Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003140.1 Hibiscus syriacus cultivar Beakdansim tig00006601_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: 75318
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3524 original size:13 final size:13
Alignment explanation
Indices: 3508--3532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3498 TTTTTAACTT
3508 TAATTTTATCATG
1 TAATTTTATCATG
3521 TAATTTTATCAT
1 TAATTTTATCAT
3533 TTTAAACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TAATTTTATCATG
Found at i:7530 original size:17 final size:17
Alignment explanation
Indices: 7505--7538 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7495 AAATGTTATG
*
7505 AGGGTATCGATACCCCC
1 AGGGAATCGATACCCCC
7522 AGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
7539 TAAAGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (17 bp):
AGGGAATCGATACCCCC
Found at i:9249 original size:101 final size:101
Alignment explanation
Indices: 8955--9266 Score: 478
Period size: 96 Copynumber: 3.1 Consensus size: 101
8945 AGAGAGGCTC
8955 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGA-ACATAC
*
9020 TTGATCC--CTATATG--TAT-A-TCTTAAGGAATGA
65 TTGATCCTAGTATATGTATATGATTCTTAAGGAATGA
*
9051 TATGTTGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGA-ACATAC
9116 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGAT-CCTAGTATATGTATATGATTCTTAAGGAATGA
* * *
9154 TATATGGTCCTTTTGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCT-GTGAG-ACATAC
1 TATGTGGTCC-TTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGAACATAC
9217 TTGATCCGTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCC-TAGTATATGTATATGATTCTTAAGGAATGA
9255 TATGTGGTCCTT
1 TATGTGGTCCTT
9267 ATGGACTTAT
Statistics
Matches: 200, Mismatches: 7, Indels: 14
0.90 0.03 0.06
Matches are distributed among these distances:
96 69 0.34
97 2 0.01
99 6 0.03
100 4 0.02
101 53 0.26
102 1 0.00
103 26 0.13
104 39 0.19
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGAACATACT
TGATCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:11534 original size:135 final size:135
Alignment explanation
Indices: 11292--11566 Score: 496
Period size: 135 Copynumber: 2.0 Consensus size: 135
11282 TCATGTATTG
* * *
11292 TGCAGGATCAGTGAGTTTACCATATGTAGAAAGATGAGGTTTATCACTTACTTGAGAGTGGTTTG
1 TGCAGGATCAGTGAGTTTACCATATGTAGAAAGATGAGGTTCATCACTTACTTAAGAGTAGTTTG
* *
11357 TATCCGTTGGCTTACGTGGAATTAACTTGTGCTGGGAGTTCTCTTGTGTGGTATGCGAGATGATA
66 TATCCGTTGGCTTACGTGGAATTAACTTGTGCTGGGAGTTCTCTTGTGTGGCATACGAGATGATA
11422 TCATC
131 TCATC
*
11427 TGCAGGATCAGTGAGTTTACCATATGTAGAAAGATGAGGTTCATCACTTACTTAAGCGTAGTTTG
1 TGCAGGATCAGTGAGTTTACCATATGTAGAAAGATGAGGTTCATCACTTACTTAAGAGTAGTTTG
11492 TATCCGTTGGCTTACGTGGAATTAACTTGTGCTGGGAGTTCTCTTGTGTGGCATACGAGATGATA
66 TATCCGTTGGCTTACGTGGAATTAACTTGTGCTGGGAGTTCTCTTGTGTGGCATACGAGATGATA
11557 TCATC
131 TCATC
11562 TGCAG
1 TGCAG
11567 TGTTCGGATT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 134 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (135 bp):
TGCAGGATCAGTGAGTTTACCATATGTAGAAAGATGAGGTTCATCACTTACTTAAGAGTAGTTTG
TATCCGTTGGCTTACGTGGAATTAACTTGTGCTGGGAGTTCTCTTGTGTGGCATACGAGATGATA
TCATC
Found at i:12936 original size:17 final size:17
Alignment explanation
Indices: 12914--12947 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12904 CTAGGTTTTC
12914 CATTTTAACTTTTTTAA
1 CATTTTAACTTTTTTAA
* *
12931 CATTTTGATTTTTTTAA
1 CATTTTAACTTTTTTAA
12948 ATCGATTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (17 bp):
CATTTTAACTTTTTTAA
Found at i:21674 original size:22 final size:23
Alignment explanation
Indices: 21636--21679 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
21626 GTAAATATTG
21636 TCATGTTCATATCATTTAAAATAA
1 TCATGTTCA-ATCATTTAAAATAA
21660 TCATGTTC-ATCATTTAAAAT
1 TCATGTTCAATCATTTAAAAT
21680 TTATTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
24 8 0.40
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (23 bp):
TCATGTTCAATCATTTAAAATAA
Found at i:21692 original size:24 final size:22
Alignment explanation
Indices: 21646--21693 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
21636 TCATGTTCAT
*
21646 ATCATTTAAAATAATCATGTTC
1 ATCATTTAAAATAATCATATTC
*
21668 ATCATTTAAAATTTATTCATATTC
1 ATCATTTAAAA--TAATCATATTC
21692 AT
1 AT
21694 ATTAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (22 bp):
ATCATTTAAAATAATCATATTC
Found at i:25845 original size:16 final size:16
Alignment explanation
Indices: 25824--25855 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25814 ACAACCATCA
25824 AACAATAAAATTTTGC
1 AACAATAAAATTTTGC
25840 AACAATAAAATTTTGC
1 AACAATAAAATTTTGC
25856 CATGACTTTC
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:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
AACAATAAAATTTTGC
Found at i:30230 original size:24 final size:24
Alignment explanation
Indices: 30203--30273 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
30193 CACCACAGCT
*
30203 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
30227 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
30251 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
30274 TATAATATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 13 0.32
24 28 0.68
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:37126 original size:31 final size:32
Alignment explanation
Indices: 37074--37134 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
37064 TTTGATATTG
37074 ATTTTAATATTCAATGTGATACTT-AATTTTC
1 ATTTTAATATTCAATGTGATACTTGAATTTTC
37105 ATTTTAATA-TCTAAT-TAGATACTTGAATTT
1 ATTTTAATATTC-AATGT-GATACTTGAATTT
37135 AACTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 19 0.70
32 5 0.19
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (32 bp):
ATTTTAATATTCAATGTGATACTTGAATTTTC
Found at i:37570 original size:16 final size:16
Alignment explanation
Indices: 37546--37593 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
37536 TATAAATTAA
*
37546 ATTAATGATGCTCATC
1 ATTAGTGATGCTCATC
*
37562 ATTAGTGATGCTCGTC
1 ATTAGTGATGCTCATC
*
37578 ATTAGTGGTGCTCATC
1 ATTAGTGATGCTCATC
37594 GCTGCTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (16 bp):
ATTAGTGATGCTCATC
Found at i:38157 original size:26 final size:26
Alignment explanation
Indices: 38123--38177 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
38113 TTAATATTTT
* *
38123 CCTTCTAAAATTTTATAAATTCAC-C
1 CCTTCTAAAAATTTAGAAATTCACTC
38148 CCTTCCTAAAAATTTAGAAATTCACTC
1 CCTT-CTAAAAATTTAGAAATTCACTC
38175 CCT
1 CCT
38178 CTGTGTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (26 bp):
CCTTCTAAAAATTTAGAAATTCACTC
Found at i:44859 original size:22 final size:24
Alignment explanation
Indices: 44810--44859 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
44800 ACGTATAAGT
44810 ATAAATTAGTTAAAAATTTAAAGG
1 ATAAATTAGTTAAAAATTTAAAGG
*
44834 -TAAATTA-TTTAAAA-TTAAAGG
1 ATAAATTAGTTAAAAATTTAAAGG
44855 ATAAA
1 ATAAA
44860 CTATATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (24 bp):
ATAAATTAGTTAAAAATTTAAAGG
Found at i:45609 original size:22 final size:22
Alignment explanation
Indices: 45583--45635 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
45573 GATCAGTGGT
45583 ATAATTTACCCTTT-AATTTTAA
1 ATAATTTA-CCTTTAAATTTTAA
*
45605 ATAATTCACCTTTAAAATTTTAA
1 ATAATTTACCTTT-AAATTTTAA
*
45628 CTAATTTA
1 ATAATTTA
45636 TAATTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 14 0.54
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATTTACCTTTAAATTTTAA
Found at i:48093 original size:143 final size:141
Alignment explanation
Indices: 47856--48113 Score: 358
Period size: 143 Copynumber: 1.8 Consensus size: 141
47846 AAAATAATCA
* * * *
47856 TATTTTAATATTTATTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTCT
1 TATTTTAATAGTTATTTTT-ATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCATTTTCT
* *
47921 GATATTCTTGAATAAATAAATATCATATTTTTATAAATTATATATATATTAATTTATTTTAATTA
65 GATATTCTTAAATAAATAAATATCATA--TTTATAAA-TATATATAAATTAATTTATTTTAATTA
47986 TTTTTAGAAAGATGT
127 TTTTTAGAAAGATGT
*
48001 TATTTTAATAGTTATTTATT-T-TTAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCT
1 TATTTTAATAGTTATTT-TTATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCATTTTCT
* ** *
48064 GATATTTTTAAATAAATAAATATTTTATTTATAAATATGTATAAATTAAT
65 GATATTCTTAAATAAATAAATATCATATTTATAAATATATATAAATTAAT
48114 AGATTTTCTT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
140 13 0.13
141 8 0.08
143 61 0.60
144 1 0.01
145 16 0.16
146 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (141 bp):
TATTTTAATAGTTATTTTTATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCATTTTCTG
ATATTCTTAAATAAATAAATATCATATTTATAAATATATATAAATTAATTTATTTTAATTATTTT
TAGAAAGATGT
Found at i:48611 original size:20 final size:21
Alignment explanation
Indices: 48588--48630 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
48578 AGAAATTAAA
48588 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
*
48608 AATTCATTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
48630 A
1 A
48631 TTACTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:50294 original size:12 final size:13
Alignment explanation
Indices: 50277--50305 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50267 ACATTCACAT
50277 ATTTACA-TTTGC
1 ATTTACATTTTGC
50289 ATTTACATTTTGC
1 ATTTACATTTTGC
50302 ATTT
1 ATTT
50306 TTACGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:52424 original size:2 final size:2
Alignment explanation
Indices: 52417--52478 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
52407 TTATCCTTTA
52417 AT AT AT AT 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 AT AT AT AT
52459 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
52479 CCTTTATTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52803 original size:24 final size:23
Alignment explanation
Indices: 52776--52860 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 23
52766 TCCAGCAAAG
*
52776 AAAGAAGAAGGAAAAAAGAAAAAA
1 AAAGAAAAAGGAAAAAA-AAAAAA
*
52800 AAAGAAAAAGG-AAAAAAAATAA
1 AAAGAAAAAGGAAAAAAAAAAAA
* * *
52822 AAATAAAAA--TAAAAAAAACAA
1 AAAGAAAAAGGAAAAAAAAAAAA
*
52843 AAACAAAAAGGAAAAAAA
1 AAAGAAAAAGGAAAAAAA
52861 GGAAAATTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.35
22 13 0.25
23 11 0.21
24 10 0.19
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (23 bp):
AAAGAAAAAGGAAAAAAAAAAAA
Found at i:52818 original size:21 final size:22
Alignment explanation
Indices: 52783--52860 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
52773 AAGAAAGAAG
* *
52783 AAGGAAAAAAGAAAAAAAAAGAAA
1 AAGG-AAAAA-AAACAAAAACAAA
* *
52807 AAGGAAAAAAAATAAAAATAAA
1 AAGGAAAAAAAACAAAAACAAA
*
52829 AA-TAAAAAAAACAAAAACAAA
1 AAGGAAAAAAAACAAAAACAAA
52850 AAGGAAAAAAA
1 AAGGAAAAAAA
52861 GGAAAATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.38
22 20 0.43
23 5 0.11
24 4 0.09
ACGTcount: A:0.83, C:0.03, G:0.10, T:0.04
Consensus pattern (22 bp):
AAGGAAAAAAAACAAAAACAAA
Found at i:52824 original size:17 final size:15
Alignment explanation
Indices: 52787--52851 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
52777 AAGAAGAAGG
52787 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
52802 AGAAAAAGGAAAAAAAA
1 A-AAAAA-GAAAAAAAA
* * *
52819 TAAAAATAAAAATAA
1 AAAAAAGAAAAAAAA
*
52834 AAAAAACAAAAACAAA
1 AAAAAAGAAAAA-AAA
52850 AA
1 AA
52852 GGAAAAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 18 0.44
16 14 0.34
17 9 0.22
ACGTcount: A:0.86, C:0.03, G:0.06, T:0.05
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:57831 original size:22 final size:22
Alignment explanation
Indices: 57803--57859 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
57793 ACATCTATAT
57803 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
57825 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
57847 TTTTCAAAGATGA
1 TCTTCAAAGATGA
57860 AAACTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:58625 original size:113 final size:113
Alignment explanation
Indices: 58410--58700 Score: 494
Period size: 113 Copynumber: 2.6 Consensus size: 113
58400 ATAGATCAGC
* *
58410 ATCAACATTTCCA-GAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCA
1 ATCAACATTACCAGGTA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCA
*
58474 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCATTCGATGG
65 TAATGAGAAGAACTTATTCAACTTTTTGCTCGAATTCATCATTCGATGG
* * *
58523 ATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAATAAGTTCAT
1 ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
58588 AATGAGAAGAACTTATTCAACTTTTTGCTCGAATTCATCATTCGATGG
66 AATGAGAAGAACTTATTCAACTTTTTGCTCGAATTCATCATTCGATGG
* *
58636 ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
58701 TGTAACACCC
Statistics
Matches: 167, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 165 0.99
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
AATGAGAAGAACTTATTCAACTTTTTGCTCGAATTCATCATTCGATGG
Found at i:59489 original size:13 final size:13
Alignment explanation
Indices: 59489--59548 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
59479 CCGTTGACCC
59489 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
59502 TACCTGACCCGTT
1 GACCCGACCCGTT
59515 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
59533 GACCCGACCCGTT
1 GACCCGACCCGTT
59546 GAC
1 GAC
59549 TGTTGACCCG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 26 0.68
18 12 0.32
ACGTcount: A:0.17, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:59490 original size:18 final size:18
Alignment explanation
Indices: 59467--59543 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
59457 ACCGGTCACA
59467 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
59485 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
59502 ----TACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
59516 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
59534 ACCCGACCCG
1 ACCCGACCCG
59544 TTGACTGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.22
18 39 0.78
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:59514 original size:31 final size:31
Alignment explanation
Indices: 59471--59548 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
59461 GTCACAACCC
59471 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
59502 TACCTGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
59533 GACCCGACCCGTTGAC
1 GACCCGACCCGTTGAC
59549 TGTTGACCCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:59569 original size:15 final size:14
Alignment explanation
Indices: 59525--59571 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
59515 GACCCGACCC
*
59525 GACCCGTTGACC-C
1 GACCCGTTGACCTT
*
59538 GACCCGTTGACTGTT
1 GACCCGTTGAC-CTT
59553 GACCCGTTGACCATT
1 GACCCGTTGACC-TT
59568 GACC
1 GACC
59572 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 11 0.39
15 17 0.61
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (14 bp):
GACCCGTTGACCTT
Found at i:60892 original size:18 final size:18
Alignment explanation
Indices: 60866--60900 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60856 TCGAAAGGAC
*
60866 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
60884 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
60901 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:63799 original size:225 final size:224
Alignment explanation
Indices: 63294--64001 Score: 987
Period size: 225 Copynumber: 3.1 Consensus size: 224
63284 GGGTGTTACA
* * * *
63294 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCATCATTTCT
1 TTCATAATAAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTTCT
* * * *
63359 AGAGAAAATTCATAATGAGAAGATCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
66 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAGC
*
63424 TTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
131 TTGTTCAACCTTTTGC-TAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
**
63489 AGAAGAACCCATCTGAAGAAGAAAGAAGAAG
195 AGAAGAACTTATCTGAAGAAGAAA-AAGAAG
* * *
63520 TTCATAATGAA-AAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTC
1 TTCATAAT-AAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTTC
63584 TAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAG
65 TAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAG
*
63649 CTTGTTCAACCTTTTGCTCAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
130 CTTGTTCAACCTTTTGCTAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
*
63714 AGAAAAACTTATCTGAAGAAGGAAAAAGAAG
195 AGAAGAACTTATCTGAAGAA-GAAAAAGAAG
* * * * *
63745 TTCATAATAAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCC
1 TTCATAATAAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTTCT
* *
63810 AG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGATAA
66 AGAG-AAAGTTCATAATGAGAAGAACT--T-ATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAA
** * * * * *
63870 GAATTTGTTCAACTTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCAT
127 GAGCTTGTTCAACCTTTTG-CTAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCAT
* *
63935 AATGAGAAGAACTTATCTGAAGAACAAGAAGAAG
191 AATGAGAAGAACTTATCTGAAGAAGAAAAAGAAG
* *
63969 TTCATAATGAGAAGAGCTTCTTCAACCTTTTGC
1 TTCATAATAAGAAGAGCTTGTTCAACCTTTTGC
64002 ATAACTCTAT
Statistics
Matches: 435, Mismatches: 39, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
224 69 0.16
225 212 0.49
226 138 0.32
227 6 0.01
228 10 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (224 bp):
TTCATAATAAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGGATCAACATTTCT
AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAGC
TTGTTCAACCTTTTGCTAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGA
GAAGAACTTATCTGAAGAAGAAAAAGAAG
Found at i:64014 original size:112 final size:113
Alignment explanation
Indices: 63294--64001 Score: 962
Period size: 113 Copynumber: 6.3 Consensus size: 113
63284 GGGTGTTACA
* * * * * * *
63294 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCATCATTTCT
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
* * *
63359 AGAGAAAATTCATAATGAGAAGATCTCATCTGAAGAAGGAAGAAGAAG
66 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
* * *
63407 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGATCAGCTTTTCC
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
** *
63472 AGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGAAAGAAGAAG
66 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
* *
63520 TTCATAATGAAAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCT
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
63585 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
66 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
* *
63633 TTCATAATGAAAAGAGCTTGTTCAACCTTTTGCTC-AATCCATCACTCGATGGATCAGCTTTTCC
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
* *
63697 AGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAAAAAGAAG
66 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
* * * * * * * *
63745 TTCATAATAAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCC
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
*
63810 AG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-
66 AGAG-AAAGTTCATAATGAGAAGAACT--T-ATCTGAAGAAGGAAGAAGAAG
* ** * * ** *
63857 TTCATAATGATAAGAATTTGTTCAACTTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCC
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
*
63922 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-CAAGAAGAAG
66 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
*
63969 TTCATAATGAGAAGAGCTTCTTCAACCTTTTGC
1 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
64002 ATAACTCTAT
Statistics
Matches: 530, Mismatches: 56, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
109 13 0.02
110 2 0.00
111 2 0.00
112 210 0.40
113 288 0.54
114 1 0.00
115 4 0.01
116 10 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (113 bp):
TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCC
AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
Found at i:64085 original size:121 final size:123
Alignment explanation
Indices: 63917--64225 Score: 327
Period size: 121 Copynumber: 2.6 Consensus size: 123
63907 TGGATCAACT
* * *
63917 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAACAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAAG-AAGTTCATAATGAGAAAAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGA
* * *
63981 AGAGCTTCTTCAACCTTTTGCA-TA-ACT-CTATCACAGAAGGAGAT-ATCATCATCAGCA
65 AGAACTTCTTCAAACTTTT-CACTAGACTAC-ATCACAGAAGGAGATAATCATCATCACCA
* * *
64038 TTTCCAGAAGAAGTTCATAATGACAAAAACTCATCT---GACGAAGAAGAAGTTCATAATTAGAA
1 TTTCCAGAAGAAGTTCATAATGAGAAAAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* * * ** *
64100 GAACTTGTTCAAACTTTTTACTAGATTACATCACAGAAGGAGATGAATTGTCATCCCCA
66 GAACTTCTTCAAACTTTTCACTAGACTACATCACAGAAGGAGAT-AATCATCATCACCA
* * *
64159 -GT--GGAAG-AGTTCATAATGAGAAAAACTCATCTGAAGAATGAAGAAGAAATTCATAATGAGA
1 TTTCCAGAAGAAGTTCATAATGAGAAAAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGA
64220 AGAACT
65 AGAACT
64226 CATCTAAAGA
Statistics
Matches: 157, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
117 25 0.16
118 44 0.28
119 17 0.11
120 4 0.03
121 65 0.41
122 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (123 bp):
TTTCCAGAAGAAGTTCATAATGAGAAAAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
GAACTTCTTCAAACTTTTCACTAGACTACATCACAGAAGGAGATAATCATCATCACCA
Found at i:64205 original size:39 final size:39
Alignment explanation
Indices: 64162--64303 Score: 207
Period size: 39 Copynumber: 3.6 Consensus size: 39
64152 ATCCCCAGTG
*
64162 GAAG-AGTTCATAATGAGAAAAACTCATCTGAAGAATGAA
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAA
* *
64201 GAAGAAATTCATAATGAGAAGAACTCATCTAAAGAAGAA
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* *
64240 GAATAAGTTCATAATGAGAAGAACTCATCTTG-AGAGGAA
1 GAAGAAGTTCATAATGAGAAGAACTCATC-TGAAGAAGAA
64279 GAAGAAGTTCATAATGAGAAGAACT
1 GAAGAAGTTCATAATGAGAAGAACT
64304 TGTTCGACAT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
39 64 0.69
40 29 0.31
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (39 bp):
GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
Found at i:74748 original size:15 final size:16
Alignment explanation
Indices: 74707--74751 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 16
74697 GTAAGTCTAT
*
74707 ATATTTAAATTTAAATA
1 ATATTT-AATTTTAATA
74724 ATATTT--TTTTAA-A
1 ATATTTAATTTTAATA
74737 ATATTTAATTTTAAT
1 ATATTTAATTTTAAT
74752 TTCACCCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 6 0.25
17 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTAATTTTAATA
Found at i:74889 original size:3 final size:3
Alignment explanation
Indices: 74881--74905 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
74871 TTTAAATAAG
74881 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
74906 TCAATTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.