Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004975.1 Hibiscus syriacus cultivar Beakdansim tig00011170_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: 99105
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:57 original size:13 final size:12
Alignment explanation
Indices: 39--93 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
29 AAATTTTAGC
*
39 TTTTTTTGGCTT
1 TTTTTTTTGCTT
51 TTTTTTTTG--T
1 TTTTTTTTGCTT
*
61 TTTTTTTGGCTT
1 TTTTTTTTGCTT
73 TTTTTTTTGCTT
1 TTTTTTTTGCTT
85 TTTTGTTTT
1 TTTT-TTTT
94 TTTTGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.24
12 24 0.65
13 4 0.11
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (12 bp):
TTTTTTTTGCTT
Found at i:64 original size:22 final size:22
Alignment explanation
Indices: 32--88 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
22 TTTTTTGAAA
*
32 TTTTAGCTTTTTTTGGCTTTTT
1 TTTTTGCTTTTTTTGGCTTTTT
*
54 TTTTTGTTTTTTTTGGCTTTTT
1 TTTTTGCTTTTTTTGGCTTTTT
76 TTTTTGCTTTTTT
1 TTTTTGCTTTTTT
89 GTTTTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.02, C:0.07, G:0.12, T:0.79
Consensus pattern (22 bp):
TTTTTGCTTTTTTTGGCTTTTT
Found at i:96 original size:22 final size:21
Alignment explanation
Indices: 39--97 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
29 AAATTTTAGC
*
39 TTTTTTTGGCTTTTTTTTTTG
1 TTTTTTTTGCTTTTTTTTTTG
60 TTTTTTTTGGCTTTTTTTTTTG
1 TTTTTTTT-GCTTTTTTTTTTG
*
82 -CTTTTTTG-TTTTTTTT
1 TTTTTTTTGCTTTTTTTT
98 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
21 13 0.37
22 13 0.37
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (21 bp):
TTTTTTTTGCTTTTTTTTTTG
Found at i:7127 original size:24 final size:24
Alignment explanation
Indices: 7081--7132 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
7071 TCTTGGCACT
* * *
7081 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
* *
7105 TCAAGTGGCATAGCTGTTGGAACG
1 TCAAGTGGCACAGCTGTTGGAACA
7129 TCAA
1 TCAA
7133 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:8428 original size:24 final size:23
Alignment explanation
Indices: 8400--8460 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
8390 ACTTTTCTTT
8400 CTTTCTTTTTCTTTTTTTCAAGTG
1 CTTTCTTTTTCTTTTTTT-AAGTG
** * *
8424 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTTTTTTAAGTG
8447 CTTT-TGTTTTCTTT
1 CTTTCT-TTTTCTTT
8461 GCTGAATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.08, C:0.16, G:0.10, T:0.66
Consensus pattern (23 bp):
CTTTCTTTTTCTTTTTTTAAGTG
Found at i:9454 original size:90 final size:90
Alignment explanation
Indices: 9280--9456 Score: 248
Period size: 90 Copynumber: 2.0 Consensus size: 90
9270 AATGATGTTT
** *
9280 GGCCGAATAGGGAGAGAGTTCTTCATCTTGGTGCCTAAATAAACCACATGCAAGGCACATGGGGC
1 GGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGGGC
* *
9345 TGTTCACATGTAAAACACATGGCTA
66 TGGTCACATGCAAAACACATGGCTA
* * *
9370 GGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATGGGGG
1 GGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-GGGG
* *
9435 CTGGT-ATATGCAAAGCACATGG
65 CTGGTCACATGCAAAACACATGG
9457 GTGTTCTAGG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
90 68 0.89
91 8 0.11
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.21
Consensus pattern (90 bp):
GGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGGGC
TGGTCACATGCAAAACACATGGCTA
Found at i:11273 original size:576 final size:572
Alignment explanation
Indices: 10484--11598 Score: 1701
Period size: 576 Copynumber: 1.9 Consensus size: 572
10474 GGATCGTATA
10484 AGGTTTCATATTTCATTTGTAAGGCAGACTTGTTTTAATCAAATATTGTGAGAGTTTTTCTCTTT
1 AGGTTTCATATTTCATTTGTAAGGCAGACTTGTTTTAATCAAATATTGTGAGAGTTTTTCTCTTT
*
10549 AGTTTTAATTGAACTTTATCGACTTATCAAGCTTATGCTTGTGGCATCAACCCCATCTATTTATC
66 AGTTTTAATTGAACTTTATCGACTTATCAAGCTTATGCTTGTGGCATCAACCCCATCTATTCATC
** *
10614 CTGATACTTCTGATTTTTATCTCTTATAGATAGTGGGTCAAAGTCCTTATTTACCACCCCTTTAA
131 CTGATACTTCTGATTCCTATCCCTTATAGATAGTGGGTCAAAGTCCTTATTTACCACCCCTTTAA
* * *
10679 GAAGTAATATAAAGTCTGGGTCTTTGTTCTTTAACATTATTTCTTCTTTGAGTCTTCTTGGAG-A
196 GAAGCAATATAAAGTCTGGGTCTTTGTTCTTTAACATCAGTTCTTCTTTGAGTCTTCTTGGAGAA
* *
10743 -TA-C-TA-TC-TTT-CAT-AT-T-CATTCTACCATACTTCACCATTTCCTTTAAAAATATCACC
261 TTATCATATTCATTTCCATCATATCCATTCTACCATACTTCACAATTTCCTTTAAAAATAT-AAC
*
10799 CAATATATATATATATATATATTCTGCTGCCATATCTTTCTATTCCATTACTTCTATTTAGCCAT
325 CAATATATAT-T-T-TATACATTCTGCTGCCATA----TCT-TTCCATT-C--C-ATTTAGCCAT
* *
10864 TCTATTTTGAGTTTTCTTGTTTGTGCAGGATCCTTATTGTTTTCCTAGATCGAGTCAATCAAAGG
378 TCTATTTTGAGTTTTCTTGTTTGTGCAGGATCCTTATTGCTTTCCTAGATCGAGACAATCAAAGG
* *
10929 TACATCCTTATCTTCCAAGGAATGTTAGGTCGTATCTTATCAAGTGGTATCAGAACTAAGGTGGA
443 TACATCCTTATCTTCCAAGGAATGCTAGGCCGTATCTTATCAAGTGGTATCAGAACTAAGGTGGA
* *
10994 TTGCAAGAATAACAAGCAAAAACAATACTTTACCATTCGACCACATTCTCTCAAACTCTATAAAT
508 TTGCAACAAGAACAAGCAAAAACAATACTTTACCATTCGACCACATTCTCTCAAACTCTATAAAT
*
11059 AGGTTTCATATTTCATTTGTAAGGCATACTTGTTTTAATCAAATATTGTGAGAGTTTTTCTCTTT
1 AGGTTTCATATTTCATTTGTAAGGCAGACTTGTTTTAATCAAATATTGTGAGAGTTTTTCTCTTT
**
11124 AGTTCTTAATTGAACTTTATCGACTTATCAAGCTTATGCTTGTGGTGTCAACCCCATCTATTCAT
66 AGTT-TTAATTGAACTTTATCGACTTATCAAGCTTATGCTTGTGGCATCAACCCCATCTATTCAT
* * * *
11189 CCTGATACTTTTGGTTCCTATCCCTTATAGATAGTTGGTCAAAGTCCTTGTTTACCACCCCTTTA
130 CCTGATACTTCTGATTCCTATCCCTTATAGATAGTGGGTCAAAGTCCTTATTTACCACCCCTTTA
*
11254 AGAAGCAATATAAAGTCTGGGTCTTTGTTCTTTAACATCGGTTCTTCTTTGAGTCTTCTTGGAGA
195 AGAAGCAATATAAAGTCTGGGTCTTTGTTCTTTAACATCAGTTCTTCTTTGAGTCTTCTTGGAGA
11319 TATTATCTTTCATATTCATTTCCATCATATCCATTCTACCATACTTCACAATTTCCTTTAAAAAT
260 -ATTA----TCATATTCATTTCCATCATATCCATTCTACCATACTTCACAATTTCCTTTAAAAAT
* *
11384 ATAACCAATATATATTTTTTCCATTCTGCTGCCATATCTTTCCATTCCATTTAGCCATTCTATTT
320 ATAACCAATATATATTTTATACATTCTGCTGCCATATCTTTCCATTCCATTTAGCCATTCTATTT
*
11449 TGAGTTTTCTTGTTTGTGCAGGATCCTTGTTGCTTTCCTAGATCGAGACAATCAAAGGTACATCC
385 TGAGTTTTCTTGTTTGTGCAGGATCCTTATTGCTTTCCTAGATCGAGACAATCAAAGGTACATCC
* * * *
11514 TTGTCTTCCAAGGTATGCTAGGCCGTATCTTATCAAGTGGTATCATAGCTAAGGTGGATTGCAAC
450 TTATCTTCCAAGGAATGCTAGGCCGTATCTTATCAAGTGGTATCAGAACTAAGGTGGATTGCAAC
*
11579 AAGAACAAGCAAAACCAATA
515 AAGAACAAGCAAAAACAATA
11599 TTCAACCATT
Statistics
Matches: 492, Mismatches: 32, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
575 68 0.14
576 175 0.36
578 156 0.32
579 3 0.01
581 1 0.00
582 7 0.01
583 3 0.01
584 1 0.00
585 2 0.00
586 2 0.00
587 19 0.04
588 4 0.01
589 3 0.01
590 13 0.03
591 35 0.07
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (572 bp):
AGGTTTCATATTTCATTTGTAAGGCAGACTTGTTTTAATCAAATATTGTGAGAGTTTTTCTCTTT
AGTTTTAATTGAACTTTATCGACTTATCAAGCTTATGCTTGTGGCATCAACCCCATCTATTCATC
CTGATACTTCTGATTCCTATCCCTTATAGATAGTGGGTCAAAGTCCTTATTTACCACCCCTTTAA
GAAGCAATATAAAGTCTGGGTCTTTGTTCTTTAACATCAGTTCTTCTTTGAGTCTTCTTGGAGAA
TTATCATATTCATTTCCATCATATCCATTCTACCATACTTCACAATTTCCTTTAAAAATATAACC
AATATATATTTTATACATTCTGCTGCCATATCTTTCCATTCCATTTAGCCATTCTATTTTGAGTT
TTCTTGTTTGTGCAGGATCCTTATTGCTTTCCTAGATCGAGACAATCAAAGGTACATCCTTATCT
TCCAAGGAATGCTAGGCCGTATCTTATCAAGTGGTATCAGAACTAAGGTGGATTGCAACAAGAAC
AAGCAAAAACAATACTTTACCATTCGACCACATTCTCTCAAACTCTATAAAT
Found at i:15352 original size:10 final size:10
Alignment explanation
Indices: 15330--15386 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 10
15320 ATTTATTTTC
15330 AAAAAAACAA
1 AAAAAAACAA
15340 AAAATAAACAA
1 AAAA-AAACAA
15351 AAAAAGGAACAA
1 AAAAA--AACAA
*
15363 AAAAAAAGGAA
1 AAAAAAA-CAA
15374 CAAAAAAACAA
1 -AAAAAAACAA
15385 AA
1 AA
15387 CAAATGCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 9 0.22
11 14 0.35
12 17 0.43
ACGTcount: A:0.82, C:0.09, G:0.07, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:15355 original size:12 final size:11
Alignment explanation
Indices: 15330--15386 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
15320 ATTTATTTTC
15330 AAAAAAACAAA
1 AAAAAAACAAA
*
15341 AAATAAACAAA
1 AAAAAAACAAA
*
15352 AAAAGGAACAAA
1 AAAA-AAACAAA
** *
15364 AAAAAAGGAAC
1 AAAAAAACAAA
15375 AAAAAAACAAA
1 AAAAAAACAAA
15386 A
1 A
15387 CAAATGCCAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.82, C:0.09, G:0.07, T:0.02
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:15366 original size:14 final size:14
Alignment explanation
Indices: 15349--15381 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
15339 AAAAATAAAC
15349 AAAAAAAGGAACAA
1 AAAAAAAGGAACAA
15363 AAAAAAAGGAACAA
1 AAAAAAAGGAACAA
15377 AAAAA
1 AAAAA
15382 CAAAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAACAA
Found at i:19698 original size:15 final size:16
Alignment explanation
Indices: 19670--19706 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
19660 CTTTATTATC
19670 TTATTTCATCTTTCAT
1 TTATTTCATCTTTCAT
19686 TTATTTC-TCTTTCAT
1 TTATTTCATCTTTCAT
19701 TTATTT
1 TTATTT
19707 TATTCTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATCTTTCAT
Found at i:25441 original size:9 final size:10
Alignment explanation
Indices: 25419--25451 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
25409 ATTGGAGTGC
25419 AAAAAGAAAG
1 AAAAAGAAAG
*
25429 AAAAAGACA-
1 AAAAAGAAAG
25438 AAAAAGAAAG
1 AAAAAGAAAG
25448 AAAA
1 AAAA
25452 TTAGAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:25460 original size:13 final size:12
Alignment explanation
Indices: 25437--25478 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
25427 AGAAAAAGAC
25437 AAAAAAG-AAAG
1 AAAAAAGAAAAG
*
25448 AAAATTAGAAAAG
1 AAAA-AAGAAAAG
25461 AAGAAAAGAAAAG
1 AA-AAAAGAAAAG
25474 AAAAA
1 AAAAA
25479 TTCAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 15 0.58
14 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:25485 original size:26 final size:26
Alignment explanation
Indices: 25430--25485 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
25420 AAAAGAAAGA
*
25430 AAAAGACAAAAAAGAAAGAAAATTAG
1 AAAAGACAAAAAAGAAAGAAAATTAC
*
25456 AAAAGA-AGAAAAGAAAAGAAAAATT-C
1 AAAAGACAAAAAAG-AAAG-AAAATTAC
25482 AAAA
1 AAAA
25486 AGAGAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 6 0.23
26 14 0.54
27 6 0.23
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (26 bp):
AAAAGACAAAAAAGAAAGAAAATTAC
Found at i:32865 original size:13 final size:12
Alignment explanation
Indices: 32846--32910 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
32836 ATATAGGCGT
32846 GATATGGTGATG
1 GATATGGTGATG
32858 GAATATGGTGAT-
1 G-ATATGGTGATG
*
32870 GATATAGGCG-T-
1 GATAT-GGTGATG
32881 GATAATGGTGATG
1 GAT-ATGGTGATG
32894 GACTATGGTGAT-
1 GA-TATGGTGATG
32906 GATAT
1 GATAT
32911 AAGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:32901 original size:36 final size:36
Alignment explanation
Indices: 32828--32932 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
32818 ATTTATAAGT
* *
32828 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
32863 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
32899 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
32933 GGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:36901 original size:22 final size:23
Alignment explanation
Indices: 36873--36924 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
36863 ATTTATAAGT
36873 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
36895 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
36918 TGGTGAT
1 TGGTGAT
36925 GGACAGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:37929 original size:18 final size:18
Alignment explanation
Indices: 37885--37923 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
37875 ACGGTGCAAC
* *
37885 TCTCCAGTTAAAATGAGG
1 TCTCCAGCTGAAATGAGG
37903 TCTCCAGCTGAAATGAGG
1 TCTCCAGCTGAAATGAGG
37921 TCT
1 TCT
37924 TTAGCTAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (18 bp):
TCTCCAGCTGAAATGAGG
Found at i:56303 original size:22 final size:24
Alignment explanation
Indices: 56284--56333 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
56274 AAGGAAAATC
56284 AGAAA-AG-AAACACTCAAAAAGA
1 AGAAATAGAAAACACTCAAAAAGA
*
56306 AGAAATTGAAAACACTC-AAAAGA
1 AGAAATAGAAAACACTCAAAAAGA
56329 AGAAA
1 AGAAA
56334 AAAAAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 8 0.32
ACGTcount: A:0.66, C:0.12, G:0.14, T:0.08
Consensus pattern (24 bp):
AGAAATAGAAAACACTCAAAAAGA
Found at i:57495 original size:11 final size:11
Alignment explanation
Indices: 57479--57504 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57469 TCAAGCAACC
57479 AACACCCATTA
1 AACACCCATTA
57490 AACACCCATTA
1 AACACCCATTA
57501 AACA
1 AACA
57505 ACTATTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (11 bp):
AACACCCATTA
Found at i:58165 original size:19 final size:20
Alignment explanation
Indices: 58127--58179 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
58117 GAAACCCCTT
*
58127 TGAAAATACATGATTTTTTTGA
1 TGAAAATACATGA--TTTTTAA
58149 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
58168 TGAAGATACATG
1 TGAAAATACATG
58180 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:61578 original size:8 final size:8
Alignment explanation
Indices: 61565--61609 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
61555 ATCTTTTTCT
61565 TTTTCTTC
1 TTTTCTTC
61573 TTTTCTTC
1 TTTTCTTC
61581 TTTTCTTC
1 TTTTCTTC
61589 TTTT-TGTC
1 TTTTCT-TC
61597 TTTTCTTTC
1 TTTTC-TTC
61606 TTTT
1 TTTT
61610 TGTACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:61611 original size:17 final size:16
Alignment explanation
Indices: 61556--61612 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
61546 CTTTTTGAAA
*
61556 TCTTTTTCT-TTTTCT
1 TCTTTTTGTCTTTTCT
61571 TCTTTTCT-TCTTTTCT
1 TCTTTT-TGTCTTTTCT
61587 TCTTTTTGTCTTTTCTT
1 TCTTTTTGTCTTTTC-T
61604 TCTTTTTGT
1 TCTTTTTGT
61613 ACTCCAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.21
16 20 0.53
17 10 0.26
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (16 bp):
TCTTTTTGTCTTTTCT
Found at i:62373 original size:19 final size:20
Alignment explanation
Indices: 62335--62385 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
62325 GAAACCCCTT
62335 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
62355 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
62374 TGAAGATACATG
1 TGAAAATACATG
62386 CTCTTTGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:63131 original size:20 final size:21
Alignment explanation
Indices: 63093--63132 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
63083 GATCATCTAG
* *
63093 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
63114 AAGCT-AGATAAAAGGTATA
1 AAGCTAAGATAAAAGGTATA
63133 GGACGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:65237 original size:15 final size:15
Alignment explanation
Indices: 65217--65252 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
65207 ATTATTAGCT
*
65217 TTATAATATATGTTA
1 TTATAATATATATTA
65232 TTATAATATATATTA
1 TTATAATATATATTA
*
65247 TGATAA
1 TTATAA
65253 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:65428 original size:42 final size:42
Alignment explanation
Indices: 65369--65452 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
65359 TATACATCAA
65369 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
65411 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
65453 ATATTAACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (42 bp):
GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
Found at i:67060 original size:19 final size:21
Alignment explanation
Indices: 67036--67087 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
67026 CGGCCAAGAG
*
67036 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
67055 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
67076 CATGTATTTTCA
1 CATGTATTTTCA
67088 AAGGGGATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:67769 original size:11 final size:11
Alignment explanation
Indices: 67753--67779 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
67743 TCATTGGCGT
67753 GAAAAGCAAAA
1 GAAAAGCAAAA
67764 GAAAAGCAAAA
1 GAAAAGCAAAA
67775 GAAAA
1 GAAAA
67780 TACTCCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAGCAAAA
Found at i:69636 original size:16 final size:16
Alignment explanation
Indices: 69615--69647 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
69605 TAGTTAGCTC
69615 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
69631 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
69647 A
1 A
69648 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:73073 original size:16 final size:16
Alignment explanation
Indices: 73052--73084 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
73042 TAGTTAGCTC
73052 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
73068 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
73084 A
1 A
73085 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:74366 original size:19 final size:20
Alignment explanation
Indices: 74342--74384 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
74332 AGCATTTATC
*
74342 TTCATT-AAAATTATGTATT
1 TTCATTGAAAATCATGTATT
*
74361 TTCATTGAAAATCATGTGTT
1 TTCATTGAAAATCATGTATT
74381 TTCA
1 TTCA
74385 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTCATTGAAAATCATGTATT
Found at i:74771 original size:36 final size:36
Alignment explanation
Indices: 74724--74828 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
74714 GATACAATCT
74724 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
74760 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
74796 TTCCACCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
74829 ACTTACAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:78951 original size:36 final size:36
Alignment explanation
Indices: 78904--78987 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
78894 GATACAATTT
78904 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
78940 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
78976 TTCCATCACCAT
1 GTCCATCACCAT
78988 ATCTTTCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:81488 original size:22 final size:22
Alignment explanation
Indices: 81463--81505 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
81453 TTCTTTGGAG
*
81463 TGTATTGGTGAGATTTTTTTTT
1 TGTATTGGTGAGATTTATTTTT
*
81485 TGTATTGGTGAGGTTTATTTT
1 TGTATTGGTGAGATTTATTTT
81506 CATCTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (22 bp):
TGTATTGGTGAGATTTATTTTT
Found at i:83241 original size:18 final size:18
Alignment explanation
Indices: 83218--83263 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
83208 ATTCATGCAT
*
83218 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAATA
83236 TTAGTTCATTGAATAATA
1 TTAGTTCATTGAATAATA
*
83254 TTATTTCATT
1 TTAGTTCATT
83264 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.50
Consensus pattern (18 bp):
TTAGTTCATTGAATAATA
Found at i:84463 original size:19 final size:20
Alignment explanation
Indices: 84422--84472 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
84412 GAAACCCCTT
*
84422 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
84442 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
84461 TGAAGATACATG
1 TGAAAATACATG
84473 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:86811 original size:15 final size:14
Alignment explanation
Indices: 86777--86813 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
86767 AGAAATGGAA
86777 AAAGAAAGGAAATG
1 AAAGAAAGGAAATG
86791 ATAAGAAAGGAAATGG
1 A-AAGAAAGGAAAT-G
86807 AAAGAAA
1 AAAGAAA
86814 TGATATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.27, T:0.08
Consensus pattern (14 bp):
AAAGAAAGGAAATG
Found at i:86990 original size:35 final size:35
Alignment explanation
Indices: 86951--87019 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
86941 AAATGGGATG
* * *
86951 GTGATTATATAAGCGTGAAATGTAGATAGAAGATT
1 GTGATGATATAAGCGCGAAATGAAGATAGAAGATT
* * *
86986 GTGATGATATAGGCGCGATATGAAGATGGAAGAT
1 GTGATGATATAAGCGCGAAATGAAGATAGAAGAT
87020 GGTATAGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.30, T:0.28
Consensus pattern (35 bp):
GTGATGATATAAGCGCGAAATGAAGATAGAAGATT
Found at i:90145 original size:20 final size:20
Alignment explanation
Indices: 90102--90152 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
90092 CGGCCAGGAG
* *
90102 CATGTATTTTC-TTTAAAGT
1 CATGTATTTTCATTAAAAAT
90121 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
90141 CATGTATTTTCA
1 CATGTATTTTCA
90153 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:90471 original size:11 final size:11
Alignment explanation
Indices: 90452--90499 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
90442 CTCTATAGCA
*
90452 TTGATTCTTCT
1 TTGAGTCTTCT
90463 TTGAGTCTTCT
1 TTGAGTCTTCT
90474 TT-ATGGTTCTTCT
1 TTGA--G-TCTTCT
90487 TTGAGTCTTCT
1 TTGAGTCTTCT
90498 TT
1 TT
90500 AAGATACTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 1 0.03
11 20 0.62
12 2 0.06
13 8 0.25
14 1 0.03
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (11 bp):
TTGAGTCTTCT
Found at i:92133 original size:34 final size:33
Alignment explanation
Indices: 92066--92133 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
92056 AAGTACCAAC
* *
92066 AAAATTTGAAAAATAAAAAAAAAACATATTAAA
1 AAAATTTGAAAAATAAAAAAAAAACAGAATAAA
*
92099 AAAATTCTGAAAATTACAAAAAAAAA-AGAATAAA
1 AAAATT-TGAAAAATA-AAAAAAAAACAGAATAAA
92133 A
1 A
92134 GAAAATAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 6 0.20
34 15 0.50
35 9 0.30
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (33 bp):
AAAATTTGAAAAATAAAAAAAAAACAGAATAAA
Found at i:92649 original size:16 final size:16
Alignment explanation
Indices: 92628--92667 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
92618 TAAGGGGGAT
92628 TTTCTTTAAATTAATC
1 TTTCTTTAAATTAATC
92644 TTTCTTTAAATTAATC
1 TTTCTTTAAATTAATC
*
92660 ATTCTTTA
1 TTTCTTTA
92668 TACCATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTCTTTAAATTAATC
Found at i:96959 original size:16 final size:15
Alignment explanation
Indices: 96921--96959 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
96911 TAAGATTAGA
96921 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
96936 ATAAATAAACGGAAG
1 ATAAATAAACAAAAG
96951 ATGAAATAA
1 AT-AAATAA
96960 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Done.