Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014945.1 Corchorus olitorius cultivar O-4 contig14978, 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: 73096
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:285 original size:6 final size:5
Alignment explanation
Indices: 262--295 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
252 GAGGATAATC
*
262 AAAGA AAAGA AAAAA AAACGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAA-GA AAAGA AAAGA AAA
296 AAACCTCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:286 original size:16 final size:17
Alignment explanation
Indices: 265--296 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
255 GATAATCAAA
265 GAAAAGAAAA-AAAAAC
1 GAAAAGAAAAGAAAAAC
281 GAAAAGAAAAGAAAAA
1 GAAAAGAAAAGAAAAA
297 AACCTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAGAAAAAC
Found at i:5274 original size:39 final size:39
Alignment explanation
Indices: 5230--5308 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
5220 TTACAAGCAA
5230 AAGTATTAACCTTTTCATATTCACTAGTATTAATTTAAC
1 AAGTATTAACCTTTTCATATTCACTAGTATTAATTTAAC
5269 AAGTATTAACCTTTTCATATTCACTAGTATTAATTTAAC
1 AAGTATTAACCTTTTCATATTCACTAGTATTAATTTAAC
5308 A
1 A
5309 TTAGAATGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (39 bp):
AAGTATTAACCTTTTCATATTCACTAGTATTAATTTAAC
Found at i:12292 original size:6 final size:6
Alignment explanation
Indices: 12281--12310 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12271 CTACCCTTCA
12281 CAAACT CAAACT CAAACT CAAACT CAAACT
1 CAAACT CAAACT CAAACT CAAACT CAAACT
12311 GACTTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
CAAACT
Found at i:12609 original size:26 final size:26
Alignment explanation
Indices: 12580--12631 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12570 ATCTTAGTTC
12580 CAGTGATTGGTGGTAGAGTACTAGAA
1 CAGTGATTGGTGGTAGAGTACTAGAA
12606 CAGTGATTGGTGGTAGAGTACTAGAA
1 CAGTGATTGGTGGTAGAGTACTAGAA
12632 TCTTAGTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.35, T:0.27
Consensus pattern (26 bp):
CAGTGATTGGTGGTAGAGTACTAGAA
Found at i:19010 original size:19 final size:19
Alignment explanation
Indices: 18986--19022 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18976 CTATTTAACA
*
18986 ATTGTACATATGAGATTAC
1 ATTGTACAAATGAGATTAC
*
19005 ATTGTACAAATTAGATTA
1 ATTGTACAAATGAGATTA
19023 GATACTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (19 bp):
ATTGTACAAATGAGATTAC
Found at i:20685 original size:19 final size:21
Alignment explanation
Indices: 20637--20685 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 21
20627 TCTGATTCCT
20637 TTCTCTCT-CT-CTGTTTTAC
1 TTCTCTCTCCTACTGTTTTAC
*
20656 TTCTCT-GCCTACT-TTTT-C
1 TTCTCTCTCCTACTGTTTTAC
20674 TTCTCTCTCCTA
1 TTCTCTCTCCTA
20686 TTCTGCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.28
19 16 0.64
20 2 0.08
ACGTcount: A:0.06, C:0.35, G:0.04, T:0.55
Consensus pattern (21 bp):
TTCTCTCTCCTACTGTTTTAC
Found at i:22552 original size:15 final size:15
Alignment explanation
Indices: 22519--22671 Score: 69
Period size: 15 Copynumber: 9.8 Consensus size: 15
22509 AGAGCCAGAG
*
22519 AAGAAGGAAGAGCCA
1 AAGAAGGAAGAACCA
22534 AAGAAGGAAGAACCCA
1 AAGAAGGAAGAA-CCA
* * **
22550 AGAAAGAGGAGGAAGGGA
1 A-AGA-AGGAAGAA-CCA
*
22568 AA-AAGGAAGAACCC
1 AAGAAGGAAGAACCA
*
22582 AAGAAAGAAGAAGAAGCA
1 AAG-AAG--GAAGAACCA
* *
22600 AAGAAAGAAGAGCCTA
1 AAGAAGGAAGAACC-A
**
22616 AA-AAGGAAGAAGGA
1 AAGAAGGAAGAACCA
* *
22630 AAGAAAGAAGAACCC
1 AAGAAGGAAGAACCA
* *
22645 AAGAAGGAGGAA-GA
1 AAGAAGGAAGAACCA
22659 GAAGAAGGAAGAA
1 -AAGAAGGAAGAA
22672 GAGAAAAAAC
Statistics
Matches: 100, Mismatches: 28, Indels: 20
0.68 0.19 0.14
Matches are distributed among these distances:
14 5 0.05
15 60 0.60
16 11 0.11
17 5 0.05
18 19 0.19
ACGTcount: A:0.58, C:0.09, G:0.32, T:0.01
Consensus pattern (15 bp):
AAGAAGGAAGAACCA
Found at i:22575 original size:33 final size:32
Alignment explanation
Indices: 22533--22671 Score: 128
Period size: 30 Copynumber: 4.4 Consensus size: 32
22523 AGGAAGAGCC
*
22533 AAAGAAGGAAGAACCCAAGAAAGAGGAGGAAGGG
1 AAAGAAGGAAGAACCCAAGAAA-AGGAAGAA-GG
* *
22567 AAA-AAGGAAGAACCCAAGAAAGAAGAAGAAGC
1 AAAGAAGGAAGAACCCAAGAAA-AGGAAGAAGG
* * *
22599 AAAGAAAGAAG-AGCCTA-AAAAGGAAGAAGG
1 AAAGAAGGAAGAACCCAAGAAAAGGAAGAAGG
* *
22629 AAAGAAAGAAGAACCCAAG--AAGGAGGAA-G
1 AAAGAAGGAAGAACCCAAGAAAAGGAAGAAGG
22658 AGAAGAAGGAAGAA
1 A-AAGAAGGAAGAA
22672 GAGAAAAAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
29 2 0.02
30 38 0.43
31 7 0.08
32 8 0.09
33 31 0.35
34 3 0.03
ACGTcount: A:0.59, C:0.09, G:0.32, T:0.01
Consensus pattern (32 bp):
AAAGAAGGAAGAACCCAAGAAAAGGAAGAAGG
Found at i:22594 original size:18 final size:18
Alignment explanation
Indices: 22533--22610 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
22523 AGGAAGAGCC
22533 AAAGAAGGAAGAACCCAAG
1 AAAGAA-GAAGAACCCAAG
* * ***
22552 AAAGAGGAGGAAGGGAA-
1 AAAGAAGAAGAACCCAAG
22569 AAAG--GAAGAACCCAAG
1 AAAGAAGAAGAACCCAAG
* *
22585 AAAGAAGAAGAAGCAAAG
1 AAAGAAGAAGAACCCAAG
22603 AAAGAAGA
1 AAAGAAGA
22611 GCCTAAAAAG
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 4 0.09
18 25 0.56
19 5 0.11
ACGTcount: A:0.60, C:0.09, G:0.31, T:0.00
Consensus pattern (18 bp):
AAAGAAGAAGAACCCAAG
Found at i:22672 original size:33 final size:32
Alignment explanation
Indices: 22533--22673 Score: 110
Period size: 33 Copynumber: 4.4 Consensus size: 32
22523 AGGAAGAGCC
* * *
22533 AAAGAAGGAAGAACCCAAGAAAGAGGAGGAAG-GG
1 AAAGAAAGAAGAACCCAAG--A-AGGAAGAAGAGA
* * *
22567 AAA-AAGGAAGAACCCAAGAAAGAAGAAGAAGC
1 AAAGAAAGAAGAACCCAAGAAGGAAGAAG-AGA
* * *
22599 AAAGAAAGAAGAGCCTAAAAAGGAAGAAG-G-
1 AAAGAAAGAAGAACCCAAGAAGGAAGAAGAGA
*
22629 AAAGAAAGAAGAACCCAAGAAGGAGGAAGAGA
1 AAAGAAAGAAGAACCCAAGAAGGAAGAAGAGA
*
22661 AGAAGGAAGAAGA
1 A-AAGAAAGAAGA
22674 GAAAAAACCA
Statistics
Matches: 88, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
30 32 0.36
31 3 0.03
32 5 0.06
33 45 0.51
34 3 0.03
ACGTcount: A:0.59, C:0.09, G:0.32, T:0.01
Consensus pattern (32 bp):
AAAGAAAGAAGAACCCAAGAAGGAAGAAGAGA
Found at i:27450 original size:12 final size:12
Alignment explanation
Indices: 27433--27457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27423 TTCTGACCCA
27433 AAAAAAAAAATC
1 AAAAAAAAAATC
27445 AAAAAAAAAATC
1 AAAAAAAAAATC
27457 A
1 A
27458 TGCATGTCCA
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:31679 original size:2 final size:2
Alignment explanation
Indices: 31672--31711 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
31662 AAAATGGGTA
* * *
31672 AT AT AT AT AT AT AA AT AA AT AA 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
31712 CCCAACATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:37440 original size:17 final size:17
Alignment explanation
Indices: 37415--37447 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37405 CCTAAATGTC
*
37415 AGAAGTTGAAAATTAAA
1 AGAAATTGAAAATTAAA
37432 AGAAATTGAAAATTAA
1 AGAAATTGAAAATTAA
37448 CTGCTGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
AGAAATTGAAAATTAAA
Found at i:43961 original size:29 final size:31
Alignment explanation
Indices: 43927--43993 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
43917 ATTTACTAAC
* * * *
43927 GTTTAGCCTCAATTTGATCATGTTTA-AAA-
1 GTTTAGACTCAAATTGAGCAAGTTTATAAAG
43956 GTTTAGACTCAAATTGAGCAAGTTTATAAAG
1 GTTTAGACTCAAATTGAGCAAGTTTATAAAG
43987 GTTTAGA
1 GTTTAGA
43994 TCCAATTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 22 0.69
30 3 0.09
31 7 0.22
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (31 bp):
GTTTAGACTCAAATTGAGCAAGTTTATAAAG
Found at i:44811 original size:29 final size:31
Alignment explanation
Indices: 44769--44827 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
44759 TTAGACCGTT
44769 TAATAATTATATATA-TT-ATTATATATATC
1 TAATAATTATATATATTTAATTATATATATC
* *
44798 TAATATTTTTATATATTTAATTATATATAT
1 TAATAATTATATATATTTAATTATATATAT
44828 TACTAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.50
30 2 0.08
31 11 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
TAATAATTATATATATTTAATTATATATATC
Found at i:45970 original size:2 final size:2
Alignment explanation
Indices: 45952--46013 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
45942 GTTTAATAAT
45952 TA TA TA T- TA T- TA T- TA TA TA TA TA -A TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
45988 TA TA -A TA TA TA TT TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46014 TATTAAACGG
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
1 9 0.18
2 40 0.82
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:45974 original size:17 final size:17
Alignment explanation
Indices: 45952--46018 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
45942 GTTTAATAAT
*
45952 TATATATTATTATTATA
1 TATATAATATTATTATA
45969 TATATAATATTATTATA
1 TATATAATATTATTATA
45986 TATATAATATATATT-TA
1 TATATAATAT-TATTATA
46003 -ATTATATATATTATTA
1 TA-TATA-ATATTATTA
46019 AACGGTTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
16 1 0.02
17 36 0.80
18 8 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATAATATTATTATA
Found at i:45985 original size:28 final size:29
Alignment explanation
Indices: 45945--46018 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 29
45935 TTAGAAGGTT
*
45945 TAATAATTA-TATATTATTATTATATATA
1 TAATAATTATTATATTATTATAATATATA
45973 TAAT-ATTATTATA-TA-TATAATATATA
1 TAATAATTATTATATTATTATAATATATA
*
45999 T-TTAATTATATATATTATTA
1 TAATAATTAT-TATATTATTA
46019 AACGGTTCGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 1 0.03
26 16 0.41
27 10 0.26
28 10 0.26
29 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATAATTATTATATTATTATAATATATA
Found at i:45991 original size:23 final size:22
Alignment explanation
Indices: 45947--46013 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 22
45937 AGAAGGTTTA
45947 ATAAT-TATATATTATTAT-TAT
1 ATAATATA-ATATTATTATATAT
45968 AT-ATATAATATTATTATATAT
1 ATAATATAATATTATTATATAT
45989 ATAATAT-ATATTTAATTATATAT
1 ATAATATAATA-TT-ATTATATAT
46012 AT
1 AT
46014 TATTAAACGG
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
20 12 0.29
21 12 0.29
22 6 0.15
23 11 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATATAATATTATTATATAT
Found at i:61657 original size:30 final size:31
Alignment explanation
Indices: 61598--61682 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 31
61588 ATTTGATGAT
*
61598 GTGGCAATGCCATGTAGGACCAAAAATGCCAC
1 GTGGCAATGCCAGGTAGGACC-AAAATGCCAC
* * *
61630 GTGGCAATGTCAGGTCGGACC-AAATGCCAT
1 GTGGCAATGCCAGGTAGGACCAAAATGCCAC
* *
61660 GTGGC-ATGGCCATGTTGGACCAA
1 GTGGCAAT-GCCAGGTAGGACCAA
61683 GACACTGACG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 2 0.05
30 23 0.52
31 1 0.02
32 18 0.41
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (31 bp):
GTGGCAATGCCAGGTAGGACCAAAATGCCAC
Found at i:66363 original size:19 final size:20
Alignment explanation
Indices: 66318--66365 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
66308 GACGGATAAT
66318 AAAATTTTTCGGAATTATTCA
1 AAAATTTTTC-GAATTATTCA
*
66339 ATAATTTTT-GAATT-TTCAA
1 AAAATTTTTCGAATTATTC-A
66358 AAAATTTT
1 AAAATTTT
66366 AAAAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 13 0.54
21 8 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
AAAATTTTTCGAATTATTCA
Found at i:67534 original size:27 final size:28
Alignment explanation
Indices: 67498--67561 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
67488 CCTTAATTTT
*
67498 TAAACATATTTCTAAAT-TGACATTATTA
1 TAAATATATTT-TAAATATGACATTATTA
* *
67526 -AAATATATTTTAATTATGCCATTATTA
1 TAAATATATTTTAAATATGACATTATTA
*
67553 TTAATATAT
1 TAAATATAT
67562 AATATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 4 0.13
27 19 0.63
28 7 0.23
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (28 bp):
TAAATATATTTTAAATATGACATTATTA
Found at i:67633 original size:51 final size:52
Alignment explanation
Indices: 67517--67634 Score: 118
Period size: 51 Copynumber: 2.3 Consensus size: 52
67507 TTCTAAATTG
* * *
67517 ACATTATTAAAATATATTTTAATTATGCCATTATTATTAATATATAATATAT
1 ACATTATTAAAATATATTTTAATAATGCCATTATTATAAATATATAAAATAT
* ** * *
67569 A-A-AATTGCCAATATGTTTTAATAATGGCATTATTA-AAATATATAAAAT-T
1 ACATTATT-AAAATATATTTTAATAATGCCATTATTATAAATATATAAAATAT
67618 ACCATTATTAAAATATA
1 A-CATTATTAAAATATA
67635 AAATCATAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
49 2 0.04
50 14 0.28
51 30 0.60
52 4 0.08
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (52 bp):
ACATTATTAAAATATATTTTAATAATGCCATTATTATAAATATATAAAATAT
Found at i:68500 original size:22 final size:22
Alignment explanation
Indices: 68412--68662 Score: 158
Period size: 22 Copynumber: 11.4 Consensus size: 22
68402 AATGATATAT
** *
68412 AATTTCATAGAGAAATTATCGA
1 AATTTCATAGAGAGGTTATCAA
* *
68434 AATTTCATATTA-TGG-TATCAAA
1 AATTTCATA-GAGAGGTTATC-AA
* *
68456 AATTT-ATAGGGAGATTGAT-AA
1 AATTTCATAGAGAGGTT-ATCAA
68477 AATTTCATAGAGAGGTTATCAAA
1 AATTTCATAGAGAGGTTATC-AA
**
68500 AAAATCATATG-GAGGTTATCAA
1 AATTTCATA-GAGAGGTTATCAA
* * *
68522 AATTTCATAGAAAAGTTTATGAA
1 AATTTCATAG-AGAGGTTATCAA
** *
68545 AATTTCATAGTTAGGTTATCAG
1 AATTTCATAGAGAGGTTATCAA
* * * * *
68567 TATTTCATTGGGAGTTTATCAC
1 AATTTCATAGAGAGGTTATCAA
*
68589 AATTTCATAG-GTA-ATTATCAA
1 AATTTCATAGAG-AGGTTATCAA
* *
68610 AATTTCATAGTGTGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
*
68632 AATTTCATA-AGATGATTATCAA
1 AATTTCATAGAGA-GGTTATCAA
68654 AATTTCATA
1 AATTTCATA
68663 AAAATATTTA
Statistics
Matches: 176, Mismatches: 38, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
21 36 0.20
22 100 0.57
23 39 0.22
24 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
AATTTCATAGAGAGGTTATCAA
Found at i:68627 original size:65 final size:66
Alignment explanation
Indices: 68475--68666 Score: 178
Period size: 65 Copynumber: 2.9 Consensus size: 66
68465 GGAGATTGAT
** **
68475 AAAATTTCATAGAGAGGTTATCAAAAAAATCATAT-GGAGGTTATCAAAATTTCATAGAAAAGTT
1 AAAATTTCATAGTTAGGTTATC-AAAATTTCAT-TGGGAGGTTATCAAAATTTCATAGAAAAG-T
*
68539 TATG
63 TATC
** * * **
68543 AAAATTTCATAGTTAGGTTATCAGTATTTCATTGGGAGTTTATCACAATTTCATAGGTAA-TTAT
1 AAAATTTCATAGTTAGGTTATCAAAATTTCATTGGGAGGTTATCAAAATTTCATAGAAAAGTTAT
68607 C
66 C
** *
68608 AAAATTTCATAGTGT-GGTTATCAAAATTTCA-TAAGATGATTATCAAAATTTCATA-AAAA
1 AAAATTTCATAGT-TAGGTTATCAAAATTTCATTGGGA-GGTTATCAAAATTTCATAGAAAA
68667 TATTTAATTA
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
64 5 0.05
65 47 0.46
66 2 0.02
67 28 0.27
68 20 0.20
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (66 bp):
AAAATTTCATAGTTAGGTTATCAAAATTTCATTGGGAGGTTATCAAAATTTCATAGAAAAGTTAT
C
Done.