Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015077.1 Corchorus olitorius cultivar O-4 contig15110, 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: 26030
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:4809 original size:332 final size:322
Alignment explanation
Indices: 4073--4826 Score: 773
Period size: 332 Copynumber: 2.3 Consensus size: 322
4063 TTAGCCCCGG
* *
4073 CTCAATTTTGCTATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACTAAATC
1 CTCAATTTTGC-ATGATTTTTGGC--AAAGACTCCTTGAAATATCTATATTAATCGAACCAAATC
* * *
4138 -CTAGCCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTCATTTCGATTTAATTAG
63 TC-AGCCACATTGGATTTAAGGATTTGTTTTTACGAACATCTAAATCTCATTTCAATTTAATTAG
* * *
4202 AAATTAATTTGGAAAAAAAAGAAAAGAAAAAACGATATTAGAAGCGTGAAAAAACCATCCATCAT
127 AAATTAAATTCGAAAAAAAAG---AGAAAAAACGATATTAGAAGCGTGAAAAAACCATCAATCAT
* * * * *
4267 TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGA
189 TTTGGCATTGAATTAAATATTATTTATGAGTATTATGGAAAAAAATTGAGAAAAAACTTTTCGGA
** * ** ** *
4332 TAAGTTTTTAGCCAAAATCGGGTACTAACCATCACGATTTTTGCCTAAAAACGCATTTCGGGGTA
254 TAAAATTTTAGCCAAAATCAGGTACTAACCATCACGACCTTTGCCTAAAAACGCATTTCGAAGCA
***
4397 TTGA
319 CCAA
* * *
4401 CT-AAGTTTTGCATGGTTTTTGGCATAAAGACTCCTTGAAATATGTATATTAATCTAACCAAATC
1 CTCAA-TTTTGCATGATTTTTGGC--AAAGACTCCTTGAAATATCTATATTAATCGAACCAAATC
* * * **
4465 TCAGCCACATTGGATTTAAGGATTTGTTTTTATGAACATTTGAATCTTGTTTCAATTTAATTAG-
63 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAACATCTAAATCTCATTTCAATTTAATTAGA
* * * **
4529 AATTAAATTCGAAAAAAATG-G-AAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTG
128 AATTAAATTCGAAAAAAAAGAGAAAAAACGATATTAGAAGCGTGAAAAAACCATCAATCATTTTG
* *
4592 GCATT-ATATTAAATATTATTTCTGAGTATTATGGAAAAAAATTGAGGAAAAACTTTTCGAGTCA
193 GCATTGA-ATTAAATATTATTTATGAGTATTATGGAAAAAAATTGAGAAAAAACTTTTCG-G--A
*** * * * *
4656 GTTTTTGCAAAATTTTAGTTGAAATCATGTACTAACCCATCACGGCCTTTGGCTAAAAACGCGTT
254 -----T--AAAATTTTAGCCAAAATCAGGTACTAA-CCATCACGACCTTTGCCTAAAAACGCATT
*
4721 TCGAAGCCCCAA
311 TCGAAGCACCAA
* *
4733 CTCAATTTTGCATGATTTTTGATGCAAAGACTCATTGAAATATTTATATTAATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTG--GCAAAGACTCCTTGAAATATCTATATTAATCGAACCAAATCT
* * * *
4798 CAACGACATTGGATATAAGAATTTGTTTT
64 CAGCCACATTGGATTTAAGGATTTGTTTT
4827 ACTCCCTCAG
Statistics
Matches: 353, Mismatches: 56, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
320 1 0.00
321 87 0.25
322 2 0.01
324 1 0.00
326 17 0.05
327 103 0.29
328 9 0.03
329 1 0.00
331 20 0.06
332 108 0.31
333 2 0.01
334 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (322 bp):
CTCAATTTTGCATGATTTTTGGCAAAGACTCCTTGAAATATCTATATTAATCGAACCAAATCTCA
GCCACATTGGATTTAAGGATTTGTTTTTACGAACATCTAAATCTCATTTCAATTTAATTAGAAAT
TAAATTCGAAAAAAAAGAGAAAAAACGATATTAGAAGCGTGAAAAAACCATCAATCATTTTGGCA
TTGAATTAAATATTATTTATGAGTATTATGGAAAAAAATTGAGAAAAAACTTTTCGGATAAAATT
TTAGCCAAAATCAGGTACTAACCATCACGACCTTTGCCTAAAAACGCATTTCGAAGCACCAA
Found at i:7199 original size:327 final size:327
Alignment explanation
Indices: 6479--8969 Score: 1238
Period size: 327 Copynumber: 7.7 Consensus size: 327
6469 GCACTAATTA
*
6479 GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGA-TTTAGGGTTCTGTTTTTACGAG
1 GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTTAGGATT-TGTTTTTACGAG
* *
6543 AATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAATTGAAAAACGATATTA
65 AATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G-AAAAAAAATGGAAAAACGATATTA
* * * * * * *
6608 GAAGCGTGAAAACCCCTTCAATTTTTTTGGTGTTAAATTATATATTTTTTCTTATTATAGTAGCA
128 GAAGCGTGAAAACCCCATCAATCTTATTGGCGATAAATTATATATTTTTTCTTAGTATAGCAGCA
** * *
6673 AAAAAATTGAGGGAAAACATTACCGGTCAGTTTTTGCAAAATTTTAGCGGAAATCGTTTACTAAC
193 AAAAAATTGAGAAAAAACATTACCGGTCAGTTTTT----AA--TGAGCGGAAATCGTGTACTAAC
* * * * *
6738 CATCACGATTTTTGGCTAAAAACGCGTTCGGGAGCTCCGGCTCAATTTTTCATGATTTTTGGCGC
252 CATCACGATTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTTACATGATTTTTGGCGC
6803 AAAGACTCCTT
317 AAAGACTCCTT
* * * * * *
6814 AAAAAATCTATATTCATCGAACCAAATCTCAGCCACATTAGATATAAGGATTTGTTTTTACGAGA
1 GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTTAGGATTTGTTTTTACGAGA
* * *
6879 ATCTGAATCTTGTTTCGATTTAATTAGAAGTTAATTC-AGAAAAAATGGAAAAACGATATTAGAA
66 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAACGATATTAGAA
** * * *
6943 TTGTGAAAAGCCCATCAATCTTATTGGCGATGAATTATATATTTTTT-TTAGTAGT-GCGGCAAA
131 GCGTGAAAACCCCATCAATCTTATTGGCGATAAATTATATATTTTTTCTTAGTA-TAGCAGCAAA
* * * * * *
7006 AATATT-AGAAAAAAGATT-CCAGTTCAGTTTTT-A-GA-C-GAAATTGTGTATTATCCATCACT
195 AAAATTGAGAAAAAACATTACC-GGTCAGTTTTTAATGAGCGGAAATCGTGTACTAACCATCAC-
*
7065 GTTTTTTTTTTTTCGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTTACATG-TTTTTGGCA
258 G------ATTTTT-GGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTTACATGATTTTTGGC-
**
7129 G-AAAGTTTCCTT
315 GCAAAGACTCCTT
* * * * *
7141 GAAATATCTATATTTATCTAACCAAATCTTTGCCACATTGGATTTTAGGATTTGTTTTTATGAGC
1 GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTTAGGATTTGTTTTTACGAGA
* * * *
7206 ATCTAAAGCCTGTTTCAATTTAATTAGAAATAAATTCCGAAAAAAAATGGAAAAAAAAAACGATA
66 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT-CGAAAAAAAATGG-----AAAAACGATA
* * * * * * ** * *** * * * *
7271 TTTGAAGCGTGAAAAACCCTTCAGTTTTTTTTTC-ATTGAATTATATATTTTTTAAGACTGTTGT
125 TTAGAAGCGTGAAAACCCCATCAATCTTATTGGCGA-TAAATTATATATTTTTTCTTAGTATAGC
* * ** *** * *
7335 GGCAAAACAATTGAGAAAAAAGTTTTTGGGTCAGTTTTTGCAAAATTTAGCCGAAATCGTG----
189 AGCAAAAAAATTGAGAAAAAACATTACCGGTCAGTTTTT----AA-TGAGCGGAAATCGTGTACT
* * * * * * * * * *
7396 ------CA-GTTTTTTTGTTAAAAGCGTC-TTCC-AAGGCCCTAGCTCAGTTTTGCATAAATTTT
249 AACCATCACGATTTTTGGCTAAAAACG-CGTTCCGAAGCCCCGA-CTCAATTTTACATGATTTTT
* *
7452 GGCGTAAAGACCCCTT
312 GGCGCAAAGACTCCTT
* * ** * * * * *
7468 GAAATATCTATATTCATCGAACCCAATCCCAGCCACATTCGATCTAAGGATTTG-TTTTACAAGC
1 GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTTAGGATTTGTTTTTACGAGA
* * * *
7532 ATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACAATATTAAAA
66 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAACGATATTAGAA
* * * * * * * * *
7597 GCCTGAGAACCCCTTCAATATTTTTGGCATTGAATTATATATATATATATTTTTATGAGTATTG-
131 GCGTGAAAACCCCATCAATCTTATTGGC---G-A-TAAAT-TATATAT-TTTTTCTTAGTATAGC
* ** * * * * *
7661 TG-GTAAAAATTGAGAAATAAC-TAACTTGGTCAG-TTTT-AT---CCGAAATCGAGTACTAACC
189 AGCAAAAAAATTGAGAAAAAACATTAC-CGGTCAGTTTTTAATGAGCGGAAATCGTGTACTAACC
* *** * * ** ** * * * * * * **
7719 ATCATGGGGTTTGGCAAAAAAACGCGTTTCGGGGCCTTGCCTCAGTATTGCATGGTTTTTGACAT
253 ATCACGATTTTTGGC-TAAAAACGCGTTCCGAAGCCCCGACTCAATTTTACATGATTTTTGGCGC
7784 AAAGACTCCTT
317 AAAGACTCCTT
* ** * * *
7795 CAAATATCTATATAT-ATCTAAGAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
1 GAAATATCTATAT-TCATCTAACCAAATCTTAGCCACATTAGATTTTAGGATTTGTTTTTACGAG
* * * * *
7859 CATCTAAATCTTGTTTTGA-TTAATTAGAAAAAAATTCGAAAAAAAATGGAAAAACAATATTAGA
65 AATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAACGATATTAGA
* * * * * * * * *
7923 AGCATAAAAAACCCTTCAATATTTTTGCCGTTGAATTATATA---TTT-TT--TAT-G-AG----
130 AGCGTGAAAACCCCATCAATCTTATTGGCGATAAATTATATATTTTTTCTTAGTATAGCAGCAAA
* * ** * * * * * *
7976 --TATTGTG---GCACATTTCGGGTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAA
195 AAAATTGAGAAAAAACATTACCGGTCAGTTTTT----AA--TGAGCGGAAATCGTGTACTAACCA
* * * * * * * **
8036 TCACGGTTTTTGGCTAAAAACGCGTTTC-AGGGCCTCGACTCAGTTTTGCATGGTTTTTGGCATA
254 TCACGATTTTTGGCTAAAAACGCGTTCCGA-AGCCCCGACTCAATTTTACATGATTTTTGGCGCA
8100 AAGACTCCTT
318 AAGACTCCTT
* * * * *
8110 GAAATATCTATATTCATCTAAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTA-GTT
1 GAAATATCTATATTCATCT-AACCAAATCTTAGCCACATTAGATTTTAGGATTTGTTTTTACG-A
** * *
8174 TTATCTGAATCTTGTTTCGATTT-ATTAGAAATGAATTCG-AAAAAAA-GGAAAAACAATATTAG
64 GAATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAACGATATTAG
* * * * * * * **
8236 CAGCGTGAATAA-CCCTTCAATTCTT-TTGGCGTTGAATTATATATTTTTCCTGAGTATTGTGGC
129 AAGCGTGAA-AACCCCATCAA-TCTTATTGGCGATAAATTATATATTTTTTCTTAGTATAGCAGC
* * * *
8299 -AACAAATTGAG---GAA-A--A----TCAG-TTTT--T--GC-AAAAT--T-T--T-AGCATCA
192 AAAAAAATTGAGAAAAAACATTACCGGTCAGTTTTTAATGAGCGGAAATCGTGTACTAACCATCA
* * ** * **
8341 CTG-TTTTTGGCTAAAAACGCATTTCGAA-CCCTCGGTTCAATTTTGCATGATTTTTGGCTTAAA
257 C-GATTTTTGGCTAAAAACGCGTTCCGAAGCCC-CGACTCAATTTTACATGATTTTTGGCGCAAA
* *
8404 GGCTACTT
320 GACTCCTT
* * * * * * *
8412 GAAATATCTATATTCATCGAATCAAGTCTCAGTCACATTGGATATAATTAAGGATTTGTTCTTAC
1 GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGAT-T--TT-AGGATTTGTTTTTAC
* * * *
8477 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAA-ATAATTC-AGAAAAAA-GGAAAAAACAAGA
62 GAGAATCTGAATCTTGTTTCGATTTAATTAGAAATA-AATTCGAAAAAAAATGG-AAAAACGATA
* * ** * * * * * **
8539 TTAGAAGCGTGAAAAGCTCGCCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTG
125 TTAGAAGCGTGAAAACCCCATCAATCTTATTGGCGATAAATTATATATTTTTTCTTAGTATAGCA
* * * * * * *
8604 GC-AAAAAATTCAGAAAAAAAAAAAATT-TCGGTTTAGTTTTT-A-G-TC-AAAATCATGTACTA
190 GCAAAAAAATT--G--AGAAAAAACATTACCGG-TCAGTTTTTAATGAGCGGAAATCGTGTACTA
* * * * ** ** * * * *
8663 ACCATCACAATTTTGGGGCTAAAAAGGCGTTTCGGGGTTCCGCCTTAGTTTTGCATGATTTTTGG
250 ACCATCACGATTTT-TGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTTACATGATTTTTGG
** *
8728 CATAAAGACTCTTT
314 CGCAAAGACTCCTT
* * *
8742 GAAATACCTATATTCATCTAACCAAATCTCT-GCCACATTGGATTTAAGGATTTGTTTTTACGAG
1 GAAATATCTATATTCATCTAACCAAATCT-TAGCCACATTAGATTTTAGGATTTGTTTTTACGAG
* * * *
8806 CATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGA
65 AATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAACGATATTAGA
* * * * **
8871 AGCGTGAAAA-ACCAGTCAATAC-T-TTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGCA
130 AGCGTGAAAACCCCA-TCAAT-CTTATTGGCGATAAATTATATATTTTTTCTTAGTATAGCAGCA
* * *
8933 AAAAAATTTGAGAAAAAACTTTTCGGGTCAGTTTTTA
193 AAAAAA-TTGAGAAAAAACATTACCGGTCAGTTTTTA
8970 GCCGGAATTG
Statistics
Matches: 1710, Mismatches: 302, Indels: 298
0.74 0.13 0.13
Matches are distributed among these distances:
301 22 0.01
302 78 0.05
303 3 0.00
304 1 0.00
305 42 0.02
306 35 0.02
307 70 0.04
308 9 0.01
309 3 0.00
311 3 0.00
313 3 0.00
314 53 0.03
315 93 0.05
316 98 0.06
317 7 0.00
318 2 0.00
319 5 0.00
320 58 0.03
321 12 0.01
322 9 0.01
323 6 0.00
324 23 0.01
325 50 0.03
326 172 0.10
327 381 0.22
328 73 0.04
329 24 0.01
330 102 0.06
331 17 0.01
332 64 0.04
333 2 0.00
334 52 0.03
335 100 0.06
336 27 0.02
341 1 0.00
343 1 0.00
344 1 0.00
345 8 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (327 bp):
GAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTTAGGATTTGTTTTTACGAGA
ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAAAAACGATATTAGAA
GCGTGAAAACCCCATCAATCTTATTGGCGATAAATTATATATTTTTTCTTAGTATAGCAGCAAAA
AAATTGAGAAAAAACATTACCGGTCAGTTTTTAATGAGCGGAAATCGTGTACTAACCATCACGAT
TTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTTACATGATTTTTGGCGCAAAGACTCC
TT
Found at i:13769 original size:10 final size:10
Alignment explanation
Indices: 13754--13785 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13744 TTATAAGTTT
13754 AAAAAACAAA
1 AAAAAACAAA
13764 AAAAAACAAA
1 AAAAAACAAA
13774 AAAAAA-AAA
1 AAAAAACAAA
13783 AAA
1 AAA
13786 CTTCAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:14318 original size:53 final size:53
Alignment explanation
Indices: 14260--14369 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
14250 TATTTATTCA
*
14260 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAATT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
* *
14313 ATTGAATCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
14366 ATTG
1 ATTG
14370 GATTTAAAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.25
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGCAATGAACT
Found at i:17895 original size:2 final size:2
Alignment explanation
Indices: 17888--17915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17878 AACCGTTAAT
17888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17916 ATCAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21594 original size:25 final size:25
Alignment explanation
Indices: 21549--21597 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21539 TTTTGAACTC
*
21549 ATTATTTATTATTCAAAATATATTT
1 ATTATTTATTAATCAAAATATATTT
*
21574 ATTATTTATTTAAT-AATATATATT
1 ATTATTTA-TTAATCAAAATATATT
21598 ACATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTATTTATTAATCAAAATATATTT
Found at i:23322 original size:2 final size:2
Alignment explanation
Indices: 23315--23344 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23305 ATTATTTGTT
23315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23345 CTAGTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.