Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015676.1 Corchorus olitorius cultivar O-4 contig15709, 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: 13044
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Found at i:1295 original size:17 final size:17
Alignment explanation
Indices: 1273--1308 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1263 AGCCCTCTTA
1273 ATCCATGATGATACCAC
1 ATCCATGATGATACCAC
1290 ATCCATGATGATACCAC
1 ATCCATGATGATACCAC
1307 AT
1 AT
1309 GTGGATGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (17 bp):
ATCCATGATGATACCAC
Found at i:8846 original size:16 final size:17
Alignment explanation
Indices: 8809--8846 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
8799 TTCTAACAAT
8809 TATT-TTTAGATTATAA
1 TATTATTTAGATTATAA
8825 TA-TATTTA-ATTATAA
1 TATTATTTAGATTATAA
8840 TATTATT
1 TATTATT
8847 ATTTATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTATTTAGATTATAA
Found at i:10028 original size:332 final size:328
Alignment explanation
Indices: 9202--11030 Score: 1509
Period size: 332 Copynumber: 5.6 Consensus size: 328
9192 ATACTTTACA
* * * * * *
9202 TCATCTAACCAAATCTCAGCAATATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
* * * * * * *
9267 TTCGATTTAATTAGAAATTAATTTAGAAAAAAATAAGAAATACAATATTAAAAGCGTAAAAATCC
66 TTCGATTTAATTAAAAATTAATCTAG--AAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCC
* *
9332 CTACAATC-TTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAAATGA-GAAGA
129 CTTCAA-CATTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAA-A
* * * * *
9395 AACCTTTCGTGTCAATTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACAAACCATCACGGTTT
192 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAA-TAA-CATCACAGTTT
* * * * * * * * ** *
9460 TTTGCTAAAAACA-TGTTCCGGGGACCTGACTCAATTTTGCATGATTTCTGGCTCTGAGACTACT
252 TTGGCTAAAAA-AGCGTTTCGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
9524 TGAAATATCTATAT
315 TGAAATATCTATAT
* * * * * * * * *
9538 TCATCTAATCAAATCTCACCCACTTTAGATTTAAGGATTTGTCTTTACGAGCGTCTGAATTTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
* * * *
9603 TTCGATTTAATTAGAAATTAATTTGGAAGAAATAGGAAAAACGATATTAGAAA-CGTCAAAAGCC
66 TTCGATTTAATTAAAAATTAATCTAGAA-AAATATGAAAAACGATATTA-AAAGCGTCAAAAGCC
* *
9667 CTTCAATC-TTTTTGGCGTTGAGTTATATATTTTTTATAAGTATTTTAGCCAAAAATTGAGGAAA
129 CTTCAA-CATTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * *
9731 TATCTTTCGGGTCAACTTTTACAAAATTTTAGTCGAAATCGTGTAATAACCATCACAGTTTTTGG
192 AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA-CATCACAGTTTTTGG
* * * *
9796 ATAAAAAAGCGTTTTGTGGCTCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAGA
256 CTAAAAAAGCGTTTCGGGGC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
9861 TATCTATAT
320 TATCTATAT
* * * *
9870 TCATCTAATCAAATCCCAGCCACATTGGATTTAAAAAATTATTTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
* * *
9935 TTCGA-TTAATTAAAAATTAATACT-GAAAAATATGAAAAATGATATTAAAAGCATGAAAAGTCC
66 TTCGATTTAATTAAAAATTAAT-CTAGAAAAATATGAAAAACGATATTAAAAGCGTCAAAAG-CC
* * * * *
9998 CCT-AACATTTTTGCCGTTAAATTATATATATTTTAGGAGTATTTTATCCAAAAATTGAGGAAAA
129 CTTCAACATTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * * * * * *
10062 ATTTTTCGGGTCATTTTTTACAAAACTTTAGCCAAAATCGTGTACGT--TATCACGGTTTTTGGC
193 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-ATAACATCACAGTTTTTGGC
* * * ** *
10125 TAAAAATGCGTTTCGGGGCACCAGCTCTGTTTTGCATGATTTTTGGCGCTGACACTCCTTGAAAT
257 TAAAAAAGCGTTTCGGGGC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* *
10190 AACTATGT
321 ATCTATAT
* * * * * * * * * * *
10198 TCATCTAATAAAATCTTAGCTAAATTGCATTTAAGATTTTTTTTTTTGACGAGTATTTGAATCAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGA-ATTTATTTTT-ACAAGCATCTGAATCTT
* * *
10263 ATTTCGATTTAATTAAAAATTAATTTAGAAAAAATATGGAAAACGATATTAAAAGCGTCAAAAGC
64 GTTTCGATTTAATTAAAAATTAATCTAG-AAAAATATGAAAAACGATATTAAAAGCGTCAAAAGC
* * * * * * *
10328 CCTTCAA-ACTTTTTGCCGTTGAATTATATATTTTTTACGAGAATTATGGCTAAAAATTGAGGAT
128 CCTTCAACA-TTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* * *
10392 ATATCTTTCGTGTCAATTTTTGC--AA----AGCCGAAATCGTGCAATAATCATCAC-GATTTTT
191 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA-CATCACAG-TTTTT
* * *** * *
10450 GGCTAAAAATGCGTTTCGTGGCCCATTTCAGTTTTGAATGATTTTTAGCGCCGAA-ACTCCTTGA
254 GGCTAAAAAAGCGTTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGA
*
10514 AATATCTATAC
318 AATATCTATAT
* * * *
10525 TCATCTAACCAAATCCCAG-C-CATT-G--TT-----TTTA----T--AAGAATCTGAATCGTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
* * * * * * * * *
10574 TTTGTTTTAATTAGAAATTAAT-TCAAAAAAAAAAGAAAAACGGTATTAGAAA-CGTGAAAAACC
66 TTCGATTTAATTAAAAATTAATCT-AGAAAAATATGAAAAACGATATTA-AAAGCGTCAAAAGCC
* *
10637 CTTCAATC-TTTTTGGCGTTGCATTATATATTTTTATGAGTATTGTTA-CTAAAAATTGAGGAAA
129 CTTCAA-CATTTTTGGCGTTGAATTATATATTTTTATGAGTATT-TTAGCCAAAAATTGAGGAAA
* * *
10700 AATATTTCGGGTC-ATTGTTTGCAAAATATTAGCCGAAAT--TGTAA-AACATCACGATTTTTTT
192 AATCTTTCGGGTCAATT-TTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCAC-A---GTTT
* * ** * *
10761 TTGTTATTGCTAAAAACGCGTTCCAGGACCCCAGG-TCAGTATTGCATGATTTTTGGCGCCAATA
252 TTG-----GCTAAAAAAGCGTTTC-GGGGCCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
**
10825 CTCCTTGAGCTATCTATAT
310 CTCCTTGAAATATCTATAT
* *
10844 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTTTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
* * * * * * **
10909 TTAGATTTAATTAAAAATTAAATC-GGAAAAATAGGAAAAACAATATTAGAAGCGTAAAAAATCC
66 TTCGATTTAATTAAAAATT-AATCTAGAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCCC
* * * * *
10973 TTCAATATTTTTGGCGTAGAATTACATATTTTTTATGA-TAATTTAGCAAAAAATTGAG
130 TTCAACATTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAG
11031 CAAATCGTGT
Statistics
Matches: 1206, Mismatches: 215, Indels: 145
0.77 0.14 0.09
Matches are distributed among these distances:
306 3 0.00
307 42 0.03
308 54 0.04
309 43 0.04
310 2 0.00
311 4 0.00
312 1 0.00
313 15 0.01
316 3 0.00
318 16 0.01
319 60 0.05
320 1 0.00
321 4 0.00
322 3 0.00
324 2 0.00
325 4 0.00
326 13 0.01
327 57 0.05
328 135 0.11
329 15 0.01
330 134 0.11
331 47 0.04
332 226 0.19
333 5 0.00
334 7 0.01
335 149 0.12
336 158 0.13
337 3 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (328 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
TTCGATTTAATTAAAAATTAATCTAGAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCCCT
TCAACATTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATC
TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCACAGTTTTTGGCTAAA
AAAGCGTTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTA
TAT
Found at i:11822 original size:337 final size:328
Alignment explanation
Indices: 11032--13037 Score: 1689
Period size: 337 Copynumber: 6.1 Consensus size: 328
11022 AAAATTGAGC
* * * *
11032 AAATCGTGTA-AATCATCACAGTTTTTGGCTAAAAATGCGTTCCTGGGCCCCGGGTCAGTTTTGC
1 AAATCGTGTACTATCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGC
* * * *
11096 ATGATTTTTG-GCACTAAGACTACTTGAGATATCCATATTCATCTAATCAAATCTCAGACACATT
65 ATGATTTTTGTGC-C-AAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
* * * * *
11160 GCATTTAAGGATTTGTTTTAACAAGC-TTCTAAATCATATTTCGATTTAATTAGAAATTAATTCA
128 GGATTTAAGGATTT-TTTTTACGAGCATT-TGAATCATGTTTCGATTTAATTAGAAATTAATTCA
* ** * * * * *
11224 GAAAAAATAAGAAAAGTGAT-TTATAAATCGTGAAACGTCCTC-CAATCTTTTTGGCATTAAATT
191 G-AAAAATATGAAAAACGATATTA-AAAGCATGAAAAGTCCTCTCAATCTTTTTGGCGTTGAATT
* *
11287 ATATATATTTCATGAG-ATTTTA-ACCAAAAATTGAGGAAAATTTTTTCTTG-TC-ATCTTTTGC
254 ATATATATTTCATGAGTATTTTAGA-CAAAAATTGAGGAAAATTATTTC-GGATCAAT-TTTTGC
*
11348 AAAATTTTAGGCG
316 AAAATTTTAGCCG
* * ** * * * *
11361 AAATCGTGTACTAACCATCACGTTTTTTTTTCTCTAAAAACGCATTTCAGGGTCGCGGCTCAGTT
1 AAATCGTGTACT-ATCATCACG---GTTTTTGGCTAAAAACGC-GTTCCGGGCCCCGGCTCAGTT
* *
11426 TTGCATGA--TTTG-G-CATTGAGGCTCCTTGAAATATATATATAT-ATTCATATGATCAAATCT
61 TTGCATGATTTTTGTGCCA---AGACTCCTTGAAATATCTATAT-TCA-TC-TA--ATCAAATCT
* * * * *
11486 CAGCTACATTGCATTTAAAGATTTTTTTTCACGAGCATCTGAAATCTTGTTTCGATTTAATTAGA
118 CAGCCACATTGGATTTAAGGATTTTTTTT-ACGAGCATTTG-AATCATGTTTCGATTTAATTAGA
** * * * *
11551 TTTTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCCTCT-AATATTTTTGGA
181 AATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCTCAATCTTTTTGGC
* * *
11615 GTTGAATTATATATATTTCATGAGTATTTTAGACAAAAATTGGGGAAAACTATTTCTGATCAATT
246 GTTGAATTATATATATTTCATGAGTATTTTAGACAAAAATTGAGGAAAATTATTTCGGATCAATT
* *
11680 ATTGCAAAATATTAGCCG
311 TTTGCAAAATTTTAGCCG
** * *
11698 AAATCGTGTACGTCAGTCGAAATCACGGTTTTTTCCTAAAAACGCGTTCCAGGGCCTCGGTTCAG
1 AAATCGTGTAC-T-A-TC---ATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAG
* * * * * * *
11763 TGTTGCTTGATTTTTTGTGCCGAGACTCCTTGAAATATCTCTATTAATCTAACCAAATCTCATCC
59 TTTTGCATGA-TTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
* * *** * * * *
11828 ACAATGGATTTAAGGATTTGTAAAACAAGCATATGAATCATGTTTCAATTTATTTAGAAATTAAT
123 ACATTGGATTTAAGGATTTTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAAT
* * * * *
11893 TCGGAAAATATTAGGAAAAACGATATTAGAAGCATGAAAA-TCC-CTTCAACCTTTTTGGTGTTG
188 TCAGAAAA-A-TATGAAAAACGATATTAAAAGCATGAAAAGTCCTC-TCAATCTTTTTGGCGTTG
* * * ** * * * *
11956 AATTATATA-ATTT-TTAAGAATATTGCGGCTAAAACTTGAGG-AAATAAATTT-AGAGTCAATT
250 AATTATATATATTTCATGAGTAT-TTTAGAC-AAAAATTGAGGAAAAT-TATTTCGGA-TCAATT
*
12017 TTTGCAAAATTCTAGCCG
311 TTTGCAAAATTTTAGCCG
* * * * *
12035 AAATCGTGTAATAATCTTCACGGTTGTTGGCTAAAAACGCGTTCCGGG-GCCGGCTAAGTTTTGC
1 AAATCGTGTACT-ATCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGC
* * * * *
12099 ATGATTTTTGTCACCAAAACTCTTTGATATAT-TCATATTCATCTAATCAAATCTCAGCTACATT
65 ATGATTTTTGT-GCCAAGACTCCTTGAAATATCT-ATATTCATCTAATCAAATCTCAGCCACATT
** * *
12163 GGATTTAAAAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATAAGAAATTAATTCAG
128 GGATTTAAGGATTT-TTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTCAG
* * *
12228 AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTC-CAATCCTTTTGGCGTTAAATTATA
192 AAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCTCAATCTTTTTGGCGTTGAATTATA
* * * *
12292 TATATTTCATGAGTA-TTTATGCCAAAAATTGACGGAAAAATT-TTTCGGGTCATTTTTTTACAA
257 TATATTTCATGAGTATTTTA-GACAAAAATTGA-GG-AAAATTATTTCGGATCA-ATTTTTGCAA
*
12355 AATTTTAGCCA
318 AATTTTAGCCG
* * * * * * *
12366 AAATCATGTACTAACCATCAAGGTTTTTGGCTAAAAACGCGTTTCGAGACCCCGACTTAGTTTTG
1 AAATCGTGTACT-ATCATCACGGTTTTTGGCTAAAAACGCGTTCCG-GGCCCCGGCTCAGTTTTG
* * ** *
12431 CATGGTTTTTGGTGCCGAGACTTTTTGAAATATCTATATTCATTTAATCAAATCTCAGCCACATT
64 CATGATTTTT-GTGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
* * * * *
12496 GAATTGAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAT
128 GGATTTAAGGATTT-TTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTCAG
* * * *
12561 AAAAATATGAAAAACGAT-TTAAAAGCATGAAAAGGCCT-TCAATCTTTTTGGCTTTTAGTTATA
192 AAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCTCAATCTTTTTGGCGTTGAATTATA
* * * * *
12624 TATA-TTCTATGAGTATTGT-GGCTTAAAATGGAGG-AAATTATTTCGGGTCAATTTTTGCAAAA
257 TATATTTC-ATGAGTATTTTAGAC-AAAAATTGAGGAAAATTATTTCGGATCAATTTTTGCAAAA
12686 TTTTAGCCG
320 TTTTAGCCG
* * * ** *
12695 AAATCGTGTAC---CATCACGGGTTTTTTGTTACAAACGCGTTTTGGGGCCCCGGGTCAG-TTTG
1 AAATCGTGTACTATCATCAC-GGTTTTTGGCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTG
** * * * * *
12756 CATGATTTTTAGTTTCAACATTCCTTGAAATATCTATATTCATCTAACCAAATCTTAACCACATT
64 CATGATTTTT-GTGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
* * * * *
12821 GGATTTAAGGA-TTTGTTTACGAGTATTTGAATCATGTTTCAATTTAATTAGAAATTAATTTGAA
128 GGATTTAAGGATTTTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAA-TTCAG
* * * *
12885 AACAAATAGGAAAAACGATATTAGAAGCATGAGAAGCCCT-TCAATCTTTTTGGCGTTGAATTAT
192 AA-AAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCTCAATCTTTTTGGCGTTGAATTAT
* * * * * * * *
12949 ATTTTTTTTATGAGTATTGT-GGCTAAAATTTGA-G-AAATATATTTCGGGTCAATTTTTGTAAA
256 ATATATTTCATGAGTATTTTAGAC-AAAAATTGAGGAAAAT-TATTTCGGATCAATTTTTGCAAA
*
13011 ATTTTAGCCA
319 ATTTTAGCCG
* *
13021 AAATTGTGTATTATCAT
1 AAATCGTGTACTATCAT
13038 GTTTTTT
Statistics
Matches: 1361, Mismatches: 241, Indels: 150
0.78 0.14 0.09
Matches are distributed among these distances:
323 41 0.03
324 7 0.01
325 90 0.07
326 128 0.09
327 6 0.00
329 113 0.08
330 94 0.07
331 122 0.09
332 109 0.08
333 145 0.11
334 40 0.03
335 47 0.03
336 131 0.10
337 208 0.15
338 8 0.01
339 37 0.03
340 3 0.00
341 20 0.01
342 10 0.01
343 1 0.00
344 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
AAATCGTGTACTATCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCA
TGATTTTTGTGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA
TTTAAGGATTTTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAA
ATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCTCAATCTTTTTGGCGTTGAATTATATATA
TTTCATGAGTATTTTAGACAAAAATTGAGGAAAATTATTTCGGATCAATTTTTGCAAAATTTTAG
CCG
Done.