Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003582.1 Hibiscus syriacus cultivar Beakdansim tig00007558_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: 40178
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:6903 original size:37 final size:37
Alignment explanation
Indices: 6812--6931 Score: 158
Period size: 36 Copynumber: 3.3 Consensus size: 37
6802 TGGTAATCAA
*
6812 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
6849 CTTT-AAAAAT-GAATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAG-ATTTTCAAAGTTTGGTAAATGTTT
* *
6885 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
6922 -GTTGAAAAAT
1 CTTTGAAAAAT
6932 GATAATGGGA
Statistics
Matches: 75, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
35 1 0.01
36 41 0.55
37 32 0.43
38 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Found at i:11421 original size:21 final size:21
Alignment explanation
Indices: 11397--11457 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
11387 AACTTTGAAA
11397 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
11418 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
11432 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
11453 AAATG
1 AAATG
11458 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:11488 original size:37 final size:37
Alignment explanation
Indices: 11389--11507 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
11379 TGGTAACCAA
11389 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
11426 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
11461 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
11498 -GTTGAAAAAT
1 CTTTGAAAAAT
11508 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:18158 original size:4 final size:4
Alignment explanation
Indices: 18149--18179 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
18139 TTCACCTATG
18149 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
18180 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:22672 original size:20 final size:20
Alignment explanation
Indices: 22647--22689 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
22637 TTCATATTTT
*
22647 CATCTTTACAGTTGCGTTCA
1 CATCTTTACAGTTACGTTCA
*
22667 CATCTTTACATTTACGTTCA
1 CATCTTTACAGTTACGTTCA
22687 CAT
1 CAT
22690 ATTTGCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (20 bp):
CATCTTTACAGTTACGTTCA
Found at i:22698 original size:20 final size:20
Alignment explanation
Indices: 22651--22699 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
22641 TATTTTCATC
* * *
22651 TTTACAGTTGCGTTCACATC
1 TTTACATTTACGTTCACATA
22671 TTTACATTTACGTTCACATA
1 TTTACATTTACGTTCACATA
*
22691 TTTGCATTT
1 TTTACATTT
22700 GCACTCTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTACATTTACGTTCACATA
Found at i:23718 original size:32 final size:32
Alignment explanation
Indices: 23677--23738 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
23667 AACAGGGTTG
*
23677 GTCGCCATCCCTTCCATGCGATACCAAAGGAA
1 GTCGCCATCCCTTCCATGCGACACCAAAGGAA
23709 GTCGCCATCCCTTCCATGCGACACCAAAGG
1 GTCGCCATCCCTTCCATGCGACACCAAAGG
23739 GTATTTCTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.37, G:0.19, T:0.18
Consensus pattern (32 bp):
GTCGCCATCCCTTCCATGCGACACCAAAGGAA
Found at i:23942 original size:23 final size:23
Alignment explanation
Indices: 23916--23960 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
23906 TCGCATTCAC
23916 GTTGATG-CATTTCTGGTTTAGCT
1 GTTGATGCCA-TTCTGGTTTAGCT
*
23939 GTTGCTGCCATTCTGGTTTAGC
1 GTTGATGCCATTCTGGTTTAGC
23961 AGACAGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.44
Consensus pattern (23 bp):
GTTGATGCCATTCTGGTTTAGCT
Found at i:25213 original size:20 final size:19
Alignment explanation
Indices: 25190--25235 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
25180 CGATATACCA
25190 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
25210 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
25230 GGTAAA
1 GGTAAA
25236 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:25385 original size:20 final size:20
Alignment explanation
Indices: 25360--25397 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25350 ATAACAGGTA
25360 AAAATGATAAAACCGGTATC
1 AAAATGATAAAACCGGTATC
25380 AAAATGATAAAACCGGTA
1 AAAATGATAAAACCGGTA
25398 AAATGATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAATGATAAAACCGGTATC
Found at i:29478 original size:19 final size:19
Alignment explanation
Indices: 29456--29503 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
29446 AAAGTCGAGT
29456 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
29475 TAA-TTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
29493 TATTTTTGTAT
1 TAATTTTGTAT
29504 GTGAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:30600 original size:194 final size:199
Alignment explanation
Indices: 30007--31502 Score: 2555
Period size: 195 Copynumber: 7.7 Consensus size: 199
29997 GGTGCACCCT
30007 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGT-ATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
30071 CGGTAC-ATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC---TATA--TT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
**
30130 GTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
30195 ATAA
196 ATAA
*
30199 AAAGTGTCGATCCCAAAATCATCGAAACCAAAAGTATAATGT-ATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
* *
30263 C-GTAC-A--ATACCGGTTTTATGAAAGGATATGTCTAAAT-ATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
*
30323 GTGTCGATA-TTTTTTTCCAGAATGAATGGAAAAC-AGGTGCACTCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
30386 AT-A
196 ATAA
30389 AAAGTGTCGATCCCAAAATCA-CGAACCC-AAAGTATAATGTAATATGT-ATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
30451 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
**
30516 GTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCC-TAAAGTGTCGAT-CATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
30579 ATAA
196 ATAA
*
30583 AAAGTGTCGATCCCAAAATCATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
30648 CCGGTACAA-T-TACCGGTTTTATGAGAG-ATATGTCTAAATAATGTATCGACACT-A-ATAGTT
65 CCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTT
*
30708 TGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
130 TGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATA
30773 TATAA
195 TATAA
30778 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
30843 CGGTACAATTATACC-GTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
*
30907 GTGTCGATATTTTTTTTCCAGAATGAAT-TAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
30971 ATAA
196 ATAA
*
30975 AAAGTGTCGATCCCAAAATCATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
31040 CCGGTACAATTATACCGGTTTTATGAGAGGATATGTCTAAATAATGTGTCGACACTAATATAGTT
65 CCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTT
*
31105 TGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
130 TGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATA
31169 TAT-A
195 TATAA
31173 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
31238 TGGTACAATTATACCGG-TTTATGAGAGAATATGTCT-AATAATGTGTCGACACT-ATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
*
31300 GTGTCGATATTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCC-TAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
31364 ATAA
196 ATAA
31368 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT-A-ATGTAA-TTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
31430 CGGTACAATTATACCGGTTTT-TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
31494 GTGTCGATA
131 GTGTCGATA
31503 CTAATTTAAA
Statistics
Matches: 1239, Mismatches: 31, Indels: 66
0.93 0.02 0.05
Matches are distributed among these distances:
188 40 0.03
189 45 0.04
190 23 0.02
191 45 0.04
192 153 0.12
193 126 0.10
194 160 0.13
195 191 0.15
196 68 0.05
197 139 0.11
198 156 0.13
199 93 0.08
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (199 bp):
AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATAT
ATAA
Found at i:31160 original size:590 final size:585
Alignment explanation
Indices: 30007--31502 Score: 2566
Period size: 590 Copynumber: 2.6 Consensus size: 585
29997 GGTGCACCCT
30007 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGT-ATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
30071 CGGTACATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACT-ATA--TTGTG
66 CGGTACAATATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTG
**
30133 TCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATA
131 TCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATA
*
30198 AAAAGTGTCGATCCCAAAATCATCGAAACCAAAAGTATAATGTATATGTAATTTTTCAATCTAAC
196 AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTATATGTAATTTTTCAATCTAAC
* *
30263 C-GTAC-A--ATACCGGTTTTATGAAAGGATATGTCTAAAT-ATGTGTCGACACTAATATAGTTT
261 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
*
30323 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGTGCACTCATAAAGTGTCGATCCATATAT
326 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATAT
*
30388 AAAAGTGTCGATCCCAAAATCACGAACCCAAAGTATAATGTAATATGTATTTTTCAATCTAACCG
391 AAAAGTGTCGATCCCAAAATCACGAACCAAAAGTATAATGTAATATGTATTTTTCAATCTAACCG
30453 GTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGT
456 GTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGT
*
30518 GTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCCTAAAGTGTCGAT-CATATATA
521 GTCGATATTTTTTTTCCAGAATGAATGAAAAACAAGGTGCACCCTAAAGTGTCGATCCATATAT-
30582 A
585 A
*
30583 AAAGTGTCGATCCCAAAATCATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
30648 CCGGTACAAT-TACCGGTTTTATGAGAG-ATATGTCTAAATAATGTATCGACACTAATAGTTTGT
65 CCGGTACAATATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGT
*
30711 GTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT
130 GTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT
30776 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTA
195 AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT-ATATGTAATTTTTCAATCTA
30841 ACCGGTACAATTATACC-GTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
259 ACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
*
30905 TTGTGTCGATATTTTTTTTCCAGAATGAAT-TAAAACAAGGTGCACCCATAAAGTGTCGATCCAT
324 TTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAAC-AGGTGCACCCATAAAGTGTCGATCCAT
30969 ATATAAAAAGTGTCGATCCCAAAATCATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
387 ATAT-AAAAGTGTCGATCCCAAAATCA-CG--AACCAAAAGTATAATGTAATATGT-ATTTTTCA
*
31034 ATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATGTCTAAATAATGTGTCGACACTAAT
447 ATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAAT
* *
31099 ATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGA
512 ATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGAAAAACAAGGTGCACCC-TAAAGTGTCGA
31163 TCCATATATA
576 TCCATATATA
31173 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
31238 TGGTACAATTATACCGG-TTTATGAGAGAATATGTCT-AATAATGTGTCGACACTATATAGTTTG
66 CGGTACAA-TATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTA-ATAGTTTG
*
31301 TGTCGATATTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCC-TATA
129 TGTCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATA
31365 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA-ATGTAA-TTTTCAATCTA
194 TAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTATATGTAATTTTTCAATCTA
31428 ACCGGTACAATTATACCGGTTTT-TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
259 ACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGT
31492 TTGTGTCGATA
324 TTGTGTCGATA
31503 CTAATTTAAA
Statistics
Matches: 874, Mismatches: 21, Indels: 39
0.94 0.02 0.04
Matches are distributed among these distances:
576 49 0.06
577 44 0.05
578 23 0.03
579 109 0.12
580 23 0.03
581 4 0.00
582 1 0.00
583 23 0.03
584 42 0.05
585 48 0.05
586 22 0.03
587 82 0.09
588 11 0.01
589 104 0.12
590 202 0.23
591 87 0.10
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (585 bp):
AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAATATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTG
TCGATATTTTTTTTCCAGAATGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATA
AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTATATGTAATTTTTCAATCTAAC
CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATAT
AAAAGTGTCGATCCCAAAATCACGAACCAAAAGTATAATGTAATATGTATTTTTCAATCTAACCG
GTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGT
GTCGATATTTTTTTTCCAGAATGAATGAAAAACAAGGTGCACCCTAAAGTGTCGATCCATATATA
Found at i:32944 original size:6 final size:6
Alignment explanation
Indices: 32920--33011 Score: 58
Period size: 6 Copynumber: 15.3 Consensus size: 6
32910 AGCGGTCGCA
* * * * * *
32920 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
32968 GAAGCT GGCGAT GAAGAT GATGAC GACGAT GATGAT GATGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
33012 TGAAGATGAT
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.36, C:0.09, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:32955 original size:3 final size:3
Alignment explanation
Indices: 32935--33024 Score: 81
Period size: 3 Copynumber: 30.0 Consensus size: 3
32925 TGAAGCTGAC
* * * * * ** *
32935 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
32983 GAT GAT GAC GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
33025 CCAAACAAGT
Statistics
Matches: 68, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:32998 original size:12 final size:12
Alignment explanation
Indices: 32920--33024 Score: 81
Period size: 12 Copynumber: 9.0 Consensus size: 12
32910 AGCGGTCGCA
* *
32920 GAAGATGAAGCT
1 GAAGATGATGAT
* *
32932 GACGATGAAGAT
1 GAAGATGATGAT
*
32944 GACGATGATGAT
1 GAAGATGATGAT
* *
32956 GATGATGACGAT
1 GAAGATGATGAT
* **
32968 GAAGCTGGCGAT
1 GAAGATGATGAT
*
32980 GAAGATGATGAC
1 GAAGATGATGAT
*
32992 GACGATGATGAT
1 GAAGATGATGAT
33004 ---GATGATGAT
1 GAAGATGATGAT
33013 GAAGATGATGAT
1 GAAGATGATGAT
33025 CCAAACAAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
9 9 0.12
12 67 0.88
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.22
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:34792 original size:179 final size:181
Alignment explanation
Indices: 34474--34800 Score: 534
Period size: 179 Copynumber: 1.8 Consensus size: 181
34464 ATTATAATAA
* *
34474 AATAGGTAAATTTGCAATATAACCGGTATAAATATACGGTCTTATGCGCGAATAGGTCTACAACC
1 AATAGATAAATTTGCAATATAACCGGTATAAATATACGGTCTTATGAGCGAATAGGTCTACAACC
* *
34539 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
66 TATATCGA-ACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGAT
*
34604 ACGATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
130 ACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
* * *
34655 AATAGATAATTTTGTAATATAACCGGTA-AAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
1 AATAGATAAATTTGCAATATAACCGGTATAAATATA-CGGTCTTATGAGCGAATAGGTCTACAAC
*
34719 CTATATCG-ACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAAAATGTGTCGAT
65 CTATATCGAACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGAT
34783 ACCATTTAAAAAAGTGTC
130 ACCATTTAAAAAAGTGTC
34801 AGTAATTTGA
Statistics
Matches: 135, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
179 59 0.44
180 17 0.13
181 59 0.44
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (181 bp):
AATAGATAAATTTGCAATATAACCGGTATAAATATACGGTCTTATGAGCGAATAGGTCTACAACC
TATATCGAACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA
CCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATATGT
Found at i:37361 original size:22 final size:23
Alignment explanation
Indices: 37328--37390 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
37318 ATAGGTAAAC
*
37328 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
37351 AT-TAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
37373 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
37391 GTTATATTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:37425 original size:20 final size:20
Alignment explanation
Indices: 37400--37438 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37390 GGTTATATTG
* *
37400 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
37420 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
37439 CACTGTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:37768 original size:23 final size:23
Alignment explanation
Indices: 37737--37800 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
37727 ATAGGTAAAC
*
37737 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
37760 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
37783 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
37801 TGTTATATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:37846 original size:19 final size:19
Alignment explanation
Indices: 37811--37847 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37801 TGTTATATTG
* *
37811 TAAAGTGTCTATCCTTTTA
1 TAAAGTGTCCATACTTTTA
37830 TAAAGTGTCCATACTTTT
1 TAAAGTGTCCATACTTTT
37848 TTCACTGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (19 bp):
TAAAGTGTCCATACTTTTA
Found at i:38103 original size:25 final size:25
Alignment explanation
Indices: 38069--38119 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
38059 ACAACAAATC
*
38069 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
38094 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
38119 A
1 A
38120 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:38371 original size:24 final size:25
Alignment explanation
Indices: 38344--38398 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
38334 TTCAAAATTC
*
38344 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
38368 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
38392 ATTTCAA
1 ATTTCAA
38399 TATATTTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:38384 original size:18 final size:18
Alignment explanation
Indices: 38363--38399 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38353 GTAATTGGAG
38363 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
38381 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
38399 T
1 T
38400 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:38688 original size:38 final size:37
Alignment explanation
Indices: 38646--38726 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 37
38636 TCCGATGCTC
* *
38646 ATCAAAATCC-AAGCTCCTATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATAT-ATGCCAAGCAAAAGG-A
*
38684 ATCAAAATCCAAATCTCATATATGCCAAGCAAAAGGA
1 ATCAAAATCCAAAGCTCATATATGCCAAGCAAAAGGA
38721 ATCAAA
1 ATCAAA
38727 TCTACAACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 7 0.18
38 24 0.62
39 8 0.21
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (37 bp):
ATCAAAATCCAAAGCTCATATATGCCAAGCAAAAGGA
Found at i:39086 original size:21 final size:20
Alignment explanation
Indices: 39055--39098 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
39045 ATTACATAAG
*
39055 TTTTAAAAAAGTATCGATCC
1 TTTTAAAAAAGTATCGACCC
*
39075 TTTTATAAAAAGTATGGACCC
1 TTTTA-AAAAAGTATCGACCC
39096 TTT
1 TTT
39099 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTAAAAAAGTATCGACCC
Found at i:39147 original size:23 final size:23
Alignment explanation
Indices: 39116--39178 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
39106 ATAGGTAAAC
*
39116 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
39139 ATATAATGT-ATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
*
39161 ATATAATGTACTAGGTAG
1 ATATAATGTAATAGGTAG
39179 TGGTTATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:39185 original size:23 final size:22
Alignment explanation
Indices: 39137--39187 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
39127 TAGGTAGCCC
*
39137 TTATATAATGTATAGGTATCGT
1 TTATATAATGTATAGGTATCGG
39159 TTATATAATGTACTAGGTAGT-GG
1 TTATATAATGTA-TAGGTA-TCGG
39182 TTATAT
1 TTATAT
39188 TGTAAAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.46
23 13 0.50
24 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (22 bp):
TTATATAATGTATAGGTATCGG
Found at i:39686 original size:17 final size:16
Alignment explanation
Indices: 39647--39688 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
39637 ACCGGTCTAA
*
39647 ATTTAACCGGTCACTT
1 ATTTAACCGGTCACGT
*
39663 GTTTAACCGGTCACCGT
1 ATTTAACCGGTCA-CGT
39680 ATTTAACCG
1 ATTTAACCG
39689 TTTTTTAGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (16 bp):
ATTTAACCGGTCACGT
Done.