Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024303.1 Corchorus olitorius cultivar O-4 contig24336, 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: 60694
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:17152 original size:2 final size:2
Alignment explanation
Indices: 17145--17179 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17135 CCCTTCAAAA
17145 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 A
17180 AATTAATTTA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19055 original size:19 final size:20
Alignment explanation
Indices: 19019--19056 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
19009 AATTCAAAAC
*
19019 AAAATAAAAATTACCCATTT
1 AAAATAAAAACTACCCATTT
*
19039 AAAAT-AAAACTATCCATT
1 AAAATAAAAACTACCCATT
19057 AGAGAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAAAACTACCCATTT
Found at i:20466 original size:10 final size:9
Alignment explanation
Indices: 20453--20527 Score: 61
Period size: 10 Copynumber: 8.4 Consensus size: 9
20443 AATTGTTAAA
20453 TTTAATTAAG
1 TTTAATT-AG
20463 TTTAA-T-G
1 TTTAATTAG
20470 -TTAATTAG
1 TTTAATTAG
20478 TGTTAATTAG
1 T-TTAATTAG
*
20488 TTT-ATAAG
1 TTTAATTAG
*
20496 TGTTAATTAA
1 T-TTAATTAG
20506 TTT-ATTAG
1 TTTAATTAG
20514 TGTTAATTAG
1 T-TTAATTAG
20524 TTTA
1 TTTA
20528 CAGTGTTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
8 11 0.21
9 12 0.23
10 24 0.45
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (9 bp):
TTTAATTAG
Found at i:20499 original size:18 final size:18
Alignment explanation
Indices: 20476--20539 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
20466 AATGTTAATT
20476 AGTGTTAATTAGTTTATA
1 AGTGTTAATTAGTTTATA
* *
20494 AGTGTTAATTAATTTATT
1 AGTGTTAATTAGTTTATA
*
20512 AGTGTTAATTAGTTTA-C
1 AGTGTTAATTAGTTTATA
20529 AGTGTTAATTA
1 AGTGTTAATTA
20540 ATGTTAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 11 0.26
18 31 0.74
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (18 bp):
AGTGTTAATTAGTTTATA
Found at i:20515 original size:36 final size:37
Alignment explanation
Indices: 20464--20546 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 37
20454 TTAATTAAGT
20464 TTAATGTTAATTAGTGTTAATTAGTTTATAAGTGTTAA
1 TTAATGTTAATTAGTGTTAATTAGTTTA-AAGTGTTAA
*
20502 TTAAT-TT-ATTAGTGTTAATTAGTTTACAGTGTTAA
1 TTAATGTTAATTAGTGTTAATTAGTTTAAAGTGTTAA
20537 TTAATGTTAA
1 TTAATGTTAA
20547 ATAACTAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 13 0.31
36 21 0.50
37 3 0.07
38 5 0.12
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (37 bp):
TTAATGTTAATTAGTGTTAATTAGTTTAAAGTGTTAA
Found at i:20625 original size:16 final size:15
Alignment explanation
Indices: 20604--20640 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
20594 ACAAAAATTC
20604 ATAATACTAATATTAA
1 ATAATACTAATATT-A
20620 ATAATACTAATATTA
1 ATAATACTAATATTA
20635 ATAATA
1 ATAATA
20641 ACACTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATACTAATATTA
Found at i:20660 original size:18 final size:18
Alignment explanation
Indices: 20619--20654 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20609 ACTAATATTA
* *
20619 AATAATACTAATATTAAT
1 AATAACACTAATATCAAT
20637 AATAACACTAATATCAAT
1 AATAACACTAATATCAAT
20655 TCTAACTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAACACTAATATCAAT
Found at i:21219 original size:32 final size:32
Alignment explanation
Indices: 21178--21241 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
21168 AGAGTTTCAA
21178 ACAGATATCACTCATCTCACAAACCAACTCCT
1 ACAGATATCACTCATCTCACAAACCAACTCCT
* *
21210 ACAGATATCACTCATCTCACAGACCAGCTCCT
1 ACAGATATCACTCATCTCACAAACCAACTCCT
21242 GCAGCTAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.38, G:0.06, T:0.22
Consensus pattern (32 bp):
ACAGATATCACTCATCTCACAAACCAACTCCT
Found at i:21445 original size:51 final size:51
Alignment explanation
Indices: 21349--21448 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
21339 TCAATATTTT
** * **
21349 CTTGTTTCAATCCTGTCTCCGGACACCTAAATACTCTTTTAGTGTTTCTTC
1 CTTGTTTCAATCCTGTCTCCGGACACAAAAATACTCGTACAGTGTTTCTTC
* *
21400 CTTGTTTCAATCTTGTCTCCGGACATAAAAATACT-GTACACGTGTTTCT
1 CTTGTTTCAATCCTGTCTCCGGACACAAAAATACTCGTACA-GTGTTTCT
21449 CTCTCAGCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (51 bp):
CTTGTTTCAATCCTGTCTCCGGACACAAAAATACTCGTACAGTGTTTCTTC
Found at i:29372 original size:14 final size:15
Alignment explanation
Indices: 29353--29381 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29343 TGATATATAG
29353 AAGAAAAATT-AATT
1 AAGAAAAATTCAATT
29367 AAGAAAAATTCAATT
1 AAGAAAAATTCAATT
29382 CAATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGAAAAATTCAATT
Found at i:29649 original size:16 final size:16
Alignment explanation
Indices: 29628--29715 Score: 81
Period size: 16 Copynumber: 5.5 Consensus size: 16
29618 TTAGTATTGA
29628 ATTCGGGTATTTTCGG
1 ATTCGGGTATTTTCGG
*
29644 ATTCGGGTATTTTTGG
1 ATTCGGGTATTTTCGG
*
29660 ATTTGGGTATTTT-GAG
1 ATTCGGGTATTTTCG-G
* *
29676 GTTCGGGTTTCTTTCGG
1 ATTCGGGTAT-TTTCGG
**
29693 GCTCGGGT-TTTTCGG
1 ATTCGGGTATTTTCGG
*
29708 GTTCGGGT
1 ATTCGGGT
29716 TTTGGGCGGC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
15 14 0.23
16 36 0.58
17 11 0.18
18 1 0.02
ACGTcount: A:0.08, C:0.11, G:0.35, T:0.45
Consensus pattern (16 bp):
ATTCGGGTATTTTCGG
Found at i:29707 original size:15 final size:15
Alignment explanation
Indices: 29687--29718 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29677 TTCGGGTTTC
29687 TTTCGGGCTCGGGTT
1 TTTCGGGCTCGGGTT
*
29702 TTTCGGGTTCGGGTT
1 TTTCGGGCTCGGGTT
29717 TT
1 TT
29719 GGGCGGCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.38, T:0.47
Consensus pattern (15 bp):
TTTCGGGCTCGGGTT
Found at i:31495 original size:24 final size:24
Alignment explanation
Indices: 31463--31511 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
31453 AGATCAACGA
31463 AGTTTTAGAGAGCATATACCCACC
1 AGTTTTAGAGAGCATATACCCACC
*
31487 AGTTTTAGAGAGCATGTACCCACC
1 AGTTTTAGAGAGCATATACCCACC
31511 A
1 A
31512 TTTGAGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (24 bp):
AGTTTTAGAGAGCATATACCCACC
Found at i:32956 original size:239 final size:239
Alignment explanation
Indices: 32537--33016 Score: 951
Period size: 239 Copynumber: 2.0 Consensus size: 239
32527 AATGATTATA
*
32537 ATCATTCTTTGATGATTTGATTTTTTTCCACCAGGCATCTGGTCTAGTGTGGTTGGTCAGTGTTC
1 ATCATTCTTTGATGATTTGATTTTTTTCCACCAAGCATCTGGTCTAGTGTGGTTGGTCAGTGTTC
32602 AACTATTAGTTCTAGTGATTAGAGTTTAATCCTTAACAAATCAAGTATCTCAAGGACTAATTATA
66 AACTATTAGTTCTAGTGATTAGAGTTTAATCCTTAACAAATCAAGTATCTCAAGGACTAATTATA
32667 ATCATTAACTTGCTCTCGAATTATTCTTGAAATTGAAATGATCCTTTTAATTGATTCTAATTAGC
131 ATCATTAACTTGCTCTCGAATTATTCTTGAAATTGAAATGATCCTTTTAATTGATTCTAATTAGC
32732 TCTAAAAGTTATGATTTTCAACCAAATAAGGAGATTCCAACGTC
196 TCTAAAAGTTATGATTTTCAACCAAATAAGGAGATTCCAACGTC
32776 ATCATTCTTTGATGATTTGATTTTTTTCCACCAAGCATCTGGTCTAGTGTGGTTGGTCAGTGTTC
1 ATCATTCTTTGATGATTTGATTTTTTTCCACCAAGCATCTGGTCTAGTGTGGTTGGTCAGTGTTC
32841 AACTATTAGTTCTAGTGATTAGAGTTTAATCCTTAACAAATCAAGTATCTCAAGGACTAATTATA
66 AACTATTAGTTCTAGTGATTAGAGTTTAATCCTTAACAAATCAAGTATCTCAAGGACTAATTATA
32906 ATCATTAACTTGCTCTCGAATTATTCTTGAAATTGAAATGATCCTTTTAATTGATTCTAATTAGC
131 ATCATTAACTTGCTCTCGAATTATTCTTGAAATTGAAATGATCCTTTTAATTGATTCTAATTAGC
32971 TCTAAAAGTTATGATTTTCAACCAAATAAGGAGATTCCAACGTC
196 TCTAAAAGTTATGATTTTCAACCAAATAAGGAGATTCCAACGTC
33015 AT
1 AT
33017 GATCAACTTT
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 240 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (239 bp):
ATCATTCTTTGATGATTTGATTTTTTTCCACCAAGCATCTGGTCTAGTGTGGTTGGTCAGTGTTC
AACTATTAGTTCTAGTGATTAGAGTTTAATCCTTAACAAATCAAGTATCTCAAGGACTAATTATA
ATCATTAACTTGCTCTCGAATTATTCTTGAAATTGAAATGATCCTTTTAATTGATTCTAATTAGC
TCTAAAAGTTATGATTTTCAACCAAATAAGGAGATTCCAACGTC
Found at i:33449 original size:16 final size:15
Alignment explanation
Indices: 33424--33453 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33414 GAGGTACTTA
33424 TGGGCCGGGCCGGGC
1 TGGGCCGGGCCGGGC
33439 TGGGTCCGGGCCGGG
1 TGGG-CCGGGCCGGG
33454 TTTTGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.30, G:0.60, T:0.10
Consensus pattern (15 bp):
TGGGCCGGGCCGGGC
Found at i:33639 original size:13 final size:13
Alignment explanation
Indices: 33623--33649 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33613 TTTTTTAATA
33623 AAAATTAAAATTT
1 AAAATTAAAATTT
33636 AAAATTAAAATTT
1 AAAATTAAAATTT
33649 A
1 A
33650 TATAAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:33783 original size:29 final size:30
Alignment explanation
Indices: 33730--33790 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
33720 GTTCTAGTTA
*
33730 ATGTAAAGATATAAATTATTCAATTTTATT
1 ATGTAAAGATATAAATTATTCAATTATATT
*
33760 ATGTATAA-ATAT-AATTATTTAATTATATT
1 ATGTA-AAGATATAAATTATTCAATTATATT
33789 AT
1 AT
33791 ATTATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 17 0.61
30 9 0.32
31 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
ATGTAAAGATATAAATTATTCAATTATATT
Found at i:37066 original size:41 final size:43
Alignment explanation
Indices: 36964--37074 Score: 147
Period size: 44 Copynumber: 2.6 Consensus size: 43
36954 TTACCCAATA
*
36964 ACTAAAGTCCCCAAACACATTTATAACACAAGGGCACCTCACTT
1 ACTAAAGTCCCCAAACACATTTATAACACAAGGGCA-CTCACAT
* * *
37008 TCTAAAGTCCTCAAACACATTTATAACA-TAGAGGCA-TC-CAT
1 ACTAAAGTCCCCAAACACATTTATAACACAAG-GGCACTCACAT
37049 ACTAAAGTCCCCAAACACATTTATAA
1 ACTAAAGTCCCCAAACACATTTATAA
37075 TTCCAAAGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
41 26 0.43
42 2 0.03
43 2 0.03
44 30 0.50
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (43 bp):
ACTAAAGTCCCCAAACACATTTATAACACAAGGGCACTCACAT
Found at i:37124 original size:41 final size:41
Alignment explanation
Indices: 37078--37236 Score: 203
Period size: 41 Copynumber: 3.8 Consensus size: 41
37068 TTTATAATTC
*
37078 CAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
* *
37119 CAAAGTCCCCAAACACATTTATAACACA-AGTGCAATTCTCTCT
1 CAAAGTCCCCAAACACATTTATAACACAGAG-GC-A-TCTATAT
* * *
37162 AAAAGTCCTCAAACGCATTTATAACACAGAGGCATCTATAT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
* * *
37203 TAAAGTCCCCAAACACAATTATAACACAGGGGCA
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCA
37237 ATTCTCTCTA
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
40 2 0.02
41 63 0.62
42 2 0.02
43 32 0.32
44 2 0.02
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.23
Consensus pattern (41 bp):
CAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATAT
Found at i:37124 original size:68 final size:68
Alignment explanation
Indices: 37011--37142 Score: 230
Period size: 68 Copynumber: 1.9 Consensus size: 68
37001 CTCACTTTCT
*
37011 AAAGTCCTCAAACACATTTATAACATAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAAT
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAAT
37076 TCC
66 TCC
*
37079 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATA-TCAAAGTCCCCAAACACATTTATAA
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACT-AAAGTCCCCAAACACATTTATAA
37143 CACAAGTGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 1 0.02
68 60 0.98
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (68 bp):
AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAAT
TCC
Found at i:37181 original size:84 final size:84
Alignment explanation
Indices: 37079--37246 Score: 291
Period size: 84 Copynumber: 2.0 Consensus size: 84
37069 TTATAATTCC
*
37079 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATTTATAAC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATAAC
*
37144 ACAAGTGCAATTCTCTCTA
66 ACAAGGGCAATTCTCTCTA
* *
37163 AAAGTCCTCAAACGCATTTATAACACAGAGGCATCTATATTAAAGTCCCCAAACACAATTATAAC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATAAC
*
37228 ACAGGGGCAATTCTCTCTA
66 ACAAGGGCAATTCTCTCTA
37247 TGGCAAAGGC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (84 bp):
AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATAAC
ACAAGGGCAATTCTCTCTA
Found at i:37311 original size:2 final size:2
Alignment explanation
Indices: 37304--37399 Score: 165
Period size: 2 Copynumber: 46.5 Consensus size: 2
37294 ATTCCTAACT
37304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
37346 TA TA GTA TA GTA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
37389 TA TA TA TA TA T
1 TA TA TA TA TA T
37400 GTAGCAAAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 85 0.93
3 6 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41007 original size:21 final size:21
Alignment explanation
Indices: 40963--41008 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
40953 GTGAGGGAGG
* *
40963 AATGAGGTCGAGAGTGAGAGA
1 AATGAGGTCGAGAGTGAAAAA
*
40984 AATGAGGTCGAGGGTGAAAAA
1 AATGAGGTCGAGAGTGAAAAA
41005 AATG
1 AATG
41009 GCGAGGTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.39, T:0.15
Consensus pattern (21 bp):
AATGAGGTCGAGAGTGAAAAA
Found at i:55732 original size:43 final size:41
Alignment explanation
Indices: 55594--55872 Score: 269
Period size: 41 Copynumber: 6.6 Consensus size: 41
55584 CCAATAACTA
* * * *
55594 AAAGTCCCCAAACACATTTATAACATAGGGGCACCTCTCTTTCT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCA--TCT-ATTCC
* * * *
55638 AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCATCTATTCC
* * *
55679 AAAGTCCTCAACCACATTTATAATATAGGGGCACCTCTATTCC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCA--TCTATTCC
*
55722 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT-C
1 AAAGTCCTCAAACACATTTATAACACAGGGGCATCTAT-TCC
* *
55763 AAAGTCAC-CAAACACATTTATAACACAGGGGCAATTCT-CTCTA
1 AAAGTC-CTCAAACACATTTATAACACAGGGGC-A-TCTATTC-C
* *
55806 AAAGTCCTCAAACACATTTATAACAGAGAGGCATCTATAT-C
1 AAAGTCCTCAAACACATTTATAACACAGGGGCATCTAT-TCC
* *
55847 AAAGTCCACAAACACAATTATAACAC
1 AAAGTCCTCAAACACATTTATAACAC
55873 CTGGGCAATT
Statistics
Matches: 197, Mismatches: 27, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
41 94 0.48
42 7 0.04
43 66 0.34
44 30 0.15
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.24
Consensus pattern (41 bp):
AAAGTCCTCAAACACATTTATAACACAGGGGCATCTATTCC
Found at i:55753 original size:84 final size:82
Alignment explanation
Indices: 55594--55871 Score: 369
Period size: 84 Copynumber: 3.3 Consensus size: 82
55584 CCAATAACTA
*
55594 AAAGTCCCCAAACACATTTATAACATAGGGGCACCTCTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGT-CCCAAACACATTTATAACATAGGGGCA-C-CTCTTTCAAAAGTCCTCAAACACATTTAT
*
55659 AACACAGAGGCATCCATA-C
63 AACACAGAGGCATCTATATC
* * *
55678 TAAAGTCCTCAACCACATTTATAATATAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTAT
1 -AAAGTCC-CAAACACATTTATAACATAGGGGCACCTCT-TTCAAAAGTCCTCAAACACATTTAT
55743 AACACAGAGGCATCTATATC
63 AACACAGAGGCATCTATATC
* ** *
55763 AAAGTCACCAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAACACATTTATA
1 AAAGTC-CCAAACACATTTATAACATAGGGGCACCTCTTTC-AAAAGTCCTCAAACACATTTATA
*
55828 ACAGAGAGGCATCTATATC
64 ACACAGAGGCATCTATATC
*
55847 AAAGTCCACAAACACAATTATAACA
1 AAAGTCC-CAAACACATTTATAACA
55872 CCTGGGCAAT
Statistics
Matches: 174, Mismatches: 13, Indels: 13
0.87 0.06 0.06
Matches are distributed among these distances:
83 7 0.04
84 137 0.79
85 30 0.17
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (82 bp):
AAAGTCCCAAACACATTTATAACATAGGGGCACCTCTTTCAAAAGTCCTCAAACACATTTATAAC
ACAGAGGCATCTATATC
Done.