Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005540.1 Hibiscus syriacus cultivar Beakdansim tig00012820_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: 62247
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:466 original size:17 final size:15
Alignment explanation
Indices: 427--457 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
417 ATATAGTTAG
*
427 AATTGTATTTTTTTT
1 AATTTTATTTTTTTT
442 AATTTTATTTTTTTT
1 AATTTTATTTTTTTT
457 A
1 A
458 TATATTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
AATTTTATTTTTTTT
Found at i:504 original size:13 final size:13
Alignment explanation
Indices: 488--527 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
478 ATATAATAAA
488 TAAATATTTATTT
1 TAAATATTTATTT
*
501 TAAATAAATTATTT
1 TAAAT-ATTTATTT
515 T-AATATTTATTT
1 TAAATATTTATTT
527 T
1 T
528 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1209 original size:28 final size:28
Alignment explanation
Indices: 1167--1221 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1157 AATTTTTTTC
*
1167 TTTTCAAAATTTTTATATTTACTTATTA
1 TTTTCAAAATATTTATATTTACTTATTA
* *
1195 TTTTCATAATATTTATATTTATTTATT
1 TTTTCAAAATATTTATATTTACTTATT
1222 TGCAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTCAAAATATTTATATTTACTTATTA
Found at i:11810 original size:8 final size:8
Alignment explanation
Indices: 11791--11843 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
11781 ATTATGCTTG
11791 AAGAAAAA
1 AAGAAAAA
*
11799 AA-AAAGA
1 AAGAAAAA
11806 AA-AAAAA
1 AAGAAAAA
11813 AAGAAAAA
1 AAGAAAAA
11821 AAGAAAAA
1 AAGAAAAA
*
11829 GAG-AAAA
1 AAGAAAAA
11836 AAGAAAAA
1 AAGAAAAA
11844 GGGGGGGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 18 0.46
8 21 0.54
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:11844 original size:15 final size:14
Alignment explanation
Indices: 11794--11844 Score: 63
Period size: 15 Copynumber: 3.7 Consensus size: 14
11784 ATGCTTGAAG
11794 AAAAAAAAA-AG-A
1 AAAAAAAAAGAGAA
11806 AAAAAAAAAGA-AA
1 AAAAAAAAAGAGAA
11819 AAAAGAAAAAGAGAA
1 AAAA-AAAAAGAGAA
11834 AAAAGAAAAAG
1 AAAA-AAAAAG
11845 GGGGGGTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.26
13 6 0.17
14 7 0.20
15 13 0.37
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAGAA
Found at i:13102 original size:83 final size:83
Alignment explanation
Indices: 12963--13315 Score: 629
Period size: 83 Copynumber: 4.3 Consensus size: 83
12953 AACATTAACT
12963 GGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 GGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
13027 AGAACCAATCATTGAATTG
65 AGAACCAATCATTGAATTG
*
13046 GGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
13111 GAACCAATCATTGAATTG
66 GAACCAATCATTGAATTG
*
13129 GGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGAC
1 GGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-C
*
13193 AGAACCAATCATTGAATTT
65 AGAACCAATCATTGAATTG
*
13212 GGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
*
13277 GAACCAATCATTGAATTT
66 GAACCAATCATTGAATTG
13295 GGAAGATGAATTTGCTCATAG
1 GGAAGATGAATTTGCTCATAG
13316 TAGAAATAAG
Statistics
Matches: 262, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
82 4 0.02
83 253 0.97
84 5 0.02
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (83 bp):
GGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
GAACCAATCATTGAATTG
Found at i:14317 original size:114 final size:114
Alignment explanation
Indices: 14117--14517 Score: 576
Period size: 114 Copynumber: 3.5 Consensus size: 114
14107 AATCTATCAT
*
14117 TTGATGGATT-GATATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTAGCT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
14181 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTACCTGAATTCATCAAA
65 AAGTTCATAATGAGAAGAATTTGTTCAACTTTTTACCTGAATTCATCAAA
*
14231 TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
14296 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACTTTTTACCTGAATTCATCAAA
* *
14345 TTGATGGATTATCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * * * *
14410 AGTTCATAATGAGAAGAACTTGTTCAA-TCTTTTGCTTGATTTCAT-TAT
66 AGTTCATAATGAGAAGAATTTGTTCAACT-TTTTACCTGAATTCATCAAA
* * * * *
14458 TTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 TTGATGGATTAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
14518 AACTTGTTCA
Statistics
Matches: 262, Mismatches: 19, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
113 37 0.14
114 209 0.80
115 3 0.01
116 13 0.05
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (114 bp):
TTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACTTTTTACCTGAATTCATCAAA
Found at i:14862 original size:3 final size:3
Alignment explanation
Indices: 14854--14919 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
14844 ATATTAATTG
* *
14854 ATT ATT ATT ATT ATT A-T AAT AAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14901 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
14920 AATATATTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:16369 original size:12 final size:12
Alignment explanation
Indices: 16354--16378 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16344 ATATAATAAA
16354 TAATATTTATTT
1 TAATATTTATTT
16366 TAATATTTATTT
1 TAATATTTATTT
16378 T
1 T
16379 TCAATATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATATTTATTT
Found at i:19021 original size:12 final size:11
Alignment explanation
Indices: 19006--19045 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
18996 TTCGAAAATC
19006 AGAAATAAAAAA
1 AGAAA-AAAAAA
19018 AGAAAAAAAAGA
1 AGAAAAAAAA-A
19030 AGAAAAAAAAA
1 AGAAAAAAAAA
19041 GAGAA
1 -AGAA
19046 CAAAGGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:19038 original size:13 final size:13
Alignment explanation
Indices: 19006--19042 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
18996 TTCGAAAATC
*
19006 AGAAATAAAAA-A
1 AGAAAAAAAAAGA
19018 AG-AAAAAAAAGA
1 AGAAAAAAAAAGA
19030 AGAAAAAAAAAGA
1 AGAAAAAAAAAGA
19043 GAACAAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 7 0.32
12 5 0.23
13 10 0.45
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AGAAAAAAAAAGA
Found at i:29097 original size:49 final size:49
Alignment explanation
Indices: 29036--29244 Score: 260
Period size: 49 Copynumber: 4.3 Consensus size: 49
29026 AATGCCTAAC
29036 GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAACT
1 GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAACT
* * * *
29085 GGGTG-ATTTTTGGTAGAAAGGTGCCACTAATTCAAGTTAGATGACAAAT
1 -GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAACT
* ** * * * *
29134 TGAACATTTTTGGCAGAAAGGTACCACTAATGCAAGTTAAATGCCTAAC-
1 GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGAC-AACT
*
29183 GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAAAT
1 GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAACT
* *
29232 AGTGCATATTTGG
1 GGTGCATTTTTGG
29245 TAGGAATTTA
Statistics
Matches: 133, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
48 3 0.02
49 124 0.93
50 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (49 bp):
GGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAACT
Found at i:29192 original size:98 final size:97
Alignment explanation
Indices: 29040--29231 Score: 287
Period size: 98 Copynumber: 2.0 Consensus size: 97
29030 CCTAACGGTG
* * * *
29040 CATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAGATGACAACTGGGTGATTTTTGGTAGAAAG
1 CATTTTTGGCAAAAAGGTACCACTAATGCAAGTTAAATGACAAC-GGGTGATTTTTGGCAAAAAG
*
29105 GTGCCACTAATTCAAGTTAGATGACAAATTGAA
65 GTGCCACTAATGCAAGTTAGATGACAAATTGAA
* *
29138 CATTTTTGGCAGAAAGGTACCACTAATGCAAGTTAAATGCCTAAC-GGTGCATTTTTGGCAAAAA
1 CATTTTTGGCAAAAAGGTACCACTAATGCAAGTTAAATGAC-AACGGGTG-ATTTTTGGCAAAAA
29202 GGTGCCACTAATGCAAGTTAGATGACAAAT
64 GGTGCCACTAATGCAAGTTAGATGACAAAT
29232 AGTGCATATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
97 4 0.05
98 78 0.92
99 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (97 bp):
CATTTTTGGCAAAAAGGTACCACTAATGCAAGTTAAATGACAACGGGTGATTTTTGGCAAAAAGG
TGCCACTAATGCAAGTTAGATGACAAATTGAA
Found at i:29874 original size:24 final size:24
Alignment explanation
Indices: 29842--29905 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
29832 GACTTAAGAC
29842 GTTG-ATCGGGTCAAAGTCAATGG
1 GTTGAATCGGGTCAAAGTCAATGG
29865 GTTGAATCGGGTCAAAGTCAATGG
1 GTTGAATCGGGTCAAAGTCAATGG
*
29889 GTTGAATCAGGTCAAAG
1 GTTGAATCGGGTCAAAG
29906 AGTTAAGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 4 0.10
24 35 0.90
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (24 bp):
GTTGAATCGGGTCAAAGTCAATGG
Found at i:35540 original size:64 final size:63
Alignment explanation
Indices: 35457--35613 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 63
35447 TTCAGTGTGT
** * *
35457 ATCGATGCATAGAAAGTGCATCGATGCACCCATTAAAAATGGAAACATCAAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCACCCATT-AAAATGAAAACATCAAAGGCAATTGGTGC
* * * * ** * *
35521 ATTGATGCATAAGG-AGTGCATTGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAAAATGAAAACATCAAAGGCAATTGGTGC
*
35585 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGTAGTGCATCGATGCAC
35614 ATGTTAAAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
63 3 0.04
64 66 0.87
65 7 0.09
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (63 bp):
ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAATGAAAACATCAAAGGCAATTGGTGC
Found at i:35646 original size:20 final size:22
Alignment explanation
Indices: 35601--35658 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
35591 GCATGGGTAG
35601 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
35625 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
35645 TGCATCGATGCACT
1 TGCATCGATGCACT
35659 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:37475 original size:19 final size:19
Alignment explanation
Indices: 37426--37486 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
37416 GATTATCCGT
*
37426 TAGCA-GCAGAGAGGTCAG
1 TAGCAGGCAGAGAGGTCTG
*
37444 TA-CAGGCAAAGAGGTCTG
1 TAGCAGGCAGAGAGGTCTG
*
37462 TAGCAGGTAGAGAGGTCTG
1 TAGCAGGCAGAGAGGTCTG
37481 TAGCAG
1 TAGCAG
37487 TGTGTCAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 2 0.05
18 15 0.41
19 20 0.54
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.16
Consensus pattern (19 bp):
TAGCAGGCAGAGAGGTCTG
Found at i:50130 original size:25 final size:25
Alignment explanation
Indices: 50096--50165 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
50086 TTAAAACAGT
50096 TTTGAAAAATATTAAATATAATAGC
1 TTTGAAAAATATTAAATATAATAGC
50121 TTTGAAAAATATTAAATATAATAGC
1 TTTGAAAAATATTAAATATAATAGC
*
50146 TTTGAAAAATATTATATATA
1 TTTGAAAAATATTAAATATA
50166 TATATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (25 bp):
TTTGAAAAATATTAAATATAATAGC
Found at i:50187 original size:43 final size:46
Alignment explanation
Indices: 50140--50230 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 46
50130 TATTAAATAT
* *
50140 AATAGCTTTGAAAAATATTAT-ATATATA-TATATATAG-TTTGAA
1 AATAGCTTTGAAAAATATTATCAAAAATACTATATATAGTTTTGAA
* * *
50183 AATAGTTTTGAAAAATGTTTTCAAAAATACTATATATAGTTTTGAA
1 AATAGCTTTGAAAAATATTATCAAAAATACTATATATAGTTTTGAA
50229 AA
1 AA
50231 CCTTTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
43 18 0.45
44 5 0.12
45 9 0.22
46 8 0.20
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (46 bp):
AATAGCTTTGAAAAATATTATCAAAAATACTATATATAGTTTTGAA
Found at i:50253 original size:30 final size:33
Alignment explanation
Indices: 50184--50266 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 33
50174 TAGTTTGAAA
** *
50184 ATAGTTTTGAAAAATGTTTTCAAAAATACTATAT
1 ATAGTTTTG-AAAACCTTTTCAAAAATACAATAT
50218 ATAGTTTTGAAAACCTTTT-AAAAATA-AAT-T
1 ATAGTTTTGAAAACCTTTTCAAAAATACAATAT
50248 ATAGTTTTGAAAACCTTTT
1 ATAGTTTTGAAAACCTTTT
50267 GAGAGTAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 20 0.43
31 2 0.04
32 7 0.15
33 8 0.17
34 9 0.20
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (33 bp):
ATAGTTTTGAAAACCTTTTCAAAAATACAATAT
Found at i:50434 original size:6 final size:5
Alignment explanation
Indices: 50417--50460 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
50407 ATGCTTTATA
* *
50417 ATTTT ATTTT ATTTTT ATTTT ATTTT ATTCT AATTT ATTTT ATT
1 ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
50461 ATCTTATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:51368 original size:14 final size:13
Alignment explanation
Indices: 51338--51381 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
51328 ATGAAGGAAA
*
51338 AAAAGAGAAAATTG
1 AAAA-AGAAAATAG
51352 AAAAAGAAAATAAG
1 AAAAAGAAAAT-AG
*
51366 AAAAAGAAAAGAG
1 AAAAAGAAAATAG
51379 AAA
1 AAA
51382 TGAATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (13 bp):
AAAAAGAAAATAG
Found at i:53131 original size:2 final size:2
Alignment explanation
Indices: 53120--53158 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
53110 GTTTTGAAAA
53120 AT AT -T 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 AT AT
53159 TTTTGAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:53275 original size:30 final size:30
Alignment explanation
Indices: 53151--53287 Score: 136
Period size: 30 Copynumber: 4.6 Consensus size: 30
53141 ATATATATAT
*
53151 ATATATATTTTTGAAAACCTTTTGAAAA-A
1 ATATATAGTTTTGAAAACCTTTTGAAAATA
* * *
53180 ATATGTAGTTTTTTAAAACTATTTTGAAAAATA
1 ATATATAG-TTTTGAAAAC-CTTTTG-AAAATA
* * * *
53213 TTATATAATTTTGAAAAACTTTTAAAAATA
1 ATATATAGTTTTGAAAACCTTTTGAAAATA
*
53243 ATATATAGTTTTGAAAACCTTTTGAAAGTA
1 ATATATAGTTTTGAAAACCTTTTGAAAATA
*
53273 ATACA-A-TTTTGAAAA
1 ATATATAGTTTTGAAAA
53288 ATGTTTTGAA
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 9 0.10
29 7 0.08
30 44 0.51
31 9 0.10
32 12 0.14
33 6 0.07
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (30 bp):
ATATATAGTTTTGAAAACCTTTTGAAAATA
Found at i:53288 original size:29 final size:28
Alignment explanation
Indices: 53201--53299 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 28
53191 TTTAAAACTA
*
53201 TTTTGAAAAATATTATATAATTTTGAAAAAC
1 TTTTG-AAAATA--ATACAATTTTGAAAAAC
* * *
53232 TTTTAAAAATAATATATAGTTTTGAAAACC
1 TTTTGAAAATAATACA-A-TTTTGAAAAAC
* *
53262 TTTTGAAAGTAATACAATTTTGAAAAATG
1 TTTTGAAAATAATACAATTTTGAAAAA-C
53291 TTTTGAAAA
1 TTTTGAAAA
53300 ACATTATACT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 14 0.25
29 10 0.18
30 29 0.51
31 4 0.07
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTTGAAAATAATACAATTTTGAAAAAC
Found at i:57552 original size:20 final size:20
Alignment explanation
Indices: 57514--57552 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57504 AAGAGCCCAT
*
57514 TTAGGACCATTTAGATGCAG
1 TTAGGACCATATAGATGCAG
* *
57534 TTAGGAGCATATAGTTGCA
1 TTAGGACCATATAGATGCA
57553 TGTGGTGGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (20 bp):
TTAGGACCATATAGATGCAG
Done.