Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004817.1 Hibiscus syriacus cultivar Beakdansim tig00010853_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: 37462
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3486 original size:27 final size:27
Alignment explanation
Indices: 3456--3507 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3446 ATTCCCCCAT
3456 TGTTCAT-CGTCACTATTCACTATTCAC
1 TGTTCATGCGT-ACTATTCACTATTCAC
* *
3483 TGTTCATGGGTACTGTTCACTATTC
1 TGTTCATGCGTACTATTCACTATTC
3508 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (27 bp):
TGTTCATGCGTACTATTCACTATTCAC
Found at i:11504 original size:48 final size:48
Alignment explanation
Indices: 11445--11725 Score: 339
Period size: 48 Copynumber: 5.9 Consensus size: 48
11435 ACCCTCGTCT
* * * *
11445 GTGGACATTCCTGGTGTGATATCTTGTGAAATCAATCCACCTTCTTCA
1 GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCATCA
* * *
11493 GTGGACATTCCTGGTGCAATATCTTGTGGAATCACCCCGCCTTCATCA
1 GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCATCA
* * * *
11541 GTGGACACTCCTGGTGCGATATCTTGCGGAATCACCCCACCTTCAACA
1 GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCATCA
* * * *
11589 GTGGACACTCCTGGTGCGTTATCTTGTGGAATCAACCCACCTTCGTCG
1 GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCATCA
*
11637 GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCGTC-
1 GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCATCA
* * * * * * *
11684 GATGGCCGTTTCAGGTGCGAGATCCTGTGGAATCAGCCCACC
1 G-TGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACC
11726 CTCGTCGATT
Statistics
Matches: 205, Mismatches: 27, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
47 1 0.00
48 204 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (48 bp):
GTGGACATTCCTGGTGCGATATCTTGTGGAATCAACCCACCTTCATCA
Found at i:12525 original size:37 final size:36
Alignment explanation
Indices: 12476--12824 Score: 273
Period size: 37 Copynumber: 9.6 Consensus size: 36
12466 TTTGAAAATG
12476 TATATAATATATAGTTTTTAAAAAAACATTTTTAAAAAC
1 TATATAATATATAGTTTTT--AAAAACA-TTTTAAAAAC
*
12515 TATATAATATATAGTTTTT-AAAACATTTTAGAAAATA
1 TATATAATATATAGTTTTTAAAAACATTTTA-AAAA-C
* *
12552 TATATAATATATAGTTTTTAAAATCATTTTGAAAAC
1 TATATAATATATAGTTTTTAAAAACATTTTAAAAAC
* **
12588 TTATATAATATATAG-TTTTGAAAACATTTTTGAAAATT
1 -TATATAATATATAGTTTTTAAAAACA-TTTT-AAAAAC
*
12626 TATATAATATATAAG-TTTTGAAAA-A-TTT----A-
1 TATATAATATAT-AGTTTTTAAAAACATTTTAAAAAC
12655 TATAT--TATATAGTTTTTAAAAACATTTTGAAAATA-
1 TATATAATATATAGTTTTTAAAAACATTTT-AAAA-AC
12690 TATATAATATATAGTTTTT-AAAACATTTTTAAAAA-
1 TATATAATATATAGTTTTTAAAAACA-TTTTAAAAAC
* *
12725 TATATATATTATATAATTTTTTAAAACATTTTTGAAAATAC
1 TATATA-A-TATATAGTTTTTAAAAACA-TTTT-AAAA-AC
* * **
12766 -GTATAATATATAATTTTTTAAAAACATTTTAGAAATT
1 TATATAATATAT-AGTTTTTAAAAACATTTTA-AAAAC
* *
12803 TATATATTATAT-GTTTTGAAAA
1 TATATAATATATAGTTTTTAAAA
12825 TATTTTATTA
Statistics
Matches: 261, Mismatches: 21, Indels: 59
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.01
27 13 0.05
28 1 0.00
29 8 0.03
35 21 0.08
36 38 0.15
37 82 0.31
38 55 0.21
39 36 0.14
40 5 0.02
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAAACATTTTAAAAAC
Found at i:12562 original size:74 final size:74
Alignment explanation
Indices: 12439--12830 Score: 386
Period size: 74 Copynumber: 5.4 Consensus size: 74
12429 TTTTTTTATA
* * * *
12439 TATATATTATATAG-TTTGCAAACGGTTTTTGAAAATGTATATAATATATAGTTTTTAAAAAAAC
1 TATATAATATATAGTTTTGAAAAC-ATTTTTGAAAATATATATAATATATAGTTTTT--AAAAAC
12503 ATTTTTAAAAAC-
63 A-TTTTAAAAACT
* * *
12515 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAAACATT
*
12580 TTGAAAACT
66 TTAAAAACT
* *
12589 TATATAATATATAGTTTTGAAAACATTTTTGAAAATTTATATAATATATAAG-TTTTGAAAA-A-
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATAT-AGTTTTTAAAAACAT
12651 TTT----A--
65 TTTAAAAACT
*
12655 TATAT--TATATAGTTTTTAAAAACA-TTTTGAAAATATATATAATATATAGTTTTT-AAAACAT
1 TATATAATATATAG-TTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAAACA-
12716 TTTTAAAAA-T
64 TTTTAAAAACT
* * * ** *
12726 ATATATATTATATAATTTTTTAAAACATTTTTGAAAATACGTATAATATATAATTTTTTAAAAAC
1 -TATATAATATAT-AGTTTTGAAAACATTTTTGAAAATATATATAATATAT-AGTTTTTAAAAAC
* *
12791 ATTTTAGAAATT
63 ATTTTAAAAACT
* *
12803 TATATATTATAT-GTTTTGAAAATATTTT
1 TATATAATATATAGTTTTGAAAACATTTT
12831 ATTATTATTA
Statistics
Matches: 271, Mismatches: 24, Indels: 44
0.80 0.07 0.13
Matches are distributed among these distances:
63 6 0.02
64 34 0.13
65 10 0.04
66 8 0.03
68 1 0.00
70 1 0.00
72 8 0.03
73 10 0.04
74 87 0.32
75 24 0.09
76 68 0.25
77 14 0.05
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (74 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAAACATT
TTAAAAACT
Found at i:12664 original size:64 final size:63
Alignment explanation
Indices: 12578--12717 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 63
12568 TTTAAAATCA
* * *
12578 TTTTG-AAAACTTATATAATATATAG-TTTTGAAAACATTTTTGAAAATTTATATAATATATAAG
1 TTTTGAAAAATTTATATAATATATAGTTTTTAAAAACA-TTTTGAAAATATATATAATATAT-AG
*
12641 TTTTGAAAAATTTATATATTATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAG
1 TTTTGAAAAATTTATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAG
*
12704 TTTTTAAAACATTT
1 TTTTGAAAA-ATTT
12718 TTAAAAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
63 15 0.22
64 44 0.64
65 10 0.14
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (63 bp):
TTTTGAAAAATTTATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAG
Found at i:12664 original size:101 final size:101
Alignment explanation
Indices: 12546--12755 Score: 314
Period size: 101 Copynumber: 2.1 Consensus size: 101
12536 AACATTTTAG
* *
12546 AAAATATATATAATATATAGTTTTTAAAATCATTTTGAAAACT-TATATAATATATAGTTTTGAA
1 AAAATTTATATAATATATAGTTTTTAAAAACATTTTGAAAA-TATATATAATATATAGTTTTGAA
* *
12610 AACATTTTTGAAAATTTATATAATATATAAGTTTTGA
65 AACATTTTTAAAAATATATATAATATATAAGTTTTGA
* *
12647 AAAATTTATATATTATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTTAAA
1 AAAATTTATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAA
* * *
12712 ACATTTTTAAAAATATATATATTATATAATTTTTTA
66 ACATTTTTAAAAATATATATAATATATAAGTTTTGA
12748 AAACATTT
1 AAA-ATTT
12756 TTGAAAATAC
Statistics
Matches: 98, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 1 0.01
101 93 0.95
102 4 0.04
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (101 bp):
AAAATTTATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAA
ACATTTTTAAAAATATATATAATATATAAGTTTTGA
Found at i:12676 original size:26 final size:27
Alignment explanation
Indices: 12614--12676 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
12604 TTTGAAAACA
*
12614 TTTTTGAAAATTTATATAATATATAAG
1 TTTTTAAAAATTTATATAATATATAAG
* *
12641 TTTTGAAAAATTTATATATTATAT-AG
1 TTTTTAAAAATTTATATAATATATAAG
12667 TTTTTAAAAA
1 TTTTTAAAAA
12677 CATTTTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (27 bp):
TTTTTAAAAATTTATATAATATATAAG
Found at i:12687 original size:138 final size:139
Alignment explanation
Indices: 12515--12789 Score: 412
Period size: 138 Copynumber: 2.0 Consensus size: 139
12505 TTTTAAAAAC
12515 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAA-CATT
* **
12580 TTGAAAACT-TATATAATATAT-AGTTTTGAAAACATTTTTGAAAATTTATATAATATATAAGTT
65 TTGAAAAATATATATAATATATAAGTTTTGAAAACATTTTTGAAAATACATATAATATATAAGTT
12643 TTGAAAAATT
130 TTGAAAAATT
*
12653 TATATATTATATAGTTTTTAAAAACATTTT-GAAAATATATATAATATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTT-AAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAACATT
* * * * * *
12717 TTTAAAAATATATATATTATATAATTTTTTAAAACATTTTTGAAAATACGTATAATATATAATTT
65 TTGAAAAATATATATAATATATAAGTTTTGAAAACATTTTTGAAAATACATATAATATATAAGTT
*
12782 TTTAAAAA
130 TTGAAAAA
12790 CATTTTAGAA
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
137 11 0.09
138 59 0.48
139 53 0.43
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (139 bp):
TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAACATTT
TGAAAAATATATATAATATATAAGTTTTGAAAACATTTTTGAAAATACATATAATATATAAGTTT
TGAAAAATT
Found at i:12837 original size:3 final size:3
Alignment explanation
Indices: 12825--12867 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
12815 GTTTTGAAAA
*
12825 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TCT TAAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
12868 TATTTCTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12876 original size:18 final size:17
Alignment explanation
Indices: 12829--12886 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
12819 TGAAAATATT
*
12829 TTATTA-TTATTATT-A
1 TTATTATTTATTCTTAA
12844 TTATTA-TTATTCTTAA
1 TTATTATTTATTCTTAA
*
12860 TTATTATTTATTTCTTAT
1 TTATTATTTA-TTCTTAA
*
12878 TTTTTATTT
1 TTATTATTT
12887 TTTGTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.35
16 7 0.19
17 3 0.08
18 14 0.38
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTTATTCTTAA
Found at i:15902 original size:21 final size:21
Alignment explanation
Indices: 15876--15924 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
15866 AATTGGACGA
*
15876 AGAGGACAAAA-CAAAGAATAT
1 AGAGGACAAAATCAAACAAT-T
*
15897 AGAGGAAAAAATCAAACAATT
1 AGAGGACAAAATCAAACAATT
15918 AGAGGAC
1 AGAGGAC
15925 CAGATGAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.59, C:0.10, G:0.20, T:0.10
Consensus pattern (21 bp):
AGAGGACAAAATCAAACAATT
Found at i:17670 original size:99 final size:99
Alignment explanation
Indices: 17512--17712 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 99
17502 TATAATATTT
* *
17512 TATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCTCCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATGGA
* *
17577 TAAGATTCAGCTAAGCCTGATAAAAGTGATTATAA
66 TAAGATTCAACT-AGCCTAATAAAAGTGATTATAA
* *
17612 TATATATACAATAAAGCTTGAGTTGT-CCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGA
1 TATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATGGA
* *
17676 TAATATTCAACTAGCCTAATAAAGGTGATTATAA
66 TAAGATTCAACTAGCCTAATAAAAGTGATTATAA
17710 TAT
1 TAT
17713 CTTGAGCTGT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 23 0.25
99 45 0.48
100 25 0.27
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (99 bp):
TATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATGGA
TAAGATTCAACTAGCCTAATAAAAGTGATTATAA
Found at i:19029 original size:84 final size:84
Alignment explanation
Indices: 18883--19550 Score: 698
Period size: 84 Copynumber: 8.0 Consensus size: 84
18873 AAACTATTGA
* * * * * *
18883 CAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTTCGCTCAG
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
18948 CTCCAAGGCACATCATTTG
66 CTCCAAGGCACATCATTTG
* ** * * * *
18967 TAGCATAGTTTACGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGCTCAG
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
19032 CTCCAAGGCACATCATTTG
66 CTCCAAGGCACATCATTTG
* * * * * * * ** * *
19051 CAACATAGCTCAAGGCAAGAAGGGCTATTTACCAATAAAATACCTTCGAGTTCGACTACACTCAA
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* *
19116 TTCCAAGGCACATCATTTA
66 CTCCAAGGCACATCATTTG
* * * * ** *
19135 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTTGAGTTTTATTACACTCAG
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
** * *
19199 CTTAAAGACACATGATTTG
66 CTCCAAGGCACATCATTTG
* * * * * * *
19218 CAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAATACCTTCAAGTTTGACTACGCTCAG
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
19283 CTCCAAGGCACATCATTTG
66 CTCCAAGGCACATCATTTG
* ** * *
19302 CAGCATAACTCAAGGT-TAGAAGGGTTATCTATCAA-CAAAGACCTACGAGTTCGATTACACTCA
1 CAGCATAACTCAA-GTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCA
*
19365 GCTCAAAGGCACAAT-ATTTG
65 GCTCCAAGGCAC-ATCATTTG
* * * * * *
19385 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCGAGTTCGATTGCACTCAG
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
*
19450 CTCCAAGGCATATCATTTG
66 CTCCAAGGCACATCATTTG
* * * * * *
19469 CAGCACAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCAAGTTCTATTACACTCAG
1 CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
* *
19533 CTCAAAGACACATCATTT
66 CTCCAAGGCACATCATTT
19551 ACATCATAGC
Statistics
Matches: 476, Mismatches: 102, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
82 2 0.00
83 170 0.36
84 302 0.63
85 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (84 bp):
CAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAG
CTCCAAGGCACATCATTTG
Found at i:19290 original size:167 final size:167
Alignment explanation
Indices: 18900--19562 Score: 824
Period size: 167 Copynumber: 4.0 Consensus size: 167
18890 ACTCAAGGCT
* * *
18900 AGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTTCGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
* ** * * * * * *
18965 TGTAGCATAGTTTACGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGCTC
66 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCTATTACACTC
* * * * * *
19030 AGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCA
130 AGCTCAAAGACACATCATTTGCAGCATAGCTTAAGTCG
* * * **
19068 AGAAGGGCTATTTACCAATAAAATACCTTCGAGTTCGACTACACTCAATTCCAAGGCACATCATT
1 AGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
* * * *
19133 TACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTTTTATTACACTCA
66 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCTATTACACTCA
* * * *
19198 GCTTAAAGACACATGATTTGCAGTATAACTTAAGTCG
131 GCTCAAAGACACATCATTTGCAGCATAGCTTAAGTCG
* * * * * *
19235 AGAAGGGCTATCTGCCAACCAAATACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
* ** * *
19300 TGCAGCATAACTCAAGGTTAGAAGGGTTATCTATCAACAAAGACCTACGAGTTCGATTACACTCA
66 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCTATTACACTCA
*
19365 GCTCAAAGGCACAAT-ATTTGCAGCATAGCTTAAGTCG
131 GCTCAAAGACAC-ATCATTTGCAGCATAGCTTAAGTCG
* * * * * *
19402 AGAAGGGCTATCTGCCATCCAAAGACCTTCGAGTTCGATTGCACTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
* *
19467 TGCAGCACAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCAAGTTCTATTACACTCA
66 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCTATTACACTCA
* *
19532 GCTCAAAGACACATCATTTACATCATAGCTT
131 GCTCAAAGACACATCATTTGCAGCATAGCTT
19563 CTTCGAGTTC
Statistics
Matches: 424, Mismatches: 69, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
166 2 0.00
167 335 0.79
168 87 0.21
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (167 bp):
AGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCTATTACACTCA
GCTCAAAGACACATCATTTGCAGCATAGCTTAAGTCG
Found at i:19668 original size:84 final size:84
Alignment explanation
Indices: 19563--19756 Score: 241
Period size: 84 Copynumber: 2.3 Consensus size: 84
19553 ATCATAGCTT
* * * *
19563 CTTCGAGTTCGATTACACTCAGCTCCAAGGCAC-ATCATTTGCAGCATAACTCAAGGCTAGAA-G
1 CTTCGAGTTCGATTACACTCAGCTCAAAGGAACAAT-ATTTGCAACATAACTCAAGGCGAGAATG
*
19626 AGTTATCTGCCAAT-AAAAGAC
65 -GCTATCTGCC-ATCAAAAGAC
* * *
19647 CTTCGAGTTCGATTACACTCAGCTCAAAGGAACAATATTTGCAACATAGCTTAAGTCGAGAATGG
1 CTTCGAGTTCGATTACACTCAGCTCAAAGGAACAATATTTGCAACATAACTCAAGGCGAGAATGG
* *
19712 CTATTTGCCATCCAAAGAC
66 CTATCTGCCATCAAAAGAC
*
19731 CTTCGAGTTCGATTACATTCAGCTCA
1 CTTCGAGTTCGATTACACTCAGCTCA
19757 GAGGCAAATA
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
83 2 0.02
84 91 0.95
85 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (84 bp):
CTTCGAGTTCGATTACACTCAGCTCAAAGGAACAATATTTGCAACATAACTCAAGGCGAGAATGG
CTATCTGCCATCAAAAGAC
Found at i:20532 original size:37 final size:34
Alignment explanation
Indices: 20439--20758 Score: 336
Period size: 37 Copynumber: 9.1 Consensus size: 34
20429 TTTTTTATAA
20439 AAAACACTTTTGAAAACTATATAATATATAGTTTTT
1 AAAACA-TTTTGAAAA-TATATAATATATAGTTTTT
20475 AAAACATTTTAGAAAATATATAATATATAGTTTTT
1 AAAACATTTT-GAAAATATATAATATATAGTTTTT
*
20510 AAAATCATTTTGAAAACTTATATAATATATAGTTTTG
1 AAAA-CATTTTGAAAA--TATATAATATATAGTTTTT
*
20547 AAAACATTTTTGAAAATTTATATAATATATAGTTTTG
1 AAAACA-TTTTGAAAA--TATATAATATATAGTTTTT
20584 AAAACA-TTT----ATATAT--TATATAGTTTTT
1 AAAACATTTTGAAAATATATAATATATAGTTTTT
20611 AAAAACATTTTGAAAATATATATAATATATAGTTTTT
1 -AAAACATTTTG-AAA-ATATATAATATATAGTTTTT
*
20648 AAAACATTTTTGAAAATATAT--TATATAATTTTT
1 AAAACA-TTTTGAAAATATATAATATATAGTTTTT
*
20681 AAAACATTTTTGAAAATACGTATAATATATAATTTTTT
1 AAAACA-TTTTGAAAATA--TATAATATAT-AGTTTTT
* *
20719 AAAAACATTTTAGAAATTTATATATTATA-AGTTTTT
1 -AAAACATTTT-GAAA-ATATATAATATATAGTTTTT
20755 AAAA
1 AAAA
20759 ATATTTTATT
Statistics
Matches: 252, Mismatches: 8, Indels: 49
0.82 0.03 0.16
Matches are distributed among these distances:
27 11 0.04
28 6 0.02
29 8 0.03
31 1 0.00
33 29 0.12
35 54 0.21
36 34 0.13
37 79 0.31
38 18 0.07
39 10 0.04
40 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
AAAACATTTTGAAAATATATAATATATAGTTTTT
Found at i:20602 original size:27 final size:28
Alignment explanation
Indices: 20553--20620 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
20543 TTTGAAAACA
20553 TTTTTG-AAA-ATTTATATAATATATAG
1 TTTTTGAAAACATTTATATAATATATAG
*
20579 -TTTTGAAAACATTTATATATTATATAG
1 TTTTTGAAAACATTTATATAATATATAG
*
20606 TTTTTAAAAACATTT
1 TTTTTGAAAACATTT
20621 TGAAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 5 0.14
26 3 0.08
27 16 0.43
28 13 0.35
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (28 bp):
TTTTTGAAAACATTTATATAATATATAG
Found at i:20603 original size:64 final size:64
Alignment explanation
Indices: 20517--20716 Score: 235
Period size: 64 Copynumber: 3.1 Consensus size: 64
20507 TTTAAAATCA
* * *
20517 TTTTGAAAAC--TTATATAATATATAGTTTTGAAAACATTTTTGAAAATTTATATAATATATAG
1 TTTTGAAAACATTTATATATTATATAGTTTTAAAAACATTTTTGAAAATATATATAATATATAG
20579 TTTTGAAAACATTTATATATTATATAGTTTTTAAAAACA-TTTTGAAAATATATATAATATATAG
1 TTTTGAAAACATTTATATATTATATAG-TTTTAAAAACATTTTTGAAAATATATATAATATATAG
* * * **
20643 TTTTTAAAACATTTTTGAAAATATATTATATAATTTTTAAAACATTTTTGAAAATACGTATAATA
1 TTTTGAAAACA--TTT----ATATATTATATAGTTTTAAAAACATTTTTGAAAATATATATAATA
*
20708 TATAA
60 TATAG
20713 TTTT
1 TTTT
20717 TTAAAAACAT
Statistics
Matches: 119, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
62 10 0.08
64 48 0.40
65 10 0.08
66 3 0.03
69 10 0.08
70 38 0.32
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (64 bp):
TTTTGAAAACATTTATATATTATATAGTTTTAAAAACATTTTTGAAAATATATATAATATATAG
Found at i:20613 original size:101 final size:97
Alignment explanation
Indices: 20491--20689 Score: 301
Period size: 101 Copynumber: 2.0 Consensus size: 97
20481 TTTTAGAAAA
*
20491 TATATAATATATAGTTTTTAAAATCATTTTGAAAACT-TATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAA-TATATATAATATATAGTTTTGAAAACATT
*
20555 TTTGAAAATTTATATAATATATAGTTTTGAAAACATT
65 TTTGAAAA--TATAT--TATATAATTTTGAAAACATT
* *
20592 TATATATTATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
*
20657 TTGAAAATATATTATATAATTTTTAAAACATT
66 TTGAAAATATATTATATAATTTTGAAAACATT
20689 T
1 T
20690 TTGAAAATAC
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
97 19 0.21
99 5 0.05
100 1 0.01
101 67 0.73
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (97 bp):
TATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
TTGAAAATATATTATATAATTTTGAAAACATT
Found at i:20630 original size:28 final size:27
Alignment explanation
Indices: 20562--20632 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
20552 ATTTTTGAAA
* *
20562 ATTTATATAATATATAGTTTTGAAAAC
1 ATTTATAAAATATATAGTTTTAAAAAC
* *
20589 ATTTATATATTATATAGTTTTTAAAAAC
1 ATTTATAAAATATATAG-TTTTAAAAAC
20617 ATTT-TGAAAATATATA
1 ATTTAT-AAAATATATA
20633 TAATATATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (27 bp):
ATTTATAAAATATATAGTTTTAAAAAC
Found at i:20635 original size:173 final size:170
Alignment explanation
Indices: 20438--20758 Score: 454
Period size: 173 Copynumber: 1.9 Consensus size: 170
20428 TTTTTTTATA
*
20438 AAAAACACTTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTAGAAAATATATAATATAT
1 AAAAACACTTTTGAAAAATATATAATATATAGTTTTTAAAACATTTTAGAAAATATAT--TATAT
* * *
20503 AGTTTTTAAAATCA-TTTTGAAAACTTA-TATAATATAT-A-GTTTTGAAAACATTTTTGAAAAT
64 AATTTTTAAAA-CATTTTTGAAAA--TACTATAATATATAATGTTTTAAAAACATTTTAG-AAAT
20564 TTATATAATATATAGTTTTGAAAACATTTATATATTATATAGTTTTT
125 TTATATAATATA-AGTTTTGAAAACATTTATATATTATATAGTTTTT
*
20611 AAAAACA-TTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAATATATTATATA
1 AAAAACACTTTTGAAAA-ATATATAATATATAGTTTTTAAAACATTTTAGAAAATATATTATATA
*
20675 ATTTTTAAAACATTTTTGAAAATACGTATAATATATAATTTTTTAAAAACATTTTAGAAATTTAT
65 ATTTTTAAAACATTTTTGAAAATAC-TATAATATATAATGTTTTAAAAACATTTTAGAAATTTAT
* *
20740 ATATTATAAGTTTTTAAAA
129 ATAATATAAGTTTTGAAAA
20759 ATATTTTATT
Statistics
Matches: 134, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
169 2 0.01
170 2 0.01
171 44 0.33
172 25 0.19
173 61 0.46
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (170 bp):
AAAAACACTTTTGAAAAATATATAATATATAGTTTTTAAAACATTTTAGAAAATATATTATATAA
TTTTTAAAACATTTTTGAAAATACTATAATATATAATGTTTTAAAAACATTTTAGAAATTTATAT
AATATAAGTTTTGAAAACATTTATATATTATATAGTTTTT
Found at i:20772 original size:3 final size:3
Alignment explanation
Indices: 20760--20807 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
20750 TTTTTAAAAA
* *
20760 TAT T-T TAT TAT TAT TAT TATT TAT TAT TAT TCT TAT TCT TAT T-T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
20804 TAT T
1 TAT T
20808 TATTTCTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:20784 original size:16 final size:15
Alignment explanation
Indices: 20763--20826 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
20753 TTAAAAATAT
20763 TTTATTATTATTATTA
1 TTTATTATT-TTATTA
*
20779 TTTATTATTATTCTTA
1 TTTATTATT-TTATTA
*
20795 -TTCTTATTTTATTTA
1 TTTATTATTTTA-TTA
*
20810 TTTCTTATTTT-TTA
1 TTTATTATTTTATTA
20824 TTT
1 TTT
20827 TTTTGTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
14 8 0.19
15 10 0.23
16 25 0.58
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTATTTTATTA
Found at i:22017 original size:2 final size:2
Alignment explanation
Indices: 22012--22089 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
22002 TTTATCATTC
22012 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
22054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22090 ATTATTTACT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22128 original size:5 final size:5
Alignment explanation
Indices: 22118--22212 Score: 73
Period size: 5 Copynumber: 17.4 Consensus size: 5
22108 CTATTTTTCC
*
22118 TTTTA TTTTA TTTTA TTTTA TTTTA TCTTATA TTTTTA TTTTA TTTTC
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TT-TA -TTTTA TTTTA TTTTA
* * * *
22166 TTTTGG GTTTA TTTAA TATTA TTGTTA TTCTTA TTATTA TTATTA TT
1 TTTT-A TTTTA TTTTA TTTTA TT-TTA TT-TTA TT-TTA TT-TTA TT
22213 ATTTATTTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
5 41 0.55
6 28 0.38
7 4 0.05
8 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:22138 original size:15 final size:15
Alignment explanation
Indices: 22118--22212 Score: 73
Period size: 18 Copynumber: 5.8 Consensus size: 15
22108 CTATTTTTCC
22118 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
22133 TTTTATTTTATCTTATA
1 TTTTATTTTAT-TT-TA
*
22150 TTTTTATTTTATTTTC
1 -TTTTATTTTATTTTA
** *
22166 TTTTGGGTTTATTTAA
1 TTTT-ATTTTATTTTA
*
22182 TATTATTGTTATTCTTA
1 TTTTATT-TTATT-TTA
22199 TTATTATTATTATT
1 TT-TTATT-TTATT
22213 ATTTATTTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
15 16 0.26
16 18 0.29
17 7 0.11
18 21 0.34
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:22202 original size:3 final size:3
Alignment explanation
Indices: 22182--22215 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
22172 GTTTATTTAA
* *
22182 TAT TAT TGT TAT TCT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22216 TATTTCTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22421 original size:6 final size:6
Alignment explanation
Indices: 22405--22440 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
22395 AATCGAATGC
22405 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA -TTTTAA TTTT
22441 CACAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.64
7 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:22423 original size:13 final size:12
Alignment explanation
Indices: 22405--22440 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
22395 AATCGAATGC
22405 TTTTAAATTTTAA
1 TTTT-AATTTTAA
22418 TTTTAATTTTAA
1 TTTTAATTTTAA
22430 TTTTTAATTTT
1 -TTTTAATTTT
22441 CACAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:23711 original size:2 final size:2
Alignment explanation
Indices: 23706--23733 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23696 TCTAGATTTA
23706 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
23734 TGCAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24387 original size:3 final size:3
Alignment explanation
Indices: 24381--24405 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24371 ATAATAATAT
24381 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
24406 GTTAGATTAA
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):
TTA
Found at i:27293 original size:21 final size:21
Alignment explanation
Indices: 27269--27315 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
27259 AACAATTCTC
*
27269 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAACCCT
* * *
27290 TTCACGAAAAGGTTAAGCCCT
1 TTCATGAAAAGATTAAACCCT
27311 TTCAT
1 TTCAT
27316 CACAGTTGTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (21 bp):
TTCATGAAAAGATTAAACCCT
Found at i:29085 original size:22 final size:20
Alignment explanation
Indices: 29053--29092 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29043 ATATAAAAAT
29053 TATTTTTTTTAATATTTTTTG
1 TATTTTTTTTAAT-TTTTTTG
29074 TATTTTTATTTAATTTTTT
1 TATTTTT-TTTAATTTTTT
29093 AAATAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (20 bp):
TATTTTTTTTAATTTTTTTG
Found at i:34398 original size:3 final size:3
Alignment explanation
Indices: 34392--34446 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
34382 CCATTTTTTT
* * * *
34392 TTA TTA TTA TTA TTTA TTA ATA ATA ATA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34438 TTA TTA TTA
1 TTA TTA TTA
34447 CATGCCCGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:36482 original size:14 final size:14
Alignment explanation
Indices: 36463--36514 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
36453 TTTCAATTAT
36463 TTATTTTTATTTTA
1 TTATTTTTATTTTA
36477 TTATTTTTATCATTGTA
1 TTATTTTTAT--TT-TA
36494 TTAATTTTT-TTTTGA
1 TT-ATTTTTATTTT-A
36509 TTATTT
1 TTATTT
36515 CAGACATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 15 0.45
15 5 0.15
16 2 0.06
17 5 0.15
18 6 0.18
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (14 bp):
TTATTTTTATTTTA
Done.