Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017888.1 Corchorus olitorius cultivar O-4 contig17921, 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: 28570
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6504 original size:12 final size:12
Alignment explanation
Indices: 6487--6512 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6477 TTTAAAAATA
6487 AAAAAACTATTT
1 AAAAAACTATTT
6499 AAAAAACTATTT
1 AAAAAACTATTT
6511 AA
1 AA
6513 TAATATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAAACTATTT
Found at i:16815 original size:15 final size:16
Alignment explanation
Indices: 16790--16819 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16780 AATAATTATT
16790 TTTAGATTATAATATA
1 TTTAGATTATAATATA
16806 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
16820 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:17870 original size:332 final size:331
Alignment explanation
Indices: 17167--19214 Score: 1970
Period size: 332 Copynumber: 6.2 Consensus size: 331
17157 AATACTTTAC
* * * *
17167 TTCATCTAA-CTAAATCTCAGCAACATTGGATTTAAGAATTTTTTTTTTATGAGCATCTGAATCT
1 TTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAATCT
* * * *
17231 TGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTAAAAAG
64 TGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG
* * * *
17296 CACTTCAATCTTTTTTGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAG
129 CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACTAAAATTGAGGA-
* * * *
17360 AA-ATCTTT-TGTGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTTCTAACAAACCATCACGG
193 AATATTTTTCTG-GTCAATTTTTGCAAAATTTTAGCCGAAATC--G-TGTAA-TAACCATCACAG
* * * * * *
17423 TTTTTGGCTAAAAACGCATTCCCGAGAC-CTGACTCAATTTTGCATGATTTTTTGCTCCAAGACT
253 TTTTTGGCTAAAAACGCATT-CCGGGGCTC-GGCTCAATTTTGCATGATTTTTGGCGCCGAGACT
*
17487 ACTTGAAATATCTATA
316 CCTTGAAATATCTATA
** *
17503 TTTGTCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
** * * *
17568 TTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTGGAAA-CGTCAAAAGC
66 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATT-AAAAGCGTGAAAAGC
* * * * * *
17632 CCTTCAATCTTTTTGGCATTGAACTATATATTTTTTATAAGTATTTTAGCCTAAAGTTCAGGAAA
130 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACTAAAATTGAGGAAA
** * *
17697 TATTTTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATGACCATCACAGTTTTTGG
195 TATTTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGG
* * * * * * * *
17762 CTAAAAAAGCGTTCTGGGGCTTCGGCTAAATTTTGCATGATTTTTGGCGTCAAGACTCCTTTAGA
260 CTAAAAACGCATTCCGGGGC-TCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAA
*
17827 TATCCATA
324 TATCTATA
* * *
17835 TTCATCTAATCAAATCTTAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * **
17900 TTTCGATTTTACTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTT
66 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* * * * * * *
17964 CTCCAATCCTTTTGGTGTTAAATTATATATATATTTTATGAGTATTTTA-TCAAGAAATAG-GAG
131 CTTCAATCTTTTTGGCGTTGAATTATATAT-T-TTTTATGAGTATTTTAGACTA-AAATTGAG-G
* * * * * * *
18027 AAAAAATTTTCGGGTCATTTTTTGCAAAGTTTTAGCCAAAATCGTGTACTAACCATCACAGTTTT
192 AAATATTTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAG-TTT
* * * * * * * *
18092 TTTGTTAAAAACGCATTTCGGGGCCCGGTTCAGTTTTACATGATTTTTGGCGCCGACACTCCTTG
256 TTGGCTAAAAACGCATTCCGGGGCTCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTG
18157 AAATATCTATA
321 AAATATCTATA
* * * * *
18168 TTCATCTGATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
18233 TTTCGATTTAATAAAAAATTAATTCAGAAAAAATATGAAAAACGATATTAACAGCATGAAAAGCC
66 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
*
18298 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTAT-GACTAAAAATTGAGGAAA
131 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACT-AAAATTGAGGAAA
* * * * * * *
18362 TATCTTTCGGGTCAATTTTTGCAATATGTTA-CCAGGAATCGTGTAATAATCATCACTGTTTTTG
195 TATTTTTCTGGTCAATTTTTGCAAAATTTTAGCC-GAAATCGTGTAATAACCATCACAGTTTTTG
* * * * *
18426 CCTAAAAACGTATTCCGGGGC-CGGTTCAATTTTGAATGATTTTTTGCGCCGAGACTCCTTGAAA
259 GCTAAAAACGCATTCCGGGGCTCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAA
18490 TATCTATA
324 TATCTATA
* ** * * *
18498 TTAATCTAATCAAA--T---CC-C---------AACCA-TTGTTTTTACAAACATCTGAATCATG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * *
18547 TTTCGTTTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAGAGTGAAAAACC
66 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* *
18612 CTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT-GACTAAAAATTGA-GAGA
131 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACT-AAAATTGAGGA-A
* *
18675 ATATTTTTCTGGTC-ATTTCTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GTTTTT
194 ATATTTTTCTGGTCAATTT-TTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAG--TTT
*** * ** * * * * **
18738 TTTATTATTAAAACGCGTTTTGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCATCGAGACTCC
256 TTGGCTA--AAAACGCATTCCG-GGGCTCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCC
**
18803 TCAAAATATC--TA
318 TTGAAATATCTATA
* * * *
18815 -T-A--T--T-AAATCTCAGCCACATTGCATTTAAGGATTTATTTTCACGAGCATCTGAATCTTC
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* **
18873 TTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGAGAAAATTC
66 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* * * * * ** * *
18937 CTCCAATATTTTTAGAGTTAAATTATATAAATTTTATGAGTATTTTAGACAAAAATTGAGGAAAA
131 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACTAAAATTGAGGAAAT
* * * * * * * *
19002 ATGTTTCTGGTAAATTTTTCCAAAATATTAGCCAAAATCGTGTACGTTAGTCGAAATCACAGTTT
196 ATTTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA--ATA-AC--CATCACAGTTT
* * * * *
19067 TTTGCTAAAAACGCGTTCCAGGGTCTCGGTTCAATGTTGCATGATTATTT-GCGCCGAGACTCCT
256 TTGGCTAAAAACGCATTCC-GGGGCTCGGCTCAATTTTGCATGATT-TTTGGCGCCGAGACTCCT
* *
19131 TAAAATATCTACA
319 TGAAATATCTATA
* * *** * *
19144 TTCATTTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAATCATG
1 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
19208 TTTCGAT
66 TTTCGAT
19215 ATTAGAATCA
Statistics
Matches: 1406, Mismatches: 243, Indels: 127
0.79 0.14 0.07
Matches are distributed among these distances:
310 3 0.00
311 1 0.00
312 1 0.00
313 8 0.01
314 177 0.13
315 15 0.01
316 2 0.00
317 11 0.01
318 3 0.00
319 38 0.03
324 1 0.00
325 117 0.08
326 55 0.04
327 51 0.04
328 6 0.00
329 9 0.01
330 66 0.05
331 82 0.06
332 221 0.16
333 201 0.14
334 81 0.06
335 130 0.09
336 125 0.09
337 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (331 bp):
TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACTAAAATTGAGGAAAT
ATTTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGC
TAAAAACGCATTCCGGGGCTCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATA
TCTATA
Found at i:20071 original size:330 final size:329
Alignment explanation
Indices: 19234--20851 Score: 1746
Period size: 330 Copynumber: 4.9 Consensus size: 329
19224 ATGAAAAACC
* * **
19234 CTTCAATCTTTTTGGTGTTGAATTATATAATTTTTATGAGTATTGTGGA-TAAAACTTGAGGAAA
1 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT-TTCACTAAAA-TTGAGGAAA
* * * *
19298 TAA-CTTTCGAGTCAATTTTTGC-AAAATTCTAGCCGAAATCGTGTAATAATCATCACCGTTTTT
64 -AATCTTTCGAGTCAATTTTTGCAAAAATT-TAGCCGAAATCATGTACTAACCATCACAGTTTTT
* * * *
19361 GGCTAAAAACGCGTTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGTGCCAAGACTCTTTGA
127 GGCTAAAAACGCATTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGA
* * * * * * * * *
19426 GATATCCATATTCAT-TTAATCTAATGTCAGCTACATTGGATTGAAGAATTTGTTTTTACGAACA
192 AATATCTATATTCATCTT-ATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCA
* * *
19490 TCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAAAGC
256 TCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGC
19555 GTGAAAAGTA
320 GTGAAAAGTA
* * * * *
19565 CTCCAATCTTTTTGGCGTT-ATATTGTATATATTTTAT--G------CA--AAATTTGACAGAAA
1 CTTCAATCTTTTTGGCGTTGA-ATTATATATTTTTTATGAGTATTTTCACTAAAATTGA-GGAAA
* * *
19619 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGA
64 AATCTTTCGAGTCAATTTTTGCAAAAATTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGG
* * * *
19684 CTAAAAACGCATGT-C-GGGACCCGACTCAGTTTTGCATGATTTTTTGTGTCGAGACTCCTTGAA
129 CTAAAAACGCAT-TCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAA
*
19747 ATATTTATATTCATCTTATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATC
193 ATATCTATATTCATCTTATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATC
*
19812 TGAATCTTGTTTTGATTTAATTAAAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTG
258 TGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTG
*
19877 AAAAAG-G
323 -AAAAGTA
* *
19884 CTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCACTAGAAATTGTGGAAA
1 C-TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCACTA-AAATTGAGGAAA
* *
19949 AATCTTTCGAGTCAATTTTTGCAAAAATTTAGCCGAAATCATGTACTAACCATCACGGTTTTCGG
64 AATCTTTCGAGTCAATTTTTGCAAAAATTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGG
* * * * *
20014 CTAAAACCGCATTCCAGGG-CCCGGCTTAGTTTTGCATGATTTTTGGGGCCAAGACTCCTTGAAA
129 CTAAAAACGCATTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAA
* * * *
20078 TATCTATATTCATCTAACCAAATCTCAGACATATT-AGATTTAAGGATTTGTTTTTACGAGCATC
194 TATCTATATTCATCTTATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCATC
* ** * * *
20142 TGAATCTTGTTTTGATTTAATTAAAAATTAATTTGGAAAATAGGAAAAACGATATTAAAAACGTC
258 TGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTG
***
20207 AAAAACC
323 AAAAGTA
* * * *
20214 CTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATAAGTATTTT-AGCCAAAAATTGAGAAAA
1 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCA--CTAAAATTGAGGAAA
* * * * * * * * * * *
20278 TAAT-TTTCTAATCAGTTTTTACAAAATTTTAGCCGAAATCGTATAATAATCATCATAGTTTTTT
64 -AATCTTTCGAGTCAATTTTTGCAAAAATTTAGCCGAAATCATGTACTAACCATCACAGTTTTTG
* * * * *
20342 GCTAAAAAAGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAG
128 GCTAAAAACGCATTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAA
* * * * *
20407 ATAT-TCATATTCAT-TTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTATGTGCA
193 ATATCT-ATATTCATCTT-ATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCA
* * * *
20470 TTTGAATTTTGTTTCGATTTGATTACAAATTAATTCAGAAAAAATATGAAAAAC-AGTATTAAAA
256 TCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAG--AAAATATGAAAAACGA-TATTAAAA
*
20534 GCATGAAAAGTA
318 GCGTGAAAAGTA
* * * * *
20546 CTCCAATCCTTTTGACGTTGAATTATATA-TTTTTATGAGTATTTTTACTAGAAATCGAGGAAAA
1 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCACTA-AAATTGAGGAAAA
* * * *
20610 GTGTTTCTG-GTCAATTTTTGCAAAAATTTTAGCCGAAACCATGTACTAACACCATCACGGTTTT
65 ATCTTTC-GAGTCAATTTTTGCAAAAA-TTTAGCCGAAATCATGTACT-A-ACCATCACAGTTTT
* ** * * * **
20674 TGGCTAAAACCTTATTCTGGGG-CCTGACTCAGTTTTGCAGGATTTTTTATGCCAAGACTCCTTG
126 TGGCTAAAAACGCATTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTG
* * * * * *
20738 AATTATCTATATTTATCTAACCAAATCTCAGCCAC-TTAAATTTAAGGACTTGTTTTTACGAGCA
191 AAATATCTATATTCATCTTATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCA
* *
20802 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAA
256 TCTGAATCTTGTTTCGATTTAATTAAAAATTAATTC-AGAAAATATGAAA
20852 CAAAATTTTG
Statistics
Matches: 1077, Mismatches: 166, Indels: 88
0.81 0.12 0.07
Matches are distributed among these distances:
319 29 0.03
320 168 0.16
321 71 0.07
322 8 0.01
328 3 0.00
329 125 0.12
330 364 0.34
331 92 0.09
332 123 0.11
333 65 0.06
334 29 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (329 bp):
CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCACTAAAATTGAGGAAAAA
TCTTTCGAGTCAATTTTTGCAAAAATTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGGCT
AAAAACGCATTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
TCTATATTCATCTTATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
ATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAA
AGTA
Done.