Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022449.1 Corchorus olitorius cultivar O-4 contig22482, 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: 11166
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:418 original size:38 final size:39
Alignment explanation
Indices: 352--431 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
342 TGGGAGAAGT
**
352 AAATTTGCTATTTTTTTTTCTTTTGTCTCCAAATTAGCC
1 AAATTTGCTATTTTTTTTTCTTCCGTCTCCAAATTAGCC
391 AAATTTGCTA-TTTTTTTTCTTCCGTCTCCAAATTAGCC
1 AAATTTGCTATTTTTTTTTCTTCCGTCTCCAAATTAGCC
429 AAA
1 AAA
432 CCTTGGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 29 0.74
39 10 0.26
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (39 bp):
AAATTTGCTATTTTTTTTTCTTCCGTCTCCAAATTAGCC
Found at i:3125 original size:8 final size:8
Alignment explanation
Indices: 3112--3145 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
3102 TACCAAATTC
*
3112 ATCTTACT
1 ATCTTATT
3120 ATCTTATT
1 ATCTTATT
3128 ATCTTATT
1 ATCTTATT
3136 ATCTTATT
1 ATCTTATT
3144 AT
1 AT
3146 ATATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (8 bp):
ATCTTATT
Found at i:3432 original size:20 final size:18
Alignment explanation
Indices: 3407--3453 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3397 ACTTCAAATA
3407 ATTATTTTTAGATTATAAT
1 ATTATTTTTA-ATTATAAT
*
3426 A-TATATTTAATTATAAT
1 ATTATTTTTAATTATAAT
3443 ATTATTATTTA
1 ATTATT-TTTA
3454 TAGTCATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTATTTTTAATTATAAT
Found at i:3455 original size:15 final size:17
Alignment explanation
Indices: 3404--3448 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3394 TTTACTTCAA
*
3404 ATAAT-TATTTTTAGATT
1 ATAATATATATTTA-ATT
3421 ATAATATATATTTAATT
1 ATAATATATATTTAATT
3438 ATAATAT-TATT
1 ATAATATATATT
3449 ATTTATAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 15 0.58
18 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATAATATATATTTAATT
Found at i:4680 original size:328 final size:329
Alignment explanation
Indices: 3784--6847 Score: 2529
Period size: 342 Copynumber: 9.4 Consensus size: 329
3774 CTTTACATTG
* * *
3784 TCTAATCAAATCTCATCAACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTC
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG-TTTTACGAGCATCTAAATCTTGTTTC
* ** * ** * * *
3849 GAGTTAATTAGAAATTAATTTTGAAAAAAAAAAGAAGTACGATATAAAAAGCGTAAAAAGTCCTC
65 GATTTAATTAGAAATTAATTCAGAAAATATGAA-AA--ACGATATTAAAAGCGTGAAAAGTCCTT
** * * *
3914 CAATCTTTTTGGCGTCGAA-T-TATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAAT
127 CAATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAA
* * * *
3977 CTTTCGTGTCAATTTTTGCAAAATTTTAATTAGCCGAAATCGTGTACTAACAAACCATCACGGTT
192 ATTTCGGGTCAATTTTTGCAAAA--TT--TTAGCCGAAATCGTG---TAA-TAACCATCACAGTT
* * * * *
4042 TTTGGCTAAAAACGCGTTCCGGGGACCCGACTCAATTTTGCATGATTTTTGGCTCCAAGACTACT
249 TTTGGCTAAAAACGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
*
4107 TGAAGTATCTATATTCA
314 TGAAATATC-ATATTCA
* * ** * * *
4124 TCTAATCAAATCTCACCCACATTAGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTT
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG-TTTTACGAGCATCTAAATCTTGTTTC
* * * * * * **
4189 GATTTAATTATAAATTAATTTGGAAAAAATAGGAAAAACGATATTAAAAACGTCAAAAACCCTTC
65 GATTTAATTAGAAATTAA-TT-CAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTC
* * * * * * *
4254 AATCTTTTAGGCGTTGAGTTATATAT-TTTTAATGAG-GTTTTAGT-CAAAAATTGAGGAAATAT
128 AATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTA-TCCAAAAATTGAGGAAAAAA
* * * * *
4316 CTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTGTGTAATAACCACCACAGTTTTTGGATA
192 ATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTA
* * * * *
4381 AAAAAGCGTTATGGGGCCCTGCCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGATATAT
257 AAAACGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
4446 C-TATTCA
322 CATATTCA
* * * ** *
4453 TCTATTCATATCTTAGCCACATTGGATTT-ATTATTTG-TTTACAAGCATCTAAATCTTGTTTCG
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTACGAGCATCTAAATCTTGTTTCG
4516 ATTTAATTAGAAATTAATTCAGAAAAT-TGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAAT
66 ATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAAT
* *
4580 CTTTTTGCCGTTAAAATATATATATATATTTTATGAGCATTTTATCCAAAAATTGAGGAAAAAAA
131 CTTTTTGGCGTT-AAAT-TATATATAT-TTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAAA
* * * * * * *
4645 TTTTGGGTCATTTTTTACAAAATTTTAGTCGAAATTGTGTAATAACCATCACAATTTTTGGATAA
193 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAA
* * *
4710 AAAAGCGTTCT-GGGCACCGGCTCAGTTTTGCATGATTTTT-G-G-C---A---C--G-------
258 AAACGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
4756 ----TCA
323 ATATTCA
* * *
4759 TGTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGTATCTAAATCTTGTTTC
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG-TTTTACGAGCATCTAAATCTTGTTTC
* * * * * *
4824 GATTTAATTAGAAATTAATTTATAAAAGTACGAAAAACGATATTAAAAGCATAAAAAGTCCTCCA
65 GATTTAATTAGAAATTAATTCAGAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCA
* * * * *
4889 ATGTTTTTGCCGTTAAATTATATATATATATATATTTATGAGTGTTTTATCAAAAAATTGAGAAA
129 ATCTTTTTGGCGTT-AA--AT-TATATATAT-T-TTTATGAGTATTTTATCCAAAAATTGAGGAA
* * *
4954 AAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAAACCATCAC-GTTTT
188 AAAAA-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT-AACCATCACAG----
* ** * * *
5018 TTTTTGGCTAAAAACGCGTT-TCGGGGCACTAACTCAG-TTTCCATGATTTTTGGCGCCGACACT
247 TTTTTGGCTAAAAACGCGTTCT-GGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACT
*
5081 CCTTGAAAAATCTATATTCA
311 CCTTGAAATATC-ATATTCA
* * * * * * *
5101 TCTAATAAAATCTTAGCCACATTGCATTT-AAGATTTTTTTTACGAGCATCTGAATCATGTTTCG
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTACGAGCATCTAAATCTTGTTTCG
* **
5165 ATTTAATTAGAAATTAATTCAAAAAAATATG--AAACGATATTAAAAGCGCCAAAAGTCCTTCAA
66 ATTTAATTAGAAATTAATTC-AGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAA
* * * * ** * *
5228 TCTTTTTGGTGTTGAATTATACA-ATTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATAAATT
130 TCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAAATT
* * * * *
5292 TCGAGTCAATTTTTGCAAAATTCTAACCGAAATCGTGTAATAATCATCATTA-TTTTTGGCTAAA
195 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCA-CAGTTTTTGGCTAAA
** * ** * * * * **
5356 AATACGTTCCGGGGCCCCGGTTAAGTTTTGCATGATTTTGGGCGTCAAGACTCTTTGCGATATC-
259 AACGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCA
*
5420 CA-T-A
324 TATTCA
* * * ** * * * *
5424 T-T--T--AAT-T-AG--AAATT--AATTAGAAA--T-TCCTAGGGGCATCTAAGTCATGTTTCG
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTACGAGCATCTAAATCTTGTTTCG
* * * * * * * *
5475 ATTCATTTAGAAATTAATTTGGAAAAAAAAGGAAAAACGATATTAGAAA-CGTGAAAAGCCCTTA
66 ATTTAATTAGAAATTAA-TT-CAGAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCCTTC
* * * * * **
5539 AATCTTTTAGGCGTTAAGTTATATAT-TTTTAATGAGTA-TTTAGCCAAAAATTGAGGAAATATC
128 AATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAAA
** * *
5602 TTTCGGGTCAATTTTTAAAAAATTTTAG-C-----C--G--A-AACCATAACAGTTTTTGGATAA
193 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAA
* * * * * * * *
5656 AAAAGCATTCTGGGGCCCCGCCTCAGCTTTGCATGATTCTTGGTGCCTAGACTCCTTGAGATATC
258 AAACGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
5721 TATATTCA
323 -ATATTCA
*
5729 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATTCT-AATCTTGTTT
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG-TTTTACGAGCA-TCTAAATCTTGTTT
* * *
5793 CGATTTAATTGGAAATTAATACAGAAAAATATGAAAAACGACATTAAAAGCGTGAAAAGTCC-TC
64 CGATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTC
* * * * * *
5857 AAATCTTTTTGCCATTAAATTATTTATA-TTTTATGAGTATTTCATCCATAAACTGAGG-AAAAA
128 -AATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAA
* * * * * * * *
5920 TTTTGGGGTC-ATTTTTGCAAAATTTTAGCCAAAATCATATACTGATCATCA-AGGTTTTTGGCT
192 ATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACA-GTTTTTGGCT
* * * * * * *
5983 AAAAACGCGTT-TCGGGG-CACTAGCTCAGTTTTGCATGACTTTTGGCACCGACACTCCTTAAAA
256 AAAAACGCGTTCT-GGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
6046 TATCTATATTCA
319 TATC-ATATTCA
* * * * *
6058 TCTAAT-ATAATCTTAGCCACATTGCATTT-AAGATTTTTTTTACGAGCATCTAAATCATGTTTC
1 TCTAATCA-AATCTCAGCCACATTGGATTTAAAAATTTGTTTTACGAGCATCTAAATCTTGTTTC
* * *
6121 GATTTAATTAGAAATTAATTCAGAAAATATGAAAAATGATATTAAAAGCGTCAAAAGCCCTTCAA
65 GATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAA
* * ** * * *
6186 TCTTTTTGGCGTTGAATTATATA-ATTTTTATGAGTATTATGGCTAAAAATTGAGGAAATAACTT
130 TCTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAAATT
* * * * * *
6250 TCGAGTCAATTTTTGCAAAATTCTAGTCGAAATCGTGTAATAATCATCACGGGTTTTGGCTAAAA
195 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAA
** * * * *
6315 ACGCGTTCCAGGACCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAGATATCCA
260 ACGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT-CA
6380 TATTCA
324 TATTCA
* * * ** * * ** *
6386 TGTGATCAAAGCTCAGTTAAATTGGATTTAAGAATTTGTTTTTATTAGCATCTGAATCTTGTTTC
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG-TTTTACGAGCATCTAAATCTTGTTTC
* * *
6451 GATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCCTCCA
65 GATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCA
*
6516 ATCTTTTTGGCATTAAATCTTATATATATATATATATATTATGAGTA-TTTATGCCAAAAAATT-
129 ATCTTTTTGGCGTT-AA----AT-TATATATAT-T-T-TTATGAGTATTTTAT-CC-AAAAATTG
* *** * * *
6579 ACAGAAAATTTTTTCTGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-AG
183 A-GGAAAAAAATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACA-
* * * * * * * *
6643 GTTTTTGGGTAAAAACGTGTT-TCGGGACCCCGTCTTAGTTTTGAATGATTTTTGGTGCCGAGAC
246 GTTTTTGGCTAAAAACGCGTTCT-GGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGAC
*
6707 TCCTTGAAATATCTATATTTA
310 TCCTTGAAATATC-ATATTCA
* ** *
6728 TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTC
1 TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG-TTTTACGAGCATCTAAATCTTGTTTC
* * * *
6793 GATTTACTTAGAAATTAATTTAGAAAAATATGAAAAACTATATTAAAAACGTGAA
65 GATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGCGTGAA
6848 GTGTCCTCCA
Statistics
Matches: 2192, Mismatches: 400, Indels: 262
0.77 0.14 0.09
Matches are distributed among these distances:
300 1 0.00
301 66 0.03
302 1 0.00
303 1 0.00
304 2 0.00
305 2 0.00
306 30 0.01
307 6 0.00
308 1 0.00
309 49 0.02
310 40 0.02
311 60 0.03
312 48 0.02
313 69 0.03
314 43 0.02
315 37 0.02
316 19 0.01
317 1 0.00
318 27 0.01
319 104 0.05
320 57 0.03
321 5 0.00
322 2 0.00
323 44 0.02
324 11 0.01
325 13 0.01
326 147 0.07
327 118 0.05
328 226 0.10
329 142 0.06
330 82 0.04
331 151 0.07
332 5 0.00
333 2 0.00
334 5 0.00
335 16 0.01
336 2 0.00
337 9 0.00
338 40 0.02
339 80 0.04
340 132 0.06
341 32 0.01
342 264 0.12
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (329 bp):
TCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTACGAGCATCTAAATCTTGTTTCG
ATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAAT
CTTTTTGGCGTTAAATTATATATATTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAAATTT
CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA
CGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCATA
TTCA
Found at i:6883 original size:2 final size:2
Alignment explanation
Indices: 6876--6910 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6866 GTGTTGTTAT
6876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6911 TCTATGAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8542 original size:12 final size:12
Alignment explanation
Indices: 8525--8549 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8515 GCACAATATG
8525 TAACTTAAAATA
1 TAACTTAAAATA
8537 TAACTTAAAATA
1 TAACTTAAAATA
8549 T
1 T
8550 GTTTCAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAACTTAAAATA
Done.