Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015154.1 Corchorus olitorius cultivar O-4 contig15187, 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: 85816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:634 original size:31 final size:31
Alignment explanation
Indices: 577--635 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
567 TCTAAGTGAT
*
577 AAACTAATAGGATTCATTTTCACCAAAAATA
1 AAACTAATAGGATTCATTTGCACCAAAAATA
*
608 AAACTAATGGGATTCATTGTGC-CCAAAA
1 AAACTAATAGGATTCATT-TGCACCAAAA
636 TCTAGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (31 bp):
AAACTAATAGGATTCATTTGCACCAAAAATA
Found at i:1247 original size:42 final size:40
Alignment explanation
Indices: 1188--1271 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 40
1178 TTTAATTCCG
1188 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
1228 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
1270 AT
1 AT
1272 TCTTAGGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 7 0.17
41 3 0.07
42 31 0.76
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:2370 original size:36 final size:36
Alignment explanation
Indices: 2323--2392 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
2313 GAGATTTTGG
*
2323 AGAAATATGATAATC-AAAATTACAAAAAATGTAATA
1 AGAAATATGATAA-CAAAAATCACAAAAAATGTAATA
*
2359 AGAAATATGATAACAAAAATCACAAAAGATGTAA
1 AGAAATATGATAACAAAAATCACAAAAAATGTAA
2393 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACAAAAATCACAAAAAATGTAATA
Found at i:4756 original size:58 final size:58
Alignment explanation
Indices: 4653--4762 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
4643 ATAGCATCAT
*
4653 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
* * *
4711 GCCTCGGTCCGGAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACT
1 GCCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACT
4763 TGATATTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 31 0.66
59 16 0.34
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
Found at i:19959 original size:17 final size:17
Alignment explanation
Indices: 19934--19988 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
19924 TTTCATTGCT
19934 TAATAACATATTAATTA
1 TAATAACATATTAATTA
*
19951 TAATTAC--ATT-A-TA
1 TAATAACATATTAATTA
19964 T-ATAACATATTAATTA
1 TAATAACATATTAATTA
*
19980 TAATCACAT
1 TAATAACAT
19989 TACATAGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
12 4 0.13
13 3 0.10
14 4 0.13
15 4 0.13
16 3 0.10
17 12 0.40
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAACATATTAATTA
Found at i:19981 original size:14 final size:14
Alignment explanation
Indices: 19936--19982 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
19926 TCATTGCTTA
19936 ATAACATATTAATT
1 ATAACATATTAATT
* *
19950 ATAATTACATT-ATAT
1 ATAA-CATATTAAT-T
19965 ATAACATATTAATT
1 ATAACATATTAATT
19979 ATAA
1 ATAA
19983 TCACATTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAACATATTAATT
Found at i:23743 original size:11 final size:11
Alignment explanation
Indices: 23729--23766 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23719 ATTCATAACA
23729 AATTTATAATT
1 AATTTATAATT
23740 AATTTATAATT
1 AATTTATAATT
23751 -ATTTGATAATT
1 AATTT-ATAATT
*
23762 TATTT
1 AATTT
23767 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:25829 original size:29 final size:29
Alignment explanation
Indices: 25796--25851 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
25786 TGAGATTTCA
*
25796 CTGGATTTGTTTGTTGGGGTAGGGGTTCC
1 CTGGATTTGTTTGTTGGGGAAGGGGTTCC
25825 CTGGATTTGTTTGTTGGGGAAGGGGTT
1 CTGGATTTGTTTGTTGGGGAAGGGGTT
25852 TGTTGGCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.09, C:0.07, G:0.43, T:0.41
Consensus pattern (29 bp):
CTGGATTTGTTTGTTGGGGAAGGGGTTCC
Found at i:27242 original size:5 final size:5
Alignment explanation
Indices: 27225--27261 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
27215 TGGAATCAGA
*
27225 TTCTT TTCCT TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
27262 TCAAGTATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:28792 original size:15 final size:17
Alignment explanation
Indices: 28772--28804 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
28762 TGCTTGGTGA
28772 TATGTTAT-GTT-ATGT
1 TATGTTATAGTTCATGT
28787 TATGTTATAGTTCATGT
1 TATGTTATAGTTCATGT
28804 T
1 T
28805 CCTGATTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (17 bp):
TATGTTATAGTTCATGT
Found at i:30287 original size:195 final size:191
Alignment explanation
Indices: 29883--30461 Score: 823
Period size: 195 Copynumber: 3.0 Consensus size: 191
29873 GGAACTCGAG
* * *
29883 AGACAGTAATTAAGTGACTACTGTTGAGTGTAATTAAGTTTGTAATGCTTGAAAATACAGCTCTG
1 AGACAGTAATTAAGTGACTACTGTTGAGTGTAATTAAGTTTGTAATGCTTGATAATACAACTGTG
** * *
29948 AATTGTGTTATTTTTAAATCAGGTTAATCTTTATGTGTATAATAAT-TAATTACTATATAGTGGC
66 AATTGTGTTATTTTTAAATCAGGAGAATCTTTATGTATATAATAATATAATTATTATATAGTGGC
* *
30012 ATTTACAATTGATGAGGACAAACCACTTCTCTTTACATTGACAATGTTGTTGTTCCAAATT
131 ATTTACAATTGATGAGGACTAATCACTTCTCTTTACATTGACAATGTTGTTGTTCCAAATT
* *
30073 AGACAGTAATTAAGTGACTACTGTTGAGTGTAATTAAGTTTTTAACGCTTGATAATACAACTGTG
1 AGACAGTAATTAAGTGACTACTGTTGAGTGTAATTAAGTTTGTAATGCTTGATAATACAACTGTG
* *
30138 AATTGTGTTATTTTTAAATAAGAAGAATCTTTATATGTATAATAATAATTATAATTATTATATAG
66 AATTGTGTTATTTTTAAATCAGGAGAATC-TT-TATGTAT-ATAATAA-TATAATTATTATATAG
* *
30203 TGGCATTTACAATTGATGAGGACTAATCACTTCTCTTTACATTGACAATGTTGTGGTTCAAAATT
127 TGGCATTTACAATTGATGAGGACTAATCACTTCTCTTTACATTGACAATGTTGTTGTTCCAAATT
*
30268 AGACAGTAATTAAGTGACTACTGTTGAGTATAATTAAGTTTGTAATGCTTGAAAGTTGAAAGTAC
1 AGACAGTAATTAAGTGACTACTGTTGAGTGTAATTAAGTTTGTAATGCTTG--A--T--AA-TAC
* *
30333 -AGTGTGAACTGTGTTATTTTTAAATCAGGAGAATCTTTA--TATAT-ATAA-AT--TTATTATA
59 AACTGTGAATTGTGTTATTTTTAAATCAGGAGAATCTTTATGTATATAATAATATAATTATTATA
* *
30391 TAGTGGCATTTGCAATTGATGAGGACTAATCACTTCTATTTACATTGACAATGTTGTTGTTCCAA
124 TAGTGGCATTTACAATTGATGAGGACTAATCACTTCTCTTTACATTGACAATGTTGTTGTTCCAA
30456 ATT
189 ATT
30459 AGA
1 AGA
30462 TACAACTAGC
Statistics
Matches: 351, Mismatches: 26, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
190 85 0.24
191 77 0.22
192 6 0.02
193 9 0.03
194 1 0.00
195 126 0.36
196 2 0.01
197 4 0.01
199 3 0.01
200 2 0.01
201 33 0.09
202 3 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (191 bp):
AGACAGTAATTAAGTGACTACTGTTGAGTGTAATTAAGTTTGTAATGCTTGATAATACAACTGTG
AATTGTGTTATTTTTAAATCAGGAGAATCTTTATGTATATAATAATATAATTATTATATAGTGGC
ATTTACAATTGATGAGGACTAATCACTTCTCTTTACATTGACAATGTTGTTGTTCCAAATT
Found at i:30979 original size:12 final size:12
Alignment explanation
Indices: 30962--30988 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30952 TCAAGCATAT
30962 ATTATTATAATA
1 ATTATTATAATA
30974 ATTATTATAATA
1 ATTATTATAATA
30986 ATT
1 ATT
30989 TATATGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTATTATAATA
Found at i:34400 original size:3 final size:3
Alignment explanation
Indices: 34394--34418 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34384 CCATTCTTCT
34394 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
34419 AATTGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:46782 original size:106 final size:104
Alignment explanation
Indices: 46611--46871 Score: 398
Period size: 106 Copynumber: 2.5 Consensus size: 104
46601 AGTTTAGCCT
*
46611 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
46676 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA--TATTGTTATAGGATTTTAGAAATAAAATACAAAAC
*
46718 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
46783 ATAATATTGTTATAGGATTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
* * ** *
46822 TAA-TTCACTAAATTTAACCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
46872 TAGAAAAATT
Statistics
Matches: 144, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 42 0.29
104 35 0.24
106 49 0.34
107 18 0.12
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
Found at i:49721 original size:27 final size:27
Alignment explanation
Indices: 49690--49742 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
49680 GAACAGAAGA
49690 TATGCCAATTAAGATTGGTTGAGTTGG
1 TATGCCAATTAAGATTGGTTGAGTTGG
49717 TATGCCAATTAAGATTGGTTGAGTTG
1 TATGCCAATTAAGATTGGTTGAGTTG
49743 ATAAGACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (27 bp):
TATGCCAATTAAGATTGGTTGAGTTGG
Found at i:49920 original size:53 final size:53
Alignment explanation
Indices: 49831--49938 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
49821 GCATACTCTG
* *
49831 ACCCTAGGCTGGGTCAGCCTCCTCCTCGCATAATAAACTTTTGCAAGCCAAGA
1 ACCCTAGACTAGGTCAGCCTCCTCCTCGCATAATAAACTTTTGCAAGCCAAGA
* *
49884 ACCCTAGACTAGGTCAGCCTCCTCCTGGCATGATAAACTTTTGCAAGCCAAGA
1 ACCCTAGACTAGGTCAGCCTCCTCCTCGCATAATAAACTTTTGCAAGCCAAGA
49937 AC
1 AC
49939 AGAAGATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (53 bp):
ACCCTAGACTAGGTCAGCCTCCTCCTCGCATAATAAACTTTTGCAAGCCAAGA
Found at i:52530 original size:3 final size:3
Alignment explanation
Indices: 52522--52556 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
52512 ATATTCACCG
*
52522 TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
52557 AGCTTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:58954 original size:101 final size:101
Alignment explanation
Indices: 58653--58955 Score: 561
Period size: 101 Copynumber: 3.0 Consensus size: 101
58643 GATGTATTGG
*
58653 ACGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTGAATAAAGAAAGAGAAAATAGTT
1 ACGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTAAATAAAGAAAGAGAAAATAGTT
* *
58718 AAGTATTGATAGAGCTTCTTTCATTTGGGATACAAC
66 AAGCATTGATAGAGCTTCTTTCATTTGGGATACAGC
58754 ACGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTAAATAAAGAAAGAGAAAATAGTT
1 ACGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTAAATAAAGAAAGAGAAAATAGTT
58819 AAGCATTGATAGAGCTTCTTTCATTTGGGATACAGC
66 AAGCATTGATAGAGCTTCTTTCATTTGGGATACAGC
* *
58855 ATGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTAAATAAATAAAGAGAAAATAGTT
1 ACGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTAAATAAAGAAAGAGAAAATAGTT
58920 AAGCATTGATAGAGCTTCTTTCATTTGGGATACAGC
66 AAGCATTGATAGAGCTTCTTTCATTTGGGATACAGC
58956 GACTCAATTC
Statistics
Matches: 197, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 197 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (101 bp):
ACGTAGATTATTCTTAAACAAGATCTGGGATTCGAATTTTGTAAATAAAGAAAGAGAAAATAGTT
AAGCATTGATAGAGCTTCTTTCATTTGGGATACAGC
Found at i:60944 original size:30 final size:31
Alignment explanation
Indices: 60910--60969 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
60900 ACTTCGCCCA
* *
60910 CTTCCACTTCCACTTCT-CCCCCGCACGTGC
1 CTTCCACCTCCACCTCTCCCCCCGCACGTGC
* *
60940 CTTCCTCCTCCTCCTCTCCCCCCGCACGTG
1 CTTCCACCTCCACCTCTCCCCCCGCACGTG
60970 TGAGTTTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.07, C:0.57, G:0.10, T:0.27
Consensus pattern (31 bp):
CTTCCACCTCCACCTCTCCCCCCGCACGTGC
Found at i:65273 original size:6 final size:6
Alignment explanation
Indices: 65262--65291 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
65252 CAAACAGTAG
65262 TAGGAT TAGGAT TAGGAT TAGGAT TAGGAT
1 TAGGAT TAGGAT TAGGAT TAGGAT TAGGAT
65292 ATAAGGATAC
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TAGGAT
Found at i:72812 original size:18 final size:19
Alignment explanation
Indices: 72789--72831 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
72779 TGAAATTATG
* *
72789 AAAATTGTAAA-TGTAAAT
1 AAAATTATAAAGTATAAAT
72807 AAAATTATAAAGTATAAAT
1 AAAATTATAAAGTATAAAT
*
72826 GAAATT
1 AAAATT
72832 TATTTACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAGTATAAAT
Found at i:77752 original size:9 final size:8
Alignment explanation
Indices: 77738--77762 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
77728 TGCACCTTTT
77738 AAAAAAAG
1 AAAAAAAG
77746 AAAAAAAG
1 AAAAAAAG
77754 AAAAAAAG
1 AAAAAAAG
77762 A
1 A
77763 CATCTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:80503 original size:119 final size:119
Alignment explanation
Indices: 80290--80520 Score: 311
Period size: 119 Copynumber: 1.9 Consensus size: 119
80280 TCATGCTAAA
* * * * * * *
80290 ACAGGGCTATATACATACAGTAGAAATTTATCACCAGTGTAACCATCTAAATACTAAGCTGGTTC
1 ACAGGGCTAAATACAAACAGTAGAAATTAACCACCAGTCTAACCATCTAAATACTAAGCTAGCTC
* * *
80355 AATAATGAAGGCTGATCTTTTCACTAAATCTACACTTACTTTCTCTTAAGTGAT
66 AAGAATGAAGGCTGATCTTTTCACAAAATCTACACTTAATTTCTCTTAAGTGAT
* * * *
80409 ACAGGGCTAAATACAAACAGTAGAAGTTAACCACTAGTCTAACCATCTAAATATTATG-TCAGCT
1 ACAGGGCTAAATACAAACAGTAGAAATTAACCACCAGTCTAACCATCTAAATACTAAGCT-AGCT
*
80473 CAAGAATGAAGGCTGATCTTTTGACAAAATCTACACTTAATTTCTCTT
65 CAAGAATGAAGGCTGATCTTTTCACAAAATCTACACTTAATTTCTCTT
80521 CAGCATAGGA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
118 1 0.01
119 95 0.99
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (119 bp):
ACAGGGCTAAATACAAACAGTAGAAATTAACCACCAGTCTAACCATCTAAATACTAAGCTAGCTC
AAGAATGAAGGCTGATCTTTTCACAAAATCTACACTTAATTTCTCTTAAGTGAT
Found at i:84709 original size:13 final size:13
Alignment explanation
Indices: 84691--84824 Score: 128
Period size: 13 Copynumber: 10.3 Consensus size: 13
84681 ATAAAAATAG
84691 AACTGATTTCAGA
1 AACTGATTTCAGA
**
84704 AACTGAAATCAG-
1 AACTGATTTCAGA
84716 -ACTGATTTCAGA
1 AACTGATTTCAGA
* * *
84728 ATCTAATTTCGGA
1 AACTGATTTCAGA
**
84741 AATTCTGAAATCAGA
1 AA--CTGATTTCAGA
*
84756 ATCTGATTTCAGA
1 AACTGATTTCAGA
*
84769 ATCTGATTTCAGA
1 AACTGATTTCAGA
84782 AACTGATTTCAGA
1 AACTGATTTCAGA
*
84795 ATCTGATTTCAGA
1 AACTGATTTCAGA
**
84808 AACTGAAATCAGA
1 AACTGATTTCAGA
84821 AACT
1 AACT
84825 ACAAACGACA
Statistics
Matches: 97, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.09
13 80 0.82
15 8 0.08
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (13 bp):
AACTGATTTCAGA
Found at i:84749 original size:39 final size:39
Alignment explanation
Indices: 84696--84808 Score: 158
Period size: 39 Copynumber: 2.9 Consensus size: 39
84686 AATAGAACTG
84696 ATTTCAGAAACTGAAATCAG-A-CTGATTTCAGAATCTA
1 ATTTCAGAAACTGAAATCAGAATCTGATTTCAGAATCTA
* *
84733 ATTTCGGAAATTCTGAAATCAGAATCTGATTTCAGAATCTG
1 ATTTCAGAAA--CTGAAATCAGAATCTGATTTCAGAATCTA
**
84774 ATTTCAGAAACTGATTTCAGAATCTGATTTCAGAA
1 ATTTCAGAAACTGAAATCAGAATCTGATTTCAGAA
84809 ACTGAAATCA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
37 9 0.13
39 33 0.49
40 1 0.01
41 24 0.36
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (39 bp):
ATTTCAGAAACTGAAATCAGAATCTGATTTCAGAATCTA
Done.