Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013694.1 Corchorus capsularis cultivar CVL-1 contig13715, 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: 130157
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2222 original size:33 final size:32
Alignment explanation
Indices: 2175--2238 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2165 ATATATATAT
*
2175 AACTTGTAAATTGTATTTTTACAAAAAAAAAAA
1 AACTTGTAAATTGTA-TTTAACAAAAAAAAAAA
* *
2208 AACTTGTAAGTTGTATTTAACAGAAAAAAAA
1 AACTTGTAAATTGTATTTAACAAAAAAAAAA
2239 GTTGTTAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (32 bp):
AACTTGTAAATTGTATTTAACAAAAAAAAAAA
Found at i:2255 original size:26 final size:27
Alignment explanation
Indices: 2202--2255 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
2192 TTTACAAAAA
2202 AAAAAAAACTTGTAAGTTGTATTTAACAG
1 AAAAAAAACTTGTAAGTTGTA--TAACAG
* *
2231 AAAAAAAAGTTGTTAGTTGTA-AACA
1 AAAAAAAACTTGTAAGTTGTATAACA
2256 AATCCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
29 19 0.83
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.30
Consensus pattern (27 bp):
AAAAAAAACTTGTAAGTTGTATAACAG
Found at i:9305 original size:16 final size:17
Alignment explanation
Indices: 9286--9328 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
9276 CCGCCCGAAT
**
9286 CCGAACCCGAA-ATTAC
1 CCGAACCCGAAGACAAC
9302 CCGAACCC-AAGACAAC
1 CCGAACCCGAAGACAAC
9318 CCGAACCCGAA
1 CCGAACCCGAA
9329 CCCGACCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.40, C:0.42, G:0.14, T:0.05
Consensus pattern (17 bp):
CCGAACCCGAAGACAAC
Found at i:10095 original size:17 final size:18
Alignment explanation
Indices: 10073--10106 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10063 TCGAAAGTGA
10073 ACCCGAACCCGA-CCCGG
1 ACCCGAACCCGAGCCCGG
*
10090 ACCCGAGCCCGAGCCCG
1 ACCCGAACCCGAGCCCG
10107 AGCCCGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.53, G:0.26, T:0.00
Consensus pattern (18 bp):
ACCCGAACCCGAGCCCGG
Found at i:10130 original size:16 final size:16
Alignment explanation
Indices: 10103--10159 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
10093 CGAGCCCGAG
*
10103 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
*
10119 CTCGAACCCGAAAA-A
1 CCCGAACCCGAAAATA
*
10134 TCCCGAACCCG-AAGTA
1 -CCCGAACCCGAAAATA
10150 CCCGAACCCG
1 CCCGAACCCG
10160 CCCAATTGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 13 0.37
16 22 0.63
ACGTcount: A:0.35, C:0.40, G:0.18, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:11025 original size:2 final size:2
Alignment explanation
Indices: 11018--11052 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11008 GGTTAATCAA
11018 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11053 CCTGTTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12280 original size:15 final size:15
Alignment explanation
Indices: 12260--12289 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12250 ATAAACTAAG
12260 TCTAACAAATATATT
1 TCTAACAAATATATT
12275 TCTAACAAATATATT
1 TCTAACAAATATATT
12290 GATCAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
TCTAACAAATATATT
Found at i:17883 original size:29 final size:29
Alignment explanation
Indices: 17848--17918 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
17838 ACTTGTAGTG
17848 TTTGGACGTTTTGC-C-TACTGAACTTCAAT
1 TTTGGACGTTTT-CTCAT-CTGAACTTCAAT
* *
17877 TTTGGACATTTTCTCATTTGAACTTCAAT
1 TTTGGACGTTTTCTCATCTGAACTTCAAT
*
17906 TTTACGACGTTTT
1 TTT-GGACGTTTT
17919 ACCCCCTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.03
29 26 0.74
30 8 0.23
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.46
Consensus pattern (29 bp):
TTTGGACGTTTTCTCATCTGAACTTCAAT
Found at i:20342 original size:17 final size:16
Alignment explanation
Indices: 20302--20350 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
20292 CATGTAATCT
* *
20302 TTGATCACCGATGATC
1 TTGATCACTGGTGATC
20318 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
20335 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
20351 TTGGGGGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:24322 original size:36 final size:36
Alignment explanation
Indices: 24270--24341 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
24260 GTAATCGGTA
*
24270 AATATAACCGCATTTGATTACTGTAGCGAGAGTATC
1 AATATAACCGCATTTGACTACTGTAGCGAGAGTATC
* * *
24306 AATATAATCGCGTTTGACTACTGTAGCGGGAGTATC
1 AATATAACCGCATTTGACTACTGTAGCGAGAGTATC
24342 TTATATATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (36 bp):
AATATAACCGCATTTGACTACTGTAGCGAGAGTATC
Found at i:32441 original size:2 final size:2
Alignment explanation
Indices: 32434--32472 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
32424 ATTAGTAGTG
*
32434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32473 ATGTTCTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:32857 original size:11 final size:11
Alignment explanation
Indices: 32841--32865 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32831 TTTAATTTCA
32841 TATACTATATC
1 TATACTATATC
32852 TATACTATATC
1 TATACTATATC
32863 TAT
1 TAT
32866 TTGGCTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
TATACTATATC
Found at i:34552 original size:27 final size:27
Alignment explanation
Indices: 34522--34580 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
34512 TTTGCTACTC
* * **
34522 AACTTTTTCTACTCATTTACATTACCA
1 AACTTTTGCTACTCATTAACAACACCA
* *
34549 AACTGTTGCTACTCCTTAACAACACCA
1 AACTTTTGCTACTCATTAACAACACCA
34576 AACTT
1 AACTT
34581 AAGGCAATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (27 bp):
AACTTTTGCTACTCATTAACAACACCA
Found at i:37229 original size:47 final size:47
Alignment explanation
Indices: 37178--37268 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
37168 TACAAGTTAA
*
37178 CGTTGTTTGAATCAGATTAATTTTATTAAATAATAAATCCCATTTAT
1 CGTTGTTTGAATCAGATCAATTTTATTAAATAATAAATCCCATTTAT
* * *
37225 CGTTGTTTGAATCAGATCGATTTTATTAAGTAATAAATCTCATT
1 CGTTGTTTGAATCAGATCAATTTTATTAAATAATAAATCCCATT
37269 CAATAATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (47 bp):
CGTTGTTTGAATCAGATCAATTTTATTAAATAATAAATCCCATTTAT
Found at i:40172 original size:37 final size:37
Alignment explanation
Indices: 40130--40205 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
40120 TAGAACGGTG
40130 TGGTAGTGATGTGATTAACACTGTTCAGGTATTGTAT
1 TGGTAGTGATGTGATTAACACTGTTCAGGTATTGTAT
40167 TGGTAGTGATGTGATTAACACTGTTCAGGTATTGTAT
1 TGGTAGTGATGTGATTAACACTGTTCAGGTATTGTAT
40204 TG
1 TG
40206 ATGAATTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (37 bp):
TGGTAGTGATGTGATTAACACTGTTCAGGTATTGTAT
Found at i:44489 original size:35 final size:34
Alignment explanation
Indices: 44441--44506 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
44431 TTTCGTTTTC
* *
44441 AGGTCTTTTGAATAAGTAAAAATGATAAATGTTTA
1 AGGTCTTTCGAATAAGTAAAAAT-AAAAATGTTTA
44476 AGGTCTTTCGAATAAGTAAAAATAAAAATGT
1 AGGTCTTTCGAATAAGTAAAAATAAAAATGT
44507 CAAACATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 7 0.24
35 22 0.76
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (34 bp):
AGGTCTTTCGAATAAGTAAAAATAAAAATGTTTA
Found at i:46689 original size:26 final size:24
Alignment explanation
Indices: 46637--46696 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
46627 TATGCTCCCT
* *
46637 TTTAATTTTAATTATTTATTAAAA
1 TTTATTTTTAATTACTTATTAAAA
* * *
46661 TTTGTATTTTTAATTACTTCTTTATA
1 -TT-TATTTTTAATTACTTATTAAAA
46687 TTTATTTTTA
1 TTTATTTTTA
46697 TTTAATGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 8 0.28
25 4 0.14
26 17 0.59
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTATTTTTAATTACTTATTAAAA
Found at i:51716 original size:14 final size:14
Alignment explanation
Indices: 51697--51724 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
51687 TTAATAATTA
51697 AACTATAAACTTGC
1 AACTATAAACTTGC
51711 AACTATAAACTTGC
1 AACTATAAACTTGC
51725 CGTTTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AACTATAAACTTGC
Found at i:53869 original size:31 final size:29
Alignment explanation
Indices: 53824--53885 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 29
53814 TTGTGTCTTT
*
53824 ATTTGGAGCGTTTTGGAAAGATTTAGTCCTG
1 ATTTGGAGCGTTTT-GAAAG-TTTAGCCCTG
* * *
53855 ATTTGTAGCTTTTTGAACGTTTAGCCCTG
1 ATTTGGAGCGTTTTGAAAGTTTAGCCCTG
53884 AT
1 AT
53886 CCGAGCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.41
30 4 0.15
31 12 0.44
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (29 bp):
ATTTGGAGCGTTTTGAAAGTTTAGCCCTG
Found at i:54114 original size:2 final size:2
Alignment explanation
Indices: 54107--54143 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54097 TTTATTTTCG
54107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54144 CATGCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78303 original size:20 final size:20
Alignment explanation
Indices: 78272--78318 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
78262 TTGGAGGGAG
78272 ATTTTCTCTTTTAATTTTTTT
1 ATTTT-TCTTTTAATTTTTTT
* *
78293 GTTTTTCTTTTACTTTTTTT
1 ATTTTTCTTTTAATTTTTTT
78313 ATTTTT
1 ATTTTT
78319 GTCCCGTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (20 bp):
ATTTTTCTTTTAATTTTTTT
Found at i:78591 original size:21 final size:22
Alignment explanation
Indices: 78565--78609 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
78555 TATCAGGGAG
78565 TTGCTAAAT-ACCGTCCCA-TTT
1 TTGCT-AATCACCGTCCCACTTT
78586 TTGCTAATCACCGTCCCACTTT
1 TTGCTAATCACCGTCCCACTTT
78608 TT
1 TT
78610 ACACTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 14 0.64
22 5 0.23
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (22 bp):
TTGCTAATCACCGTCCCACTTT
Found at i:80268 original size:2 final size:2
Alignment explanation
Indices: 80261--80299 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
80251 CAATAGGGCA
80261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80300 GATCGAGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:90539 original size:17 final size:17
Alignment explanation
Indices: 90517--90552 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
90507 TTGAGCCCAA
90517 AAAGCT-AACTAAAGTGG
1 AAAGCTAAAC-AAAGTGG
90534 AAAGCTAAACAAAGTGG
1 AAAGCTAAACAAAGTGG
90551 AA
1 AA
90553 TGCTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.53, C:0.11, G:0.22, T:0.14
Consensus pattern (17 bp):
AAAGCTAAACAAAGTGG
Found at i:91981 original size:25 final size:25
Alignment explanation
Indices: 91951--92002 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
91941 CTTTCAACAA
*
91951 TGCATGAGGTTAGAAAGGATATAAG
1 TGCATGAGCTTAGAAAGGATATAAG
91976 TGCATGAGCTTAGAAAGGATATAAG
1 TGCATGAGCTTAGAAAGGATATAAG
92001 TG
1 TG
92003 TTGTTTACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (25 bp):
TGCATGAGCTTAGAAAGGATATAAG
Found at i:97771 original size:66 final size:61
Alignment explanation
Indices: 97642--97756 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 61
97632 TCATTTGTGC
* **
97642 AAAATAATCTCATGTCATTTAGAAACTTCTTGGAAGAAGATAAGATATGCAGTTCACCATG
1 AAAATAACCTCATGTCATCCAGAAACTTCTTGGAAGAAGATAAGATATGCAGTTCACCATG
97703 AAAATAACCTCATGTCA-CCAGAAACTTCTTGGAAGAAGATAAGATATGCAGTTC
1 AAAATAACCTCATGTCATCCAGAAACTTCTTGGAAGAAGATAAGATATGCAGTTC
97757 CAGTTCACCA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 35 0.69
61 16 0.31
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (61 bp):
AAAATAACCTCATGTCATCCAGAAACTTCTTGGAAGAAGATAAGATATGCAGTTCACCATG
Found at i:98392 original size:6 final size:6
Alignment explanation
Indices: 98381--98428 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
98371 CTGCATCTAC
* * *
98381 CGTTGG CGTTGG CGTTGG CGTTGG CGTTGG TGTTGG TGTTGG TGTTGG
1 CGTTGG CGTTGG CGTTGG CGTTGG CGTTGG CGTTGG CGTTGG CGTTGG
98429 GGGACGGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.00, C:0.10, G:0.50, T:0.40
Consensus pattern (6 bp):
CGTTGG
Found at i:99141 original size:32 final size:32
Alignment explanation
Indices: 99093--99177 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
99083 TAGTCACGCG
*
99093 GAGCCTCCCCACTAGGACGGCTCTGCCACGGC
1 GAGCCGCCCCACTAGGACGGCTCTGCCACGGC
* * *
99125 GGGCCGTCCCACTAGGACGGTTCTGCCACGGC
1 GAGCCGCCCCACTAGGACGGCTCTGCCACGGC
* *
99157 TAGCCGCCCCACTAGGGCGGC
1 GAGCCGCCCCACTAGGACGGC
99178 AAGGCCTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.14, C:0.41, G:0.32, T:0.13
Consensus pattern (32 bp):
GAGCCGCCCCACTAGGACGGCTCTGCCACGGC
Found at i:99281 original size:33 final size:33
Alignment explanation
Indices: 99238--99331 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 33
99228 TAGTACCGGT
* *
99238 GCCG-CCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
99270 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
99303 GCCGCCCCAGGAGGGCGGCTTGGCCATGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGG
99332 CTCAGCCGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 4 0.08
33 49 0.92
ACGTcount: A:0.12, C:0.32, G:0.44, T:0.13
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
Found at i:99461 original size:32 final size:32
Alignment explanation
Indices: 99420--99505 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
99410 AAAATAGCCG
*
99420 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCG-A
1 AGCCGCCCCACCGGGGCGGCCTGCCCTGG-GTA
*
99452 AGCCGCCCCACCGGGACGGCCTGCCCTGGGTA
1 AGCCGCCCCACCGGGGCGGCCTGCCCTGGGTA
**
99484 AGCCGCCCCAGTGGGGCGGCCT
1 AGCCGCCCCACCGGGGCGGCCT
99506 TTTCATGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.02
32 47 0.98
ACGTcount: A:0.10, C:0.43, G:0.38, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGGGGCGGCCTGCCCTGGGTA
Found at i:122314 original size:6 final size:6
Alignment explanation
Indices: 122303--122328 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
122293 AGCAACGAGT
122303 GTCTTC GTCTTC GTCTTC GTCTTC GT
1 GTCTTC GTCTTC GTCTTC GTCTTC GT
122329 TTAATACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.19, T:0.50
Consensus pattern (6 bp):
GTCTTC
Found at i:124362 original size:2 final size:2
Alignment explanation
Indices: 124357--124399 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
124347 AAAAAGCTAG
124357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
124400 AAATTGTAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Done.