Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008882.1 Hibiscus syriacus cultivar Beakdansim tig00112128_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: 93746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2194 original size:2 final size:2
Alignment explanation
Indices: 2181--2218 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
2171 TTAAATTATT
2181 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2219 TTAACAATCG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4479 original size:20 final size:20
Alignment explanation
Indices: 4434--4491 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
4424 TGATGGGTAG
4434 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
4458 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
4478 TGCATCGATGCACT
1 TGCATCGATGCACT
4492 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:5451 original size:2 final size:2
Alignment explanation
Indices: 5444--5533 Score: 164
Period size: 2 Copynumber: 45.5 Consensus size: 2
5434 ATACGATTAT
5444 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5485 TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5527 TA TA TA T
1 TA TA TA T
5534 GAAGGTGCAT
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 84 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11045 original size:64 final size:64
Alignment explanation
Indices: 10992--11154 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
10982 CGGTGCACCA
*
10992 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
11056 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
11121 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
11155 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:11126 original size:19 final size:19
Alignment explanation
Indices: 11102--11152 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
11092 GAAAATATTC
11102 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
11121 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
11140 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
11153 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:12165 original size:21 final size:21
Alignment explanation
Indices: 12131--12174 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12121 CAGGAGCTGG
12131 AGGAGGAGCACGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
* *
12152 AGGAGTAGCTCGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
12173 AG
1 AG
12175 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.09
Consensus pattern (21 bp):
AGGAGGAGCACGAGAAGAACT
Found at i:17637 original size:22 final size:21
Alignment explanation
Indices: 17595--17634 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17585 GAGTTTGTTT
*
17595 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
17616 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
17635 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:19707 original size:19 final size:19
Alignment explanation
Indices: 19683--19733 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
19673 GAAAATATTC
19683 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
19702 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
19721 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
19734 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:19709 original size:65 final size:65
Alignment explanation
Indices: 19558--19735 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 65
19548 GAACACTTGA
*** * *
19558 TGCATCGATGCACCAAGTGTGCATTGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGG
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGG
** * **
19622 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGA
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-
19686 G
65 G
* * *
19687 TGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
19736 CAATTAATTC
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 48 0.50
65 48 0.50
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGG
Found at i:19775 original size:65 final size:65
Alignment explanation
Indices: 19585--19784 Score: 200
Period size: 65 Copynumber: 3.1 Consensus size: 65
19575 TGTGCATTGA
* ** *
19585 TGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTTG-TGCATC
1 TGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-TGATGCATC
*
19647 GA
64 GG
* *
19649 TGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--GAGTGCATC
1 TGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA-TGCATC
19712 GG
64 GG
* *
19714 TGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGACTGATGCAT
1 TGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGACTGATGCAT
19776 CGG
63 CGG
19779 TGCATG
1 TGCATG
19785 CCTTTGAATA
Statistics
Matches: 116, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 43 0.37
65 60 0.52
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGATGCATCGG
Found at i:23778 original size:22 final size:21
Alignment explanation
Indices: 23736--23775 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23726 AAGACTATTT
23736 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
23757 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
23776 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:27021 original size:23 final size:23
Alignment explanation
Indices: 26953--27021 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
26943 ACATATTATA
*
26953 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
26976 CGGTA-TTATGGTGCAATTCTACG
1 TGGCACTT-CGGTGCATTTCTACG
*
26999 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
27022 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:27869 original size:28 final size:27
Alignment explanation
Indices: 27819--27911 Score: 161
Period size: 27 Copynumber: 3.4 Consensus size: 27
27809 TTTTTTCGGG
27819 TCGGGTCGGG-TTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
27845 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGG-TTTTTTAAGTGTGATAT
*
27873 TCGGGTTGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
27900 TCGGGTCGGGTT
1 TCGGGTCGGGTT
27912 CGGGTTTAGG
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
26 10 0.16
27 28 0.44
28 25 0.40
ACGTcount: A:0.13, C:0.08, G:0.35, T:0.44
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:36743 original size:37 final size:37
Alignment explanation
Indices: 36685--36756 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
36675 GGATGGAGAA
* *
36685 AGTTTAGTTCTTTTCTTTCTTTGTCTAATATGTGTAT
1 AGTTTAGTTCTTCTCTCTCTTTGTCTAATATGTGTAT
* *
36722 AGTTTTGTTCTTCTCTCTCTTTGTCTAATTTGTGT
1 AGTTTAGTTCTTCTCTCTCTTTGTCTAATATGTGT
36757 GTGTGCTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (37 bp):
AGTTTAGTTCTTCTCTCTCTTTGTCTAATATGTGTAT
Found at i:40992 original size:48 final size:47
Alignment explanation
Indices: 40917--41011 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 47
40907 CGGGAGCATC
*
40917 GCCGTTTTAGAAGGCAACAAATGGAGGAAATCGCTCAAGCTTTGATA
1 GCCGTTTTAGAAGGCAACAAATAGAGGAAATCGCTCAAGCTTTGATA
*
40964 GCCGTTTTAGCAAGGCAACAAATAGAGGAAATCGCTCGAGCTTTGATA
1 GCCGTTTTAG-AAGGCAACAAATAGAGGAAATCGCTCAAGCTTTGATA
41012 TCCAGTGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 10 0.22
48 35 0.78
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (47 bp):
GCCGTTTTAGAAGGCAACAAATAGAGGAAATCGCTCAAGCTTTGATA
Found at i:41899 original size:21 final size:21
Alignment explanation
Indices: 41836--41899 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
41826 ACAACTGTAG
*
41836 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
41857 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
41877 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
41898 AC
1 AC
41900 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:48633 original size:2 final size:2
Alignment explanation
Indices: 48626--48656 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48616 TTAAATTGTT
48626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48657 CTACATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49179 original size:16 final size:16
Alignment explanation
Indices: 49141--49179 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
49131 TGAAGTTGGC
*
49141 GTATCACTATAAAGTA
1 GTATCATTATAAAGTA
49157 GTATCATTATAAAGTA
1 GTATCATTATAAAGTA
49173 GTATCAT
1 GTATCAT
49180 ATCATCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (16 bp):
GTATCATTATAAAGTA
Found at i:53275 original size:15 final size:17
Alignment explanation
Indices: 53244--53278 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
53234 TAGAAAATTT
53244 TTAAAAAATATTCAAAA
1 TTAAAAAATATTCAAAA
53261 TTAAAAAA-ATT-AAAA
1 TTAAAAAATATTCAAAA
53276 TTA
1 TTA
53279 TATATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAAATATTCAAAA
Found at i:55461 original size:21 final size:22
Alignment explanation
Indices: 55424--55465 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55414 CTGAAGTCAT
55424 AAAAATTCAAATAACCAAATAA
1 AAAAATTCAAATAACCAAATAA
55446 AAAAATTCAAAT-ACCAAATA
1 AAAAATTCAAATAACCAAATA
55466 CCAAATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAAATTCAAATAACCAAATAA
Found at i:60017 original size:21 final size:20
Alignment explanation
Indices: 60000--60046 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
59990 ATAGATCGAA
60000 CCTTTGGTCAAAGGGATCAAT
1 CCTTTGG-CAAAGGGATCAAT
* *
60021 CCTTTTGCTAAGGGATCAAT
1 CCTTTGGCAAAGGGATCAAT
60041 CCTTTG
1 CCTTTG
60047 AACCAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
CCTTTGGCAAAGGGATCAAT
Found at i:60184 original size:11 final size:11
Alignment explanation
Indices: 60170--60194 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60160 ACTTTGAATT
60170 ATTTTTGATAA
1 ATTTTTGATAA
60181 ATTTTTGATAA
1 ATTTTTGATAA
60192 ATT
1 ATT
60195 CAATTAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTTTTGATAA
Found at i:71595 original size:20 final size:20
Alignment explanation
Indices: 71570--71619 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
71560 TGCATGTAGA
*
71570 GGTATCGATACCTCAAGGGT
1 GGTATCGATACCTCAAGGAT
**
71590 GGTATCGATACCTGTAGGAT
1 GGTATCGATACCTCAAGGAT
71610 GGTATCGATA
1 GGTATCGATA
71620 TCCTTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCTCAAGGAT
Found at i:71625 original size:147 final size:147
Alignment explanation
Indices: 71419--71726 Score: 553
Period size: 147 Copynumber: 2.1 Consensus size: 147
71409 TACCTGTTGA
* *
71419 TAGAGGTATCAATATCTCAAGGGTGGTATCAATACCTGTAGAATGGTATCGATATCCTTAAAACT
1 TAGAGGTATCGATACCTCAAGGGTGGTATCAATACCTGTAGAATGGTATCGATATCCTTAAAACT
* *
71484 TCGAAGGTAATTTCGGTTTTAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACATAAT
66 TCGAAGGTAATTTCGATTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACATAAT
71549 TTTGATATTGTTGCATG
131 TTTGATATTGTTGCATG
* *
71566 TAGAGGTATCGATACCTCAAGGGTGGTATCGATACCTGTAGGATGGTATCGATATCCTTAAAACT
1 TAGAGGTATCGATACCTCAAGGGTGGTATCAATACCTGTAGAATGGTATCGATATCCTTAAAACT
71631 TCGAAGGTAATTTCGATTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACATAAT
66 TCGAAGGTAATTTCGATTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACATAAT
71696 TTTGATATTGTTGCATG
131 TTTGATATTGTTGCATG
*
71713 TGGAGGTATCGATA
1 TAGAGGTATCGATA
71727 ACCTTGAGGG
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 154 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (147 bp):
TAGAGGTATCGATACCTCAAGGGTGGTATCAATACCTGTAGAATGGTATCGATATCCTTAAAACT
TCGAAGGTAATTTCGATTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACATAAT
TTTGATATTGTTGCATG
Found at i:72316 original size:21 final size:21
Alignment explanation
Indices: 72271--72316 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
72261 TCGAGGGTCT
* * **
72271 ATGTGGTCCTTCGGGATAATT
1 ATGTGGTCCTCCGGGACAAAG
72292 ATGTGGTCCTCCGGGACAAAG
1 ATGTGGTCCTCCGGGACAAAG
72313 ATGT
1 ATGT
72317 AGCACTTCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
ATGTGGTCCTCCGGGACAAAG
Found at i:78629 original size:23 final size:20
Alignment explanation
Indices: 78601--78654 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
78591 GCATATGGAT
78601 GTATCGATACCCTTGAGGGGGTG
1 GTATCGATACCCTT-A--GGGTG
*
78624 GTATCGGTACCCTTAGGGTG
1 GTATCGATACCCTTAGGGTG
*
78644 GTACCGATACC
1 GTATCGATACC
78655 TACAGATACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
22 1 0.04
23 13 0.46
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCTTAGGGTG
Found at i:79223 original size:21 final size:21
Alignment explanation
Indices: 79196--79245 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
79186 AGTCGAGGAT
79196 ATATGTGGTCATT-CGGGACAA
1 ATATGTGGTC-TTCCGGGACAA
* *
79217 TTATGTGGTCTTCCGGGATAA
1 ATATGTGGTCTTCCGGGACAA
79238 ATATGTGG
1 ATATGTGG
79246 CACTTCGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (21 bp):
ATATGTGGTCTTCCGGGACAA
Found at i:80122 original size:31 final size:31
Alignment explanation
Indices: 80087--80155 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
80077 TGATTATCGA
*
80087 ATTGGTTGTTTTCGGTTCGGATCAATATCAG
1 ATTGGTTGTTTTCGGTTCGAATCAATATCAG
*
80118 ATTGGTTGTTTTCGGTTCGAATCAATATCAT
1 ATTGGTTGTTTTCGGTTCGAATCAATATCAG
80149 ATTGGTT
1 ATTGGTT
80156 AATTTTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (31 bp):
ATTGGTTGTTTTCGGTTCGAATCAATATCAG
Found at i:80556 original size:19 final size:18
Alignment explanation
Indices: 80514--80556 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
80504 TATCTATTTA
80514 ATAAAGAAATATTTTTTT
1 ATAAAGAAATATTTTTTT
80532 ATTAAA-AAATTATTTTTATT
1 A-TAAAGAAA-TATTTTT-TT
80552 ATAAA
1 ATAAA
80557 TATAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 15 0.68
20 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATAAAGAAATATTTTTTT
Found at i:81571 original size:87 final size:86
Alignment explanation
Indices: 81421--81587 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 86
81411 CGATTATGTT
* *
81421 ATATTATTTAATCGGAAATATTATCAAGTACAATAACGTATTAGGTAACGTTTATATAATGTAAT
1 ATATTATTTAATCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAAT
81486 AGATAGCGCTTATATAATAAA
66 AGATAGCGCTTATATAATAAA
* *
81507 ATATGTATTTAA-CGGGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATGTA
1 ATAT-TATTTAATC-GGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTA
*
81571 ATAGGTAGCGCTTATAT
64 ATAGATAGCGCTTATAT
81588 TGACCTATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 5 0.07
87 69 0.93
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (86 bp):
ATATTATTTAATCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAAT
AGATAGCGCTTATATAATAAA
Found at i:85224 original size:183 final size:183
Alignment explanation
Indices: 84916--85484 Score: 973
Period size: 183 Copynumber: 3.1 Consensus size: 183
84906 TTAAAATTAG
* *
84916 CGACACAATATTAAAAAATGTCGATATAGGTTGTAGACCTATTCGCTTATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
84981 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
85046 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
85099 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGAATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
85164 ATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
85229 CACTTTTTGACAAGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
85282 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * * * *
85347 ATACTGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCAATGTTTTTCAA--TC
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG--TGTAAATGTC
* *
85410 GATAC-TTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
129 GACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
85464 CGACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
85485 GAAAACTTTG
Statistics
Matches: 367, Mismatches: 17, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
182 68 0.19
183 295 0.80
185 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:88961 original size:200 final size:200
Alignment explanation
Indices: 88242--89356 Score: 1934
Period size: 200 Copynumber: 5.6 Consensus size: 200
88232 ACATTAACAA
* * * * *
88242 TGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGATTAGATTGAA
1 TGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAA
* * * *
88306 AAATTACCTAATACATTATACTTTTGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGA
65 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGG
* *
88371 ATCGACACTTCATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
130 ATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
88436 CAAAAG
195 CAAAAG
* *
88442 TGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
88507 AATTA-CTATTACACTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
* *
88571 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCA-TCTGGACCAAAAATATCGACACAAAATAT
131 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
88635 AAAAG
196 AAAAG
*
88640 TATCGATACATTA-TTAGACCTATTCTCTCATAAAA-CGGTATACTTGTACCGGTTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
88703 AATTACCTATTACATTATACTTATAGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
* *
88768 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCAACATAAACTAC
131 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
88833 AAAAG
196 AAAAG
* *
88838 TGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
* *
88903 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGGCACATTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
88968 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
89033 AAAAG
196 AAAAG
*
89038 TGTCGATACATTATTTAGACCGATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
89103 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
89168 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
131 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
89233 AAAAG
196 AAAAG
*
89238 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
*
89303 AATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTT
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTT
89357 ATGGTTGCAC
Statistics
Matches: 869, Mismatches: 41, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
196 33 0.04
197 114 0.13
198 84 0.10
199 109 0.13
200 525 0.60
201 4 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAA
AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
AAAAG
Found at i:89623 original size:18 final size:18
Alignment explanation
Indices: 89600--89644 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
89590 TCTCATTCAT
*
89600 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
89618 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
89637 AATTATAA
1 AATTATAA
89645 ATCTTACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:89654 original size:17 final size:19
Alignment explanation
Indices: 89612--89658 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
89602 TTATATTCAC
89612 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
89631 ATACAAAATTATAAATC-T
1 ATACAAAATTATAAATCGT
89649 -TACAAAATTA
1 ATACAAAATTA
89659 ACCCTACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 17 0.61
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:91539 original size:21 final size:21
Alignment explanation
Indices: 91514--91578 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
91504 CCCCTTATGC
* *
91514 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
91535 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
91556 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
91577 CT
1 CT
91579 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Done.