Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012846.1 Corchorus olitorius cultivar O-4 contig12879, 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: 18234
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4084 original size:25 final size:24
Alignment explanation
Indices: 4056--4112 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 24
4046 GTGAATTGTA
4056 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAATAATTAA-ACATT
*
4081 AAATAAATTTAATAATTAAACATT
1 AAATAAATTGAATAATTAAACATT
4105 AAA-AAATT
1 AAATAAATT
4113 CAAGACTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 5 0.16
24 8 0.26
25 18 0.58
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTGAATAATTAAACATT
Found at i:15509 original size:318 final size:318
Alignment explanation
Indices: 14799--15747 Score: 1213
Period size: 319 Copynumber: 3.0 Consensus size: 318
14789 CCATAAGAAT
* * * *
14799 ATCACGGTTTTTGGCTAAAAACGTGTTTTGGGGCCTGACTTAGTTTTGCTTGATTTTTGGCAGAA
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCTGACTTAGTTTTGCATGATTTTTGGCAGAA
* *
14864 AGACTTCTT-AAA-A-CTATATTCATATAACCAAATCTCAGCCAATTTGGATTT---A---TTTT
66 AGACTACTTGAAATATTTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGATTTTTTT
* * * * *
14920 TACGAGCATTTGAATCTTGTTTCGATTTCATTAAAAATCAATTCGGAAAAAAAAATATCGAAAAA
131 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G-AAAAAAAA-ATGGAAAAA
* * *
14985 CGATCTCGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCAGAGTA
193 CGATATTGGAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTCAATTATATATTTTTT-AGAGTA
* *
15050 GTT-TGGCAAAAAATTGAGAAAAAAGATTTCGGGTCAATTTTTAGCCGAAATTGTGTAAAAACC
256 -TTGTGGCAAAAAATTGAGAAAAAAGATTTCGGGTCAATTTTTAGCCGAAATCGTATAAAAACC
* * * * * *
15113 ATCACGGTTTTTGCCTAAAAACACGTTTCGGGACCCCGGCTCAGTTTTGCATGATTTTTGGAAGA
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGG-CCCTGACTTAGTTTTGCATGATTTTTGGCAGA
15178 AAGACTACTTGAAATATTTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAAGATTTTT
65 AAGACTACTTGAAATATTTATATTCATATAACCAAATCTCAGCCAATTTGGATTT-AAGATTTTT
** *
15243 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGTTAAAAAAATGGAAAAAA
129 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATGGAAAAAC
* * *
15308 GATATTGGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTTAA-T-TATATTTTTTAGAGTATT
194 GATATTGGAAGCGTGAAAA-CCCTTCAATTTTTTTGGCGTTCAATTATATATTTTTTAGAGTATT
* * * * * **
15371 GTGGCAAAAAATTGAGTATAAAGCTTTCGGGTCAATATTTCGCCGAAATCGTATATTAACC
258 GTGGCAAAAAATTGAGAAAAAAGATTTCGGGTCAATTTTTAGCCGAAATCGTATAAAAACC
* *
15432 ATCACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCTGACTTAGTTTTGCATGATTTTTCGCAGAA
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCTGACTTAGTTTTGCATGATTTTTGGCAGAA
* ** *
15497 AGACTCCTTGAAATATTTATATTTGTATAACCAAATCTCAACCAATTTGGATTTAAGGATTTCTT
66 AGACTACTTGAAATATTTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA-GATTT-TT
* *
15562 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATTGGAAACA
129 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAAAATGGAAAAA
* *
15627 CGATATTGTAAACGTGGAAAACCCTTCAATTTTTTTTGGCGTTCAATTATATATTTTTTTAGAGT
193 CGATATTGGAAGCGT-GAAAACCCTTCAA-TTTTTTTGGCGTTCAATTATATA-TTTTTTAGAGT
* * * *
15692 -TGTGTGGCAAAAAAAATGAGAAAAAAGTTTTCGGATCAATTTTTATCCGAAATCGT
255 AT-TGTGGC-AAAAAATTGAGAAAAAAGATTTCGGGTCAATTTTTAGCCGAAATCGT
15748 GTAGTTCAAG
Statistics
Matches: 548, Mismatches: 64, Indels: 35
0.85 0.10 0.05
Matches are distributed among these distances:
314 28 0.05
315 35 0.06
316 3 0.01
317 3 0.01
318 122 0.22
319 134 0.24
320 43 0.08
321 24 0.04
322 44 0.08
323 11 0.02
324 18 0.03
325 83 0.15
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (318 bp):
ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCTGACTTAGTTTTGCATGATTTTTGGCAGAA
AGACTACTTGAAATATTTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGATTTTTTT
TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATGGAAAAACGA
TATTGGAAGCGTGAAAACCCTTCAATTTTTTTGGCGTTCAATTATATATTTTTTAGAGTATTGTG
GCAAAAAATTGAGAAAAAAGATTTCGGGTCAATTTTTAGCCGAAATCGTATAAAAACC
Found at i:16696 original size:326 final size:324
Alignment explanation
Indices: 16016--18227 Score: 2509
Period size: 326 Copynumber: 6.9 Consensus size: 324
16006 GGAGCAATCG
* * * * * *
16016 CATCATGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTAGGC-G
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
* ** * * * *
16080 CAAAGACTCCTTG----ATCTATATTTATCCAACAAAATCTTAGCCACA-TTAGATATAAGGATT
66 -AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCA-ATTTGGATTTAAGGATT
* * * * *
16140 TGTTTTTACAAGTATCTGAATCTTGTTTCGATATAATTAGAAATTAATTCGG---AAAATGGGAA
129 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAA
* * * * * *
16202 AATGATATCAGAAGCGTGAAAATCCCGCCAATCGTTTTGGTGTTTAATTATAT-T-TTTTTTTCA
194 AACGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTTT-A
* * * * * * * *
16265 AAGCATTGTGGCAAAAAATTGAGTAAAAATTTTTCGGGTCAATATTTCGTCGAAATCGTGTATTA
258 GAGTATTGTGGCAAAAAATTGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAATA
16330 AC
323 AC
* * * * *
16332 CATCACGATTTTTGGCTAAAAATGCGTTTCGAGGCCCCGGTTCAATTTTGCATGATTTTTGGCAG
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
*
16397 AAAGACTCCTTGAAATATCTATATTCATATAATCAAATCTCAGCCAATTTGGATTTAAGGATTTG
66 AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTG
* * * *
16462 TTTTTACGAGCATTTGAATCTTGTTTCAATTTAATTAAAAATAAATTCGGAAAAAAATCGAAAAA
131 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAA
* * * *
16527 CGATATTGGAAGCGTGAAAAACCCTTCAAT-TTTTGTGGCATTGAATTATATATATATTTTTTAG
196 CGATATTAGAAGCGTGAAAATCCCGTCAATCTTTT-TGGCGTTGAATTATATATAT-TTTTTTAG
* * * *
16591 AGTATTGTGGTAAAAAATTGAGAAAAAAGTTTTCGTGTCAATTTTTAGCTGAAAATCGTGTAATA
259 AGTATTGTGGCAAAAAATTGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCG-AAATCGTGTAATA
16656 AC
323 AC
16658 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
** * *
16723 AAAGACTCCTTGAAATATCTATATAAATATAACCAAATATCAGCTAATTTGGATTTAAGGATTTG
66 AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTG
* * *
16788 TTTTTACGAGCATCTAAATCTTATTTC-AGTTTAACTT-GAAATTAATTCCGG-AAAAAATGGAA
131 TTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAA-TTAGAAATAAATT-CGGAAAAAAATGGAA
* * * *
16850 AAACGATATTTGAAGCGTGAAAAACCCTTCAAT-TTTTTTGCGTTGAATTATATATATATATATA
193 AAACGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTG----A-AT-TATATATAT-
* *
16914 TATATATTTCAGAGTAGTT-TGGCCAAAAAA-TGA-GAAAAAGTTTTCGGGT-AAATTTTAACCG
251 T-T-T-TTT-AGAGTA-TTGTGG-CAAAAAATTGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCG
* *
16975 AAATCTTGTACTAAC
310 AAATCGTGTAATAAC
* * * * ** * * *
16990 CATCATGGATTTTTGACTAAAAACGCGTTTTGGGGTCCCAACTCGGTTTTACATGATTTTTGACA
1 CATCACGG-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCA
* * * *
17055 CAAAGACT-CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTCAAGGATTT
65 GAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTT
* * * *
17119 GTTTTTACGTGCAGCTGATTCTTGTTTCGATTTAATTAGAAATAAATTC-TAAAAAAATGGAAAA
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAA
* **
17183 ACGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTT-GCGTTTAA-T-TATAT-TTTTTCCAGA
195 ACGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTTTAGA
* * *
17244 GTATTGTGGCAAAAAATTGAGTAAAAAGTTTTCAGGTCAGTATTTTA-CCGAAATCGTGT-ATAA
260 GTATTGTGGCAAAAAATTGAGGAAAAAGTTTTCGGGTCAAT-TTTTAGCCGAAATCGTGTAATAA
17307 C
324 C
* * * * ** *
17308 CATCACGGTTTTTTGCTAAAAATGCGTTTCGAGGCCCCGGATCAGTTTAACAAGATTTTTGGCAG
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
*
17373 AAAGACTCCTTGAAATATCTATATTCATACAACCAAATCTCAGCCAATTTGGATTTAAGGATTCT
66 AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATT-T
* * * * * *
17438 G-GTTTACGAGCATTTCAATCTTGTTTCAATTTAATTAAAAATAAATTCGGAGAAAAATGGAAAA
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAA
* * * *
17502 ACGATATTAGAAGCGTGAAAATCCCG-CGAATCTTTAAT-GCGTTTAA--CTATATCTTTTTTTA
195 ACGATATTAGAAGCGTGAAAATCCCGTC-AATCTTT-TTGGCGTTGAATTATATATATTTTTTTA
* * * * *
17563 GAGTATTGTGGCCAAAAATTGAGGAAAAAGTTTCCGGGTCAATATTTAGCCGAAATTGTGTACTT
258 GAGTATTGTGGCAAAAAATTGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTA-AT
17628 AAC
322 AAC
* * * * ** *
17631 CATTAAGGTTTTAGGATAAAAACGCGTTTTC-GGGCCCCGATTTAGTTTTGCATGATTTTTGGCA
1 CATCACGGTTTTTGGCTAAAAACGCG-TTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCA
* * * *
17695 GAAAGACTTCTTGAAATATTTATATTCATATAACCAAATCTCGGCCAAGTTGGATTTAAGGATTT
65 GAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTT
* * * * *
17760 GTTTTTACGAGTATTTGAATCTTATTTCGATTTAATTAAAAATAAATTCGGAAAAAAAATATCGA
130 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAAAA-ATGGA
* * * *
17825 AAAACGATATTGGAAGCGTGAAAA-CCCTTCAATTTTTTTGGCGTTGAA-T-TATATATTTTTTC
192 AAAACGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTTT
*
17887 AGAGTAGTT-TGGCAAAAAAATTGAGGAAAAAGTTTTC-GGTCAATTTTTAGCCGAAATCATGTA
257 AGAGTA-TTGTGGC-AAAAAATTGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTA
17950 ATAAC
320 ATAAC
* * *
17955 CATCACGGATTTTGGCTAAAAACGCG-TT-GGGGCTCCGGCTCAGTTTTGCATGATTTTTGACAG
1 CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
* * * *
18018 AAAGACTACTCGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAGGGATTTA
66 AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTG
* *
18083 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTGG-AATAAATGGAAAAA
131 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAA
* *
18147 CGATATTAGAAACGTGAAAATCCCGTCAATCTTTTTGGCGTT---TAAT-TATATTTTTTTAGAG
196 CGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTTTAGAG
18208 TATTGTGGCAAAAAATTGAG
261 TATTGTGGCAAAAAATTGAG
18228 TATAAAG
Statistics
Matches: 1614, Mismatches: 218, Indels: 128
0.82 0.11 0.07
Matches are distributed among these distances:
316 88 0.05
317 83 0.05
318 144 0.09
319 85 0.05
320 106 0.07
321 56 0.03
322 140 0.09
323 205 0.13
324 32 0.02
325 116 0.07
326 275 0.17
327 6 0.00
329 1 0.00
330 2 0.00
331 60 0.04
332 112 0.07
333 66 0.04
334 17 0.01
335 12 0.01
336 8 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (324 bp):
CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
AAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTG
TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAA
CGATATTAGAAGCGTGAAAATCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTTTAGAG
TATTGTGGCAAAAAATTGAGGAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAATAAC
Done.