACATTC
7112 TGTTTTCTACAT
1 TGTTTTCTACAT
7124 GGTATCAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (14 bp):
TGTTTTCTACATTC
Found at i:16706 original size:12 final size:12
Alignment explanation
Indices: 16689--16753 Score: 130
Period size: 12 Copynumber: 5.4 Consensus size: 12
16679 CCATTGAACA
16689 CAGCTGAGCTGC
1 CAGCTGAGCTGC
16701 CAGCTGAGCTGC
1 CAGCTGAGCTGC
16713 CAGCTGAGCTGC
1 CAGCTGAGCTGC
16725 CAGCTGAGCTGC
1 CAGCTGAGCTGC
16737 CAGCTGAGCTGC
1 CAGCTGAGCTGC
16749 CAGCT
1 CAGCT
16754 TCACCATTCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (12 bp):
CAGCTGAGCTGC
Found at i:17941 original size:20 final size:20
Alignment explanation
Indices: 17916--18005 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
17906 TCCTATTACT
*
17916 TGGTAATCTTTTATTTCCAC
1 TGGTAATCTTTTATTCCCAC
*
17936 TGGTAATCTTTTATTTCCAC
1 TGGTAATCTTTTATTCCCAC
*
17956 CGGTAATCTTTTATTCCCAC
1 TGGTAATCTTTTATTCCCAC
17976 TGGTAATCTTTTATTCCCAC
1 TGGTAATCTTTTATTCCCAC
*
17996 TAGTAATCTT
1 TGGTAATCTT
18006 ACCTCCCGTG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.47
Consensus pattern (20 bp):
TGGTAATCTTTTATTCCCAC
Found at i:20849 original size:2 final size:2
Alignment explanation
Indices: 20842--20875 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20832 TTACTTGTTA
20842 AT AT 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 AT AT
20876 CACAAGGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22430 original size:157 final size:157
Alignment explanation
Indices: 22144--22457 Score: 610
Period size: 157 Copynumber: 2.0 Consensus size: 157
22134 AGAGTAATGC
22144 TATACTCCAATAATATTACTCTCAAATATAATCTTACATTATGTGAATCAAATATTCCTGCACTC
1 TATACTCCAATAATATTACTCTCAAATATAATCTTACATTATGTGAATCAAATATTCCTGCACTC
22209 TAAGAAGAGTTTATACGAGTAAGAAGAAGAATCTTTGACAAATCAATCAGTGCTTGTTACTTTCT
66 TAAGAAGAGTTTATACGAGTAAGAAGAAGAATCTTTGACAAATCAATCAGTGCTTGTTACTTTCT
22274 CATCAGATAAGTGAAAAATAAGAGATT
131 CATCAGATAAGTGAAAAATAAGAGATT
*
22301 TATACTCCAATAATATTACTCTCAAATATAGTCTTACATTATGTGAATCAAATATTCCTGCACTC
1 TATACTCCAATAATATTACTCTCAAATATAATCTTACATTATGTGAATCAAATATTCCTGCACTC
*
22366 TAAGAAGAGTTTATACGAGTAAGAAGAATAATCTTTGACAAATCAATCAGTGCTTGTTACTTTCT
66 TAAGAAGAGTTTATACGAGTAAGAAGAAGAATCTTTGACAAATCAATCAGTGCTTGTTACTTTCT
22431 CATCAGATAAGTGAAAAATAAGAGATT
131 CATCAGATAAGTGAAAAATAAGAGATT
22458 GTGAACATCA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (157 bp):
TATACTCCAATAATATTACTCTCAAATATAATCTTACATTATGTGAATCAAATATTCCTGCACTC
TAAGAAGAGTTTATACGAGTAAGAAGAAGAATCTTTGACAAATCAATCAGTGCTTGTTACTTTCT
CATCAGATAAGTGAAAAATAAGAGATT
Found at i:27031 original size:58 final size:56
Alignment explanation
Indices: 26935--27044 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 56
26925 TTAATTTATA
* *
26935 TTAGTTTGTTTGTTTGTTGAAGTTATATTATATGAAAAAAATTAGTTAATTAGGTTT
1 TTAGTTTGTTAGTTTGTTGAAGTTAGATTATATGAAAAAAA-TAGTTAATTAGGTTT
* *
26992 TTAGTTTGTTAGTTTAAGTT-AAGTTGGATTATAAT-AAAAAAATAGTTTATTAG
1 TTAGTTTGTTAGTTT--GTTGAAGTTAGATTAT-ATGAAAAAAATAGTTAATTAG
27045 TTTAAGTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 24 0.52
58 17 0.37
59 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (56 bp):
TTAGTTTGTTAGTTTGTTGAAGTTAGATTATATGAAAAAAATAGTTAATTAGGTTT
Found at i:29395 original size:15 final size:14
Alignment explanation
Indices: 29366--29404 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
29356 TGCTAAATTT
29366 TATTAAA-ACTTAAA
1 TATTAAATA-TTAAA
29380 TATTATAATATTAAA
1 TATTA-AATATTAAA
29395 TATTAAATAT
1 TATTAAATAT
29405 GCATGTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 12 0.52
16 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTAAATATTAAA
Found at i:29396 original size:7 final size:7
Alignment explanation
Indices: 29366--29404 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
29356 TGCTAAATTT
29366 TATTAAA
1 TATTAAA
29373 -ACTTAAA
1 TA-TTAAA
29380 TATTATAA
1 TATTA-AA
29388 TATTAAA
1 TATTAAA
29395 TATTAAA
1 TATTAAA
29402 TAT
1 TAT
29405 GCATGTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 20 0.69
8 8 0.28
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (7 bp):
TATTAAA
Found at i:29452 original size:16 final size:16
Alignment explanation
Indices: 29433--29493 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
29423 TGTAAAAAGA
29433 ATAAATTTGACTATTT
1 ATAAATTTGACTATTT
*
29449 ATAAATATAAATTCGACTAGTT
1 AT-AA-AT---TT-GACTATTT
*
29471 ATAGATTTGACTATTT
1 ATAAATTTGACTATTT
29487 ATAAATT
1 ATAAATT
29494 CGATTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 15 0.43
17 4 0.11
18 2 0.06
20 2 0.06
21 3 0.09
22 9 0.26
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (16 bp):
ATAAATTTGACTATTT
Found at i:29537 original size:11 final size:11
Alignment explanation
Indices: 29523--29632 Score: 60
Period size: 11 Copynumber: 9.2 Consensus size: 11
29513 TCTATTTAAA
*
29523 TATTTAATCAT
1 TATTAAATCAT
*
29534 TATTAAATAAT
1 TATTAAATCAT
29545 TATTAGTAATCAT
1 TATTA--AATCAT
*
29558 TGTTAAATCAT
1 TATTAAATCAT
*
29569 TATTAGTAATTAT
1 TATTA--AATCAT
*
29582 TA-TAATTTCAT
1 TATTAA-ATCAT
*
29593 TATTACTAATCAA
1 TATTA--AATCAT
*
29606 TACTAAATCAT
1 TATTAAATCAT
29617 TAGTATCAAATCAT
1 TA-T-T-AAATCAT
29631 TA
1 TA
29633 AATATTAATA
Statistics
Matches: 75, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
10 1 0.01
11 36 0.48
12 4 0.05
13 24 0.32
14 10 0.13
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:29554 original size:24 final size:24
Alignment explanation
Indices: 29527--29584 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
29517 TTTAAATATT
29527 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATAATTATTAG
* *
29551 TAATCATTGTTAAATCATTATTAG
1 TAATCATTATTAAATAATTATTAG
*
29575 TAATTATTAT
1 TAATCATTAT
29585 AATTTCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (24 bp):
TAATCATTATTAAATAATTATTAG
Found at i:29592 original size:24 final size:24
Alignment explanation
Indices: 29527--29618 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
29517 TTTAAATATT
*
29527 TAATCATT-ATTAAATAATTATTAG
1 TAATCATTGA-TAAATCATTATTAG
*
29551 TAATCATTGTTAAATCATTATTAG
1 TAATCATTGATAAATCATTATTAG
* * *
29575 TAATTATT-ATAATTTCATTATTAC
1 TAATCATTGATAA-ATCATTATTAG
*
29599 TAATCAAT-ACTAAATCATTA
1 TAATCATTGA-TAAATCATTA
29619 GTATCAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.05
24 50 0.89
25 3 0.05
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (24 bp):
TAATCATTGATAAATCATTATTAG
Found at i:29705 original size:15 final size:15
Alignment explanation
Indices: 29685--29727 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
29675 TATCATTACT
29685 AAATCATTAAATATA
1 AAATCATTAAATATA
29700 AAATCATTAAATATA
1 AAATCATTAAATATA
29715 AAATCATTAAATA
1 AAATCATTAAATA
29728 ATAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATCATTAAATATA
Found at i:29711 original size:8 final size:8
Alignment explanation
Indices: 29684--29726 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
29674 ATATCATTAC
29684 TAAATCAT
1 TAAATCAT
29692 TAAAT-AT
1 TAAATCAT
*
29699 AAAATCAT
1 TAAATCAT
29707 TAAAT-AT
1 TAAATCAT
*
29714 AAAATCAT
1 TAAATCAT
29722 TAAAT
1 TAAAT
29727 AATAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAATCAT
Found at i:35113 original size:16 final size:16
Alignment explanation
Indices: 35075--35106 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35065 ATTATTAGTA
35075 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
35091 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
35107 TAGATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:35427 original size:25 final size:25
Alignment explanation
Indices: 35378--35433 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
35368 TGAAAGCCAC
* *
35378 TTTTAAAGCTGCATGGCAGTAATAAA
1 TTTTAAAACTGCATGGCAGCAAT-AA
35404 TTTTAAAACTGCAT-GCAGCAATAA
1 TTTTAAAACTGCATGGCAGCAATAA
35428 TTTTAA
1 TTTTAA
35434 TTGTAAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.29
25 7 0.25
26 13 0.46
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (25 bp):
TTTTAAAACTGCATGGCAGCAATAA
Found at i:35656 original size:16 final size:17
Alignment explanation
Indices: 35618--35658 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
35608 TTCGATTATT
* *
35618 TATAAATAATAATATGA
1 TATAAATAAAAATATAA
35635 TA-AAATAAAAATA-AA
1 TATAAATAAAAATATAA
35650 TATAAATAA
1 TATAAATAA
35659 TTCAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
TATAAATAAAAATATAA
Found at i:38733 original size:16 final size:16
Alignment explanation
Indices: 38712--38743 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38702 TTGATATTTA
*
38712 ATGATTTAGTAATGAT
1 ATGATTTAATAATGAT
38728 ATGATTTAATAATGAT
1 ATGATTTAATAATGAT
38744 TACTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (16 bp):
ATGATTTAATAATGAT
Found at i:38808 original size:20 final size:21
Alignment explanation
Indices: 38771--38815 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
38761 TATAAATATT
*
38771 TAATGATTTAGATTTGA-TAC
1 TAATGATTTAGATATGATTAC
38791 TAATGATTTAG-TAATGATTAC
1 TAATGATTTAGAT-ATGATTAC
38812 TAAT
1 TAAT
38816 AATAGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 14 0.64
21 7 0.32
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (21 bp):
TAATGATTTAGATATGATTAC
Found at i:38970 original size:15 final size:15
Alignment explanation
Indices: 38950--39001 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 15
38940 CTAATATAAA
38950 TTAAACAATATATTT
1 TTAAACAATATATTT
38965 TTAAACAACAATAAATATTT
1 TT--A-AACAAT--ATATTT
*
38985 TTAAACAAAATATTT
1 TTAAACAATATATTT
39000 TT
1 TT
39002 TTAAACGGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 10 0.32
17 6 0.19
18 7 0.23
20 8 0.26
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAACAATATATTT
Found at i:38996 original size:19 final size:20
Alignment explanation
Indices: 38959--38996 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38949 ATTAAACAAT
38959 ATATTTTTAAACAACAATAA
1 ATATTTTTAAACAACAATAA
38979 ATATTTTTAAACAA-AATA
1 ATATTTTTAAACAACAATA
38997 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTTTTAAACAACAATAA
Found at i:39477 original size:46 final size:50
Alignment explanation
Indices: 39426--39544 Score: 165
Period size: 46 Copynumber: 2.4 Consensus size: 50
39416 GTTTAAACAC
*
39426 ACTAACAAACTAATTAAATAATTTTTT-TA-CATAT-A-ATATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAA
*
39472 ACTAACAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAA
*
39522 AATAACAAACTAATATAATATAA
1 ACTAACAAACTAAT-TAA-ATAA
39545 CTTAAACTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
46 26 0.41
47 2 0.03
48 4 0.06
49 1 0.02
50 24 0.38
51 3 0.05
52 3 0.05
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (50 bp):
ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAA
Found at i:39519 original size:50 final size:50
Alignment explanation
Indices: 39426--39591 Score: 168
Period size: 50 Copynumber: 3.4 Consensus size: 50
39416 GTTTAAACAC
* *
39426 ACTAACAAACTAATTAAATAATTTTTT-TA-CATAT-A-ATATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
39472 ACTAACAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
* *** * * *
39522 AATAACAAACTAATATAA-T-ATAACTTAAACTAACA-AACTA-ATAATTTAA
1 ACTAACAAACTAAT-TAACTAATTTTTTATA-TAATATAA-TATATAACTTAA
39571 ACTAACAAACTAATTAACTAA
1 ACTAACAAACTAATTAACTAA
39592 AATTTTGTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
46 26 0.26
47 2 0.02
48 7 0.07
49 31 0.31
50 32 0.32
51 3 0.03
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (50 bp):
ACTAACAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
Found at i:39542 original size:28 final size:30
Alignment explanation
Indices: 39502--39564 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
39492 ATTTTTTATA
39502 TAATATAATATATAACTTAAAATAACAAAC
1 TAATATAATATATAACTTAAAATAACAAAC
*
39532 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAAATAACAAAC
39560 TAATA
1 TAATA
39565 ATTTAAACTA
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAAATAACAAAC
Found at i:39570 original size:21 final size:21
Alignment explanation
Indices: 39541--39589 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
39531 CTAATATAAT
39541 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
*
39562 ATAATTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
39583 ATTAACT
1 A-TAACT
39590 AAAATTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:39592 original size:21 final size:21
Alignment explanation
Indices: 39537--39592 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
39527 CAAACTAATA
39537 TAATATAACTTAAACTAACAAAC
1 TAAT-TAAC-TAAACTAACAAAC
*
39560 TAA-TAATTTAAACTAACAAAC
1 TAATTAA-CTAAACTAACAAAC
39581 TAATTAACTAAA
1 TAATTAACTAAA
39593 ATTTTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 23 0.79
22 3 0.10
23 3 0.10
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
TAATTAACTAAACTAACAAAC
Found at i:39663 original size:17 final size:18
Alignment explanation
Indices: 39630--39663 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39620 AACAAACTAA
39630 TAATTTATAATAATAAAC
1 TAATTTATAATAATAAAC
*
39648 TAATTTA-AATATTAAA
1 TAATTTATAATAATAAA
39664 AATTACCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATTTATAATAATAAAC
Found at i:39983 original size:39 final size:40
Alignment explanation
Indices: 39940--40032 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
39930 TCATCGGGCG
*
39940 TGCATGGCGACCTA-GGCTTTGGCTGCTTCTCGTTCTGAT
1 TGCATGGCGACCTAGGGCTTGGGCTGCTTCTCGTTCTGAT
* * *
39979 TGCATGGTGACCTAGGGCTTGGGCTGCTTGTCGTTTTGAT
1 TGCATGGCGACCTAGGGCTTGGGCTGCTTCTCGTTCTGAT
* *
40019 TGTAGGGCGACCTA
1 TGCATGGCGACCTA
40033 CTGCTTGGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 13 0.28
40 33 0.72
ACGTcount: A:0.12, C:0.22, G:0.32, T:0.34
Consensus pattern (40 bp):
TGCATGGCGACCTAGGGCTTGGGCTGCTTCTCGTTCTGAT
Found at i:40962 original size:60 final size:60
Alignment explanation
Indices: 40852--40964 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
40842 GTGGGGTAAC
* * **
40852 CATTTTGTAACCTTTAATGGTTGAAGGACTCAACAAAGCAAAACTCTATAGTCAGAAGAT
1 CATTTTGTAACCTTTAATAGTCGAAGGACTCAACAAAGCAAAACAATATAGTCAGAAGAT
* * * *
40912 CATTTTGTAACTTTTAATAGTCGATA-GACTTAATAAAGCAATACAATATAGTC
1 CATTTTGTAACCTTTAATAGTCGA-AGGACTCAACAAAGCAAAACAATATAGTC
40965 GATGGACCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 43 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (60 bp):
CATTTTGTAACCTTTAATAGTCGAAGGACTCAACAAAGCAAAACAATATAGTCAGAAGAT
Found at i:43018 original size:22 final size:23
Alignment explanation
Indices: 42993--43037 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42983 AGTACATGAA
*
42993 TGGTGTAAT-AAATTATAGGAAT
1 TGGTATAATGAAATTATAGGAAT
*
43015 TGGTATAATGAAATTATATGAAT
1 TGGTATAATGAAATTATAGGAAT
43038 AAGTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (23 bp):
TGGTATAATGAAATTATAGGAAT
Found at i:47789 original size:21 final size:21
Alignment explanation
Indices: 47773--47813 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
47763 TAATTAGAAG
*
47773 ATATGATATA-GTTATTATAC
1 ATATGATATATGTTATTAAAC
47793 ATATGATATATGTTATTAAAC
1 ATATGATATATGTTATTAAAC
47814 TGGATAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (21 bp):
ATATGATATATGTTATTAAAC
Found at i:48277 original size:16 final size:16
Alignment explanation
Indices: 48236--48273 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
48226 AAACTATAAG
*
48236 ACATGATATATGTGATT
1 ACATG-TATAAGTGATT
48253 ACATGTATAAGTGA-T
1 ACATGTATAAGTGATT
48268 ACATGT
1 ACATGT
48274 TATATGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (16 bp):
ACATGTATAAGTGATT
Found at i:48490 original size:30 final size:30
Alignment explanation
Indices: 48407--48494 Score: 110
Period size: 30 Copynumber: 2.9 Consensus size: 30
48397 AGAGTCGAGG
* *
48407 GTTACCTATGTCTTTCGAGATATATAGACA
1 GTTACCTATGTCTTTCGAGACATATGGACA
48437 GTTTACCTA-GTCTTTCGAGACATATGGACA
1 G-TTACCTATGTCTTTCGAGACATATGGACA
48467 GTTACCTATGT-TCTTCG-GAACATATGGA
1 GTTACCTATGTCT-TTCGAG-ACATATGGA
48495 TAGGTTCTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
29 9 0.17
30 36 0.69
31 7 0.13
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (30 bp):
GTTACCTATGTCTTTCGAGACATATGGACA
Done.