Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001613.1 Hibiscus syriacus cultivar Beakdansim tig00003204_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: 119945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:774 original size:18 final size:19
Alignment explanation
Indices: 751--787 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
741 GAGAAACGAC
751 ATATATATATTAT-ATAAT
1 ATATATATATTATGATAAT
769 ATATATATATTATGATAAT
1 ATATATATATTATGATAAT
788 TGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATATATATTATGATAAT
Found at i:18911 original size:31 final size:32
Alignment explanation
Indices: 18858--18920 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
18848 AGAAAAATAT
18858 AACATTGCATGAATGTTATCTAATATAGAAAA
1 AACATTGCATGAATGTTATCTAATATAGAAAA
*
18890 AACATTGCATG-ATGTTCTCTAATATAGAAAA
1 AACATTGCATGAATGTTATCTAATATAGAAAA
18921 TTTTCTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (32 bp):
AACATTGCATGAATGTTATCTAATATAGAAAA
Found at i:21955 original size:21 final size:21
Alignment explanation
Indices: 21917--21957 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21907 TGATTGATGT
*
21917 AAAGAAAAAGAGAGAAACAAA
1 AAAGAAAAAGAGAAAAACAAA
21938 AAAG-AAAAGAAGAAAAACAA
1 AAAGAAAAAG-AGAAAAACAA
21958 TCTTAAGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGAGAAAAACAAA
Found at i:21982 original size:6 final size:6
Alignment explanation
Indices: 21971--22008 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
21961 TAAGTGTGAG
21971 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GG
22009 AGGACGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGTGGA
Found at i:25792 original size:23 final size:22
Alignment explanation
Indices: 25749--25794 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
25739 TTTAGTTAAT
*
25749 TTTTTAAAATTTAATCGTTTAG
1 TTTTTAAAATTTAATAGTTTAG
*
25771 TTTTTAAAATTTTAATATTTTAG
1 TTTTTAAAA-TTTAATAGTTTAG
25794 T
1 T
25795 CACTTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTTTAAAATTTAATAGTTTAG
Found at i:30242 original size:17 final size:17
Alignment explanation
Indices: 30222--30256 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30212 ATTACAAACT
30222 AATAAAAAGAATAAGGA
1 AATAAAAAGAATAAGGA
**
30239 AATAAAATTAATAAGGA
1 AATAAAAAGAATAAGGA
30256 A
1 A
30257 CAAAGACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (17 bp):
AATAAAAAGAATAAGGA
Found at i:31424 original size:2 final size:2
Alignment explanation
Indices: 31417--31447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31407 TATATTTTTG
31417 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
31448 TGGTTAAAAG
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:34250 original size:31 final size:31
Alignment explanation
Indices: 34206--34276 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
34196 TGATGTGGTG
*
34206 GTCCATCTACCATGTTTGAGTTACTAATTCA
1 GTCCATCTGCCATGTTTGAGTTACTAATTCA
* * *
34237 GTCTATCTGCCATGTTTGAGTTATTAATTTA
1 GTCCATCTGCCATGTTTGAGTTACTAATTCA
34268 GTCCATCTG
1 GTCCATCTG
34277 TCATATCATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (31 bp):
GTCCATCTGCCATGTTTGAGTTACTAATTCA
Found at i:38253 original size:20 final size:20
Alignment explanation
Indices: 38228--38274 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
38218 AAATCACAAT
*
38228 TAGATACATGCGCATGTGCC
1 TAGATACATGCACATGTGCC
38248 TAGATACATGCACATGTGCC
1 TAGATACATGCACATGTGCC
38268 TAGATAC
1 TAGATAC
38275 GTGTGGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (20 bp):
TAGATACATGCACATGTGCC
Found at i:44156 original size:43 final size:38
Alignment explanation
Indices: 44107--44185 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
44097 ACTCACAAAC
*
44107 TTATCAAATTAAGTTAGACTTTGTTTAACTCAACTCGT
1 TTATCAAATCAAGTTAGACTTTGTTTAACTCAACTCGT
*
44145 TTATCAAATCAAGTTAGGCTTTGTTTAACTCAACTCGT
1 TTATCAAATCAAGTTAGACTTTGTTTAACTCAACTCGT
44183 TTA
1 TTA
44186 AATTTTGAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (38 bp):
TTATCAAATCAAGTTAGACTTTGTTTAACTCAACTCGT
Found at i:48394 original size:25 final size:25
Alignment explanation
Indices: 48348--48395 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
48338 ATTTAATTCG
* *
48348 TTTAGTACCTAAACTATTAGTTTGA
1 TTTAATACCTAAACTATCAGTTTGA
48373 TTTAATACCTAAACCT-TCAGTTT
1 TTTAATACCTAAA-CTATCAGTTT
48396 TTCTCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTAATACCTAAACTATCAGTTTGA
Found at i:50559 original size:16 final size:16
Alignment explanation
Indices: 50538--50570 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
50528 TAATAAATAA
50538 ACAAACATAAACGAAC
1 ACAAACATAAACGAAC
50554 ACAAACATAAACGAAC
1 ACAAACATAAACGAAC
50570 A
1 A
50571 TTTTTTGTTC
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:0.64, C:0.24, G:0.06, T:0.06
Consensus pattern (16 bp):
ACAAACATAAACGAAC
Found at i:50661 original size:14 final size:14
Alignment explanation
Indices: 50644--50683 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
50634 AATGAACATA
*
50644 AACGAACACGAACG
1 AACGAACACAAACG
*
50658 AACGAACATAAACG
1 AACGAACACAAACG
50672 AAC-AACACAAAC
1 AACGAACACAAAC
50684 ACAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:52648 original size:41 final size:41
Alignment explanation
Indices: 52601--52683 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
52591 AGTCGCGGCT
52601 AGATACGAAGGAATGAAAATAAAGAATTTAAGTCGCCAATC
1 AGATACGAAGGAATGAAAATAAAGAATTTAAGTCGCCAATC
52642 AGATACGAAGGAATGAAAATAAAGAATTTAAGTCGCCAATC
1 AGATACGAAGGAATGAAAATAAAGAATTTAAGTCGCCAATC
52683 A
1 A
52684 TATAAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.19
Consensus pattern (41 bp):
AGATACGAAGGAATGAAAATAAAGAATTTAAGTCGCCAATC
Found at i:53949 original size:46 final size:49
Alignment explanation
Indices: 53851--53947 Score: 151
Period size: 51 Copynumber: 2.0 Consensus size: 49
53841 TGAAGCTTCA
53851 AACTCGAACTTAAATCTTATATACATTAAAATCTTATATTGTATTTTTTTT
1 AACTCGAACTTAAATCTTATATACATTAAAATCTTATA-T-TATTTTTTTT
* *
53902 AACTTGAACTTGAATCTTATATACATTAAAATCTTATATT-TTTTTT
1 AACTCGAACTTAAATCTTATATACATTAAAATCTTATATTATTTTTT
53948 AAATAAACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 6 0.14
49 1 0.02
50 1 0.02
51 36 0.82
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.49
Consensus pattern (49 bp):
AACTCGAACTTAAATCTTATATACATTAAAATCTTATATTATTTTTTTT
Found at i:61041 original size:229 final size:226
Alignment explanation
Indices: 60610--61057 Score: 806
Period size: 229 Copynumber: 2.0 Consensus size: 226
60600 GTAAATTATC
* *
60610 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
60675 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATTTT
60740 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
60805 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
60837 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
60902 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-AAATT
* *
60967 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
61032 GAAACATAAATTACATAACTTTAAAA
194 GAAACATAAATTACATAACTTTAAAA
61058 GCAGTTATAA
Statistics
Matches: 212, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
227 37 0.17
228 86 0.41
229 89 0.42
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:61146 original size:20 final size:19
Alignment explanation
Indices: 61123--61168 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
61113 CGATATACCA
61123 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
61143 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
61163 GGTAAA
1 GGTAAA
61169 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:61313 original size:20 final size:19
Alignment explanation
Indices: 61290--61336 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
61280 CGATATAACA
61290 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
61310 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
61330 GGTAAAA
1 GGTAAAA
61337 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:61338 original size:17 final size:19
Alignment explanation
Indices: 61299--61341 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
61289 AGGTAAAAAT
61299 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
61319 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
61336 ATGATA
1 ATGATA
61342 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:61693 original size:23 final size:23
Alignment explanation
Indices: 61662--61734 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
61652 ATAGGTAAAA
*
61662 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
61685 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
61708 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
61731 ATAT
1 ATAT
61735 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:63187 original size:11 final size:11
Alignment explanation
Indices: 63171--63233 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
63161 AAAATTACAT
63171 TATTAAAAATA
1 TATTAAAAATA
63182 TATTAAAAATA
1 TATTAAAAATA
***
63193 TATTATTGATA
1 TATTAAAAATA
63204 -ATTATAAAAT-
1 TATTA-AAAATA
63214 T-TTAAAAATA
1 TATTAAAAATA
63224 TATTAAAAAT
1 TATTAAAAAT
63234 TCTATAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:63369 original size:7 final size:7
Alignment explanation
Indices: 63354--63411 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
63344 CTAAGCCCTA
63354 AAACC-T
1 AAACCAT
63360 AAACCAT
1 AAACCAT
*
63367 AAATCAT
1 AAACCAT
*
63374 AAATCAT
1 AAACCAT
63381 AAACCAT
1 AAACCAT
63388 AAACCAT
1 AAACCAT
*
63395 AAATCAT
1 AAACCAT
*
63402 AAACCCT
1 AAACCAT
63409 AAA
1 AAA
63412 TCTAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 5 0.11
7 41 0.89
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCAT
Found at i:63376 original size:21 final size:21
Alignment explanation
Indices: 63359--63413 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
63349 CCCTAAAACC
63359 TAAACCATAAATCATAAATCA
1 TAAACCATAAATCATAAATCA
*
63380 TAAACCATAAACCATAAATCA
1 TAAACCATAAATCATAAATCA
*
63401 TAAACCCTAAATC
1 TAAACCATAAATC
63414 TAATTATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCATAAATCATAAATCA
Found at i:63412 original size:14 final size:14
Alignment explanation
Indices: 63359--63413 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
63349 CCCTAAAACC
63359 TAAACCATAAATCA
1 TAAACCATAAATCA
* *
63373 TAAATCATAAACCA
1 TAAACCATAAATCA
63387 TAAACCATAAATCA
1 TAAACCATAAATCA
*
63401 TAAACCCTAAATC
1 TAAACCATAAATC
63414 TAATTATGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAAATCA
Found at i:86249 original size:29 final size:29
Alignment explanation
Indices: 86199--86265 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
86189 TTAAAAAATA
*
86199 AAAAATAAATATTAAATTTTAA-TTTTATT
1 AAAAATAAATA-TAAATTTTAACTGTTATT
86228 AAAAATAAATA-AATATTATTAACTGTTATT
1 AAAAATAAATATAA-ATT-TTAACTGTTATT
86258 AAAAATAA
1 AAAAATAA
86266 TAATTAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 15 0.44
30 14 0.41
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAAATAAATATAAATTTTAACTGTTATT
Found at i:86535 original size:28 final size:28
Alignment explanation
Indices: 86495--86554 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
86485 CCTCTGCTTA
86495 AATCTCTCTTTGCAAGTAAACAATAAGC
1 AATCTCTCTTTGCAAGTAAACAATAAGC
86523 AATCTCTCTTTGCAAGTAAACAATAAGC
1 AATCTCTCTTTGCAAGTAAACAATAAGC
86551 AATC
1 AATC
86555 CCTGTTCCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (28 bp):
AATCTCTCTTTGCAAGTAAACAATAAGC
Found at i:93174 original size:71 final size:69
Alignment explanation
Indices: 93058--93292 Score: 294
Period size: 71 Copynumber: 3.3 Consensus size: 69
93048 TTTTGACGTG
* *
93058 AGTCTTTAGAGCAAGACTTATGTTAGTCTCAATGCTCTGCTTTTGGTTATATACTATCTATAAGT
1 AGTCTTTAGAGCAATACTTATGTTAGTCTCAATGCTCTGCTTTTGG-T-TATACTATCTATCAGT
93123 AATGTC
64 AATGTC
* *
93129 AGTCTTTAGATCAATACTTATGTTAGTCTCAATGCTCTGCTTTTGGTTATAC--TCTCTCAGTAA
1 AGTCTTTAGAGCAATACTTATGTTAGTCTCAATGCTCTGCTTTTGGTTATACTATCTATCAGTAA
*
93192 TATC
66 TGTC
* *
93196 AGTCTTTAGAGCAATACGTATGTTAGCCCTTAGTCTAAATGCTCTGCTTTTGGTTATACTATCTA
1 AGTCTTTAGAGCAATAC-T-T-AT-G---TTAGTCTCAATGCTCTGCTTTTGGTTATACTATCTA
93261 TCAGTAATGTC
59 TCAGTAATGTC
* *
93272 AGTCTTTGGAGCTATACTTAT
1 AGTCTTTAGAGCAATACTTAT
93293 TTCTTGGCCT
Statistics
Matches: 142, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
67 28 0.20
68 1 0.01
69 6 0.04
70 2 0.01
71 45 0.32
73 1 0.01
74 30 0.21
75 1 0.01
76 28 0.20
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (69 bp):
AGTCTTTAGAGCAATACTTATGTTAGTCTCAATGCTCTGCTTTTGGTTATACTATCTATCAGTAA
TGTC
Found at i:94322 original size:9 final size:9
Alignment explanation
Indices: 94310--94367 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
94300 AATATTTTAT
*
94310 ATATAATTA
1 ATATAAATA
*
94319 ATATAAAAA
1 ATATAAATA
94328 ATATAAAT-
1 ATATAAATA
*
94336 AT-TATAT-
1 ATATAAATA
*
94343 ATATAATTA
1 ATATAAATA
*
94352 ATATAAAAA
1 ATATAAATA
94361 ATATAAA
1 ATATAAA
94368 ATATTATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
7 6 0.15
8 5 0.13
9 28 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATAAATA
Found at i:94344 original size:33 final size:34
Alignment explanation
Indices: 94298--94381 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
94288 TCCGAATCCG
*
94298 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
94332 -AAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
94365 AAAATATTATATATATA
1 AAAATATTATATATATA
94382 TAATCGGGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 32 0.67
34 16 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:94570 original size:16 final size:18
Alignment explanation
Indices: 94549--94581 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
94539 ACCCTTAAGC
94549 GTAAA-TATA-TTTTAGG
1 GTAAATTATAGTTTTAGG
94565 GTAAATTATAGTTTTAG
1 GTAAATTATAGTTTTAG
94582 TTTCTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (18 bp):
GTAAATTATAGTTTTAGG
Found at i:110403 original size:33 final size:33
Alignment explanation
Indices: 110365--110429 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
110355 GGGTACCCTA
* *
110365 GCTACATACATGTGATTCTTTCTTTTATGAAAT
1 GCTACATACATGAGAATCTTTCTTTTATGAAAT
110398 GCTACATACATGAGAATCTTTCTTTTATGAAA
1 GCTACATACATGAGAATCTTTCTTTTATGAAA
110430 GATGCTGTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (33 bp):
GCTACATACATGAGAATCTTTCTTTTATGAAAT
Done.