Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021086.1 Corchorus olitorius cultivar O-4 contig21119, 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: 16334
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:290 original size:21 final size:20
Alignment explanation
Indices: 251--290 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
241 AGCAGTGAGG
*
251 AAAGAAAACAAAAGTGAAAC
1 AAAGAAAACAAAAGAGAAAC
*
271 AAAGAAGAAGAAAAGAGAAA
1 AAAGAA-AACAAAAGAGAAA
291 TGGCGACTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.05, G:0.20, T:0.03
Consensus pattern (20 bp):
AAAGAAAACAAAAGAGAAAC
Found at i:1489 original size:10 final size:10
Alignment explanation
Indices: 1471--1512 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1461 GTAGTTTTGC
*
1471 TAAGCTAGTT
1 TAAGTTAGTT
1481 TAAGTTAGTT
1 TAAGTTAGTT
*
1491 AAAGATTAGTT
1 TAAG-TTAGTT
1502 T-AGTTAGTT
1 TAAGTTAGTT
1511 TA
1 TA
1513 TCGAGTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.26
10 14 0.52
11 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.45
Consensus pattern (10 bp):
TAAGTTAGTT
Found at i:6367 original size:20 final size:20
Alignment explanation
Indices: 6338--6383 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
6328 CAAGGCCAAA
6338 ACCC-AAATTAAGATAAGTG
1 ACCCAAAATTAAGATAAGTG
6357 ACCCAAAATTAAGATAAGTG
1 ACCCAAAATTAAGATAAGTG
*
6377 GCCCAAA
1 ACCCAAA
6384 GAAAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (20 bp):
ACCCAAAATTAAGATAAGTG
Found at i:8376 original size:333 final size:329
Alignment explanation
Indices: 7478--8662 Score: 1447
Period size: 333 Copynumber: 3.6 Consensus size: 329
7468 TCCTTTGTTA
* * * *
7478 CCAAAAACCGTGATGATTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCGAAAAAAT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCG-AAAAAT
* ** ** * * *
7543 TTTCCTAAATTTTTTTGCCATGATACTCATAAAAAATATATAATTAAACGCCAAATATATTGAAA
65 TTTCCTCAA-TTTTCGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAA
* * * *
7608 GGCTTTTCACGCTTCTAATATCGATTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
129 GGCTTCTCACGATTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * *
7673 CATGATACAAATGCTTGTAAAACCAAATCCTTAAATCCAATGTGGTTGAGATTTTC-TTAGATGG
194 CATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTCGTTAGATGG
*
7737 ATATAGATATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGACCACGAATCA
258 ATATAGATATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGGG-CCACGAA-CG
7802 CGTTTTTAG
321 CGTTTTTAG
* * * * *
7811 GCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAACATT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
* * * *
7876 TCTTCTCAATTTTCGGCCACCATATTCAT-AAAAA-ATAT-A--CAACGCCAAAAAGATTGAAGG
66 T-TCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAG
* *
7936 GCTTCTCACGTTTCTAATATTGTTTTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGA
130 GCTTCTCACGATTCTAATATCG---TTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGA
* * *
8001 AATCAT-ATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTCGTTAGAT
192 AA-CATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGAT
** * * *
8065 AAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCACGTAA
256 GGATATAGATATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCG-GGCCACG-AA
8130 CGCGTTTTTAG
319 CGCGTTTTTAG
* * * *
8141 CCAAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATCGACCTGAAAGAA
1 CC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AA
* * * * *
8206 TTTACCTCAACTTGT-AGCCACAATACTCGTAAAAAATATATAATTCAACACCAAAAAGATTGAA
64 TTTTCCTCAA-TTTTCGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA
* * * *
8270 AGGCTAT-TCACGATTCTAATATTGTTTTTCCTAATTTGTCCGAATTAATTCCTAATTGAATCGA
128 AGGCT-TCTCACGATTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * *
8334 AACATGATTCATATGCTCGTAAAAACAAATGCTTAAATCCAATGTGGGTAAGATTTGGTTAGATG
192 AACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATG
*
8399 GATATAGATATTTCAATGAGACTTGGTGCCAAAAATCGTGCAAAACAGAGCCGGAGCTC-CGGAA
257 GATATAGATATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGG-GC-CAC-GAA
*
8463 TGCGTTTTTAG
319 CGCGTTTTTAG
* * * *
8474 TCAAAAACCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAGAAATT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
* * * * * * *
8539 TCTCCTCAATTTTGGGCCACAATACTAATAAAAAATACATAACTCAATGCCAAAAAGACTGAAGG
66 T-TCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAG
*
8604 GCTTCTCAC-ACTTCTAATATCGTTTTTCCTACCTTTTTCCGAATTAATTTCTAATTAAA
130 GCTTCTCACGA-TTCTAATATCGTTTTTCCTA-ATTTTTCCGAATTAATTTCTAATTAAA
8663 AAAATTATAT
Statistics
Matches: 730, Mismatches: 96, Indels: 52
0.83 0.11 0.06
Matches are distributed among these distances:
327 36 0.05
329 5 0.01
330 155 0.21
331 92 0.13
332 164 0.22
333 236 0.32
334 3 0.00
336 38 0.05
337 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (329 bp):
CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
TTCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGG
CTTCTCACGATTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGAAACA
TGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGGATA
TAGATATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGCCACGAACGCGTTT
TTAG
Found at i:9059 original size:25 final size:25
Alignment explanation
Indices: 9022--9069 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
9012 GGGTTTCAGA
* *
9022 CTAATTTTTTTAGATCGAAAGCAGG
1 CTAATTTTGTTAGATAGAAAGCAGG
9047 CTAATTTTGTTAGATAGAAAGCA
1 CTAATTTTGTTAGATAGAAAGCA
9070 TGAATAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (25 bp):
CTAATTTTGTTAGATAGAAAGCAGG
Found at i:13050 original size:127 final size:133
Alignment explanation
Indices: 12898--13160 Score: 344
Period size: 137 Copynumber: 2.0 Consensus size: 133
12888 TTCCCGATTG
*
12898 TACCCTTTTTTCAAATATATTTCTAAA-TT-GA-CATT-A-TTA-A-AA-TTTATTATTTAAAAA
1 TACCCTTTTTTCAAATATATTTCTAAATTTCCATCATTAATTTAGATAATTTTATTATTTAAAAA
* * *
12955 TTAATTATAAAATTTCAATTTAGACCGAATTTTAAGTTTGTAAAATTGATTTTTATTGATGAACA
66 TTAATTA-AAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTGATAAACA
13020 TGCA
130 TGCA
* * *
13024 TACCCTTTTTTTCAATTATGTTTCTAAATTTCCATTATTAAAATTTAGTATAATTTTATTATTTA
1 TACCC-TTTTTTCAAATATATTTCTAAATTTCCATCATT--AATTTAG-ATAATTTTATTATTTA
* *
13089 AAAATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTCAAATTGATTTTCGTTGATAA
62 AAAATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTGATAA
13154 ACATGCA
127 ACATGCA
13161 AATTTCCTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
126 5 0.04
127 20 0.17
128 2 0.02
129 1 0.01
130 3 0.03
133 1 0.01
134 3 0.03
136 1 0.01
137 58 0.50
138 22 0.19
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (133 bp):
TACCCTTTTTTCAAATATATTTCTAAATTTCCATCATTAATTTAGATAATTTTATTATTTAAAAA
TTAATTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTGATAAACAT
GCA
Found at i:13377 original size:22 final size:22
Alignment explanation
Indices: 13352--13522 Score: 107
Period size: 22 Copynumber: 7.7 Consensus size: 22
13342 AAAGTAGGTG
13352 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
13374 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
13397 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
13418 TGGTTACCAAAA-TTCATATTGA
1 TGGTTATCAAAATTTCATA-AGA
** **
13440 AAGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
13462 AGGTTATCAAACTTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
13484 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
13506 TCAGGTTATTAAAATTT
1 T--GGTTATCAAAATTT
13523 TTTAGGAAGG
Statistics
Matches: 111, Mismatches: 28, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 83 0.75
23 10 0.09
24 12 0.11
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:13455 original size:66 final size:66
Alignment explanation
Indices: 13349--13584 Score: 208
Period size: 66 Copynumber: 3.5 Consensus size: 66
13339 AGAAAAGTAG
* ** * *
13349 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTCCA
13413 TA
65 TA
* * *
13415 GTGTGGTTACCAAAA-TTCATATTGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAACTTTCA
1 GTGTGGTTACCAAAATTTCATA-AGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCCA
13479 TA
65 TA
* * * ** * *** *
13481 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTAGGAAGGTTATTGGAATTTC
1 GTGTGGTTACCAAAATTTCATAAGA--AAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCC
13546 ATA
64 ATA
** * *
13549 GTGTGGTTTTCACAATTTTAT-AGAAAGGTTATCAAA
1 GTGTGGTTACCAAAATTTCATAAGAAA-GTTATCAAA
13585 GAGATTATCA
Statistics
Matches: 139, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
65 9 0.06
66 73 0.53
67 8 0.06
68 49 0.35
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCCAT
A
Found at i:13614 original size:22 final size:22
Alignment explanation
Indices: 13589--13648 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
13579 ATCAAAGAGA
*
13589 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
13611 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
13633 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
13649 AGGAGGTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:13702 original size:22 final size:23
Alignment explanation
Indices: 13661--13722 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
13651 GAGGTAAGGA
13661 GGTTATC-AAATTTTCATAGTGT
1 GGTTATCAAAATTTTCATAGTGT
* * *
13683 GTTTATTAAAATTTT-TTAGTGT
1 GGTTATCAAAATTTTCATAGTGT
13705 GGTTATCAAAA-TTTCATA
1 GGTTATCAAAATTTTCATA
13723 TGAAGGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.09
22 22 0.69
23 7 0.22
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (23 bp):
GGTTATCAAAATTTTCATAGTGT
Found at i:13811 original size:22 final size:23
Alignment explanation
Indices: 13759--14013 Score: 112
Period size: 22 Copynumber: 11.6 Consensus size: 23
13749 TAAGGAGTAC
* *
13759 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
13780 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
13801 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
13826 -AGAAATTT-ATAG-GAAT-ATTAT
1 CA-AAATTTCATAGAG-ATGATTAT
* *
13847 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
13869 CAAAATTTCAAAGTGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * * *
13891 CCAAATTACATA-ATGA-AAATAT
1 CAAAATTTCATAGA-GATGATTAT
* * * *
13913 CAAAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* *
13935 CAAAATTTTATAGAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
13957 CAAAATTCCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
13979 CAAATTTTCA-AAATG-TGATTAC
1 CAAAATTTCATAGA-GATGATTAT
14001 CAAAATTTCATAG
1 CAAAATTTCATAG
14014 TGGTATTTAT
Statistics
Matches: 180, Mismatches: 34, Indels: 38
0.71 0.13 0.15
Matches are distributed among these distances:
20 10 0.06
21 22 0.12
22 125 0.69
23 5 0.03
24 6 0.03
25 12 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:13939 original size:66 final size:66
Alignment explanation
Indices: 13844--13969 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
13834 ATAGGAATAT
* ** * * * *
13844 TATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGTGAGGTTATCCAAATTACATAATGAAA
1 TATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATGAAA
13909 A
66 A
* * *
13910 TATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTCCATAA
1 TATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAA
13970 AGAGGTTATC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (66 bp):
TATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATGAAA
A
Found at i:13980 original size:66 final size:66
Alignment explanation
Indices: 13842--13988 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 66
13832 TTATAGGAAT
* ** * * * * *
13842 ATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGTGAGGTTATCCAAATTACATAATGA
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAAGA
13907 A
66 A
* * * *
13908 AATATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTCCATAAAGA
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAAGA
*
13973 G
66 A
* *
13974 GTTATCAAATTTTCA
1 ATTATCAAAATTTCA
13989 AAATGTGATT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (66 bp):
ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAAGA
A
Found at i:14141 original size:22 final size:22
Alignment explanation
Indices: 14094--14268 Score: 119
Period size: 22 Copynumber: 8.0 Consensus size: 22
14084 CTATGGAGTG
* *
14094 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATATAGAGGTT
*
14114 ATCAAAATTTCATATAAAGGTT
1 ATCAAAATTTCATATAGAGGTT
**
14136 ATCAAAATTTCATAATTTA-GTT
1 ATCAAAATTTCAT-ATAGAGGTT
* *
14158 TTCAAAATTTCATA-AGTGGGTT
1 ATCAAAATTTCATATAG-AGGTT
* * *
14180 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATAGAGGTT
* *
14202 ATCAACATCTCATAGT-GAGGTT
1 ATCAAAATTTCATA-TAGAGGTT
* * * **
14224 TTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATAGAGGTT
14246 ATCAAAATTTCATA-AGGAGGTT
1 ATCAAAATTTCATATA-GAGGTT
14268 A
1 A
14269 AGAAAAATTT
Statistics
Matches: 120, Mismatches: 26, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
20 12 0.10
21 2 0.02
22 101 0.84
23 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATAGAGGTT
Found at i:14201 original size:66 final size:66
Alignment explanation
Indices: 14107--14268 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 66
14097 AAAATTTCAA
* ** * * *
14107 GGAGGATATCAAAATTTCATATAAAGGTTATCAAAATTTCATAATTTA-GTTTTCAAAATTTCAT
1 GGAGGTTATCAAAATTTCATATGGAGGTTATCAAAATCTCAT-AGTGAGGTTTTCAAAA-TTCAT
14171 AAG
64 AAG
* * * * * *
14174 TG-GGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGAGGTTTTCAAAATTCCTTA
1 GGAGGTTATCAAAATTTCATATGGAGGTTATCAAAATCTCATAGTGAGGTTTTCAAAATTCATAA
14238 G
66 G
*
14239 GGAGGTTATCAAAATTTCATAAGGAGGTTA
1 GGAGGTTATCAAAATTTCATATGGAGGTTA
14269 AGAAAAATTT
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
65 10 0.13
66 66 0.86
67 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (66 bp):
GGAGGTTATCAAAATTTCATATGGAGGTTATCAAAATCTCATAGTGAGGTTTTCAAAATTCATAA
G
Found at i:14274 original size:22 final size:22
Alignment explanation
Indices: 14239--14282 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
14229 AATTCCTTAG
*
14239 GGAGGTTATC-AAAATTTCATAA
1 GGAGGTTAACAAAAATTT-ATAA
*
14261 GGAGGTTAAGAAAAATTTATAA
1 GGAGGTTAACAAAAATTTATAA
14283 AAGGGTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (22 bp):
GGAGGTTAACAAAAATTTATAA
Found at i:14337 original size:22 final size:22
Alignment explanation
Indices: 14309--14362 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
14299 CGATAATATC
*
14309 GTTATTAAAGTTTCAT-AGGAAG
1 GTTATTAAAATTTCATAAGG-AG
*
14331 GTTATTAAAATTTTATAAGGAG
1 GTTATTAAAATTTCATAAGGAG
*
14353 GTTATCAAAA
1 GTTATTAAAA
14363 GTAGTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.37
Consensus pattern (22 bp):
GTTATTAAAATTTCATAAGGAG
Done.