Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010162.1 Corchorus capsularis cultivar CVL-1 contig10183, 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: 72068
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3008 original size:11 final size:11
Alignment explanation
Indices: 2992--3027 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2982 ATTTATTCAT
2992 TATTAATTA-A
1 TATTAATTAGA
3002 CTATTAATTAGA
1 -TATTAATTAGA
3014 TATTAATTAGA
1 TATTAATTAGA
3025 TAT
1 TAT
3028 AGTATAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:3177 original size:2 final size:2
Alignment explanation
Indices: 3162--3195 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3152 GACAAAAATA
3162 AT AT AT A- AT A- 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
3196 TTTTTTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4051 original size:31 final size:31
Alignment explanation
Indices: 4010--4092 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
4000 TAAAAATGAC
4010 CAATTTAGTCCATCTTCTTACAGGTTTGGAT
1 CAATTTAGTCCATCTTCTTACAGGTTTGGAT
* * * *
4041 CAATTGAGTCCGTCTACTTATAGGTTTGGAT
1 CAATTTAGTCCATCTTCTTACAGGTTTGGAT
*
4072 CAATTTAGTCCCTCTTCTTAC
1 CAATTTAGTCCATCTTCTTAC
4093 GAAATTGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (31 bp):
CAATTTAGTCCATCTTCTTACAGGTTTGGAT
Found at i:8622 original size:156 final size:157
Alignment explanation
Indices: 8236--8622 Score: 403
Period size: 156 Copynumber: 2.5 Consensus size: 157
8226 CATCTAGGTG
* ** * * *
8236 AAATTTCATCTCAAACAGACTTAGCATAAAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGCTT
1 AAATTTCAGCTCATTCAGACTTAGAAT-GAAAAACTTATGCTAGTTTTTCATTTAAGGACAGCTT
* * * * * * *
8301 GAGAAGACAAACCAACTTCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCCT
65 GAGGAGAGAAACCAACATCACTATCCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCCT
8366 TATGGGGATAATCTAAGTCTACTGGTGGA
130 TATGGGGATAATCTAAGTCTACT-GTGGA
** * * *
8395 AAA-TT-AGCCTGGTT-GGACTTAGAATGAAAACCTTATGCTAGTTTTTCATTTAAGGACCA-CC
1 AAATTTCAG-CTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGA-CAGCT
* * * *
8456 TGGGGAGAGAAACCTAGATCACTA-CCAAGGGAAGCTCGGTTTTACTTAGAAATTTTT-CCATAG
64 TGAGGAGAGAAACCAACATCACTATCCAAGAG-AGCTCGGTTTTACTTAG-AATTTTTCCCATAG
* * * *
8519 TCTTATGTGGATATTCTAAGTC-CCT-TGGAA
127 CCTTATGGGGATAATCTAAGTCTACTGTGG-A
*
8549 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGCTTG
*
8614 AGGTGAGAA
66 AGGAGAGAA
8623 GCTCGGTTTA
Statistics
Matches: 185, Mismatches: 34, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 14 0.08
156 138 0.75
157 19 0.10
158 4 0.02
159 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (157 bp):
AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGCTTG
AGGAGAGAAACCAACATCACTATCCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCCTT
ATGGGGATAATCTAAGTCTACTGTGGA
Found at i:13033 original size:3 final size:3
Alignment explanation
Indices: 13025--13069 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
13015 CAAAATATTG
13025 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13070 ATATAATGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15189 original size:20 final size:20
Alignment explanation
Indices: 15164--15212 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
15154 TGTTTTTATA
15164 CATTTTTCACTTTTATAATT
1 CATTTTTCACTTTTATAATT
15184 CATTTTTCACTTTTATAATT
1 CATTTTTCACTTTTATAATT
15204 CATTTTTCA
1 CATTTTTCA
15213 ATTATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.59
Consensus pattern (20 bp):
CATTTTTCACTTTTATAATT
Found at i:15244 original size:20 final size:20
Alignment explanation
Indices: 15165--15244 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
15155 GTTTTTATAC
*
15165 ATTTTTCACTTTTATAATTC
1 ATTTTTCACTTTTATAATTA
*
15185 ATTTTTCACTTTTATAATTC
1 ATTTTTCACTTTTATAATTA
*
15205 ATTTTTCA--ATTAT-A--A
1 ATTTTTCACTTTTATAATTA
* *
15220 ATTTTTCACTTTTAGAATGA
1 ATTTTTCACTTTTATAATTA
15240 ATTTT
1 ATTTT
15245 AGAATGAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 8 0.16
17 4 0.08
18 5 0.10
20 34 0.67
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (20 bp):
ATTTTTCACTTTTATAATTA
Found at i:15246 original size:12 final size:12
Alignment explanation
Indices: 15229--15255 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15219 AATTTTTCAC
15229 TTTTAGAATGAA
1 TTTTAGAATGAA
15241 TTTTAGAATGAA
1 TTTTAGAATGAA
15253 TTT
1 TTT
15256 ATTAGCTTGA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
TTTTAGAATGAA
Found at i:16842 original size:13 final size:14
Alignment explanation
Indices: 16824--16852 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16814 GCTCATAAGA
16824 TTGTA-TTTTGAAT
1 TTGTATTTTTGAAT
16837 TTGTATTTTTGAAT
1 TTGTATTTTTGAAT
16851 TT
1 TT
16853 CCTGTAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TTGTATTTTTGAAT
Found at i:19184 original size:25 final size:28
Alignment explanation
Indices: 19114--19184 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 28
19104 AAAAATTCTG
*
19114 ATTAATTAATATATACTTATAAATTATTCA
1 ATTATTTAAT-TATA-TTATAAATTATTCA
*
19144 ATT-TTT-ATTAT-GTATAAA-TA-T-A
1 ATTATTTAATTATATTATAAATTATTCA
19166 ATTATTTAATTATATTATA
1 ATTATTTAATTATATTATA
19185 TTATTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
22 4 0.11
23 4 0.11
24 7 0.20
25 10 0.29
27 3 0.09
28 2 0.06
29 2 0.06
30 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (28 bp):
ATTATTTAATTATATTATAAATTATTCA
Found at i:24005 original size:3 final size:3
Alignment explanation
Indices: 23993--24021 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
23983 CTTTTCCTTC
23993 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24022 CTTTTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:26240 original size:1 final size:1
Alignment explanation
Indices: 26234--26264 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
26224 ACATAGTGAG
26234 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26265 GCCACCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:41016 original size:17 final size:18
Alignment explanation
Indices: 40994--41027 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40984 TCTCCTTTCC
40994 TAAATAA-AATAAATTAT
1 TAAATAATAATAAATTAT
*
41011 TAAATAATTATAAATTA
1 TAAATAATAATAAATTA
41028 ATTATAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATAATAATAAATTAT
Found at i:41043 original size:11 final size:11
Alignment explanation
Indices: 41000--41037 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40990 TTCCTAAATA
*
41000 AAATAAATTATT
1 AAATTAATTA-T
41012 AAA-TAATTAT
1 AAATTAATTAT
41022 AAATTAATTAT
1 AAATTAATTAT
41033 AAATT
1 AAATT
41038 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.71
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:50729 original size:21 final size:21
Alignment explanation
Indices: 50703--50742 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50693 ATGAAAGATC
50703 TGGTTTGAGCTAAACTAAAAT
1 TGGTTTGAGCTAAACTAAAAT
* *
50724 TGGTTTGGGCTAAATTAAA
1 TGGTTTGAGCTAAACTAAA
50743 TTAGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (21 bp):
TGGTTTGAGCTAAACTAAAAT
Found at i:51939 original size:15 final size:16
Alignment explanation
Indices: 51907--51940 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
51897 AAAGAATAAT
*
51907 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
51923 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
51938 TAA
1 TAA
51941 GACAACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:53254 original size:19 final size:18
Alignment explanation
Indices: 53221--53256 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53211 TTGAAATAAT
53221 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
53239 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
53257 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:53458 original size:20 final size:21
Alignment explanation
Indices: 53420--53458 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53410 TAGAAAATAA
*
53420 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
53441 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
53459 ATAGCTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:54418 original size:14 final size:14
Alignment explanation
Indices: 54399--54433 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
54389 AGGGATGCAT
*
54399 ATGGGTAGTAGCTA
1 ATGGGTAATAGCTA
54413 ATGGGTAATAGCTA
1 ATGGGTAATAGCTA
54427 ATCGGGT
1 AT-GGGT
54434 TAGGGTACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (14 bp):
ATGGGTAATAGCTA
Found at i:58889 original size:85 final size:87
Alignment explanation
Indices: 58755--58983 Score: 356
Period size: 85 Copynumber: 2.7 Consensus size: 87
58745 AAATTGTTAA
58755 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAG-A
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAA
58819 AATAAATAAATAATAAA-AT-T
66 AATAAATAAATAATAAAGATGT
* * * * * * *
58839 GAATAGTAATCAGAATATTTTCTAAATCATGCCAAATTGTGGAAGGTTTAGGAGATATTTTAGGA
1 -AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGA
*
58904 AAATAAATAAATTATAAAGATGT
65 AAATAAATAAATAATAAAGATGT
58927 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
58984 CAAAAAGGAA
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
85 56 0.44
86 17 0.13
87 53 0.42
88 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (87 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAA
AATAAATAAATAATAAAGATGT
Found at i:62472 original size:18 final size:15
Alignment explanation
Indices: 62443--62489 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 15
62433 GATTCCCATC
62443 AGCAAAAGAAAAAAGAAA
1 AGCAAAA-AAAAAAG--A
62461 AGCAAGAAAAAAAAGA
1 AGCAA-AAAAAAAAGA
62477 AGCAAAAAAAAAA
1 AGCAAAAAAAAAA
62490 TGGAAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
18 12 0.43
19 2 0.07
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (15 bp):
AGCAAAAAAAAAAGA
Found at i:62473 original size:12 final size:12
Alignment explanation
Indices: 62446--62487 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
62436 TCCCATCAGC
62446 AAAAGAA-AAAA
1 AAAAGAAGAAAA
62457 GAAAAGCAAGAAAA
1 -AAAAG-AAGAAAA
62471 AAAAGAAGCAAAA
1 AAAAGAAG-AAAA
62484 AAAA
1 AAAA
62488 AATGGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.30
13 15 0.56
14 4 0.15
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:62495 original size:17 final size:16
Alignment explanation
Indices: 62448--62489 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
62438 CCATCAGCAA
62448 AAGAAAAAAGAA-AAGC
1 AAGAAAAAA-AAGAAGC
62464 AAGAAAAAAAAGAAGC
1 AAGAAAAAAAAGAAGC
62480 AA-AAAAAAAA
1 AAGAAAAAAAA
62490 TGGAAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAGAAGC
Found at i:62592 original size:14 final size:14
Alignment explanation
Indices: 62575--62613 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
62565 TTAAAAATGT
62575 TTTTCAAAAAAGCG
1 TTTTCAAAAAAGCG
* *
62589 TTTTCAGAAAAGGG
1 TTTTCAAAAAAGCG
62603 TTTTCTAAAAA
1 TTTTC-AAAAA
62614 TTGGTTTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (14 bp):
TTTTCAAAAAAGCG
Found at i:62980 original size:5 final size:5
Alignment explanation
Indices: 62958--63004 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
62948 AAAAAAAATG
**
62958 AAGAA AAGAA TTGAAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
63005 GAAGTTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 34 0.92
6 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (5 bp):
AAGAA
Found at i:63282 original size:37 final size:37
Alignment explanation
Indices: 63204--63280 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
63194 TGAAGAAGAA
* *
63204 TTTTCTTCAAAGTGTGATCTTTTCAAAAGAAAAAATG
1 TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAAAAATG
*
63241 TTTTCCTCGAAGTGTAATCTTTTCAAAAG-AAAAATG
1 TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAAAAATG
63277 TTTT
1 TTTT
63281 TCAAAAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 11 0.30
37 26 0.70
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTTCCTCAAAGTGTAATCTTTTCAAAAGAAAAAATG
Found at i:64305 original size:22 final size:22
Alignment explanation
Indices: 64273--64320 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
64263 AGACAGTAGC
*
64273 CAAGAATGGGTA-AAGAAGAAGT
1 CAAGAAAGGGTAGAAGAAG-AGT
*
64295 CAAGAAAGGGTAGATGAAGAGT
1 CAAGAAAGGGTAGAAGAAGAGT
64317 CAAG
1 CAAG
64321 TACAAGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.48, C:0.06, G:0.33, T:0.12
Consensus pattern (22 bp):
CAAGAAAGGGTAGAAGAAGAGT
Found at i:64476 original size:35 final size:35
Alignment explanation
Indices: 64430--65056 Score: 965
Period size: 35 Copynumber: 17.9 Consensus size: 35
64420 ATGTACGGTC
64430 TTTCATAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCA-AGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
64466 TTTGAAGAAGTTTTCAGAGGAT-AGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGG-TCAGAGTTGATCTCA
*
64501 TTTCAAGAA-TATTTCGGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGT-TTTCAGAGGTCAGAGTTGATCTCA
* *
64536 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTTA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
64571 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
64606 TTTGAAGAAGTTTTCAGAGGTCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
64641 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
64676 TTTCAAGAAGTTTTCAAAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
64711 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
64746 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
64781 TATCAAGATGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
64816 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
64851 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * *
64886 TTTAAAGAAGTTTACAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
64921 -TACTAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTC-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * * *
64956 TTCCAAGAAGTTTCCAAAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
64991 TTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
65027 TTTCAAGAAATTTTC-GATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGA
65057 CCCAGTGCGG
Statistics
Matches: 540, Mismatches: 43, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
34 5 0.01
35 497 0.92
36 38 0.07
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
Found at i:66377 original size:85 final size:87
Alignment explanation
Indices: 66276--66500 Score: 357
Period size: 85 Copynumber: 2.6 Consensus size: 87
66266 AAATTGTTAA
66276 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAG-A
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAA
66340 AATAAATAAATAATAAA-AT-T
66 AATAAATAAATAATAAAGATAT
* * * * * *
66360 GAATAGTAATCAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAGGA
1 -AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGA
*
66425 AAATAAATAAATTATAAAGATAT
65 AAATAAATAAATAATAAAGATAT
66448 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAG
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAG
66501 TTATAAAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
85 57 0.46
86 17 0.14
87 50 0.40
88 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (87 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAA
AATAAATAAATAATAAAGATAT
Done.