Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019110.1 Corchorus olitorius cultivar O-4 contig19143, 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: 48390
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2247 original size:328 final size:326
Alignment explanation
Indices: 1561--2731 Score: 994
Period size: 328 Copynumber: 3.6 Consensus size: 326
1551 AAATTCTATT
* ** * * * * *
1561 TAAGGATTTGTTTTTAGGAGTATCTAAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAAAT
1 TAAGGATTTGTTTTTACGAAAATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAA
* * ** * * * *
1626 ATGTAAATCCGATATTAGAAGCATGAAAAATCCTTCAATCTTTTTGGCGTTGAAATATATATTTT
66 AAGGAAA-AAGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTT
* * * * * * ** **
1691 TTATGAGTATTGTGGTAAAATATTGAA-ATAATA-TATTTCGGTTAAGTTTTTAGCCGAATTCGA
130 TTCTGAGTATTGTGGCAAAAAATTGAAGA-AAAACT-TTTCGGATCAGTTTTT-GCAAAATTTTA
* * * * * * ** *
1754 GTAC-AAAAC---AT-A--ATGA--TTTTTTTGCTAAAAACGCGTTTCC-GAG-CCTTGACTCAG
192 G-CCGAAATCGTGATAACCATCACGGTTTTTGGTTAAAAACGCG-TTCCAGAGCCCCAGA-TCAA
* * ** * * *
1808 TTTTGCATGGTTTTTAG-TATAAAGACTCCTTGAAATATCTATATTCATCTAGCCAAATCTCAGG
254 TTTTCCATGATTTTGGGCT-TAAAGACTCCTT-AAATATCTA-ATTCATCGAACCAAATCTCAAG
* *
1872 GACATTGGATT
316 CACATTGGATA
* * * *
1883 TAAGGATTTCTTTTTACGAAAATCTAAATTTTGTTTCGATTTAATTAAAAATAAATTTGGAAAAA
1 TAAGGATTTGTTTTTACGAAAATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAA
* * *
1948 AATGGAAAAACGATATTTGAAGCGTAAAAAACCCTTCAATTTTTTTGGCGTTGAGTTATATATTT
66 AA-GGAAAAA-GATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTT
* *
2013 TTTCT-ATATATTGTGGCAAAAAATTGAAGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAG
129 TTTCTGA-GTATTGTGGCAAAAAATTGAAGAAAAACTTTTCGGATCAGTTTTTGCAAAATTTTAG
* *
2077 CCGAAATCGTG-T-ACCATCACGGTTTTTGGTTAAAAATGCGTTCTAGAGCCCCAGATCAATTTT
193 CCGAAATCGTGATAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAGAGCCCCAGATCAATTTT
* * * *
2140 GCATGATATTTAGTGC-T-AAGACTTCTTAAAATATCTACATTCATCGAACCAAATCTCAATCAC
258 CCATGAT-TTT-GGGCTTAAAGACTCCTT-AAATATCTA-ATTCATCGAACCAAATCTCAAGCAC
2203 ATTGGATA
319 ATTGGATA
* ** * *
2211 TAATGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT-AGAATCTAA-TTCGAAAA
1 TAAGGATTTGTTTTTACGAAAATCTGAATCTTGTTTCGATTTAATTAAAAAT-TAATTTGGAAAA
* * * *
2274 AAAGGGGAAAAAGATATTAGAGGCATGAAAAACCCTTCAATATTTTTGACGTTGAATTATATATT
65 AAA--GGAAAAAGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATT
* ** * *
2339 TTTT-TGAGTATTGTGGCAAAAATTTG-AGAAAAAGCTTTTTAGTTCAGTTTTTGTAAAATTTTA
128 TTTTCTGAGTATTGTGGCAAAAAATTGAAGAAAAA-CTTTTCGGATCAGTTTTTGCAAAATTTTA
* * * *
2402 GCCGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCGTTCCGGAGCCCCGGCTCAGT
192 GCCGAAATCGTG-A-TAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAGAGCCCCAGATCAAT
* * * * *
2467 TTTCCATGATTTTGGGCTTAAAAACTCCTT-CAGA--T-ATTCATCGAATCAAATC-CGAGC-C-
255 TTTCCATGATTTTGGGCTTAAAGACTCCTTAAATATCTAATTCATCGAACCAAATCTCAAGCACA
*
2525 ----ACA
320 TTGGATA
* * * *
2528 TAAGGATTTGTTTTTAC-AAATATCTGAATCTTGTTTCGTTTTAATTAGAAATTAATTCGGAAAT
1 TAAGGATTTGTTTTTACGAAA-ATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAA
*
2592 AAAGGAAAAAAGATATTAG-AGTCGTGAAAAACCCTTC-ATTATTTTTGGCATTGAATTATATAT
65 AAAGG-AAAAAGATATTAGAAG-CGTGAAAAACCCTTCAATT-TTTTTGGCGTTGAATTATATAT
* * * *
2655 TCTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAACTTTTCGGATCAATTTTTACAAAATTTT
127 T-TTTTCTGAGTATTGTGGCAAAAAATTGAAGAAAAACTTTTCGGATCAGTTTTTGCAAAATTTT
*
2720 AACCGAAATCGT
191 AGCCGAAATCGT
2732 ATACTAATCA
Statistics
Matches: 694, Mismatches: 118, Indels: 77
0.78 0.13 0.09
Matches are distributed among these distances:
316 6 0.01
317 93 0.13
318 15 0.02
319 53 0.08
320 6 0.01
321 1 0.00
322 70 0.10
323 93 0.13
324 20 0.03
325 7 0.01
326 59 0.09
327 68 0.10
328 130 0.19
329 13 0.02
330 60 0.09
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (326 bp):
TAAGGATTTGTTTTTACGAAAATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAA
AAGGAAAAAGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTT
TCTGAGTATTGTGGCAAAAAATTGAAGAAAAACTTTTCGGATCAGTTTTTGCAAAATTTTAGCCG
AAATCGTGATAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAGAGCCCCAGATCAATTTTCCA
TGATTTTGGGCTTAAAGACTCCTTAAATATCTAATTCATCGAACCAAATCTCAAGCACATTGGAT
A
Found at i:3740 original size:25 final size:25
Alignment explanation
Indices: 3712--3761 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3702 ATCAAAGCTT
*
3712 AATTGTTCCACCCTTTAACTAGATA
1 AATTGCTCCACCCTTTAACTAGATA
3737 AATTGCTCCACCCTTTAACTAGATA
1 AATTGCTCCACCCTTTAACTAGATA
3762 GGATAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (25 bp):
AATTGCTCCACCCTTTAACTAGATA
Found at i:9418 original size:41 final size:41
Alignment explanation
Indices: 9372--9459 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
9362 GTTCTTGCAC
9372 CACTCTCACTCTCGACACATACACTACAACACACTATACCT
1 CACTCTCACTCTCGACACATACACTACAACACACTATACCT
9413 CACTCTCACTCTCGACACATACACTACAACACACTATACCT
1 CACTCTCACTCTCGACACATACACTACAACACACTATACCT
9454 CACTCT
1 CACTCT
9460 TTCTACAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.23
Consensus pattern (41 bp):
CACTCTCACTCTCGACACATACACTACAACACACTATACCT
Found at i:11043 original size:330 final size:330
Alignment explanation
Indices: 10528--11873 Score: 1172
Period size: 330 Copynumber: 4.0 Consensus size: 330
10518 ATTTTTTATG
* * *
10528 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCATGTAAAAACAAATCATTAAATCTAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * * *
10593 GTGGTTGAGATTT-GATTAGATGAATAAAGATATTTTCAAGGAGTCGCGGCGCCAAAAATCATGC
66 GTGGCTGAGATTTAG-TTAGATGAATATAGATA-TATCAAGGAGTCTCGGCGCCAAAAATCATGC
* *
10657 AAAA-TAGAGCTGTGGCTCCGGAACGCGATTT-TAGACAAAAACCGTGA---TACGTACACGATT
129 AAAACTA-AGCCG-GGCTCCGGAACGC-ATTTCTAGCCAAAAACCGTGATGTTACGTACACGATT
* * *
10717 TCAGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGGTAAACTACTCAT
191 TCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCAT
* *
10782 AAAAAATATATAATTCGACATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTCCT
256 AAAAAATATATAATTCAAC-TCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTCCT
*
10847 ATTTTTATCCG
320 ATTTTTATCCA
* *
10858 AATTAATTTCTAATTAAATCGAAAGAAGATTCATATGCACGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * * *
10923 GTGGGTGAGATTT-GTTGAGATGAATATAGACATATCAAGGAGTCTTGGCACCAAAAATCATGCA
66 GTGGCTGAGATTTAGTT-AGATGAATATAGATATATCAAGGAGTCTCGGCGCCAAAAATCATGCA
* * * *
10987 AAACTAAGCCGGGC-CCGTAACACATTTCTAGCCGAAAACCGTGATGGTTA-GTACACGATTTTG
130 AAACTAAGCCGGGCTCCGGAACGCATTTCTAGCCAAAAACCGTGAT-GTTACGTACACGATTTCG
* * * * * *
11050 GCTAAAATTTTGCGAAAATTGACAT-GAAAGATTTTTTCTCAATTTCTT-GCGACAATAATCATA
194 GCTAAAATTTTGCAAAAATTGAC-TCGAAAGATATTTCCTCAATTT-TTGGCTAAAATACTCATA
* * * * * * *
11113 AAAAATATATAATTCAACGCTAAAAAAATTCAAAGTCTTTTTCATGCTTCTAATATCATTTTTTT
257 AAAAATATATAATTCAACTC-AAAAAGATTGAAGGGC-TTTTCACGCTTCT-A-AT-ATTGTTTT
* *
11178 CATATTTTATTTCCA
317 CCTATTTT-TATCCA
* * * * * * * *
11193 AATTAATTGCTGATTAAATCGAAACAAGATTTAGATACTCGTAAAAGCAAATACTTAAATACAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * * * **
11258 GTGGCTGAAATTTGGTTAGATGAATATATATATATATATATATTTTAAGGAGTCTTAGCGCCAAA
66 GTGGCTGAGATTTAGTTAGATG-------A-ATATAGATATA--TCAAGGAGTCTCGGCGCCAAA
* * * ** * *
11323 AATCTTGCAAAACTGA-CTCGGGGCTCTGGAACGTGTTTTTAGCCAAAAACCGTGATTTCGACTA
121 AATCATGCAAAACTAAGC-C-GGGCTCCGGAACGCATTTCTAGCCAAAAACCGTGA--T-G--TT
* * * * * * * **
11387 ACGTACACGATTTCGTCTAATATTTTGCAAAAATTAAC-CAGAAATATTTTTTCTTAATTTTTTT
179 ACGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTC-GAAAGATATTTCCTCAATTTTTGG
* * * * * *
11451 CTAAAATACTCATAATATATATATAATTCAACTCCAAGAAGATTGGAGGACTTTTCACGCTTTTA
243 CTAAAATACTCATAAAAAATATATAATTCAACT-CAAAAAGATTGAAGGGCTTTTCACGCTTCTA
* * *
11516 ATATAGTTTTTC-ATATTTT-TCTA
307 ATATTGTTTTCCTAT-TTTTATCCA
* * * * * *
11539 AATTAATTTTTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAATAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * * * **
11604 GTGGCTGAGATTTAATTAGATGAATATATATATTTCAAGGAGTGTCGATGCCAAAAATCATGCAA
66 GTGGCTGAGATTTAGTTAGATGAATATAGATATATCAAGGAGTCTCGGCGCCAAAAATCATGCAA
* * * *
11669 AACTGAATG-AGGG-TCCCGAAACGCGTTTCTAGCAACAAAAAAAAAC-TG-TGATTA-GTACAC
131 AACT-AA-GCCGGGCT-CCGGAACGCATTTCTAGC--C---AAAAACCGTGATG-TTACGTACAC
*
11729 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATAC
187 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATAC
* * * * * * *
11794 TCACAAAAAATATATAATTCAACGCCAAAAATATTGAA-GGATTTTTAC-TTTCTAATATCGTTT
252 TCATAAAAAATATATAATTCAAC-TCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTT
*
11857 TCCCTACTTTT-TCCA
316 T-CCTATTTTTATCCA
11872 AA
1 AA
11874 AGGGAAAGCT
Statistics
Matches: 816, Mismatches: 148, Indels: 101
0.77 0.14 0.09
Matches are distributed among these distances:
326 4 0.00
327 21 0.03
328 3 0.00
329 38 0.05
330 178 0.22
331 16 0.02
332 14 0.02
333 19 0.02
334 105 0.13
335 79 0.10
336 49 0.06
337 2 0.00
338 11 0.01
339 1 0.00
340 2 0.00
341 6 0.01
342 1 0.00
343 9 0.01
344 1 0.00
345 33 0.04
346 82 0.10
347 26 0.03
348 9 0.01
349 4 0.00
350 1 0.00
351 15 0.02
352 86 0.11
353 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (330 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTAGTTAGATGAATATAGATATATCAAGGAGTCTCGGCGCCAAAAATCATGCAA
AACTAAGCCGGGCTCCGGAACGCATTTCTAGCCAAAAACCGTGATGTTACGTACACGATTTCGGC
TAAAATTTTGCAAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAA
ATATATAATTCAACTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTCCTATTTTT
ATCCA
Found at i:13191 original size:336 final size:331
Alignment explanation
Indices: 12450--13336 Score: 817
Period size: 336 Copynumber: 2.7 Consensus size: 331
12440 TGTAAAAACA
* * * ** * *
12450 ATGGCTGAGATTTGCTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAA-CTATG-C
1 ATGGCTAAGATTTGATTAGATAAATATAGATATCCCAAGGAGACTCGGAGCCAAAAATC-ATGCC
* * * * ** *
12513 AAAACTGAA-TCGGGTCCC-GGAACGCGT-TTTTAGCCAAAAAAGAGTGATGATTATTACATGAT
65 AAAA-T-AAGCCGGGGCCCTAGAACGC-TCTTTTAGGC-AAAAACCGTGATGGTTATTACA-GAT
* ** * * * ***
12575 TTC-AGCTAAAATTTTTAAAAAATTGAACCGAAAGATATTTCCTCAATTTTT--A-GCCACA-TC
125 TTCGA-CTAAAGTTTTGCAAAAATTGACCCGAAAAATATTTCATCAATTTTTGGATAAAACACTC
* *
12635 AT-AAAAA-ATATAATTCAACGACAAAAAGATTGAAGGGCTTTTCACACTTTTAATATCGCTTTT
189 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTTTTAATATCGCTTTT
* *
12698 CATAATTTTTTCTGAAACAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAAAT
254 CATAATTTTTTCTGAAACAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAAAAT
*
12763 CCTAAAATGCAAT
319 CCTAAAATCCAAT
* * ** * *
12776 ATGGCTAAGATTTTATTAGATAAATATAGATTTTTCAAGGAGTCTCGGCGCCAAAAATCATGCCA
1 ATGGCTAAGATTTGATTAGATAAATATAGATATCCCAAGGAGACTCGGAGCCAAAAATCATGCCA
*
12841 AAATGAGCCGGGGCCCT-GAAACGCGT-TTTTA-GCTAAAAACCGTGATGGGTTAGTTAC-GATT
66 AAATAAGCCGGGGCCCTAG-AACGC-TCTTTTAGGC-AAAAACCGTGAT-GGTTA-TTACAGATT
* * * * *
12902 TTGGCTAAAAG-TTTGC-AAATTATGACCCGAAAAATGTTTCCTCAATTTTTGGATAAAACACTC
126 TCGACT-AAAGTTTTGCAAAAAT-TGACCCGAAAAATATTTCATCAATTTTTGGATAAAACACTC
* * * * ** * *
12965 ATAATATATATATATAATTTAACTCCAAAAAGATTGGAGGACTTTTCACGGTTTTAATATTGTTT
189 ATAA-A-AAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTTTTAATATCG--C
* *
13030 TTTTCAT-ATTTTTTCT-AAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTTGTAAAA
250 TTTTCATAATTTTTTCTGAAA-CAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAA
** * *
13093 ACAAATTTTTAAATCCTAT
314 A-AAATCCTAAAATCCAAT
* * ** * *
13112 GTGGCTGAGATTTGATTAGATGTATATAGATATCCCAAGGAGACTTGGAGTCAAAAATCATG-CA
1 ATGGCTAAGATTTGATTAGATAAATATAGATATCCCAAGGAGACTCGGAGCCAAAAATCATGCCA
* * *
13176 AAACTAAGTCGGGGCCCTAGAATGCTCTTTTAGGCAAAAACTGTGATGGTTATTACATGATTTCG
66 AAA-TAAGCCGGGGCCCTAGAACGCTCTTTTAGGCAAAAACCGTGATGGTTATTACA-GATTTCG
* * * * *
13241 ACTAAAGTTTTGTAAAAATTGATCCGAAAGATATTTCATCAATTTTTGGTTAAAATACTCATAAA
129 ACTAAAGTTTTGCAAAAATTGACCCGAAAAATATTTCATCAATTTTTGGATAAAACACTCATAAA
13306 AAATATATAATTCAACGCCAAAAAGATTGAA
194 AAATATATAATTCAACGCCAAAAAGATTGAA
13337 AAGATCGAAG
Statistics
Matches: 457, Mismatches: 74, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
325 5 0.01
326 110 0.24
327 25 0.05
328 5 0.01
329 3 0.01
330 4 0.01
331 1 0.00
332 1 0.00
333 2 0.00
334 77 0.17
335 65 0.14
336 152 0.33
337 7 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (331 bp):
ATGGCTAAGATTTGATTAGATAAATATAGATATCCCAAGGAGACTCGGAGCCAAAAATCATGCCA
AAATAAGCCGGGGCCCTAGAACGCTCTTTTAGGCAAAAACCGTGATGGTTATTACAGATTTCGAC
TAAAGTTTTGCAAAAATTGACCCGAAAAATATTTCATCAATTTTTGGATAAAACACTCATAAAAA
ATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTTTTAATATCGCTTTTCATAATT
TTTTCTGAAACAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAAAATCCTAAAA
TCCAAT
Found at i:14433 original size:6 final size:6
Alignment explanation
Indices: 14422--14481 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
14412 GTCATTTTAT
* * *
14422 ATAGTA ATAGTA ATAATA GTAAT- ATAGTA ATAGTA ATAGTA ATAGTA
1 ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA
14469 ATAGTA ATAGTA A
1 ATAGTA ATAGTA A
14482 GATAGTAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 3 0.06
6 46 0.94
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATAGTA
Found at i:14489 original size:32 final size:29
Alignment explanation
Indices: 14422--14481 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
14412 GTCATTTTAT
*
14422 ATAGTAATAGTAATAATAGTAATATAGTA
1 ATAGTAATAGTAATAATAATAATATAGTA
* *
14451 ATAGTAATAGTAATAGTAATAGTAATAGTA
1 ATAGTAATAGTAATAATAATAAT-ATAGTA
14481 A
1 A
14482 GATAGTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (29 bp):
ATAGTAATAGTAATAATAATAATATAGTA
Found at i:17564 original size:30 final size:30
Alignment explanation
Indices: 17528--17588 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
17518 TTGACAGGCG
17528 AAATGAGGCTCGAATTATGTATGAGAAGCT
1 AAATGAGGCTCGAATTATGTATGAGAAGCT
17558 AAATGAGGCTCGAATTATGTATGAGAAGCT
1 AAATGAGGCTCGAATTATGTATGAGAAGCT
17588 A
1 A
17589 CGATCTCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (30 bp):
AAATGAGGCTCGAATTATGTATGAGAAGCT
Found at i:18711 original size:34 final size:35
Alignment explanation
Indices: 18668--18737 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
18658 TCCCTTGCAC
** *
18668 TAGTTCATAGGCCAAATTTTCTAATA-TATAAGCA
1 TAGTTCATAGGCCAAATTGGCTAATATTAGAAGCA
18702 TAGTTCATAGGCCAAATTGGCTAATATTAGAAGCA
1 TAGTTCATAGGCCAAATTGGCTAATATTAGAAGCA
18737 T
1 T
18738 GCTTATAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 24 0.75
35 8 0.25
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (35 bp):
TAGTTCATAGGCCAAATTGGCTAATATTAGAAGCA
Found at i:22087 original size:47 final size:47
Alignment explanation
Indices: 21985--22092 Score: 198
Period size: 47 Copynumber: 2.3 Consensus size: 47
21975 TACGCGTCTA
* *
21985 TTTTGTTTATGATGGTGATAATGGGATTAAACTATAATTTAATTTCT
1 TTTTGTTTGTTATGGTGATAATGGGATTAAACTATAATTTAATTTCT
22032 TTTTGTTTGTTATGGTGATAATGGGATTAAACTATAATTTAATTTCT
1 TTTTGTTTGTTATGGTGATAATGGGATTAAACTATAATTTAATTTCT
22079 TTTTGTTTGTTATG
1 TTTTGTTTGTTATG
22093 TCTTGTATCT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.53
Consensus pattern (47 bp):
TTTTGTTTGTTATGGTGATAATGGGATTAAACTATAATTTAATTTCT
Found at i:25784 original size:323 final size:321
Alignment explanation
Indices: 25036--26961 Score: 1689
Period size: 323 Copynumber: 5.9 Consensus size: 321
25026 ATAGGATGGT
* * ** * ** * * *
25036 TTTTTGGTTAAAAACGC--TTCGGGGCCTCATCTTAGTTTCACATGGTTTTTGACATAAAGACTT
1 TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGAAAGACTC
* * * * * **
25099 TTTGAAATATCTATATTCATCTAACCAAATCACAACCACTTTGGATTTAAGAATTTGTTTTTATA
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * *
25164 AGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAAAATGGAAAAACGATATT
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG--GAAAAAATGGAAAAACGATATT
** * * *
25229 AGAAGCGTGAAAAATCCATAAATTTTTTTGGCGTTGAAT-TATATATTTTTT-TGAGTATTTTGG
194 AGAAGCGTGAAAAGCCCGTCAATTTTTTTGGC-TTGAATATATATATTTTTTATGAGTATTGTGG
* * * * * * *
25292 CAAAAACTTGAGGAAAAACTTTTTGGGTCAGTTTTTA-CAATATTTTAATTGAAATCATTTACT-
258 CAAAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGC-----------CGAAATCGTGTA-TA
25355 AACCATCACGG
311 AACCATCACGG
* * * * * * * *
25366 TTTTTGGCTAAAAACACG-TTCTTGAGCCCTGACTCAATTTTGCATGATTTTTTA-TGCAAAGAC
1 TTTTTGGCTAAAAACGCGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAG-AAAGAC
* * * * **
25429 TCCTTGAAATATCTATATTAATCGAACCAAATCTCAACCACATTGGATATAAGTTTTTGTTTTTA
64 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * *
25494 CGAGCATCTGAATCTTTTTTCGATTTAATTAGAAATTAATTTTGGAAAAAATGGAAAAATGATA-
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAATGGAAAAACGATAT
* * * * * * *
25558 TAGAAACGTGAAAAGTCTGTCAATTTTTTTGGCATTGTATCATATATTTTTTTTCTTAGTATTGT
193 TAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGC-TTGAAT-ATATATATTTTTTATGAGTATTGT
** * * * * *
25623 AACAGAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAACCGAAATCGTGTATTACCCATCACA
256 GGCAAAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTATAAACCATCACG
25688 G
321 G
** * *** * * *
25689 TTTTTCCCTAAAAACACGTTTCGGGGTATCGGCTCTGTTTTGCATGATTTTTGACAAAAAGACCC
1 TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGAAAGACTC
* * * *
25754 CTTGAAATATCTAAATTCATTTAACCAAATCTCAGTCACATTGGATTTAAGGATTTATTTTTACG
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * * *
25819 AGCATTTGAATCTTGTTTCGATCTAATTAGAAATTAATTCGGAAAAAAAGGAAAAACAATATTAG
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAG
* * * * *
25884 AAGCGTGAAAA-CCCGTCAATCTTTTTTACGC-TGAAATATATATATTTTTTCTCAGTATTATGT
196 AAGCGTGAAAAGCCCGTCAAT-TTTTTT-GGCTTG-AATATATATATTTTTTATGAGTATTGTGG
* *** * * *
25947 CAAAAAATTGAGAAAAAACGTTTCAAATCAGTTTTTAGCCGAAAATCGTGTACAAATCATCACGG
258 CAAAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGCCG-AAATCGTGTATAAACCATCACGG
* * * * * *
26012 TTTTTGACTAGAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCACGATTTTAG-GAGAAATACTC
1 TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGAAAGACTC
*
26076 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTTCG
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * *
26141 AGAATCTGAATCTTGTTTCAATTTAATAAGAAATTAATTCGGAAAAAAAAT-G-AAAACGATATT
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAATGGAAAAACGATATT
* * *
26204 ATAAGCGTGAAAAGCCCGTCAA-TTTTTAGACGTTGAAT-TATATATTTTTTATGAGTATTGTGG
194 AGAAGCGTGAAAAGCCCGTCAATTTTTTTGGC-TTGAATATATATATTTTTTATGAGTATTGTGG
* * * *
26267 CAAAAAATTGACAAAAAAACCTTTCGGGTAAGTTTTTTAGCCGAAATCGTGT-T--A-CGTCACG
258 CAAAAAATTGA-GAAAAAACTTTTCGGGTTAG-TTTTTAGCCGAAATCGTGTATAAACCATCACG
26328 G
321 G
* * * *
26329 TTTTTTTTTTTTTTGCTAAAAACGCG-TTCTAGGG-CCCGACTCAGTTTTGCATGATTTTTGCCA
1 --------TTTTTGGCTAAAAACGCGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGACA
* ** * * * *
26392 TAAAGACTTATTGAAATTTCTATATTCGTCGAACCAAATCCCAGCCACATTGGATTTAAGGATTT
57 GAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
* * * * * * *
26457 GTTTTTACGACCATCTTAATGTTCTTTTGATTTAATTGGAAATTAATTCGGAAAAAAATTAGAAA
122 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAA-TGGAAA
* * * * * * * *
26522 GACAATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGGTAAAT-TATATAGTTTTTATGA
185 AACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGC-TTGAATATATATATTTTTTATGA
* *
26586 GTATTGTGGCAAAAAATTGATAAAAAA-TATTTCGGGTTAGTTTTTAGCCGAAATCGTTTACTAA
249 GTATTGTGGCAAAAAATTGAGAAAAAACT-TTTCGGGTTAGTTTTTAGCCGAAATCGTGTA-TAA
**
26650 TTC-TCACGG
312 ACCATCACGG
* * *
26659 TTTTTTGGCTAAAAACGCGTTTCGGGACCCCGGCTCAGTTTTGCCTGATTTTTGGA-AGAAATAC
1 -TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTT-GACAGAAAGAC
* * *
26723 TCCTTGAAATATATATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGAATTT-TTTTTA
64 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * * * * *
26787 CGAGTATCTAAATCTTGTATCAATTTAATTAGAACAAT-ATTCGGGAACAAAAAAAAAAGGAAAA
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAA-ATTAATTC-GG------AAAAAATGGAAAA
* * * * * *
26851 ACGATATTAAAAGCGTAAAAAAAAACCCTTCAATTTTTTTGGCGTTGAAT-TTTATATTTTTTCT
186 ACGATATTAGAAGCGT---GAAAAGCCCGTCAATTTTTTTGGC-TTGAATATATATATTTTTTAT
* *
26915 GAGTATTGTGGCAAAGAATTGAGGAAGAAA-TTTTCGGGTTAGTTTTT
247 GAGTATTGTGGCAAAAAATTGA-GAAAAAACTTTTCGGGTTAGTTTTT
26962 GGAAAATTTT
Statistics
Matches: 1304, Mismatches: 235, Indels: 113
0.79 0.14 0.07
Matches are distributed among these distances:
317 7 0.01
318 1 0.00
320 33 0.03
321 31 0.02
322 223 0.17
323 298 0.23
324 129 0.10
325 119 0.09
326 19 0.01
327 44 0.03
328 65 0.05
329 7 0.01
330 54 0.04
331 97 0.07
332 133 0.10
333 43 0.03
334 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (321 bp):
TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGAAAGACTC
CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAG
AAGCGTGAAAAGCCCGTCAATTTTTTTGGCTTGAATATATATATTTTTTATGAGTATTGTGGCAA
AAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTATAAACCATCACGG
Found at i:28564 original size:2 final size:2
Alignment explanation
Indices: 28559--28587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28549 ATTAAGTGTG
28559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28588 TTGATTTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46625 original size:58 final size:58
Alignment explanation
Indices: 46529--46643 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
46519 ATTAATCAAA
*
46529 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * *
46587 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCAAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGC
46644 ATGATGCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:47948 original size:36 final size:36
Alignment explanation
Indices: 47901--47970 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
47891 TTCAATAACC
* *
47901 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
47937 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
47971 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.