Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020398.1 Corchorus olitorius cultivar O-4 contig20431, 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: 93716
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2713 original size:94 final size:94
Alignment explanation
Indices: 2573--2760 Score: 360
Period size: 94 Copynumber: 2.0 Consensus size: 94
2563 ATTGCAATGC
2573 TATAAGATCACCATCATTTAAAAAAAAACTTATTTTAGATGGATGAAAATTTAATAAGGGGTATT
1 TATAAGATCACCATCATTTAAAAAAAAACTTATTTTAGATGGATGAAAATTTAATAAGGGGTATT
2638 TTTTA-ATTAAAGAAAAAGAAACAAAAAA
66 TTTTAGATTAAAGAAAAAGAAACAAAAAA
2666 TATAAGATCACCATCATTTAAAAAAAAAACTTATTTTAGATGGATGAAAATTTAATAAGGGGTAT
1 TATAAGATCACCATCATTT-AAAAAAAAACTTATTTTAGATGGATGAAAATTTAATAAGGGGTAT
2731 TTTTTAGATTAAAGAAAAAGAAACAAAAAA
65 TTTTTAGATTAAAGAAAAAGAAACAAAAAA
2761 GAGAGTATAT
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
93 19 0.20
94 51 0.55
95 23 0.25
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (94 bp):
TATAAGATCACCATCATTTAAAAAAAAACTTATTTTAGATGGATGAAAATTTAATAAGGGGTATT
TTTTAGATTAAAGAAAAAGAAACAAAAAA
Found at i:3223 original size:90 final size:89
Alignment explanation
Indices: 3116--3293 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 89
3106 ACACATGAAT
**
3116 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTTCAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
3181 AATATTTAAAAATTAAAAAGGACAC
66 AATATTT-AAAATTAAAAAGGACAC
* *
3206 ATGATATATAATTCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
*
3271 AATATTTAAAATTAAAAATGACA
66 AATATTTAAAATTAAAAAGGACA
3294 TTTTAGATAT
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 15 0.18
90 68 0.82
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (89 bp):
ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
AATATTTAAAATTAAAAAGGACAC
Found at i:6184 original size:40 final size:41
Alignment explanation
Indices: 6129--6206 Score: 140
Period size: 40 Copynumber: 1.9 Consensus size: 41
6119 ACTCTCACGG
6129 AATGTGAGTTTGTTTGTAATTTG-TTGTTTATATGGTAAGA
1 AATGTGAGTTTGTTTGTAATTTGTTTGTTTATATGGTAAGA
*
6169 AATGTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTA
1 AATGTGAGTTTGTTTGTAATTTGTTTGTTTATATGGTA
6207 GGTAGGTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 23 0.64
41 13 0.36
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (41 bp):
AATGTGAGTTTGTTTGTAATTTGTTTGTTTATATGGTAAGA
Found at i:6935 original size:21 final size:22
Alignment explanation
Indices: 6903--6948 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
6893 AATAATCATA
*
6903 TAAAATAATAATAACTAATTTT
1 TAAAATAATAATAACTAATTAT
6925 TAAAA-AATAATAACTAATTAT
1 TAAAATAATAATAACTAATTAT
6946 TAA
1 TAA
6949 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAATAATAACTAATTAT
Found at i:10790 original size:2 final size:2
Alignment explanation
Indices: 10783--10819 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10773 CAAGGCATGA
*
10783 AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
10820 AGTCTACTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22894 original size:2 final size:2
Alignment explanation
Indices: 22887--22924 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
22877 GTTATCACTA
22887 AT AT AT AT 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
22925 TGGCATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24566 original size:174 final size:174
Alignment explanation
Indices: 24276--24624 Score: 619
Period size: 174 Copynumber: 2.0 Consensus size: 174
24266 TATTTAAAAA
* * *
24276 ATATCATTTATTAACCCGCATTGACACGATTGACCCGATGGTTAAACCGATTGATCCGTGACCCG
1 ATATCATTTATTAACCCGCATTGACACGATTGACCCGACGGTTAAACCGATTGACCCGTAACCCG
* *
24341 AAACCTCAAACGGGTCGCTCTCCGAATCGGGTTTAATAACTACGGTCGCATCATACTCTAATTAG
66 AAACCTCAAACGGATCACTCTCCGAATCGGGTTTAATAACTACGGTCGCATCATACTCTAATTAG
24406 AAGAAATTTCACCTAATACATATTTTCTCTATTTACGAGATTCG
131 AAGAAATTTCACCTAATACATATTTTCTCTATTTACGAGATTCG
24450 ATATCATTTATTAACCCGCATTGACACGATTGACCCGACGGTTAAACCGATTGACCCGTAACCCG
1 ATATCATTTATTAACCCGCATTGACACGATTGACCCGACGGTTAAACCGATTGACCCGTAACCCG
* *
24515 AAACCTCAAATGGATCACTCTCC-AGATCGGGTTTAATAACTATGGTCGCATCATACTCTAATTA
66 AAACCTCAAACGGATCACTCTCCGA-ATCGGGTTTAATAACTACGGTCGCATCATACTCTAATTA
24579 GAAGAAATTTCACCTAATACATATTTTCTCTATTTACGAGATTCG
130 GAAGAAATTTCACCTAATACATATTTTCTCTATTTACGAGATTCG
24624 A
1 A
24625 ACTGAACATT
Statistics
Matches: 167, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
173 1 0.01
174 166 0.99
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ATATCATTTATTAACCCGCATTGACACGATTGACCCGACGGTTAAACCGATTGACCCGTAACCCG
AAACCTCAAACGGATCACTCTCCGAATCGGGTTTAATAACTACGGTCGCATCATACTCTAATTAG
AAGAAATTTCACCTAATACATATTTTCTCTATTTACGAGATTCG
Found at i:29070 original size:29 final size:29
Alignment explanation
Indices: 29028--29083 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
29018 GCCAATTACA
29028 TAGAATTTGAATCCTAGTCCTAACTGAAG
1 TAGAATTTGAATCCTAGTCCTAACTGAAG
29057 TAGAATTTGAATCCTAGTCCTAACTGA
1 TAGAATTTGAATCCTAGTCCTAACTGA
29084 TAAGCAAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (29 bp):
TAGAATTTGAATCCTAGTCCTAACTGAAG
Found at i:31056 original size:128 final size:128
Alignment explanation
Indices: 30890--31148 Score: 446
Period size: 128 Copynumber: 2.0 Consensus size: 128
30880 TAATCATCCA
* *
30890 GGGGCGTGCAATTGTGGAGTACTGGGCCCTTGCACTCCACGGGTTAAGTCTTGGATGACCGGTAA
1 GGGGCGTGCAATTGTGGAGTACTGGGCCCTCGCACTCCACGGATTAAGTCTTGGATGACCGGTAA
*
30955 TTGGCTTGAGACTTGACGAGTTGGGCCGCACGGGGTAGAGATGAGGACTCACAAGTGAATCGG
66 TTGGCTTGAGACTTGACGAGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGAATCGG
* *
31018 GGGGCGTGCAATTGTGGAGTATTGGGCCCTCGCACTCCATGGATTAAGTCTTGGATGACCGGTAA
1 GGGGCGTGCAATTGTGGAGTACTGGGCCCTCGCACTCCACGGATTAAGTCTTGGATGACCGGTAA
* * *
31083 TTGGCTTGAGATTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGCATCGG
66 TTGGCTTGAGACTTGACGAGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGAATCGG
31146 GGG
1 GGG
31149 AGATTGTTAA
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.23
Consensus pattern (128 bp):
GGGGCGTGCAATTGTGGAGTACTGGGCCCTCGCACTCCACGGATTAAGTCTTGGATGACCGGTAA
TTGGCTTGAGACTTGACGAGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGAATCGG
Found at i:31328 original size:49 final size:49
Alignment explanation
Indices: 31256--31355 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
31246 AGTCTAGGCT
31256 TTTGGGTTCAGGTTGGTGTCCGACATGTATATGGGCTGTTCAGTGGGTC
1 TTTGGGTTCAGGTTGGTGTCCGACATGTATATGGGCTGTTCAGTGGGTC
*
31305 TTTGGGTTCAGGTTGGTGTCCGACATGTATATGGGCTGTTCGGTGGGTC
1 TTTGGGTTCAGGTTGGTGTCCGACATGTATATGGGCTGTTCAGTGGGTC
31354 TT
1 TT
31356 GCTGAAGCAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.11, C:0.14, G:0.37, T:0.38
Consensus pattern (49 bp):
TTTGGGTTCAGGTTGGTGTCCGACATGTATATGGGCTGTTCAGTGGGTC
Found at i:36208 original size:31 final size:31
Alignment explanation
Indices: 36165--36263 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
36155 AATTTTTTAA
*
36165 TTTGATTGAATTAGGGTCCAACATTTCAAAT
1 TTTGATTCAATTAGGGTCCAACATTTCAAAT
* * *
36196 TTTGATTCAATTA-AGT---TC-TTT-TAA-
1 TTTGATTCAATTAGGGTCCAACATTTCAAAT
* *
36220 TTTGATTGAATCAGGGTCCAACATTTCAAAT
1 TTTGATTCAATTAGGGTCCAACATTTCAAAT
36251 TTTGATTCAATTA
1 TTTGATTCAATTA
36264 AGTACTTGGC
Statistics
Matches: 50, Mismatches: 11, Indels: 14
0.67 0.15 0.19
Matches are distributed among these distances:
24 11 0.22
25 4 0.08
26 3 0.06
27 1 0.02
28 1 0.02
29 3 0.06
30 4 0.08
31 23 0.46
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTGATTCAATTAGGGTCCAACATTTCAAAT
Found at i:36243 original size:55 final size:55
Alignment explanation
Indices: 36159--36266 Score: 207
Period size: 55 Copynumber: 2.0 Consensus size: 55
36149 GGATCCAATT
*
36159 TTTTAATTTGATTGAATTAGGGTCCAACATTTCAAATTTTGATTCAATTAAGTTC
1 TTTTAATTTGATTGAATCAGGGTCCAACATTTCAAATTTTGATTCAATTAAGTTC
36214 TTTTAATTTGATTGAATCAGGGTCCAACATTTCAAATTTTGATTCAATTAAGT
1 TTTTAATTTGATTGAATCAGGGTCCAACATTTCAAATTTTGATTCAATTAAGT
36267 ACTTGGCGTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (55 bp):
TTTTAATTTGATTGAATCAGGGTCCAACATTTCAAATTTTGATTCAATTAAGTTC
Found at i:40624 original size:19 final size:19
Alignment explanation
Indices: 40604--40640 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40594 AATTAATTAT
40604 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
40622 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
40641 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:40651 original size:19 final size:19
Alignment explanation
Indices: 40610--40651 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40600 TTATTTTAAT
* * *
40610 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
40629 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
40648 ATTA
1 ATTA
40652 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:41791 original size:35 final size:35
Alignment explanation
Indices: 41745--41817 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
41735 TTTTCAAACC
41745 TTTCATGTCCATATGAAGAAAAGAGTAAACTTAGT
1 TTTCATGTCCATATGAAGAAAAGAGTAAACTTAGT
** *
41780 TTTCATGTCCATATGAAGAAGTGAGTAAATTTAGT
1 TTTCATGTCCATATGAAGAAAAGAGTAAACTTAGT
41815 TTT
1 TTT
41818 TGTTTAAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (35 bp):
TTTCATGTCCATATGAAGAAAAGAGTAAACTTAGT
Found at i:42788 original size:17 final size:17
Alignment explanation
Indices: 42766--42798 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42756 AGTTGTAATT
42766 TTTCTTTTTCCATCTTC
1 TTTCTTTTTCCATCTTC
42783 TTTCTTTTTCCATCTT
1 TTTCTTTTTCCATCTT
42799 ACCAAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTCTTTTTCCATCTTC
Found at i:50981 original size:33 final size:33
Alignment explanation
Indices: 50944--51010 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
50934 GAAATTGGTC
50944 GGGTTGGTACTAACTAGAATTAGAAACAGGGAA
1 GGGTTGGTACTAACTAGAATTAGAAACAGGGAA
50977 GGGTTGGTACTAACTAGAATTAGAAACAGGGAA
1 GGGTTGGTACTAACTAGAATTAGAAACAGGGAA
51010 G
1 G
51011 AAGGGAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.31, T:0.21
Consensus pattern (33 bp):
GGGTTGGTACTAACTAGAATTAGAAACAGGGAA
Found at i:55085 original size:33 final size:33
Alignment explanation
Indices: 55017--55104 Score: 115
Period size: 33 Copynumber: 2.5 Consensus size: 33
55007 TCTACCAATC
55017 AACTATTAATATAGTCTTTTGACCCTAAAAAAAAAAA
1 AACTATTAATATAGTC---T-ACCCTAAAAAAAAAAA
55054 AACTATTAATATAGTCTA-CCTGAAAAAAAAAAA
1 AACTATTAATATAGTCTACCCT-AAAAAAAAAAA
*
55087 ACCTATTAATATAGTCTA
1 AACTATTAATATAGTCTA
55105 GTTTTAATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
32 3 0.06
33 29 0.59
34 1 0.02
37 16 0.33
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.30
Consensus pattern (33 bp):
AACTATTAATATAGTCTACCCTAAAAAAAAAAA
Found at i:65593 original size:29 final size:29
Alignment explanation
Indices: 65560--65630 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
65550 ACTTGTAGCG
65560 TTTGGACGTTTTA-CCACATGAACTTCAAT
1 TTTGGACGTTTTATCC-CATGAACTTCAAT
* *
65589 TTTGGACATTTTATCCCCTGAACTTCAAT
1 TTTGGACGTTTTATCCCATGAACTTCAAT
*
65618 TTTGAAACGTTTT
1 TTTG-GACGTTTT
65631 GCCCCTCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 28 0.78
30 8 0.22
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (29 bp):
TTTGGACGTTTTATCCCATGAACTTCAAT
Found at i:65635 original size:29 final size:29
Alignment explanation
Indices: 65578--65636 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
65568 TTTTACCACA
* *
65578 TGAACTTCAATTTTGGACATTTTATCCCC
1 TGAACTTCAATTTTGAACATTTTAGCCCC
*
65607 TGAACTTCAATTTTGAAACGTTTT-GCCCC
1 TGAACTTCAATTTTG-AACATTTTAGCCCC
65636 T
1 T
65637 CAACATAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (29 bp):
TGAACTTCAATTTTGAACATTTTAGCCCC
Found at i:66505 original size:19 final size:20
Alignment explanation
Indices: 66460--66518 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
66450 GTATCCATCC
66460 TAAAAAAAAATGGGATTATGG
1 TAAAAAAAAATGGGATTAT-G
*
66481 CCAAAAAAAAATGGGATTAT-
1 -TAAAAAAAAATGGGATTATG
**
66501 TAAAATTAAATGGGATTA
1 TAAAAAAAAATGGGATTA
66519 CTAATCTTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.45
22 18 0.55
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (20 bp):
TAAAAAAAAATGGGATTATG
Found at i:67557 original size:31 final size:31
Alignment explanation
Indices: 67497--67585 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 31
67487 CTTTCCATCA
67497 GGGGTAAAATGTCTTGAATTTGGGAAGTTTAT
1 GGGGTAAAATGTCTTGAATTT-GGAAGTTTAT
67529 GGGGTAAAATG-CTGTGAATTTGGAAGTTTAT
1 GGGGTAAAATGTCT-TGAATTTGGAAGTTTAT
*
67560 GAGGTAAAATGTCTTG-ATTT-GAAGTT
1 GGGGTAAAATGTCTTGAATTTGGAAGTT
67586 CAAATGACAA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.11
30 4 0.07
31 24 0.44
32 20 0.37
ACGTcount: A:0.29, C:0.03, G:0.30, T:0.37
Consensus pattern (31 bp):
GGGGTAAAATGTCTTGAATTTGGAAGTTTAT
Found at i:84021 original size:332 final size:331
Alignment explanation
Indices: 83275--84053 Score: 968
Period size: 334 Copynumber: 2.3 Consensus size: 331
83265 TTCATGATTT
* *
83275 TAATATCGTTTTTCATATTTTTTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATAC
1 TAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCT-ATTAAATCGAAA-TAGATTCAGATAC
* * * *
83339 ACATAAAAACAAAT-CTCTAAATCCAATGTGGTTGAGATTTGATTAGATAAATAAAGATATTTCA
64 TCAT-AAAACAAATCCT-TAAAT-CAATGTGGCTGAGATTTGGTTAGATGAATAAAGATATTTCA
* * *
83403 AGGAGTCTCGGCACAAAAAATCATGCAAAACAGAGCCGTGACCCTGTAACGCATTTTTAGCCAAA
126 AGGAGTCTCGACACAAAAAATCATGCAAAACAGAGCCGTGACCCGGAAACGCATTTTTAGCCAAA
* *
83468 AACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTTACCCGAAAGATATTTTC
191 AACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATATTTTC
* * * * * * *
83533 TCAATTTTTGGCTAAAATACTCATAAAAATATATAATTCGATATAAAAAAGATTGAAGGGCTTTT
256 TCAATTTTTAGCGAAAATACTCATAAAAATAAATAATTCAACATAAAAAAGATTGAAAGCCTTTT
83598 ATTAACGCTTC
321 ATTAACGCTTC
* * *
83609 TAATATTGTTTTTCCTATTTTTTTCTGAATTACTTTCTACTTAAATCGAAATCAGATTCAGATGC
1 TAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTA-TTAAATCGAAAT-AGATTCAGATAC
*
83674 TCATAAAAAAAATCCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAA-ATATTTCAA
64 TCATAAAACAAATCCTTAAATC-AATGTGGCTGAGATTTGGTTAGATGAATA-AAGATATTTCAA
* * * * * *
83738 TGAGTCTTGACACCAAAAATCATGCAAAACTGAGCCG-GATCCGGAAACGCATTTTTAGCCGAAA
127 GGAGTCTCGACACAAAAAATCATGCAAAACAGAGCCGTGACCCGGAAACGCATTTTTAGCCAAAA
*
83802 ACCGTGATGGTTAGTACACGATTTCAGCT-AAATTTTGCAAAAATTGACCCGAAAGAT-TTTTC-
192 ACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATATTTTCT
* *
83864 CGCATTTTCTAGCGAAAATACTCA-AAAAATAAATAATTCAACGTCAAAAAA-ATTGAAAGCCTT
257 C-AATTTT-TAGCGAAAATACTCATAAAAATAAATAATTCAACAT-AAAAAAGATTGAAAGCCTT
*
83927 TT-TTCACGCTTC
319 TTATTAACGCTTC
** * *
83939 TAATATCGTTTTTCCTATTTTATTTCAAAATTAATTTTTGATTAAATCGAAATAGGATTTC-GAA
1 TAATATCGTTTTTCCTATTTT-TTTCTGAATTAATTTCT-ATTAAATCGAAATA-GA-TTCAGAT
* * *
84003 ACTCGTACAAACAAATCCTTAAATACAACGTCGCTGAGATTTGGTTAGATG
62 ACTCATA-AAACAAATCCTTAAAT-CAATGTGGCTGAGATTTGGTTAGATG
84054 TGTGTGTGTG
Statistics
Matches: 387, Mismatches: 43, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
330 31 0.08
331 72 0.19
332 87 0.22
333 53 0.14
334 103 0.27
335 41 0.11
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (331 bp):
TAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCTATTAAATCGAAATAGATTCAGATACTC
ATAAAACAAATCCTTAAATCAATGTGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAG
TCTCGACACAAAAAATCATGCAAAACAGAGCCGTGACCCGGAAACGCATTTTTAGCCAAAAACCG
TGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATATTTTCTCAAT
TTTTAGCGAAAATACTCATAAAAATAAATAATTCAACATAAAAAAGATTGAAAGCCTTTTATTAA
CGCTTC
Found at i:84059 original size:2 final size:2
Alignment explanation
Indices: 84052--84134 Score: 82
Period size: 2 Copynumber: 40.5 Consensus size: 2
84042 TTTGGTTAGA
84052 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TCG CTG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T-G -TG
* *
84095 AG ATT TG -G T- TAG ATG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG -TG TG TG TG T-G -TG TG TG TG TG TG TG TG TG TG TG TG TG T
84135 TAAGGAGTCT
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
1 3 0.04
2 62 0.90
3 2 0.03
4 2 0.03
ACGTcount: A:0.05, C:0.02, G:0.45, T:0.48
Consensus pattern (2 bp):
TG
Found at i:92219 original size:17 final size:16
Alignment explanation
Indices: 92165--92215 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
92155 GATCACCCCC
*
92165 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
92182 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
92199 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
92215 A
1 A
92216 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Done.