Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007827.1 Corchorus capsularis cultivar CVL-1 contig07848, 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: 66419
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:149 original size:46 final size:45
Alignment explanation
Indices: 82--176 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 45
72 CGTGCGGCTG
82 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAA-AAATCAAA
128 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAATCAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAATCAAA
173 TTTT
1 TTTT
177 GTTGTGATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 12 0.24
46 37 0.76
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (45 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAATCAAA
Found at i:290 original size:59 final size:59
Alignment explanation
Indices: 211--338 Score: 213
Period size: 59 Copynumber: 2.2 Consensus size: 59
201 GCAATGGAGT
*
211 AAAAT-TGAAGTATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAG
1 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAG
* *
269 AAAATATGAAGTATGTAAAAGACAAGAGAATAGATAGACAATAGAATATGGAGAAGAAG
1 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAG
*
328 AAAACATGAAG
1 AAAATATGAAG
339 AATGGGAGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 5 0.08
59 60 0.92
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.16
Consensus pattern (59 bp):
AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAAAAGAAG
Found at i:3493 original size:21 final size:21
Alignment explanation
Indices: 3467--3510 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3457 ATAATCTGGA
3467 TTGCTAAAT-ACTGTCCCATTT
1 TTGCT-AATCACTGTCCCATTT
*
3488 TTGCTATTCACTGTCCCATTT
1 TTGCTAATCACTGTCCCATTT
3509 TT
1 TT
3511 TACCTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (21 bp):
TTGCTAATCACTGTCCCATTT
Found at i:3851 original size:32 final size:32
Alignment explanation
Indices: 3815--3881 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
3805 CGCCCCATGA
* *
3815 GGGCGGCCTGCC-GTGGCGAAGCCGTCCCAGTG
1 GGGCGGCCTACCAATGGCGAAGCCG-CCCAGTG
*
3847 GGGCGGCCTACCAATGGTGAAGCCGCCCAGTG
1 GGGCGGCCTACCAATGGCGAAGCCGCCCAGTG
3879 GGG
1 GGG
3882 AGGCTCCGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.13, C:0.31, G:0.43, T:0.12
Consensus pattern (32 bp):
GGGCGGCCTACCAATGGCGAAGCCGCCCAGTG
Found at i:3917 original size:33 final size:33
Alignment explanation
Indices: 3867--3949 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
3857 CCAATGGTGA
* *
3867 AGCCG-CCCAGTGGGGAGGCTCCGCCGTAGTTG
1 AGCCGTCCTAGTGGGGAGGCTCCGCCGTAGCTG
* *
3899 AGCCTTCCTAGTGGGGAGGCTCCGCCGTGGCTG
1 AGCCGTCCTAGTGGGGAGGCTCCGCCGTAGCTG
*
3932 AGTCGTCCTAGTGGGGAG
1 AGCCGTCCTAGTGGGGAG
3950 ACTCAGTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 4 0.09
33 40 0.91
ACGTcount: A:0.12, C:0.28, G:0.41, T:0.19
Consensus pattern (33 bp):
AGCCGTCCTAGTGGGGAGGCTCCGCCGTAGCTG
Found at i:5092 original size:3 final size:3
Alignment explanation
Indices: 5086--5118 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5076 TAAAATTATT
5086 ATA ATA ATA ATA ATA AT- ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
5119 GTAGTAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10731 original size:25 final size:25
Alignment explanation
Indices: 10702--10754 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
10692 GAACATTGCC
10702 AAATACATTCTTATTCCAAAATTGT
1 AAATACATTCTTATTCCAAAATTGT
10727 AAATACATTCTTATTCCAAAATTGT
1 AAATACATTCTTATTCCAAAATTGT
10752 AAA
1 AAA
10755 GCTCTCCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (25 bp):
AAATACATTCTTATTCCAAAATTGT
Found at i:13936 original size:31 final size:31
Alignment explanation
Indices: 13898--13998 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
13888 CAACTTACCT
*
13898 ACTAAAATTGAAGTTTTATCATATTGACCCC
1 ACTAAAATTGAAGTTTTATCACATTGACCCC
*
13929 ACTAAAATTGAAGTTTTATCACATTGACTCTC
1 ACTAAAATTGAAGTTTTATCACATTGAC-CCC
** *
13961 -CTAAAATAAAAGATTTAT-AGCATTGACCCC
1 ACTAAAATTGAAGTTTTATCA-CATTGACCCC
*
13991 ATTAAAAT
1 ACTAAAAT
13999 GTTAGATATT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 3 0.05
31 55 0.92
32 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.34
Consensus pattern (31 bp):
ACTAAAATTGAAGTTTTATCACATTGACCCC
Found at i:14859 original size:31 final size:31
Alignment explanation
Indices: 14729--14859 Score: 160
Period size: 31 Copynumber: 4.3 Consensus size: 31
14719 AAAAATGACA
*
14729 CATGGCACGTGTC-CTTTTT-GTACACGTGG
1 CATGACACGTGTCACTTTTTGGTACACGTGG
* ** *
14758 CATGCCAATTGTCAC-TTTTGGTACACTTGG
1 CATGACACGTGTCACTTTTTGGTACACGTGG
* *
14788 CATGACACATGTCACTTTTTGGTACACATGG
1 CATGACACGTGTCACTTTTTGGTACACGTGG
*
14819 CTTGACACGTGTCACTTTTTGGTACACGTGG
1 CATGACACGTGTCACTTTTTGGTACACGTGG
*
14850 CATGCCACGT
1 CATGACACGT
14860 CGGACACCGT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 14 0.16
30 22 0.26
31 50 0.58
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (31 bp):
CATGACACGTGTCACTTTTTGGTACACGTGG
Found at i:16468 original size:18 final size:18
Alignment explanation
Indices: 16445--16481 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16435 TAGTCATTTT
16445 AAATTTCAAATAATCCGA
1 AAATTTCAAATAATCCGA
16463 AAATTTCAAATAATCCGA
1 AAATTTCAAATAATCCGA
16481 A
1 A
16482 GTGAAGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATTTCAAATAATCCGA
Found at i:26720 original size:2 final size:2
Alignment explanation
Indices: 26713--26751 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
26703 TTACAATGTA
26713 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
26752 AAATAAGATT
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:38156 original size:25 final size:25
Alignment explanation
Indices: 38128--38178 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
38118 AAATATGGGA
*
38128 ATCTTCCCCAAAAACAAAATTTGCC
1 ATCTTCACCAAAAACAAAATTTGCC
* *
38153 ATCTTGACCAAAAACAGAATTTGCC
1 ATCTTCACCAAAAACAAAATTTGCC
38178 A
1 A
38179 ACATATTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (25 bp):
ATCTTCACCAAAAACAAAATTTGCC
Found at i:41433 original size:13 final size:13
Alignment explanation
Indices: 41409--41447 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
41399 ACGTAAATAT
41409 AAAAAAACCAAAA
1 AAAAAAACCAAAA
41422 AACAAAAA-CAAAA
1 AA-AAAAACCAAAA
*
41435 AAAAAAAGCAAAA
1 AAAAAAACCAAAA
41448 TACACAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.85, C:0.13, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACCAAAA
Found at i:45094 original size:12 final size:12
Alignment explanation
Indices: 45077--45131 Score: 101
Period size: 12 Copynumber: 4.5 Consensus size: 12
45067 TTAATACAGG
45077 TATCGACGGATA
1 TATCGACGGATA
45089 TATCGAACGGATA
1 TATCG-ACGGATA
45102 TATCGACGGATA
1 TATCGACGGATA
45114 TATCGACGGATA
1 TATCGACGGATA
45126 TATCGA
1 TATCGA
45132 GGTATCGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 30 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:45111 original size:25 final size:24
Alignment explanation
Indices: 45077--45131 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
45067 TTAATACAGG
45077 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
45102 TATCGACGGATATATCGACGGATA
1 TATCGACGGATATATCGACGGATA
45126 TATCGA
1 TATCGA
45132 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:48292 original size:32 final size:32
Alignment explanation
Indices: 48256--48318 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
48246 TGCACTCAAC
48256 AGAAACCAACTTGAAAAAAAGCTAGAAGAAGA
1 AGAAACCAACTTGAAAAAAAGCTAGAAGAAGA
* *
48288 AGAAACCAGCTTGAAAAAGAGCTAGAAGAAG
1 AGAAACCAACTTGAAAAAAAGCTAGAAGAAG
48319 CCCAAAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.22, T:0.10
Consensus pattern (32 bp):
AGAAACCAACTTGAAAAAAAGCTAGAAGAAGA
Found at i:50999 original size:415 final size:415
Alignment explanation
Indices: 50229--51060 Score: 1565
Period size: 415 Copynumber: 2.0 Consensus size: 415
50219 GGATTGAACC
50229 GGTACCAATGGAGATCAACACTAATACCCAACAACTACAAATTAGCAAGATGATCTACCCCGTTA
1 GGTACCAATGGAGATCAACACTAATACCCAACAACTACAAATTAGCAAGATGATCTACCCCGTTA
*
50294 AACGCCAGTGGGTAGGATGGCTGGCAAACATTGTACTTAACCAAAGGAAAACCATTAAACTTAAG
66 AACACCAGTGGGTAGGATGGCTGGCAAACATTGTACTTAACCAAAGGAAAACCATTAAACTTAAG
*
50359 CAGAGAACCTTTTCTATCCTAGGGGGGAAAGACAAAGCAGTTTGGAGATTCAACCCCAATGGAGA
131 CAGAGAACCTTCTCTATCCTAGGGGGGAAAGACAAAGCAGTTTGGAGATTCAACCCCAATGGAGA
*
50424 ATACACAGTTAAGTCAGCTTACCTCGAGATACTTGAAGAGGAACAAGAGGAAGCCCAGCAAGGGA
196 ATACACAGTTAAGTCAGCTTACCTCAAGATACTTGAAGAGGAACAAGAGGAAGCCCAGCAAGGGA
*
50489 TTTATCCAACCTTTTGGAAAAACCTTTGGAAATTGAAAATCCCATATAAGCTTATCATGTTCATT
261 TTTATCCAACCTTTTGGAAAAACCTTTGGAAACTGAAAATCCCATATAAGCTTATCATGTTCATT
*
50554 TGGAAACTATACAACAGATGCTTAACCACAAAAGATGAACTTCAACAGAGAGGAATCTGCTAGTC
326 TGGAAACTATACAACAGATGCTTAACCACAAAAGATGAACTTCAACAGAGAGGAATCTGCCAGTC
50619 CTCATAGTGTATCTTATGCAAGAAT
391 CTCATAGTGTATCTTATGCAAGAAT
*
50644 GGTACCAATGGAGATCAACACTAATACCCAACAACTGCAAATTAGCAAGATGATCTACCCCGTTA
1 GGTACCAATGGAGATCAACACTAATACCCAACAACTACAAATTAGCAAGATGATCTACCCCGTTA
*
50709 AACACCAGTGGGTAGGATGGCTGGCAAACATTGTACTTAACCAAAGGGAAACCATTAAACTTAAG
66 AACACCAGTGGGTAGGATGGCTGGCAAACATTGTACTTAACCAAAGGAAAACCATTAAACTTAAG
50774 CAGAGAACCTTCTCTATCCTAGGGGGGAAAGACAAAGCAGTTTGGAGATTCAACCCCAATGGAGA
131 CAGAGAACCTTCTCTATCCTAGGGGGGAAAGACAAAGCAGTTTGGAGATTCAACCCCAATGGAGA
* *
50839 ATACACAGTTAAGTCAGCTTACCTCAAGATACTTGAAGAGGAACAGGAGGAAGTCCAGCAAGGGA
196 ATACACAGTTAAGTCAGCTTACCTCAAGATACTTGAAGAGGAACAAGAGGAAGCCCAGCAAGGGA
*
50904 TTTATCCAACCTTTTGGGAAAACCTTTGGAAACTGAAAATCCCATATAAGCTTATCATGTTCATT
261 TTTATCCAACCTTTTGGAAAAACCTTTGGAAACTGAAAATCCCATATAAGCTTATCATGTTCATT
*
50969 TGGAAACTATGCAACAGATGCTTAACCACAAAAGATGAACTTCAACAGAGAGGAATCTGCCAGTC
326 TGGAAACTATACAACAGATGCTTAACCACAAAAGATGAACTTCAACAGAGAGGAATCTGCCAGTC
51034 CTCATAGTGTATCTTATGCAAGAAT
391 CTCATAGTGTATCTTATGCAAGAAT
51059 GG
1 GG
51061 CTCTAAGTCC
Statistics
Matches: 406, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
415 406 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (415 bp):
GGTACCAATGGAGATCAACACTAATACCCAACAACTACAAATTAGCAAGATGATCTACCCCGTTA
AACACCAGTGGGTAGGATGGCTGGCAAACATTGTACTTAACCAAAGGAAAACCATTAAACTTAAG
CAGAGAACCTTCTCTATCCTAGGGGGGAAAGACAAAGCAGTTTGGAGATTCAACCCCAATGGAGA
ATACACAGTTAAGTCAGCTTACCTCAAGATACTTGAAGAGGAACAAGAGGAAGCCCAGCAAGGGA
TTTATCCAACCTTTTGGAAAAACCTTTGGAAACTGAAAATCCCATATAAGCTTATCATGTTCATT
TGGAAACTATACAACAGATGCTTAACCACAAAAGATGAACTTCAACAGAGAGGAATCTGCCAGTC
CTCATAGTGTATCTTATGCAAGAAT
Found at i:52110 original size:29 final size:30
Alignment explanation
Indices: 52068--52138 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
52058 GCTGAAATCT
*
52068 CAATTTGGTACCAAACCTTTTATT-TCGTC
1 CAATTTGGTACCAAACATTTTATTATCGTC
*
52097 CAATTTGGTACCAAACATTTTATTAATGGTC
1 CAATTTGGTACCAAACATTTTATT-ATCGTC
*
52128 CAATTTAGTAC
1 CAATTTGGTAC
52139 TTTTTAGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 23 0.62
31 14 0.38
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (30 bp):
CAATTTGGTACCAAACATTTTATTATCGTC
Found at i:52243 original size:14 final size:13
Alignment explanation
Indices: 52217--52263 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
52207 TCAACGTAGC
52217 TTTTTTATATTAT
1 TTTTTTATATTAT
*
52230 TTTTATTATTTTAT
1 TTTT-TTATATTAT
*
52244 TATTTTA-ATATAT
1 TTTTTTATAT-TAT
52257 TTTTTTA
1 TTTTTTA
52264 AATTTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.04
13 16 0.57
14 11 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTATATTAT
Found at i:52246 original size:17 final size:18
Alignment explanation
Indices: 52224--52259 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
52214 AGCTTTTTTA
*
52224 TATTATTTTTAT-TATTT
1 TATTATTTTAATATATTT
52241 TATTATTTTAATATATTT
1 TATTATTTTAATATATTT
52259 T
1 T
52260 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTATTTTAATATATTT
Found at i:53376 original size:19 final size:17
Alignment explanation
Indices: 53336--53384 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
53326 GAAGAAGGAA
53336 AAAG-AAAAGAAAAGGG
1 AAAGAAAAAGAAAAGGG
53352 AAAGAATAAAAGAAAA-GG
1 AAAG-A-AAAAGAAAAGGG
53370 AATAGAAAAAGAAAA
1 AA-AGAAAAAGAAAA
53385 TAAGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
18 5 0.17
19 11 0.38
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (17 bp):
AAAGAAAAAGAAAAGGG
Found at i:53380 original size:25 final size:23
Alignment explanation
Indices: 53334--53392 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
53324 TTGAAGAAGG
**
53334 AAAAAGAAAAGAAAAGGGAAAGA
1 AAAAAGAAAAGAAAAGAAAAAGA
*
53357 ATAAAAGAAAAGGAATAGAAAAAGA
1 A-AAAAGAAAA-GAAAAGAAAAAGA
53382 AAATAAGAAAA
1 AAA-AAGAAAA
53393 AATATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 11 0.37
25 18 0.60
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAGAAAAAGA
Found at i:53569 original size:29 final size:30
Alignment explanation
Indices: 53511--53573 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
53501 GCTTAAAAAA
* *
53511 GTACTAAATTGGATGATTAATAAAACGTTTG
1 GTACCAAATTGGACGA-TAATAAAACGTTTG
*
53542 GTACCAAATTGGACGA-AATAAAAGGTTTG
1 GTACCAAATTGGACGATAATAAAACGTTTG
53571 GTA
1 GTA
53574 TCAAGTTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.52
31 14 0.48
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (30 bp):
GTACCAAATTGGACGATAATAAAACGTTTG
Found at i:54966 original size:17 final size:17
Alignment explanation
Indices: 54919--54966 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
54909 TTGACAGCGC
*
54919 AACAAAAAGAAAAAGAA
1 AACAAAAACAAAAAGAA
* *
54936 AACGAAAACGAAAATG-A
1 AACAAAAAC-AAAAAGAA
54953 AACAAAAACAAAAA
1 AACAAAAACAAAAA
54967 ACAGAAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 4 0.16
17 16 0.64
18 5 0.20
ACGTcount: A:0.77, C:0.10, G:0.10, T:0.02
Consensus pattern (17 bp):
AACAAAAACAAAAAGAA
Done.