Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002083.1 Hibiscus syriacus cultivar Beakdansim tig00004255_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: 100110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:496 original size:17 final size:17
Alignment explanation
Indices: 455--492 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
445 CATTCGAGAT
455 TATAATATTATTTTTTA
1 TATAATATTATTTTTTA
*
472 TATTATATTA-TTTTTA
1 TATAATATTATTTTTTA
488 TATAA
1 TATAA
493 ATATGTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAATATTATTTTTTA
Found at i:10248 original size:28 final size:30
Alignment explanation
Indices: 10192--10248 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
10182 TAAACTTTAC
*
10192 TCTCTCTTATTTCACTCATTGTAATTTAAA
1 TCTCTCTTATTTCACTCATTGTAAATTAAA
10222 TCTCT-TTAATTTC-CTCATTG-AAATTAA
1 TCTCTCTT-ATTTCACTCATTGTAAATTAA
10249 TATAATGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (30 bp):
TCTCTCTTATTTCACTCATTGTAAATTAAA
Found at i:20604 original size:14 final size:14
Alignment explanation
Indices: 20580--20619 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20570 TTTGAGGAGG
*
20580 AAGAAGAAGAGAGA
1 AAGATGAAGAGAGA
*
20594 AAGATGGAGAGAGA
1 AAGATGAAGAGAGA
*
20608 ATGATGAAGAGA
1 AAGATGAAGAGA
20620 AGAGGAAGAG
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:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (14 bp):
AAGATGAAGAGAGA
Found at i:25741 original size:21 final size:21
Alignment explanation
Indices: 25715--25755 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25705 TCTGGGCAAA
25715 GTGTATCGATGCACATTCAAT
1 GTGTATCGATGCACATTCAAT
* *
25736 GTGTATTGATGCACTTTCAA
1 GTGTATCGATGCACATTCAA
25756 ATAAATGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (21 bp):
GTGTATCGATGCACATTCAAT
Found at i:27384 original size:23 final size:23
Alignment explanation
Indices: 27320--27376 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
27310 ATTTTATATA
* *
27320 GCACTTCGGTGTAATTCTACGCG
1 GCACTTCGGTGAAATTATACGCG
*
27343 GCACTTCGGTGAAATTATACGTG
1 GCACTTCGGTGAAATTATACGCG
*
27366 GTACTTCGGTG
1 GCACTTCGGTG
27377 CATTTATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGAAATTATACGCG
Found at i:29797 original size:20 final size:20
Alignment explanation
Indices: 29772--29842 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
29762 AAACTGAAAT
*
29772 AGTATCGATACTGACTCATC
1 AGTATCGATATTGACTCATC
* *
29792 AGTATCGATATTAACTCATT
1 AGTATCGATATTGACTCATC
* * *
29812 AGTATCGATATTGGCTTAGC
1 AGTATCGATATTGACTCATC
29832 AGTATCGATAT
1 AGTATCGATAT
29843 ATTTCCCCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
AGTATCGATATTGACTCATC
Found at i:32278 original size:49 final size:48
Alignment explanation
Indices: 32217--32309 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 48
32207 TAGAAATATA
*
32217 AATATGAAAAATATTGAATTTAATTTAGAATCATAAAAATAATAAATTT
1 AATATGAAAAATATTGAATTTAATTTAAAAT-ATAAAAATAATAAATTT
32266 AATAT-AATAAATATTGAATTTAATTTAAAATATAAAAATAATAA
1 AATATGAA-AAATATTGAATTTAATTTAAAATATAAAAATAATAA
32310 TTTTTTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
48 15 0.36
49 27 0.64
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (48 bp):
AATATGAAAAATATTGAATTTAATTTAAAATATAAAAATAATAAATTT
Found at i:32300 original size:28 final size:27
Alignment explanation
Indices: 32216--32305 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 27
32206 TTAGAAATAT
32216 AAATATGAAAAATATTGAATTTAATTTA
1 AAATAT-AAAAATATTGAATTTAATTTA
* *
32244 GAATCAT-AAAA-A-T-AA-TAAATTT-
1 AAAT-ATAAAAATATTGAATTTAATTTA
32266 -AATATAATAAATATTGAATTTAATTTA
1 AAATATAA-AAATATTGAATTTAATTTA
32293 AAATATAAAAATA
1 AAATATAAAAATA
32306 ATAATTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 19
0.69 0.04 0.26
Matches are distributed among these distances:
20 2 0.04
21 4 0.08
22 3 0.06
23 7 0.14
24 3 0.06
25 3 0.06
26 7 0.14
27 9 0.18
28 10 0.20
29 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (27 bp):
AAATATAAAAATATTGAATTTAATTTA
Found at i:33559 original size:21 final size:21
Alignment explanation
Indices: 33534--33578 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
33524 TGATGTTAAA
33534 GAGGTGATGAATGAATATGTT
1 GAGGTGATGAATGAATATGTT
33555 GAGGTGATGAATGAATATGTT
1 GAGGTGATGAATGAATATGTT
33576 GAG
1 GAG
33579 TTAATCGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (21 bp):
GAGGTGATGAATGAATATGTT
Found at i:37039 original size:23 final size:21
Alignment explanation
Indices: 36980--37060 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
36970 CCAGAACCCC
* **
36980 AGGGGGTATCGATTCCCCTGT
1 AGGGGGAATCGATTCCCCTCA
*
37001 GGGGGGAATC-AGTTCCCCTTCAA
1 AGGGGGAATCGA-TTCCCC-TC-A
37024 AGGGGGAATCGATT-CCCTCA
1 AGGGGGAATCGATTCCCCTCA
* *
37044 TGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
37061 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 14 0.29
21 18 0.38
22 4 0.08
23 11 0.23
24 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTCA
Found at i:37054 original size:20 final size:20
Alignment explanation
Indices: 37025--37062 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37015 CCCCTTCAAA
37025 GGGGGAATCGATTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
37045 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
37063 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:37936 original size:37 final size:37
Alignment explanation
Indices: 37846--37950 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
37836 CCTTTTCGTC
*
37846 CTACTAGGATTCAAACTCCAAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
37883 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
37920 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
37951 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:38461 original size:26 final size:26
Alignment explanation
Indices: 38404--38479 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 26
38394 TTCTTTGCGT
* *
38404 TATATTATATTATTTTCTATTATATA
1 TATATTATACTATTTTATATTATATA
* *
38430 TATATTATA-TATTTTATTTTATCTA
1 TATATTATACTATTTTATATTATATA
* * *
38455 TCTTATT-TACTATTTTTTACTATAT
1 T-ATATTATACTATTTTATATTATAT
38480 TTTCCTAACG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 16 0.40
26 24 0.60
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (26 bp):
TATATTATACTATTTTATATTATATA
Found at i:38536 original size:29 final size:29
Alignment explanation
Indices: 38490--38597 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 29
38480 TTTCCTAACG
* * *
38490 TTATATATATATTCTTACT-TTATTTTATT
1 TTATATTTATATTATTACTATT-TTTTAGT
*
38519 TTATATTTCTATTATTACTATTTTTTAGT
1 TTATATTTATATTATTACTATTTTTTAGT
* *
38548 TAATA-TTATATGATATT--TATTTTTCA-T
1 TTATATTTATAT--TATTACTATTTTTTAGT
38575 TTAT-TTTATTATTATTACTATTT
1 TTATATTTA-TATTATTACTATTT
38598 AGTATTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
26 4 0.06
27 7 0.11
28 21 0.33
29 26 0.41
30 6 0.09
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (29 bp):
TTATATTTATATTATTACTATTTTTTAGT
Found at i:38667 original size:20 final size:21
Alignment explanation
Indices: 38628--38681 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
38618 ATACATTTTT
* *
38628 TATATTTTTATATATATATA-
1 TATATTATTATTTATATATAC
*
38648 TATATTATTATTTATTTATAC
1 TATATTATTATTTATATATAC
38669 TAT-TTATTTATTT
1 TATATTA-TTATTT
38682 TCATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TATATTATTATTTATATATAC
Found at i:38689 original size:17 final size:17
Alignment explanation
Indices: 38622--38690 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 17
38612 TTATACATAC
38622 ATTT-TTTATATT-TTT
1 ATTTATTTATATTATTT
38637 ATATATATATATATATTA-TT
1 AT-T-TAT-T-TATATTATTT
*
38657 ATTTATTTATACTATTT
1 ATTTATTTATATTATTT
38674 ATTTATTT-TCATTATTT
1 ATTTATTTAT-ATTATTT
38691 TTAGTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
15 2 0.05
16 8 0.18
17 18 0.41
18 4 0.09
19 2 0.05
20 10 0.23
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTATTTATATTATTT
Found at i:41465 original size:15 final size:15
Alignment explanation
Indices: 41442--41471 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41432 AAGTCAAGGA
*
41442 TAACTCCTGAGAATC
1 TAACGCCTGAGAATC
41457 TAACGCCTGAGAATC
1 TAACGCCTGAGAATC
41472 CAAATGGCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (15 bp):
TAACGCCTGAGAATC
Found at i:43147 original size:15 final size:14
Alignment explanation
Indices: 43129--43176 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
43119 GGCAAAAACA
43129 AAAAAGAAAAGAAGC
1 AAAAAGAAAAGAA-C
43144 AAAAAAGAAGAA-AAC
1 -AAAAAGAA-AAGAAC
43159 AAAAA-AAAAGAAC
1 AAAAAGAAAAGAAC
43172 AAAAA
1 AAAAA
43177 TCAAAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.07
13 10 0.33
14 5 0.17
15 1 0.03
16 10 0.33
17 2 0.07
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAC
Found at i:43156 original size:19 final size:18
Alignment explanation
Indices: 43121--43175 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
43111 ACAAAAAGGG
43121 CAAAAACAAAA-AAGAAAA
1 CAAAAA-AAAAGAAGAAAA
* *
43139 GAAGCAAAAAAGAAGAAAA
1 CAA-AAAAAAAGAAGAAAA
*
43158 CAAAAAAAAAGAACAAAA
1 CAAAAAAAAAGAAGAAAA
43176 ATCAAAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAGAAGAAAA
Found at i:43182 original size:15 final size:15
Alignment explanation
Indices: 43125--43176 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
43115 AAAGGGCAAA
43125 AACAAAAAAGAAAAG
1 AACAAAAAAGAAAAG
43140 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAAGAA-AAG
43156 AAC-AAAAA-AAAAG
1 AACAAAAAAGAAAAG
43169 AACAAAAA
1 AACAAAAA
43177 TCAAAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 5 0.15
14 9 0.27
15 3 0.09
16 12 0.36
17 2 0.06
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAAAG
Found at i:44913 original size:106 final size:106
Alignment explanation
Indices: 44785--45955 Score: 1759
Period size: 106 Copynumber: 11.0 Consensus size: 106
44775 ATATCATGCC
* * * * *
44785 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTTTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
44850 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
44891 ACTCCAGACAACACAAGTTCAACTTGACGACGAAGAGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
44956 AATTTCAGAGCCAATTTTAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
44997 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
45062 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
45103 ACTCAAGATAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
45168 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
45209 ACTCCAGACAACGCAAGTTCAACTTCATGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
45274 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
45315 ACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
45380 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
45421 AATCGAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
45486 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
45527 ACTCCAGACAACGTAAGTTCAACTTCACGGCGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
45592 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAATAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
45633 ACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
45698 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
45739 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
45804 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
45845 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-CTTCC
* * ** *
45910 CGATTCCAGATTCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
45952 ACTC
1 ACTC
45956 GAAACAATGC
Statistics
Matches: 973, Mismatches: 90, Indels: 3
0.91 0.08 0.00
Matches are distributed among these distances:
106 932 0.96
107 41 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:46758 original size:37 final size:37
Alignment explanation
Indices: 46705--46809 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
46695 CCTTTTCGTC
46705 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* * *
46742 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
** * *
46779 CTACTATTATTTAAACTCCTAAAGATATGAT
1 CTACTAGGATTCAAACTCCTAAAAATATGAT
46810 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:47431 original size:29 final size:29
Alignment explanation
Indices: 47394--47449 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
47384 TATACATATA
* *
47394 TATTCTTACT-TTATTTTATTTTATATTTC
1 TATTCTTACTATT-TTTTAGTTAATATTTC
*
47423 TATTGTTACTATTTTTTAGTTAATATT
1 TATTCTTACTATTTTTTAGTTAATATT
47450 ATATGTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.66
Consensus pattern (29 bp):
TATTCTTACTATTTTTTAGTTAATATTTC
Found at i:47551 original size:19 final size:19
Alignment explanation
Indices: 47514--47578 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
47504 TATTACATAC
* *
47514 ATTTT-TATATTTATATAT
1 ATTTTATATTTTTATTTAT
47532 ATTTTATATTTTTATTTAT
1 ATTTTATATTTTTATTTAT
*
47551 ACTATTTATTTATTTTCA-TTAT
1 A-T-TTTA--TATTTTTATTTAT
47573 ATTTTA
1 ATTTTA
47579 GTTTCTTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 5 0.13
19 12 0.31
20 5 0.13
21 5 0.13
22 5 0.13
23 7 0.18
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTATATTTTTATTTAT
Found at i:47558 original size:13 final size:12
Alignment explanation
Indices: 47521--47563 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 12
47511 TACATTTTTA
*
47521 TATTTATATATA
1 TATTTATATATT
*
47533 T-TTTATATTTT
1 TATTTATATATT
47544 TATTTATACTATT
1 TATTTATA-TATT
47557 TATTTAT
1 TATTTAT
47564 TTTCATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.35
12 7 0.27
13 10 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTATATATT
Found at i:54253 original size:2 final size:2
Alignment explanation
Indices: 54248--54287 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
54238 ATATTATATA
54248 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
54288 AACATAAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:55306 original size:23 final size:23
Alignment explanation
Indices: 55238--55295 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
55228 CAACCTTATA
55238 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
55261 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
55284 TGGCACTTCGGT
1 TGGCACTTCGGT
55296 ACATTTATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:56305 original size:67 final size:69
Alignment explanation
Indices: 56224--56358 Score: 220
Period size: 67 Copynumber: 2.0 Consensus size: 69
56214 TCAAATGCCT
*
56224 TTTTATAGTAAGATATGAAGTTACCTTGCC-TTTCAATTATTTTT-TAGGCATTCTTTTATTTAA
1 TTTTATAGTAAGATAAGAAGTTACCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTTAA
56287 TTTC
66 TTTC
* * *
56291 TTTTATAGTTAGATAAGAAGTTATCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTTCA
1 TTTTATAGTAAGATAAGAAGTTACCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTTAA
56356 TTT
66 TTT
56359 AAATGAAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 27 0.44
68 14 0.23
69 21 0.34
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (69 bp):
TTTTATAGTAAGATAAGAAGTTACCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTTAA
TTTC
Found at i:75665 original size:4 final size:4
Alignment explanation
Indices: 75656--75685 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
75646 GCAGCCTATT
75656 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
75686 CGTAAATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:76309 original size:31 final size:31
Alignment explanation
Indices: 76267--76334 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
76257 GTCGGGGACT
*
76267 ATATTGCAAACGGACTAAATGTTGAGGGATC
1 ATATTGAAAACGGACTAAATGTTGAGGGATC
* * *
76298 ATATTGAAAACGGACTAAGTGTTGGGGGATT
1 ATATTGAAAACGGACTAAATGTTGAGGGATC
76329 ATATTG
1 ATATTG
76335 CAAGTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (31 bp):
ATATTGAAAACGGACTAAATGTTGAGGGATC
Found at i:78028 original size:42 final size:42
Alignment explanation
Indices: 77969--78063 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 42
77959 AGACGTAACT
*
77969 TAAAATATTATAAAATATTAATATTTTCGGTTGAGTG-TGACC
1 TAAAATATTATAAAATATTAACATTTTCGGTTGAGTGTTG-CC
78011 TAAAATATTATAAAATATTAACATTTTCGGTTGAGTGTTGCC
1 TAAAATATTATAAAATATTAACATTTTCGGTTGAGTGTTGCC
*
78053 TAAAATGTTAT
1 TAAAATATTAT
78064 TTTTTCATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 48 0.96
43 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (42 bp):
TAAAATATTATAAAATATTAACATTTTCGGTTGAGTGTTGCC
Found at i:80577 original size:21 final size:21
Alignment explanation
Indices: 80553--80631 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
80543 ATCGTAGCCG
*
80553 TTTCAGATGGCACCACAACCA
1 TTTCAGATGCCACCACAACCA
* ** *
80574 TTTCAGATGCCATCACAGTCG
1 TTTCAGATGCCACCACAACCA
* *
80595 GTTCAGACGCCACCACAACCA
1 TTTCAGATGCCACCACAACCA
80616 GTTT-AGATGCCACCAC
1 -TTTCAGATGCCACCAC
80632 CGCAGGGTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
21 42 0.95
22 2 0.05
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.20
Consensus pattern (21 bp):
TTTCAGATGCCACCACAACCA
Found at i:83268 original size:27 final size:27
Alignment explanation
Indices: 83229--83283 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
83219 TGATCTGACC
* *
83229 TAAAAAATTTATATCTTTCACCCGATT
1 TAAAAAATATATATCTTTCACCCAATT
83256 TAAAAAATATATATCTTTCACCCAATT
1 TAAAAAATATATATCTTTCACCCAATT
83283 T
1 T
83284 GAATCCGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAAAAATATATATCTTTCACCCAATT
Found at i:87242 original size:25 final size:25
Alignment explanation
Indices: 87213--87267 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
87203 GTTTAAGTTG
87213 TGTTTT-GGTATCAATTTGTGTTATT
1 TGTTTTAGGTA-CAATTTGTGTTATT
* *
87238 TGTTTTTATGTAGAATTTGTGTTATT
1 TG-TTTTAGGTACAATTTGTGTTATT
87264 TGTT
1 TGTT
87268 AAATGAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 19 0.73
27 3 0.12
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (25 bp):
TGTTTTAGGTACAATTTGTGTTATT
Found at i:87302 original size:45 final size:44
Alignment explanation
Indices: 87251--87343 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 44
87241 TTTTATGTAG
** *
87251 AATTTGTGTTATTTGTTAAATGAAATTAAGTTGTGTTTTGGTATT
1 AATTTGTGCCATTTGTTAAATGAAATTAAGTAGTG-TTTGGTATT
*
87296 AATTTGTGCCATTTGTTGAATGAAATTAAGTAGTGTTTGGTATT
1 AATTTGTGCCATTTGTTAAATGAAATTAAGTAGTGTTTGGTATT
87340 AATT
1 AATT
87344 AAGTGCCGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 13 0.30
45 31 0.70
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.49
Consensus pattern (44 bp):
AATTTGTGCCATTTGTTAAATGAAATTAAGTAGTGTTTGGTATT
Done.