Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001293.1 Hibiscus syriacus cultivar Beakdansim tig00002529_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: 47534
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6327 original size:29 final size:30
Alignment explanation
Indices: 6281--6340 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
6271 TAAAGTTTGG
*
6281 AAAAGTTTAAAGACCAAAAG-GTAATTTTC
1 AAAAGTTTAAAGAACAAAAGTGTAATTTTC
** *
6310 AAAAGTTTAGGGAACAAAAGTTTAATTTTC
1 AAAAGTTTAAAGAACAAAAGTGTAATTTTC
6340 A
1 A
6341 TTTTTATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (30 bp):
AAAAGTTTAAAGAACAAAAGTGTAATTTTC
Found at i:7513 original size:20 final size:19
Alignment explanation
Indices: 7488--7533 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
7478 GTCTATGCTA
*
7488 GAAATTAATGTTAGAATGTT
1 GAAATTAATGTTAGAAT-AT
*
7508 GAAATTGATGTTAGAATAT
1 GAAATTAATGTTAGAATAT
7527 GAAATTA
1 GAAATTA
7534 GGTCACTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (19 bp):
GAAATTAATGTTAGAATAT
Found at i:8851 original size:26 final size:26
Alignment explanation
Indices: 8815--8917 Score: 145
Period size: 26 Copynumber: 4.0 Consensus size: 26
8805 AAGTCTTGGT
8815 ATAAATAGCACTTTCGAGTGCGAGTG
1 ATAAATAGCACTTTCGAGTGCGAGTG
*
8841 ATAAATAGCACTTTCGAGTACGAGTG
1 ATAAATAGCACTTTCGAGTGCGAGTG
* *
8867 ATAAATAGAAC-CTCGAGTGCGAGTG
1 ATAAATAGCACTTTCGAGTGCGAGTG
* * *
8892 ATAAATGGCATTTTCGAGTGCAAGTG
1 ATAAATAGCACTTTCGAGTGCGAGTG
8918 GAAAATGGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
25 20 0.30
26 47 0.70
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (26 bp):
ATAAATAGCACTTTCGAGTGCGAGTG
Found at i:11461 original size:44 final size:44
Alignment explanation
Indices: 11411--11502 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
11401 ACCGATATCA
** *
11411 ATACTACTTTACATAGTAGTATGGATACTCCTTGGAT-GGTATTG
1 ATACTACTACACATAGTAGTATCGATACTCCTT-GATAGGTATTG
*
11455 ATACTACTACACATAGTAGTATCGATACTCCTTTATAGGTATTG
1 ATACTACTACACATAGTAGTATCGATACTCCTTGATAGGTATTG
11499 ATAC
1 ATAC
11503 CGTTAGGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (44 bp):
ATACTACTACACATAGTAGTATCGATACTCCTTGATAGGTATTG
Found at i:12617 original size:103 final size:102
Alignment explanation
Indices: 12397--12618 Score: 225
Period size: 103 Copynumber: 2.2 Consensus size: 102
12387 GATTTTTGGT
*
12397 TTTTGATCAAGAAAAATAGGTTGAGTTAAGATTTTTGGTGTTTGTAAAGATCAAATAACATTTTT
1 TTTTGATCAA-AAAAATAGGTTGAGTTAAGATTTTTGGTGTTTGTAAAGATCAAATAACAATTTT
* * * * * * *
12462 GGGGATGAATAAAGGATGAAAAGGCTTAAAGTTTTGGA
65 AGGGATGAACAAAGGATGAAAAGGATGAAACTATAGGA
* ** * * *
12500 TTTTCATTTTAAAAAATAGGTT-AGGTTAAGGTTTTTGGTGTTTGTAATGATTAAATAA-AGATT
1 TTTTGA-TCAAAAAAATAGGTTGA-GTTAAGATTTTTGGTGTTTGTAAAGATCAAATAACA-ATT
* *
12563 TTAGGGATGAACAAAGGATGAACACGGATGAAACTATAGTA
63 TTAGGGATGAACAAAGGATGAA-AAGGATGAAACTATAGGA
*
12604 -TTTGATCGAAAAAAT
1 TTTTGATCAAAAAAAT
12619 TAAAATTTTA
Statistics
Matches: 96, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
102 10 0.10
103 73 0.76
104 13 0.14
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (102 bp):
TTTTGATCAAAAAAATAGGTTGAGTTAAGATTTTTGGTGTTTGTAAAGATCAAATAACAATTTTA
GGGATGAACAAAGGATGAAAAGGATGAAACTATAGGA
Found at i:14398 original size:2 final size:2
Alignment explanation
Indices: 14391--14426 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14381 TAAAAACAAG
14391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14427 GTTGTGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14576 original size:17 final size:17
Alignment explanation
Indices: 14554--14587 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14544 TCAAGCTAGC
*
14554 ATAAATAACCAAGTCAT
1 ATAAATAACCAAATCAT
*
14571 ATAAATACCCAAATCAT
1 ATAAATAACCAAATCAT
14588 CCAAGTCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAATAACCAAATCAT
Found at i:17282 original size:53 final size:53
Alignment explanation
Indices: 17197--17497 Score: 297
Period size: 53 Copynumber: 5.7 Consensus size: 53
17187 GTCTGCTCGC
* *** *
17197 TCTTG-TTCAGGGATTAAGGAACT-ATAACAATCTTCTAAAAATTGGTTCGCTCCT
1 TCTTGCTTCAGGGAGT-A-GAACTCA-AACAATCTTCTACCTATGGGTTCGCTCCT
* * * * * * *
17251 TATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTACGGGTTCGCTCCC
1 TCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTACCTATGGGTTCGCTCCT
* * * *
17304 TCTTGCTTCAGAGG-GTAGAACTAAAAAAATCTTCTGCCTATGGGTTCACT-CT
1 TCTTGCTTCAG-GGAGTAGAACTCAAACAATCTTCTACCTATGGGTTCGCTCCT
* *
17356 CCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTACCTACGGGTTCGCT-CT
1 TCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTACCTATGGGTTCGCTCCT
* * * * *
17408 GTCTTGCTTCAGGGAGTAAAACTCAAACAATCTTATGCCTATGGGTTCGCCCCC
1 -TCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTACCTATGGGTTCGCTCCT
* *
17462 TCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTA
1 TCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTA
17498 GTGTGATTTT
Statistics
Matches: 204, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
51 2 0.01
52 44 0.22
53 141 0.69
54 8 0.04
55 9 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (53 bp):
TCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTACCTATGGGTTCGCTCCT
Found at i:17376 original size:105 final size:106
Alignment explanation
Indices: 17253--17497 Score: 341
Period size: 105 Copynumber: 2.3 Consensus size: 106
17243 TCGCTCCTTA
* * *
17253 TTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTCAGAGG
1 TTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAG-GG
* * * *
17318 -GTAGAACTAAAAAAATCTTCTGCCTATGGGTTCACTCTC-C
65 AGTAAAACTAAAAAAATCTTATGCCTATGGGTTCACCCCCTC
* **
17358 TTGCTTCAGGGAGTAGAACTCAAACAATCTTCTACCTACGGGTTCGCTCTGTCTTGCTTCAGGGA
1 TTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGA
* * *
17423 GTAAAACTCAAACAATCTTATGCCTATGGGTTCGCCCCCTC
66 GTAAAACTAAAAAAATCTTATGCCTATGGGTTCACCCCCTC
*
17464 TTACTTCAGGGAGTAGAACTCGAACAATCTTCTA
1 TTGCTTCAGGGAGTAGAACTCGAACAATCTTCTA
17498 GTGTGATTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
104 2 0.02
105 88 0.72
106 33 0.27
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (106 bp):
TTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGA
GTAAAACTAAAAAAATCTTATGCCTATGGGTTCACCCCCTC
Found at i:17774 original size:42 final size:42
Alignment explanation
Indices: 17717--17827 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
17707 GGCCCGAAGA
* * **
17717 ACTT-ATCATCTTGCTCGAAAGACTTACAAATGTCCCGAACG
1 ACTTAATCATCATGCTCGAAAGACTTACAAATGGCCAAAACG
* ** *
17758 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCAAAATG
1 ACTTAATCATCATGCTCGAAAGACTTACAAATGGCCAAAACG
* *
17800 ACTTCATCATCATGCTAGAAAGACTTAC
1 ACTTAATCATCATGCTCGAAAGACTTAC
17828 TGATGGGTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 3 0.05
42 55 0.95
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (42 bp):
ACTTAATCATCATGCTCGAAAGACTTACAAATGGCCAAAACG
Found at i:17920 original size:42 final size:42
Alignment explanation
Indices: 17872--17955 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
17862 TTACAAATTT
*
17872 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
17914 CCCGAAGGACTTCATCATCATGCTGGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGG
17956 TAGTTACTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (42 bp):
CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:22161 original size:6 final size:6
Alignment explanation
Indices: 22150--22183 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
22140 AAATACATAT
*
22150 AATGCA AATGCA AATGCA TATGTCA AATGCA AAT
1 AATGCA AATGCA AATGCA AATG-CA AATGCA AAT
22184 AGAAAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (6 bp):
AATGCA
Found at i:32462 original size:3 final size:3
Alignment explanation
Indices: 32454--32563 Score: 204
Period size: 3 Copynumber: 36.7 Consensus size: 3
32444 GTTTATTAAT
32454 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32502 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32548 TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
32564 GATTGTATAT
Statistics
Matches: 105, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.02
3 100 0.95
4 3 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37575 original size:37 final size:36
Alignment explanation
Indices: 37534--37627 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 36
37524 CAAAGTGTCA
* * *
37534 TCTCGCTAGAGATAATTTTTC-TTAAAAACAAATTTTT
1 TCTCGCTA-AGACAA-TTTTCACTAAAAACAAATTTTG
37571 TCTCGCTTAAGACAATTTTCACTAAAAACAAATTTTG
1 TCTCGC-TAAGACAATTTTCACTAAAAACAAATTTTG
37608 TCTCGCTTGAA-ACAATTTTC
1 TCTCGC-T-AAGACAATTTTC
37628 TCTCAAATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
36 5 0.10
37 42 0.82
38 4 0.08
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (36 bp):
TCTCGCTAAGACAATTTTCACTAAAAACAAATTTTG
Found at i:37641 original size:37 final size:38
Alignment explanation
Indices: 37556--37658 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 38
37546 TAATTTTTCT
*
37556 TAAAAACAAATTTTTTCTCGCTT-AAGACAATTTTCAC
1 TAAAAACAAATTTTATCTCGCTTGAAGACAATTTTCAC
* *
37593 TAAAAACAAATTTTGTCTCGCTTGAA-ACAATTTTCTC
1 TAAAAACAAATTTTATCTCGCTTGAAGACAATTTTCAC
* ** *
37630 TCAAATTAAATTTCATCTCGCTTG-AGACA
1 TAAAAACAAATTTTATCTCGCTTGAAGACA
37659 GTTCTCCCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 1 0.02
37 54 0.95
38 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (38 bp):
TAAAAACAAATTTTATCTCGCTTGAAGACAATTTTCAC
Found at i:38071 original size:67 final size:66
Alignment explanation
Indices: 37962--38177 Score: 211
Period size: 67 Copynumber: 3.2 Consensus size: 66
37952 ATTTGGAAAT
* * ** * * *
37962 TGTTTCTCTTAAAACATAGAAAAACTGAGATTGTTTCTCTTGAAACAAGTTTTGTCTCGCTTGAG
1 TGTTTCTCTTGAAACATA-CAAATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAG
38027 AC
65 AC
* *
38029 TGTTTCTCTTGAAACATA-AAGTATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTTA
1 TGTTTCTCTTGAAACATACAA--ATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGA
38093 GAC
64 GAC
* * * * * * * *
38096 AT-ATTCTCTTAAAATATACAACTTTAACATCGTTTCCCTTGAAACAAATTTTGTCTCACTGGAG
1 -TGTTTCTCTTGAAACATACAAATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAG
38160 AC
65 AC
* *
38162 AGTTTATCTTGAAACA
1 TGTTTCTCTTGAAACA
38178 AATTATCCCT
Statistics
Matches: 122, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
65 2 0.02
66 48 0.39
67 69 0.57
68 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (66 bp):
TGTTTCTCTTGAAACATACAAATTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGA
C
Found at i:39000 original size:137 final size:137
Alignment explanation
Indices: 38179--39002 Score: 918
Period size: 137 Copynumber: 6.0 Consensus size: 137
38169 CTTGAAACAA
* * *
38179 ATTATCCCTAAAGGTGGCCAGCCGTCCTCATCATGTAGGAACCATGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* ** * * *
38244 CCTCATCACGTAGGAGCCACGAGATCCTTAGATAACCAGACTTCCTCATCATGTAGGAACCATAT
66 CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
*
38309 TATTTCC
131 TATCTCC
* * ***
38316 ATTATCCCTAAAGATGGCCAAGACGTCCTCATCACGTAAGAACAAAGTCATCCACC-ATCCAGAT
1 ATTATCCCTAAAGATGGCC-AGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGA-CCAGAT
* * * * * * * *
38380 CTCCTCATCACATAGGAGCCATGTCATCCTTAGATAATCAAACTTCCTCATCGCGTAGGAATCAT
64 CTCCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCAT
*
38445 GTTATCTTC
129 GTTATCTCC
* * * * *
38454 ATTATCCCTAAAGATGGCCTGACGTCTTAATCACGTAGGAACCGTGTCATCTACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * *
38519 CCTTATCACGTAAGAG-AAGCGTCACCCTTAGATAGA-CATACTTCCCCATCACGTAGGAACCAT
66 CCTCATCACGTAGGAGCAA-CGTCACCCTTAGATA-ACCAGACTTCCTCATCACGTAGGAACCAT
*
38582 GTTATCTCT
129 GTTATCTCC
* * * *** * *
38591 ATTATTCCTAAAGATGGCCAGTCGTCCTCATCGCGTAGG-ATTTTCATCATCCACCGACCAAATC
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGT-GTCATCCACCGACCAGATC
** ** * ** * * *
38655 TCCTTGTCATATAGGAGCAGCGTCACCCTTAGATAGTCAGACTTCCTCATCACGTAGGAATCGTT
65 TCCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATG
38720 TTATCTCC
130 TTATCTCC
* * * * * *
38728 ATTTTGCCTAAAGATGGTCATCCATCCTCATCACGTATGAACCGTGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
*** * * * **
38793 CCTCATCACGTAGGAGCAGTTTTACCTTTAGATAACCAGACTTCCACATCACGTAGGAACTGTGT
66 CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
38858 TATCTCC
131 TATCTCC
* * *
38865 ATTATCCCTAAAGACGGCCAGCCGTCCTCATCACGTAGGAATCGTGTCATCCACCGACCAAATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * *
38930 CCTCATCACGTAAGAGCAACGTCACCCTTAGATAACCAGATTTCCTCATCACATAGGAACCGTGT
66 CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
38995 TATCTCC
131 TATCTCC
39002 A
1 A
39003 AATTTACCAA
Statistics
Matches: 570, Mismatches: 108, Indels: 18
0.82 0.16 0.03
Matches are distributed among these distances:
136 3 0.01
137 444 0.78
138 123 0.22
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (137 bp):
ATTATCCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
CCTCATCACGTAGGAGCAACGTCACCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
TATCTCC
Found at i:39210 original size:3 final size:3
Alignment explanation
Indices: 39202--39245 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
39192 GTATATTAAT
*
39202 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39246 ATTGTATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:39402 original size:23 final size:23
Alignment explanation
Indices: 39372--39416 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
39362 AAGACTTGGA
39372 GCCCAGACCCGAGGCCCATGATT
1 GCCCAGACCCGAGGCCCATGATT
39395 GCCCAGACCCGAGGCCCATGAT
1 GCCCAGACCCGAGGCCCATGAT
39417 CTGACCTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.40, G:0.27, T:0.11
Consensus pattern (23 bp):
GCCCAGACCCGAGGCCCATGATT
Found at i:43818 original size:29 final size:30
Alignment explanation
Indices: 43749--43807 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
43739 CAATTTAAGG
43749 CAAAATGTTTTTGGACTTAAATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
*
43779 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
43808 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTAAATTGAATTTA
Found at i:43912 original size:21 final size:21
Alignment explanation
Indices: 43886--44004 Score: 145
Period size: 21 Copynumber: 5.7 Consensus size: 21
43876 AGGGTGTCAA
43886 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
43907 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
43928 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCATCCCTGC
43949 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCATCCCTG--C
* * *
43970 TAATGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCCTGC
*
43991 AATGCATCCATGCA
1 AGTGCATCCATGCA
44005 CTCAAACATC
Statistics
Matches: 88, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.03
20 13 0.15
21 57 0.65
22 12 0.14
23 3 0.03
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:44054 original size:20 final size:20
Alignment explanation
Indices: 44029--44092 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
44019 GCACTTAGTA
44029 CATCGATGCAT-CAATCCATG
1 CATCGATGCATGC-ATCCATG
*
44049 CATCGATGCATGCATCGATG
1 CATCGATGCATGCATCCATG
*
44069 CATC-CTGCCATGCATCCATG
1 CATCGATG-CATGCATCCATG
44089 CATC
1 CATC
44093 AAGGCTGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
CATCGATGCATGCATCCATG
Found at i:44065 original size:12 final size:12
Alignment explanation
Indices: 44034--44071 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
44024 TAGTACATCG
* *
44034 ATGCATCAATCC
1 ATGCATCGATGC
44046 ATGCATCGATGC
1 ATGCATCGATGC
44058 ATGCATCGATGC
1 ATGCATCGATGC
44070 AT
1 AT
44072 CCTGCCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (12 bp):
ATGCATCGATGC
Found at i:44231 original size:20 final size:22
Alignment explanation
Indices: 44193--44232 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
44183 TTTTAGTAGA
44193 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
44215 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
44233 ATATAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:47340 original size:28 final size:29
Alignment explanation
Indices: 47309--47372 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
47299 TTGATATAAC
* *
47309 AATTTAAGGT-AAAATGTTTTTGGACTTA
1 AATTGAAGGTAAAAATATTTTTGGACTTA
**
47337 AATTGAATTTACAAAATATTTTTGGACTT-
1 AATTGAAGGTA-AAAATATTTTTGGACTTA
47366 AATTGAA
1 AATTGAA
47373 TTTATTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 7 0.23
30 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (29 bp):
AATTGAAGGTAAAAATATTTTTGGACTTA
Found at i:47387 original size:29 final size:30
Alignment explanation
Indices: 47319--47376 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47309 AATTTAAGGT
47319 AAAATGTTTTTGGACTTAAATTGAATTTAC
1 AAAATGTTTTTGGACTTAAATTGAATTTAC
*
47349 AAAATATTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTAAATTGAATTTA
47377 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTAAATTGAATTTAC
Found at i:47482 original size:21 final size:21
Alignment explanation
Indices: 47456--47511 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
47446 AGGGTGTCAA
47456 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
47477 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
47498 AGTGCATCCATGCA
1 AGTGCATCCATGCA
47512 CCTGCACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Done.