Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003671.1 Hibiscus syriacus cultivar Beakdansim tig00007844_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: 84168
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8259 original size:21 final size:21
Alignment explanation
Indices: 8233--8277 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8223 GTATCAAGGT
*
8233 CTTTGTGGAAGCCATGAAATC
1 CTTTGTCGAAGCCATGAAATC
* *
8254 CTTTGTCGAGGCCATGAATTC
1 CTTTGTCGAAGCCATGAAATC
8275 CTT
1 CTT
8278 CAATGATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (21 bp):
CTTTGTCGAAGCCATGAAATC
Found at i:11374 original size:24 final size:24
Alignment explanation
Indices: 11339--11387 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
11329 AGTCTTCTAG
* *
11339 ATGATGTGTAAAACATCTATATAC
1 ATGATGTATAAAACATATATATAC
*
11363 ATGATGTATAAAACATATATGTAC
1 ATGATGTATAAAACATATATATAC
11387 A
1 A
11388 ATGTCATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATATATATAC
Found at i:19578 original size:2 final size:2
Alignment explanation
Indices: 19571--19598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19561 AGCCATGAAC
19571 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
19599 TCGACACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20137 original size:27 final size:27
Alignment explanation
Indices: 20057--20137 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
20047 AATAAAATTT
* *
20057 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
20084 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
*
20111 ATATTATTTATATATTTAATATTAATA
1 ATATTATTTATATATTTAATATAAATA
20138 CAATAATCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
25 1 0.02
26 7 0.16
27 24 0.56
28 10 0.23
29 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:20183 original size:23 final size:24
Alignment explanation
Indices: 20157--20202 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
20147 AATAATATTT
20157 TAATAAAGA-TATTTAAAATATAC
1 TAATAAAGATTATTTAAAATATAC
* * *
20180 TAATTAATATTTTTTAAAATATA
1 TAATAAAGATTATTTAAAATATA
20203 ATATGACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAAGATTATTTAAAATATAC
Found at i:20320 original size:14 final size:14
Alignment explanation
Indices: 20252--20321 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
20242 ATAATATTTT
*
20252 TATTTCAATAA-AA
1 TATTTTAATAATAA
* * *
20265 TATATCAATACTAA
1 TATTTTAATAATAA
*
20279 TATTTTTATTAATAA
1 TA-TTTTAATAATAA
* * *
20294 AATTATAAAAATAA
1 TATTTTAATAATAA
20308 TATTTTAATAATAA
1 TATTTTAATAATAA
20322 ATAAATTATT
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
13 9 0.21
14 24 0.57
15 9 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:20336 original size:28 final size:28
Alignment explanation
Indices: 20305--20358 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
20295 ATTATAAAAA
*
20305 TAATATTTTAATAATAAATAA-ATTATTT
1 TAATATTTTAAAAAT-AATAATATTATTT
20333 TAATATTTTAAAAATAATAATATTAT
1 TAATATTTTAAAAATAATAATATTAT
20359 GTTTTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATATTTTAAAAATAATAATATTATTT
Found at i:20372 original size:25 final size:25
Alignment explanation
Indices: 20271--20391 Score: 76
Period size: 25 Copynumber: 4.9 Consensus size: 25
20261 AAAATATATC
*
20271 AATACTAATATT-TTTATTAATAA-A
1 AATAATAATATTATTTATT-ATAATA
* * *
20295 ATTATAAAAATAATATTT-TAATAATA
1 A--ATAATAATATTATTTATTATAATA
* *
20321 AATAA-ATTATT-TTAATATTTTAA-A
1 AATAATAATATTATT--TATTATAATA
20345 AATAATAATATTATGTT-TTATAATA
1 AATAATAATATTAT-TTATTATAATA
*
20370 AATAATATTATTATTTATTATA
1 AATAATAATATTATTTATTATA
20392 TTTAATATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
22 2 0.03
23 4 0.05
24 19 0.26
25 33 0.45
26 12 0.16
27 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
AATAATAATATTATTTATTATAATA
Found at i:20386 original size:22 final size:21
Alignment explanation
Indices: 20296--20387 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 21
20286 ATTAATAAAA
*
20296 TTATAAAAATAATATT-TTAA
1 TTATAAAAATAATATTATTAT
* * * *
20316 TAATAAATAAATTATTTTAATAT
1 TTAT-AA-AAATAATATTATTAT
*
20339 TT-TAAAAATAATAATATTATGTT
1 TTATAAAAATAATATTATTA---T
20362 TTATAATAAATAATATTATTAT
1 TTATAA-AAATAATATTATTAT
20384 TTAT
1 TTAT
20388 TATATTTAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
20 13 0.25
21 4 0.08
22 14 0.26
23 6 0.11
24 3 0.06
25 13 0.25
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TTATAAAAATAATATTATTAT
Found at i:23404 original size:13 final size:13
Alignment explanation
Indices: 23388--23416 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
23378 CACAATATAG
23388 TATTTAAAAAAAT
1 TATTTAAAAAAAT
23401 TA-TTAAAAAAAT
1 TATTTAAAAAAAT
23413 TATT
1 TATT
23417 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTTAAAAAAAT
Found at i:23408 original size:12 final size:12
Alignment explanation
Indices: 23391--23417 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23381 AATATAGTAT
23391 TTAAAAAAATTA
1 TTAAAAAAATTA
23403 TTAAAAAAATTA
1 TTAAAAAAATTA
23415 TTA
1 TTA
23418 TATTTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:23825 original size:2 final size:2
Alignment explanation
Indices: 23818--23851 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23808 TTTTTCTTTA
23818 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
23852 TATTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29280 original size:32 final size:32
Alignment explanation
Indices: 29221--29282 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
29211 ATATTAACCT
* *
29221 GACTCAAAAATCAACTGATATGGTATTGACTG
1 GACTCAAAAACCAACTGATATGATATTGACTG
* * *
29253 GACTCGAAAACCAATTGATTTGATATTGAC
1 GACTCAAAAACCAACTGATATGATATTGAC
29283 CAGACCCGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (32 bp):
GACTCAAAAACCAACTGATATGATATTGACTG
Found at i:29349 original size:44 final size:44
Alignment explanation
Indices: 29286--29383 Score: 160
Period size: 44 Copynumber: 2.2 Consensus size: 44
29276 TATTGACCAG
* *
29286 ACCCGACCCGAAAACCAACCGATCTAAGTTTTACCCTGTCCGAT
1 ACCCGACCCGAAAACCAACCGATATAAGTTTTACCCTGCCCGAT
* *
29330 ACCCGACCCGAAAACCAACCGATATGAGTTTTACCTTGCCCGAT
1 ACCCGACCCGAAAACCAACCGATATAAGTTTTACCCTGCCCGAT
29374 ACCCGACCCG
1 ACCCGACCCG
29384 TTATGACTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.29, C:0.38, G:0.15, T:0.18
Consensus pattern (44 bp):
ACCCGACCCGAAAACCAACCGATATAAGTTTTACCCTGCCCGAT
Found at i:33817 original size:13 final size:13
Alignment explanation
Indices: 33799--33825 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33789 CATAGTTGAA
33799 CAGTCTTCATATG
1 CAGTCTTCATATG
33812 CAGTCTTCATATG
1 CAGTCTTCATATG
33825 C
1 C
33826 GCGTATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:36348 original size:42 final size:42
Alignment explanation
Indices: 36244--36383 Score: 178
Period size: 42 Copynumber: 3.4 Consensus size: 42
36234 TTTAATATAC
* *
36244 AAACGCCACTAAAGTACGAG-ATTTTAGCGGTGTTTGTGCTT-
1 AAACGCCACTAAAGTACGAGTA-TATAGCGGCGTTTGTGCTTA
36285 AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTGCTTA
1 AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTGCTTA
* * * * *
36327 AAACGCCACTAAAATAAGAGTATATAGTGGCGTTTGTAC-AA
1 AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTGCTTA
36368 GAAACGCCACTAAAGT
1 -AAACGCCACTAAAGT
36384 TTAGTATTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 38 0.43
42 50 0.57
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTGCTTA
Found at i:38500 original size:51 final size:51
Alignment explanation
Indices: 38424--38529 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
38414 AAGGAGAGAA
38424 AATAGAATTAAGAACTGATGATTTGTTTCTTCCCCTCATGACGCTATTTAT
1 AATAGAATTAAGAACTGATGATTTGTTTCTTCCCCTCATGACGCTATTTAT
*
38475 AATAGAATTAAGAATTGATGATTTGTTTCTTCCCCTCATGACGCTATTTAT
1 AATAGAATTAAGAACTGATGATTTGTTTCTTCCCCTCATGACGCTATTTAT
38526 AATA
1 AATA
38530 AGAGTCATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (51 bp):
AATAGAATTAAGAACTGATGATTTGTTTCTTCCCCTCATGACGCTATTTAT
Found at i:44460 original size:19 final size:20
Alignment explanation
Indices: 44418--44460 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
44408 TAATATATAT
* *
44418 AAAATTTAAAATAAAAGAAT
1 AAAATTTAAAATAAAAAAAA
*
44438 AAAATTT-AAGTAAAAAAAA
1 AAAATTTAAAATAAAAAAAA
44457 AAAA
1 AAAA
44461 GTTGAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATTTAAAATAAAAAAAA
Found at i:46093 original size:5 final size:5
Alignment explanation
Indices: 46085--46113 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
46075 TAAAATTTAC
46085 GATGT GATGT GATGT GATGT GATGT GATG
1 GATGT GATGT GATGT GATGT GATGT GATG
46114 ATATGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (5 bp):
GATGT
Found at i:50752 original size:23 final size:23
Alignment explanation
Indices: 50726--50769 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
50716 TATCATATGT
*
50726 TATCATTTATTTGCATGATTTGA
1 TATCATTCATTTGCATGATTTGA
50749 TATCATTCATTTGCATGATTT
1 TATCATTCATTTGCATGATTT
50770 TACTTGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (23 bp):
TATCATTCATTTGCATGATTTGA
Found at i:53727 original size:12 final size:12
Alignment explanation
Indices: 53710--53735 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53700 TGCATATTTA
53710 ATTATCACTGTT
1 ATTATCACTGTT
53722 ATTATCACTGTT
1 ATTATCACTGTT
53734 AT
1 AT
53736 GGAACTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTATCACTGTT
Found at i:54948 original size:28 final size:28
Alignment explanation
Indices: 54917--55075 Score: 146
Period size: 28 Copynumber: 5.6 Consensus size: 28
54907 TAAAAAAAAC
54917 TCTTTATTATAATTTATAAAAAATTTTG
1 TCTTTATTATAATTTATAAAAAATTTTG
* * *
54945 TCTTTATTGTAATTTATACAAAATTTGG
1 TCTTTATTATAATTTATAAAAAATTTTG
*
54973 TCTTTATTATAATTTAT-AAAAGTTTTG
1 TCTTTATTATAATTTATAAAAAATTTTG
* *
55000 TCCTTTATTGA-AATTTATAAAAAAAGTTCTA
1 T-CTTTATT-ATAATTTAT-AAAAAA-TTTTG
* * **
55031 TCCTTTATTAT-ATTTTTTAAAAATTAAG
1 T-CTTTATTATAATTTATAAAAAATTTTG
55059 -CTATTATTATAATTTAT
1 TCT-TTATTATAATTTAT
55076 TATTATTATT
Statistics
Matches: 107, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
26 2 0.02
27 15 0.14
28 62 0.58
29 6 0.06
30 10 0.09
31 12 0.11
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (28 bp):
TCTTTATTATAATTTATAAAAAATTTTG
Found at i:54951 original size:56 final size:55
Alignment explanation
Indices: 54891--55024 Score: 171
Period size: 56 Copynumber: 2.4 Consensus size: 55
54881 GATGTATGTA
54891 TTTATTGTAATTTATATAAAAAAAACTCTTTATTATAATTTATAAAAAATTTTGT-C
1 TTTATTGTAATTTATA-AAAAAAAACTCTTTATTATAATTTAT-AAAAATTTTGTCC
***** *
54947 TTTATTGTAATTTATACAAAATTTGGTCTTTATTATAATTTATAAAAGTTTTGTCC
1 TTTATTGTAATTTATA-AAAAAAAACTCTTTATTATAATTTATAAAAATTTTGTCC
*
55003 TTTATTGAAATTTATAAAAAAA
1 TTTATTGTAATTTATAAAAAAA
55025 GTTCTATCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
55 14 0.21
56 53 0.79
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (55 bp):
TTTATTGTAATTTATAAAAAAAAACTCTTTATTATAATTTATAAAAATTTTGTCC
Found at i:58375 original size:17 final size:17
Alignment explanation
Indices: 58355--58388 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
58345 TGTTTATACG
58355 TGTAAAAATTTTAAGTT
1 TGTAAAAATTTTAAGTT
58372 TGTAAAAATTTTAAGTT
1 TGTAAAAATTTTAAGTT
58389 GCATAAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
TGTAAAAATTTTAAGTT
Found at i:66705 original size:21 final size:21
Alignment explanation
Indices: 66679--66730 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
66669 CCTCTATCAT
*
66679 GGGTTGTAAGTATT-GTCGTAG
1 GGGTTGTAAGTATTACT-GTAG
66700 GGGTTGTAAGTATTACTGTAG
1 GGGTTGTAAGTATTACTGTAG
*
66721 GGGTTATAAG
1 GGGTTGTAAG
66731 ATCATTGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.04, G:0.37, T:0.37
Consensus pattern (21 bp):
GGGTTGTAAGTATTACTGTAG
Found at i:74110 original size:18 final size:18
Alignment explanation
Indices: 74087--74122 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
74077 TCCTGTAGGA
*
74087 CTTCAACGCCTCCAATAG
1 CTTCAACCCCTCCAATAG
74105 CTTCAACCCCTCCAATAG
1 CTTCAACCCCTCCAATAG
74123 GACCAGCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.42, G:0.08, T:0.22
Consensus pattern (18 bp):
CTTCAACCCCTCCAATAG
Found at i:76660 original size:33 final size:31
Alignment explanation
Indices: 76620--76696 Score: 111
Period size: 33 Copynumber: 2.5 Consensus size: 31
76610 AATAAATTAT
*
76620 ATATACATACATATCATACATTCGATTGAAC
1 ATATACATACATATCATACATTCGATCGAAC
*
76651 ATGAATACATACATATCATACATTCGGTCGAAC
1 AT--ATACATACATATCATACATTCGATCGAAC
76684 ATAT-CATACATAT
1 ATATACATACATAT
76697 ATGATGCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 9 0.21
31 4 0.10
33 29 0.69
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (31 bp):
ATATACATACATATCATACATTCGATCGAAC
Found at i:76733 original size:19 final size:19
Alignment explanation
Indices: 76682--76733 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
76672 ATTCGGTCGA
*
76682 ACATATCATACATATATGAT
1 ACATA-CATACATAAATGAT
* * * *
76702 GCATGCATTCATAAATTAT
1 ACATACATACATAAATGAT
76721 ACATACATACATA
1 ACATACATACATA
76734 CATACGTATC
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (19 bp):
ACATACATACATAAATGAT
Found at i:79279 original size:19 final size:19
Alignment explanation
Indices: 79255--79304 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
79245 TTCCCAATTT
*
79255 TATTCCCCCATTTGCTGTG
1 TATTCCCCCATTTACTGTG
79274 TATTCCCCCATTTACTGTG
1 TATTCCCCCATTTACTGTG
79293 TATTCCCCCATT
1 TATTCCCCCATT
79305 CTTCTCACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.34, G:0.10, T:0.42
Consensus pattern (19 bp):
TATTCCCCCATTTACTGTG
Found at i:82614 original size:64 final size:63
Alignment explanation
Indices: 82527--82679 Score: 184
Period size: 64 Copynumber: 2.4 Consensus size: 63
82517 GTACACTTGG
* * * * *
82527 GTGCATCGTACACTAATTACATTCGATGTTTCAA-AAGAGGCAAGA-TGCATCGATTCATGGTCT
1 GTGCATCGTACACAAAATGCATTCGATGTTTCAATAA-AAGCAAGACTGCATCGATGCATGGT-T
* * *
82590 GTGCATCGATACACAAAGTGCATTCAATGTTTCAATAAAATCAAGACTGCATCGATGCATGGTT
1 GTGCATCG-TACACAAAATGCATTCGATGTTTCAATAAAAGCAAGACTGCATCGATGCATGGTT
*
82654 GTGCATCGTACACAAAATGCAATCGA
1 GTGCATCGTACACAAAATGCATTCGA
82680 AATAGGGTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 23 0.30
64 37 0.48
65 17 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (63 bp):
GTGCATCGTACACAAAATGCATTCGATGTTTCAATAAAAGCAAGACTGCATCGATGCATGGTT
Found at i:83230 original size:30 final size:31
Alignment explanation
Indices: 83180--83238 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
83170 TTTGTGATGG
83180 AATATGTGGACCCATCACAAATTTATGACGA
1 AATATGTGGACCCATCACAAATTTATGACGA
* *
83211 AATATGTGGATCC-TCACAAATTTCTGAC
1 AATATGTGGACCCATCACAAATTTATGAC
83239 AGATTCATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (31 bp):
AATATGTGGACCCATCACAAATTTATGACGA
Found at i:83962 original size:21 final size:20
Alignment explanation
Indices: 83923--83962 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
83913 TGATTTATAA
* *
83923 TATTTTTTTTGGAGCGAATG
1 TATTTTTTTTCGAGAGAATG
83943 TATTTTTTTTCGAGTAGAAT
1 TATTTTTTTTCGAG-AGAAT
83963 CCCGATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.53
Consensus pattern (20 bp):
TATTTTTTTTCGAGAGAATG
Done.