Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006834.1 Corchorus capsularis cultivar CVL-1 contig06855, 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: 31098
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:1303 original size:50 final size:51
Alignment explanation
Indices: 1234--1345 Score: 201
Period size: 50 Copynumber: 2.2 Consensus size: 51
1224 CAGAGGCTGA
*
1234 AGAA-AGGATGAAACTCAGAAGGATGGCTAGGATGGGGCATGGAGTGGAGG
1 AGAAGAGGATGAAACTCAGAAGGATGGCCAGGATGGGGCATGGAGTGGAGG
1284 AGAAGAGGAT-AAACTCAGAAGGATGGCCAGGATGGGGCATGGAGTGGAGG
1 AGAAGAGGATGAAACTCAGAAGGATGGCCAGGATGGGGCATGGAGTGGAGG
1334 AGAAGAGGATGA
1 AGAAGAGGATGA
1346 GGTTCCCACC
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
50 53 0.90
51 6 0.10
ACGTcount: A:0.36, C:0.08, G:0.44, T:0.12
Consensus pattern (51 bp):
AGAAGAGGATGAAACTCAGAAGGATGGCCAGGATGGGGCATGGAGTGGAGG
Found at i:6629 original size:29 final size:29
Alignment explanation
Indices: 6541--6617 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
6531 GGGTCGCCCA
*
6541 GGGGTATTTTGGTCATTTTCACATCTAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
*
6570 GGGGCATTTTGGTCATTTTCACATCCAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
6599 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
6618 TGCATTTAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.40
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCACATCTAGG
Found at i:6761 original size:32 final size:32
Alignment explanation
Indices: 6720--6794 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
6710 ATCTTAATAT
* *
6720 GTAATTTAGTAATTTA-G-TTTTGTTGCACTTTA
1 GTAATTTAGTAAGTTATGATATTGTT-CA-TTTA
6752 GTAATTTAGTAAGTTATGCATATTGTTCATTTA
1 GTAATTTAGTAAGTTATG-ATATTGTTCATTTA
6785 GTAATTTAGT
1 GTAATTTAGT
6795 TTTGCAGCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 15 0.39
33 15 0.39
34 2 0.05
35 6 0.16
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (32 bp):
GTAATTTAGTAAGTTATGATATTGTTCATTTA
Found at i:9134 original size:51 final size:50
Alignment explanation
Indices: 9045--9236 Score: 199
Period size: 50 Copynumber: 3.8 Consensus size: 50
9035 AAATTTATCA
* * *
9045 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGAAAATAAAAATGTCATC
1 TTTGAATTAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCATC
* ** * * *
9095 TTTGAGTTAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGGTTTAACC
1 TTTGAATTAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCATC
* * *
9146 TTTGAATAAAAGTTTGAATTTTTAAGTAATTAGTAAAT-AAAATGTCATT
1 TTTGAATTAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCATC
* * **
9195 TTTGAATTAGAAG-TGTGAACTTTTAGGCCATTAGTAAATAAA
1 TTTGAATTA-AAGAT-TGAATTTTTAAGTAATTAGTAAATAAA
9237 TTAATTGGTT
Statistics
Matches: 115, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 14 0.12
50 59 0.51
51 42 0.37
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.39
Consensus pattern (50 bp):
TTTGAATTAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCATC
Found at i:9252 original size:101 final size:101
Alignment explanation
Indices: 9045--9236 Score: 273
Period size: 101 Copynumber: 1.9 Consensus size: 101
9035 AAATTTATCA
* *
9045 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGAAAATAAAAATGTCATCTTTGAGTTAAAGATT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGAAAATAAAAATGTCATCTTTGAATTAAAGATT
* *
9110 GAATTTTTAGAGTAATTAGTAAATAAAGGTTTAACC
66 GAACTTTTAGAGCAATTAGTAAATAAAGGTTTAACC
* * *
9146 TTTGAATAAAAGTTTGAATTTTTAAGTAATTAGTAAAT-AAAATGTCATTTTTGAATTAGAAG-T
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGAAAATAAAAATGTCATCTTTGAATTA-AAGAT
*
9209 GTGAACTTTTAG-GCCATTAGTAAATAAA
65 -TGAACTTTTAGAGCAATTAGTAAATAAA
9237 TTAATTGGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 33 0.41
101 48 0.59
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.39
Consensus pattern (101 bp):
TTTGAATAAAAGATTGAATTTTTAAGTAATTAGAAAATAAAAATGTCATCTTTGAATTAAAGATT
GAACTTTTAGAGCAATTAGTAAATAAAGGTTTAACC
Found at i:9984 original size:55 final size:55
Alignment explanation
Indices: 9923--10049 Score: 182
Period size: 55 Copynumber: 2.3 Consensus size: 55
9913 GAAAAAGGGC
* * *
9923 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATCAATCAGAATCAAGGAAATAGT
* * *
9978 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATCAATCAGAATCAAGGTAATGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATCAATCAGAATCAAGGAAATAGT
* *
10033 AATAAGTAAATCGGTAA
1 AATCAGTAAATCAGTAA
10050 AAAGAGATTG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (55 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATCAATCAGAATCAAGGAAATAGT
Found at i:10124 original size:72 final size:70
Alignment explanation
Indices: 10037--10375 Score: 280
Period size: 72 Copynumber: 4.8 Consensus size: 70
10027 AATGGTAATA
* * * * *
10037 AGTAAATCGGTAAAAAGAGATTGATCAGTAAAGTGATAATCAAGAATCAAGGTAATATTAATCTA
1 AGTAAAGC-GTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATAGTAAT-TA
*
10102 TAAAA-C
64 GAAAATC
* * * *
10108 TAGTAAAGCAGTAAAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAGTAATTA
1 -AGTAAAGC-GTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATAGTAATTA
**
10173 GGCAATC
64 GAAAATC
* *
10180 AGTAATTAG-GT-AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAG--ATTA
1 AGTAA--AGCGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATAGTAATTA
* *
10241 -AACAGTA
64 GAA-AATC
* * * * * *
10248 ATTAAAGAGTCTAGGTAAAGATAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAGTAAT
1 AGTAAAGCG--TA--AAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATAGTAAT
**
10313 TAGGCAATC
62 TAGAAAATC
*
10322 AGTAATTAG-GT-AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAA
1 AGTAA--AGCGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAA
10376 GAGATTAAAC
Statistics
Matches: 212, Mismatches: 40, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
66 2 0.01
67 1 0.00
68 10 0.05
69 1 0.00
70 78 0.37
71 11 0.05
72 93 0.44
73 3 0.01
74 10 0.05
75 1 0.00
76 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (70 bp):
AGTAAAGCGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATAGTAATTAGA
AAATC
Found at i:10207 original size:142 final size:140
Alignment explanation
Indices: 10049--10581 Score: 529
Period size: 142 Copynumber: 3.7 Consensus size: 140
10039 TAAATCGGTA
* * * * *
10049 AAAAGAGATTGATCAGTAAAGTGATAATCAAGAATCAAGGTAATATTAATCTATAAAACT-AGTA
1 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGA--AAT-TA-AAAACTAAGTA
10113 AAGCAG-TA-AAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAGTAATTAGGC
62 AAG-AGCTAGAAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAGTAATTAGGC
10176 AATCAGTAATTAGGT
126 AATCAGTAATTAGGT
* * * *
10191 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATTAAAGA
1 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAAAAACTAAGTAAAGA
* *
10256 GTCTAGGTAAAGATAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAGTAATTAGGCAAT
66 G-CTA-GAAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAGTAATTAGGCAAT
10321 CAGTAATTAGGT
129 CAGTAATTAGGT
* * * *
10333 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATTAAAGA
1 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAAAAACTAAGTAAAGA
* * * * ** * ** *
10398 GTTTAGGTAAAGATAGTAATCAGTAAATTGATAAGTAAGAGTCAAGGTAAGAGATTAAACA-GTA
66 G-CTA-GAAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAG--TAATTAGGCA
* *
10462 ATTAAAG-AGTCTAGGT
127 A-T-CAGTAAT-TAGGT
* * ** * * *
10478 -AAAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAATCAGTAATTAAGGA
1 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAAAAACTAAGTAAAGA
* * * *
10542 GTCAAGGTAAAAAATAGTAATCAGTAAATCGATAATTAAG
66 G-CTA-G-AAAAGATAGTAATCAGTAAATTGACAATTAAG
10582 GGTTAAAGTG
Statistics
Matches: 348, Mismatches: 32, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
138 6 0.02
139 8 0.02
140 4 0.01
142 221 0.64
143 3 0.01
144 71 0.20
145 35 0.10
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (140 bp):
AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAAAAACTAAGTAAAGA
GCTAGAAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAGTAATTAGGCAATCA
GTAATTAGGT
Found at i:10212 original size:70 final size:70
Alignment explanation
Indices: 10121--10375 Score: 309
Period size: 70 Copynumber: 3.6 Consensus size: 70
10111 TAAAGCAGTA
* *
10121 AAAAGATAGTAATCAGTAAATTGACAATTAAGAACCAAGGTAATAGTAATTAGGCAATCAGTAAT
1 AAAAGAGAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAGTAATTAGGCAATCAGTAAT
10186 TAGGT
66 TAGGT
* ** * ** * *
10191 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACA-GTAATTAAAG
1 AAAAGAGAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAG--TAATTAGGCAA-T-CAG
*
10255 -AGTCTAGGT
62 TAAT-TAGGT
*
10264 -AAAGATAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAGTAATTAGGCAATCAGTAAT
1 AAAAGAGAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAGTAATTAGGCAATCAGTAAT
10328 TAGGT
66 TAGGT
* **
10333 AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAA
1 AAAAGAGAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAA
10376 GAGATTAAAC
Statistics
Matches: 152, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
69 7 0.05
70 85 0.56
71 6 0.04
72 47 0.31
73 7 0.05
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (70 bp):
AAAAGAGAGTAATCAGTAAATTGATAATTAAGAACCAAGGTAATAGTAATTAGGCAATCAGTAAT
TAGGT
Found at i:10232 original size:41 final size:40
Alignment explanation
Indices: 10187--10305 Score: 119
Period size: 39 Copynumber: 3.1 Consensus size: 40
10177 ATCAGTAATT
10187 AGGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCA
1 AGGT-AAAGAGATTAATCAGTAAATTGATAATTAAGAGTCA
* *
10228 AGGT-AAGAGATTAAACAGT-AA-T--T-A--AAGAGTCT
1 AGGTAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCA
* * **
10260 AGGTAAAGATAGTAATCAGTAAATTGATAATTAAGAACCA
1 AGGTAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCA
10300 AGGTAA
1 AGGTAA
10306 TAGTAATTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
32 11 0.18
33 12 0.19
34 3 0.05
35 2 0.03
37 2 0.03
38 3 0.05
39 14 0.23
40 11 0.18
41 4 0.06
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (40 bp):
AGGTAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCA
Found at i:10406 original size:32 final size:31
Alignment explanation
Indices: 10357--10552 Score: 124
Period size: 32 Copynumber: 5.7 Consensus size: 31
10347 AGTAAATTGA
10357 TAATT-AAGAGTCAAGGTAAGAGATTAAACAG
1 TAATTAAAGAGTCAAGGTAA-AGATTAAACAG
** *
10388 TAATTAAAGAGTTTAGGTAAAGATAGTAATCAG
1 TAATTAAAGAGTCAAGGTAAAGAT--TAAACAG
10421 TAAATTGATAAGTAAGAGTCAAGGTAAGAGATTAAACAG
1 T-AA-T--T-A--AAGAGTCAAGGTAA-AGATTAAACAG
* *
10460 TAATTAAAGAGTCTAGGTAAAGATAGTAATCAG
1 TAATTAAAGAGTCAAGGTAAAGAT--TAAACAG
* *
10493 TAAATTGATAATTAAGAGTCAAGGTAAGAAATTAATCAG
1 T-AA-T--T-A--AAGAGTCAAGGTAA-AGATTAAACAG
*
10532 TAATTAAGGAGTCAAGGTAAA
1 TAATTAAAGAGTCAAGGTAAA
10553 AAATAGTAAT
Statistics
Matches: 133, Mismatches: 11, Indels: 42
0.72 0.06 0.23
Matches are distributed among these distances:
31 14 0.11
32 38 0.29
33 14 0.11
34 6 0.05
35 4 0.03
37 4 0.03
38 6 0.05
39 15 0.11
40 25 0.19
41 7 0.05
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.26
Consensus pattern (31 bp):
TAATTAAAGAGTCAAGGTAAAGATTAAACAG
Found at i:10419 original size:72 final size:73
Alignment explanation
Indices: 10328--10581 Score: 404
Period size: 72 Copynumber: 3.5 Consensus size: 73
10318 AATCAGTAAT
* *
10328 TAGGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATT
1 TAGGTAAAAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATT
*
10393 AAAGAGTT
66 AAAGAGTC
*
10401 TAGGT-AAAGATAGTAATCAGTAAATTGATAAGTAAGAGTCAAGGTAAGAGATTAAACAGTAATT
1 TAGGTAAAAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATT
10465 AAAGAGTC
66 AAAGAGTC
* *
10473 TAGGT-AAAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAATCAGTAATT
1 TAGGTAAAAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATT
*
10537 AAGGAGTC
66 AAAGAGTC
* * *
10545 AAGGTAAAAAATAGTAATCAGTAAATCGATAATTAAG
1 TAGGTAAAAGATAGTAATCAGTAAATTGATAATTAAG
10582 GGTTAAAGTG
Statistics
Matches: 169, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
72 135 0.80
73 34 0.20
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.26
Consensus pattern (73 bp):
TAGGTAAAAGATAGTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAGATTAAACAGTAATT
AAAGAGTC
Found at i:10568 original size:34 final size:31
Alignment explanation
Indices: 10501--10568 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 31
10491 AGTAAATTGA
*
10501 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
1 TAATTAAGAGTCAAGGTAAAAAATTAATCAG
10532 TAATTAAGGAGTCAAGGTAAAAAATAGTAATCAG
1 TAATTAA-GAGTCAAGGTAAAAAAT--TAATCAG
10566 TAA
1 TAA
10569 ATCGATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 7 0.21
32 16 0.48
34 10 0.30
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAAAAATTAATCAG
Found at i:10892 original size:27 final size:27
Alignment explanation
Indices: 10849--10921 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 27
10839 AAGAAAAGAG
10849 AGAGTAAAAAAATGGTAATTAAAGTA-AA
1 AGAGT-AAAAAATGGTAATT-AAGTACAA
** *
10877 AGAGTAAAATGTGGTAA-TCAGTACAA
1 AGAGTAAAAAATGGTAATTAAGTACAA
10903 AGAGTAAAAAATGGTAATT
1 AGAGTAAAAAATGGTAATT
10922 GGCAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 4 0.11
26 18 0.47
27 11 0.29
28 5 0.13
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.23
Consensus pattern (27 bp):
AGAGTAAAAAATGGTAATTAAGTACAA
Found at i:19742 original size:12 final size:11
Alignment explanation
Indices: 19713--19743 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
19703 TAAATAATCA
19713 TCCAAAAAGGC
1 TCCAAAAAGGC
19724 TCCAAAAAGGC
1 TCCAAAAAGGC
19735 TCCAAAAAG
1 TCCAAAAAG
19744 ATACAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (11 bp):
TCCAAAAAGGC
Found at i:26724 original size:18 final size:17
Alignment explanation
Indices: 26697--26732 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
26687 TTTCTCTTCA
26697 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
26714 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
26732 T
1 T
26733 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:27556 original size:18 final size:17
Alignment explanation
Indices: 27529--27564 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
27519 TTTCTCTTCA
27529 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
27546 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
27564 T
1 T
27565 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:28103 original size:832 final size:832
Alignment explanation
Indices: 26500--28168 Score: 3329
Period size: 832 Copynumber: 2.0 Consensus size: 832
26490 ACGATTCCAG
26500 AAAATTCCAGGATCCTATTTTGACTTGGACTCTACTCTAGGATGACACCTAATCCAACCTGGAGA
1 AAAATTCCAGGATCCTATTTTGACTTGGACTCTACTCTAGGATGACACCTAATCCAACCTGGAGA
26565 CCAAGTCAGCCCCTAGAACGTCCTAGACTTATATCCTAAGTCTAATAGGAGTCTTTAGATTATTT
66 CCAAGTCAGCCCCTAGAACGTCCTAGACTTATATCCTAAGTCTAATAGGAGTCTTTAGATTATTT
26630 TTCCACTATAAATAGCCACCTTATATAGCCTTAGAAGATATAACATCTAGATACAATTTTCTCTT
131 TTCCACTATAAATAGCCACCTTATATAGCCTTAGAAGATATAACATCTAGATACAATTTTCTCTT
26695 CATCTATTTTTCTTCTAGTTCTAGTTTTTCTTCTAGTTTTAGGTTGAGGGTGTCGACACCTCTCT
196 CATCTATTTTTCTTCTAGTTCTAGTTTTTCTTCTAGTTTTAGGTTGAGGGTGTCGACACCTCTCT
26760 TTGCATAGAGAGGTGTGATAACTCTCCTTGTTGAAGGCTAAGGAGATTCCGCCCCAAGGTCTTGT
261 TTGCATAGAGAGGTGTGATAACTCTCCTTGTTGAAGGCTAAGGAGATTCCGCCCCAAGGTCTTGT
26825 AAGTTTTCTTATGCCTCTCATGGATTTTCCCAAATCCATGAGTAGCTAAACCCTTAATACTTCCT
326 AAGTTTTCTTATGCCTCTCATGGATTTTCCCAAATCCATGAGTAGCTAAACCCTTAATACTTCCT
26890 ATCCTTTGGTGAATCAATCAATTGATTATGGTGAGATTTGTGTGCTTATAATTTGATGTTTGTTC
391 ATCCTTTGGTGAATCAATCAATTGATTATGGTGAGATTTGTGTGCTTATAATTTGATGTTTGTTC
26955 TTGGTTGATAGTTATTAATTCTCTGTTTTAATTTTATGATCTTCATGATTGTGGATTTAGAACTG
456 TTGGTTGATAGTTATTAATTCTCTGTTTTAATTTTATGATCTTCATGATTGTGGATTTAGAACTG
27020 CAGCTATTGATACGATTTGATAGATCTATTGTTAAATCAAACTTAGACCAATTCAAGTTTGATTG
521 CAGCTATTGATACGATTTGATAGATCTATTGTTAAATCAAACTTAGACCAATTCAAGTTTGATTG
*
27085 TGTGGTAACAATTGGGGGTGAAGGACCAATTCCTCCCAAGGGATTAATTAACCTTATTTGAAAGA
586 TGCGGTAACAATTGGGGGTGAAGGACCAATTCCTCCCAAGGGATTAATTAACCTTATTTGAAAGA
27150 ATAAGTTTGGTTATACTTGTTATGCATGTGTGAAAACTGTTCTTAATGTTTTGTTTTTATCAACT
651 ATAAGTTTGGTTATACTTGTTATGCATGTGTGAAAACTGTTCTTAATGTTTTGTTTTTATCAACT
27215 GAGAAGCTGGACCAAGGCAATTGGTTGTTAAGAAAAAAAGGGATAATATAAGCTGGACCAAGGTA
716 GAGAAGCTGGACCAAGGCAATTGGTTGTTAAGAAAAAAAGGGATAATATAAGCTGGACCAAGGTA
27280 ATATTATCTAATATACATGTTAGGGTTTCCTAGACCAAGGATCATCGAGAAT
781 ATATTATCTAATATACATGTTAGGGTTTCCTAGACCAAGGATCATCGAGAAT
27332 AAAATTCCAGGATCCTATTTTGACTTGGACTCTACTCTAGGATGACACCTAATCCAACCTGGAGA
1 AAAATTCCAGGATCCTATTTTGACTTGGACTCTACTCTAGGATGACACCTAATCCAACCTGGAGA
27397 CCAAGTCAGCCCCTAGAACGTCCTAGACTTATATCCTAAGTCTAATAGGAGTCTTTAGATTATTT
66 CCAAGTCAGCCCCTAGAACGTCCTAGACTTATATCCTAAGTCTAATAGGAGTCTTTAGATTATTT
27462 TTCCACTATAAATAGCCACCTTATATAGCCTTAGAAGATATAACATCTAGATACAATTTTCTCTT
131 TTCCACTATAAATAGCCACCTTATATAGCCTTAGAAGATATAACATCTAGATACAATTTTCTCTT
27527 CATCTATTTTTCTTCTAGTTCTAGTTTTTCTTCTAGTTTTAGGTTGAGGGTGTCGACACCTCTCT
196 CATCTATTTTTCTTCTAGTTCTAGTTTTTCTTCTAGTTTTAGGTTGAGGGTGTCGACACCTCTCT
27592 TTGCATAGAGAGGTGTGATAACTCTCCTTGTTGAAGGCTAAGGAGATTCCGCCCCAAGGTCTTGT
261 TTGCATAGAGAGGTGTGATAACTCTCCTTGTTGAAGGCTAAGGAGATTCCGCCCCAAGGTCTTGT
27657 AAGTTTTCTTATGCCTCTCATGGATTTTCCCAAATCCATGAGTAGCTAAACCCTTAATACTTCCT
326 AAGTTTTCTTATGCCTCTCATGGATTTTCCCAAATCCATGAGTAGCTAAACCCTTAATACTTCCT
27722 ATCCTTTGGTGAATCAATCAATTGATTATGGTGAGATTTGTGTGCTTATAATTTGATGTTTGTTC
391 ATCCTTTGGTGAATCAATCAATTGATTATGGTGAGATTTGTGTGCTTATAATTTGATGTTTGTTC
27787 TTGGTTGATAGTTATTAATTCTCTGTTTTAATTTTATGATCTTCATGATTGTGGATTTAGAACTG
456 TTGGTTGATAGTTATTAATTCTCTGTTTTAATTTTATGATCTTCATGATTGTGGATTTAGAACTG
27852 CAGCTATTGATACGATTTGATAGATCTATTGTTAAATCAAACTTAGACCAATTCAAGTTTGATTG
521 CAGCTATTGATACGATTTGATAGATCTATTGTTAAATCAAACTTAGACCAATTCAAGTTTGATTG
27917 TGCGGTAACAATTGGGGGTGAAGGACCAATTCCTCCCAAGGGATTAATTAACCTTATTTGAAAGA
586 TGCGGTAACAATTGGGGGTGAAGGACCAATTCCTCCCAAGGGATTAATTAACCTTATTTGAAAGA
27982 ATAAGTTTGGTTATACTTGTTATGCATGTGTGAAAACTGTTCTTAATGTTTTGTTTTTATCAACT
651 ATAAGTTTGGTTATACTTGTTATGCATGTGTGAAAACTGTTCTTAATGTTTTGTTTTTATCAACT
28047 GAGAAGCTGGACCAAGGCAATTGGTTGTTAAGAAAAAAAGGGATAATATAAGCTGGACCAAGGTA
716 GAGAAGCTGGACCAAGGCAATTGGTTGTTAAGAAAAAAAGGGATAATATAAGCTGGACCAAGGTA
28112 ATATTATCTAATATACATGTTAGGGTTTCCTAGACCAAGGATCATCGAGAAT
781 ATATTATCTAATATACATGTTAGGGTTTCCTAGACCAAGGATCATCGAGAAT
28164 AAAAT
1 AAAAT
28169 ATTAAATTCA
Statistics
Matches: 836, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
832 836 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (832 bp):
AAAATTCCAGGATCCTATTTTGACTTGGACTCTACTCTAGGATGACACCTAATCCAACCTGGAGA
CCAAGTCAGCCCCTAGAACGTCCTAGACTTATATCCTAAGTCTAATAGGAGTCTTTAGATTATTT
TTCCACTATAAATAGCCACCTTATATAGCCTTAGAAGATATAACATCTAGATACAATTTTCTCTT
CATCTATTTTTCTTCTAGTTCTAGTTTTTCTTCTAGTTTTAGGTTGAGGGTGTCGACACCTCTCT
TTGCATAGAGAGGTGTGATAACTCTCCTTGTTGAAGGCTAAGGAGATTCCGCCCCAAGGTCTTGT
AAGTTTTCTTATGCCTCTCATGGATTTTCCCAAATCCATGAGTAGCTAAACCCTTAATACTTCCT
ATCCTTTGGTGAATCAATCAATTGATTATGGTGAGATTTGTGTGCTTATAATTTGATGTTTGTTC
TTGGTTGATAGTTATTAATTCTCTGTTTTAATTTTATGATCTTCATGATTGTGGATTTAGAACTG
CAGCTATTGATACGATTTGATAGATCTATTGTTAAATCAAACTTAGACCAATTCAAGTTTGATTG
TGCGGTAACAATTGGGGGTGAAGGACCAATTCCTCCCAAGGGATTAATTAACCTTATTTGAAAGA
ATAAGTTTGGTTATACTTGTTATGCATGTGTGAAAACTGTTCTTAATGTTTTGTTTTTATCAACT
GAGAAGCTGGACCAAGGCAATTGGTTGTTAAGAAAAAAAGGGATAATATAAGCTGGACCAAGGTA
ATATTATCTAATATACATGTTAGGGTTTCCTAGACCAAGGATCATCGAGAAT
Done.