Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014886.1 Corchorus olitorius cultivar O-4 contig14919, 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: 67623
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:417 original size:11 final size:11
Alignment explanation
Indices: 401--440 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
391 TATTTAAAAG
401 TAAATATACGA
1 TAAATATACGA
*
412 TAAATATAAG-
1 TAAATATACGA
422 TAAATATACGA
1 TAAATATACGA
*
433 GAAATATA
1 TAAATATA
441 AATAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (11 bp):
TAAATATACGA
Found at i:439 original size:21 final size:21
Alignment explanation
Indices: 398--441 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
388 CTATATTTAA
*
398 AAGTAAATATACGATAAATAT
1 AAGTAAATATACGAGAAATAT
419 AAGTAAATATACGAGAAATAT
1 AAGTAAATATACGAGAAATAT
440 AA
1 AA
442 ATAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (21 bp):
AAGTAAATATACGAGAAATAT
Found at i:451 original size:4 final size:4
Alignment explanation
Indices: 438--478 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
428 TACGAGAAAT
438 ATAA AT-A ATAA ATAA AT-- ATAA AT-A ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
479 AGGCCACTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.06
3 6 0.18
4 25 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:454 original size:17 final size:17
Alignment explanation
Indices: 434--472 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
424 AATATACGAG
434 AAATATAAATAATAAAT
1 AAATATAAATAATAAAT
451 AAATATAAATAATAAAT
1 AAATATAAATAATAAAT
468 AAATA
1 AAATA
473 AATAAAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATAAATAATAAAT
Found at i:1062 original size:2 final size:2
Alignment explanation
Indices: 1055--1087 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1045 ATATCGAACC
1055 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 A
1088 CGCTTAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1717 original size:21 final size:21
Alignment explanation
Indices: 1675--1717 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1665 AACTTAAAGA
* *
1675 TCAGTAATCTTGCGCTCCACT
1 TCAGTAATCTTGCGATCAACT
*
1696 TCAGTAATCTTGCTATCAACT
1 TCAGTAATCTTGCGATCAACT
1717 T
1 T
1718 GAAATTCCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.37
Consensus pattern (21 bp):
TCAGTAATCTTGCGATCAACT
Found at i:19013 original size:23 final size:22
Alignment explanation
Indices: 18970--19013 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
18960 TTACTTCATT
* *
18970 AATTTTTCTAGTTGGTTACAAC
1 AATTTTTCTAGTTGATGACAAC
*
18992 AATTTTTATTAGTTGATGACAA
1 AATTTTT-CTAGTTGATGACAA
19014 AATCTGATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
AATTTTTCTAGTTGATGACAAC
Found at i:22661 original size:15 final size:16
Alignment explanation
Indices: 22632--22661 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22622 CCCACAAAGA
22632 GCAATTAATTTCTATT
1 GCAATTAATTTCTATT
22648 GCAATTAA-TTCTAT
1 GCAATTAATTTCTAT
22662 CAAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (16 bp):
GCAATTAATTTCTATT
Found at i:24097 original size:14 final size:15
Alignment explanation
Indices: 24078--24106 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24068 TTTCTTGTTC
24078 TTTTTCTTT-TTCCT
1 TTTTTCTTTCTTCCT
24092 TTTTTCTTTCTTCCT
1 TTTTTCTTTCTTCCT
24107 CCCTCACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTTCTTCCT
Found at i:27032 original size:16 final size:15
Alignment explanation
Indices: 26996--27039 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
26986 CAATTGGGCG
* *
26996 GGTTCGGGTACTTCG
1 GGTTCGGGTATTTCA
27011 GGTTCGGGCTATTTCA
1 GGTTCGGG-TATTTCA
27027 GGTTCGGGTATTT
1 GGTTCGGGTATTT
27040 TCGGGCTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.09, C:0.16, G:0.36, T:0.39
Consensus pattern (15 bp):
GGTTCGGGTATTTCA
Found at i:27041 original size:16 final size:16
Alignment explanation
Indices: 26994--27113 Score: 104
Period size: 16 Copynumber: 7.6 Consensus size: 16
26984 AGCAATTGGG
*
26994 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
27009 CGGGTTCGGGCTA-TTT
1 CGGGTTCGGG-TATTTT
*
27025 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* **
27041 CGGGCTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
*
27057 CGGATTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
27073 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
*
27089 CGAGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
27105 CGGGTTCGG
1 CGGGTTCGG
27114 TCTCGGGTAG
Statistics
Matches: 82, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
15 14 0.17
16 66 0.80
17 2 0.02
ACGTcount: A:0.09, C:0.17, G:0.38, T:0.36
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:27050 original size:32 final size:31
Alignment explanation
Indices: 26996--27113 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 31
26986 CAATTGGGCG
* * * *
26996 GGTTCGGGTA-CTTCGGGTTCGGGCTATTTC
1 GGTTCGGGTATTTTCGGGCTCGGGTTATGTC
*
27026 AGGTTCGGGTATTTTCGGGCTCGGGTTAAGTC
1 -GGTTCGGGTATTTTCGGGCTCGGGTTATGTC
27058 GGATTCGGGTATTTTCGGGCTCGGGTTATGTC
1 GG-TTCGGGTATTTTCGGGCTCGGGTTATGTC
*
27090 GAGTTCGGGTATTTTCGGGTTCGG
1 G-GTTCGGGTATTTTCGGGCTCGG
27114 TCTCGGGTAG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
31 12 0.16
32 64 0.83
33 1 0.01
ACGTcount: A:0.09, C:0.16, G:0.38, T:0.36
Consensus pattern (31 bp):
GGTTCGGGTATTTTCGGGCTCGGGTTATGTC
Found at i:27624 original size:31 final size:31
Alignment explanation
Indices: 27589--27660 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
27579 TAAATTATTG
*
27589 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
27620 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
27651 CAAATTAAAA
1 CAAATTAAAA
27661 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:28014 original size:25 final size:25
Alignment explanation
Indices: 27971--28021 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
27961 TGATAAAGTT
27971 TTATATATAATTATGATTTCTTAAAAA
1 TTATATATAATTATGA-TT-TTAAAAA
*
27998 TTATATGT-ATTAT-ATTTTAAAAA
1 TTATATATAATTATGATTTTAAAAA
28021 T
1 T
28022 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 5 0.22
27 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATATATAATTATGATTTTAAAAA
Found at i:31059 original size:22 final size:22
Alignment explanation
Indices: 31031--31111 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
31021 ATTATGCTAT
31031 TATATATAAAATATATTTATGA
1 TATATATAAAATATATTTATGA
* *
31053 TATATATAGAATATATGTA--A
1 TATATATAAAATATATTTATGA
* *
31073 AATATATAAATTATATTTATGA
1 TATATATAAAATATATTTATGA
31095 TATATATAAAAATATAT
1 TATATAT-AAAATATAT
31112 ATAACAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 16 0.33
22 24 0.50
23 8 0.17
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TATATATAAAATATATTTATGA
Found at i:31176 original size:20 final size:20
Alignment explanation
Indices: 31151--31202 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
31141 TATATTATTA
*
31151 AAAACCCG-CCAAATATCGCC
1 AAAACCCGACCAAA-ACCGCC
*
31171 AAAACCCGACCGAAACCGCC
1 AAAACCCGACCAAAACCGCC
31191 AAAACCCGACCA
1 AAAACCCGACCA
31203 CCTCAGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.42, C:0.42, G:0.12, T:0.04
Consensus pattern (20 bp):
AAAACCCGACCAAAACCGCC
Found at i:31678 original size:2 final size:2
Alignment explanation
Indices: 31671--31712 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
31661 TCAAGAATAC
**
31671 AT AT AT AT AT GG 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 AT
31713 GTGTGTGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33218 original size:23 final size:23
Alignment explanation
Indices: 33168--33218 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
33158 TTCAAATTAT
*
33168 TTCGGATTCGGATTCGGGTCGGG
1 TTCGGATTCGGATTCGGGTCAGG
* *
33191 ATCGGATTTGG-TCTCGGGTCAGG
1 TTCGGATTCGGAT-TCGGGTCAGG
33214 TTCGG
1 TTCGG
33219 GCTGCCTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.10, C:0.18, G:0.41, T:0.31
Consensus pattern (23 bp):
TTCGGATTCGGATTCGGGTCAGG
Found at i:40266 original size:31 final size:31
Alignment explanation
Indices: 40195--40266 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
40185 GTCTATCATC
*
40195 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* * *
40226 TAATT-ATTTGTTTAATTTGATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTAATTT
40256 GTTTTAATTTG
1 -TTTTAATTTG
40267 CAATAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:40556 original size:18 final size:18
Alignment explanation
Indices: 40518--40575 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
40508 TATTCAATCT
*
40518 TTATAT-ATATATTCATA
1 TTATATAATATAATCATA
*
40535 --ATATAATATAATCATT
1 TTATATAATATAATCATA
* * *
40551 TTATATTATATTATTATA
1 TTATATAATATAATCATA
40569 TTATATA
1 TTATATA
40576 TTATCAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
18 18 0.58
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATAATATAATCATA
Found at i:40755 original size:16 final size:15
Alignment explanation
Indices: 40716--40784 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
40706 CCCGAACCAA
*
40716 AACCCGACATAACCCG
1 AACCCGA-AAAACCCG
* *
40732 AGCTCGAAAATACCCG
1 AACCCGAAAA-ACCCG
*
40748 AACCCGAATAAACCCA
1 AACCCGAA-AAACCCG
40764 AACCCGAAAAAGCCCG
1 AACCCGAAAAA-CCCG
40780 AACCC
1 AACCC
40785 ACCCAATTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 5 0.12
16 36 0.84
17 2 0.05
ACGTcount: A:0.42, C:0.39, G:0.13, T:0.06
Consensus pattern (15 bp):
AACCCGAAAAACCCG
Found at i:42031 original size:22 final size:21
Alignment explanation
Indices: 41985--42031 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
41975 ATATGTGTGT
*
41985 GTATATATTATTTTATATATA
1 GTATATATTATTGTATATATA
42006 -TATATA-TATTGTATAATATAA
1 GTATATATTATTGTAT-ATAT-A
42027 GTATA
1 GTATA
42032 ATAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 7 0.32
20 10 0.45
21 1 0.05
22 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
GTATATATTATTGTATATATA
Found at i:42524 original size:76 final size:77
Alignment explanation
Indices: 42433--42588 Score: 305
Period size: 76 Copynumber: 2.0 Consensus size: 77
42423 CGGTAAACCT
42433 GGTGTCCGTGTCCCCGCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAA-
1 GGTGTCCGTGTCCCCGCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAG
42497 TCTTGGATGGCC
66 TCTTGGATGGCC
42509 GGTGTCCGTGTCCCCGCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAG
1 GGTGTCCGTGTCCCCGCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAG
42574 TCTTGGATGGCC
66 TCTTGGATGGCC
42586 GGT
1 GGT
42589 AATTGGCTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 64 0.81
77 15 0.19
ACGTcount: A:0.12, C:0.23, G:0.37, T:0.29
Consensus pattern (77 bp):
GGTGTCCGTGTCCCCGCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAG
TCTTGGATGGCC
Found at i:42719 original size:73 final size:73
Alignment explanation
Indices: 42600--42746 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
42590 ATTGGCTTAA
42600 GACTTGACGGGTTGGGCCGCACAGGGGAGAGATGAGGACTCACATGTAAATCGAGGGAGATAAAT
1 GACTTGACGGGTTGGGCCGCACAGGGGAGAGATGAGGACTCACATGTAAATCGAGGGAGATAAAT
42665 CCCGTGTT
66 CCCGTGTT
*
42673 GACTTGACGGGTTGGGCCGCACAGGGGAGAGATGAGGACTCACATGTAAATCGGGGGAGATAAAT
1 GACTTGACGGGTTGGGCCGCACAGGGGAGAGATGAGGACTCACATGTAAATCGAGGGAGATAAAT
42738 CCCGTGTT
66 CCCGTGTT
42746 G
1 G
42747 CATACAACAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.27, C:0.18, G:0.37, T:0.19
Consensus pattern (73 bp):
GACTTGACGGGTTGGGCCGCACAGGGGAGAGATGAGGACTCACATGTAAATCGAGGGAGATAAAT
CCCGTGTT
Found at i:47472 original size:16 final size:16
Alignment explanation
Indices: 47451--47495 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
47441 TCGTTTAAAG
*
47451 TTTTTTCGAGTTCGGA
1 TTTTTTCGAGTTCGAA
* *
47467 TTTTTTCAAGTTTGAA
1 TTTTTTCGAGTTCGAA
*
47483 TTTTTTTGAGTTC
1 TTTTTTCGAGTTC
47496 AAGTTATTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.58
Consensus pattern (16 bp):
TTTTTTCGAGTTCGAA
Found at i:47832 original size:11 final size:11
Alignment explanation
Indices: 47808--47842 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47798 TTGACAACGC
47808 AACAAAAACAA
1 AACAAAAACAA
* *
47819 AACGAAAACGA
1 AACAAAAACAA
47830 AACAAAAACAA
1 AACAAAAACAA
47841 AA
1 AA
47843 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:55798 original size:18 final size:18
Alignment explanation
Indices: 55775--55814 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
55765 CTCCTCTATC
*
55775 ATGAAAACACTTTTTTTT
1 ATGAAAACAATTTTTTTT
55793 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTTTTTTT
55811 -TGAA
1 ATGAA
55815 TTACCCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (18 bp):
ATGAAAACAATTTTTTTT
Found at i:55808 original size:17 final size:18
Alignment explanation
Indices: 55775--55814 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
55765 CTCCTCTATC
*
55775 ATGAAAACACTTTTTTTT
1 ATGAAAACACATTTTTTT
55793 ATGAAAACA-ATTTTTTT
1 ATGAAAACACATTTTTTT
*
55810 TTGAA
1 ATGAA
55815 TTACCCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (18 bp):
ATGAAAACACATTTTTTT
Found at i:56499 original size:30 final size:30
Alignment explanation
Indices: 56460--56518 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56450 GTTTATTAAT
56460 GAAACTTGAAAATTAAAGACATAAAATAAAG
1 GAAACTTGAAAATTAAAG-CATAAAATAAAG
*
56491 GAAA-TTGAAAATTAAAGCATAAATTAAA
1 GAAACTTGAAAATTAAAGCATAAAATAAA
56519 TAACTAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (30 bp):
GAAACTTGAAAATTAAAGCATAAAATAAAG
Done.