Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000545.1 Corchorus olitorius cultivar O-4 contig00545, 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: 4679
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 6--51 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 GTTAG
6 TA TA GTA TA TA TA 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 TA TA TA TA TA TA
49 TA T
1 TA T
52 GAGTCTTGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1345 original size:34 final size:34
Alignment explanation
Indices: 1307--1378 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
1297 ACATCATTTA
* *
1307 GATGCTTGTTTTAAAAATCCTTCAATCCATTGTG
1 GATGCTAGTTTTAAAAATCCTTAAATCCATTGTG
*
1341 GATGCTAGTTTTATAAATCCTTAAATCCATTGTG
1 GATGCTAGTTTTAAAAATCCTTAAATCCATTGTG
1375 GATG
1 GATG
1379 AAATTTAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (34 bp):
GATGCTAGTTTTAAAAATCCTTAAATCCATTGTG
Found at i:2344 original size:332 final size:323
Alignment explanation
Indices: 1355--2969 Score: 1408
Period size: 332 Copynumber: 4.9 Consensus size: 323
1345 CTAGTTTTAT
* * * * *
1355 AAATCCTTAAATCCATTGTGGATGAAATTT-AGTTAGATTAATATAGATATTTCAAGGAGTC-TC
1 AAATCCTTAAATGCAATGTGGTTGATATTTGA-TTAGATGAATATAGATATTTCAAGGAGTCTTC
* *
1418 GGCGCAAAAAATCATGCAACACTGAACC-GGGGCCCCGGAACGCGTTTTTAGTCAAAAACCGTGA
65 -GC-C-AAAAATCATGCAAAACTG-ACCTGGGG--CCGGAACGCGTTTTTAGCCAAAAACCGTGA
* * * * * *
1482 TTTTGGCTAACATACACGATTGCGGCTAATATTTTGCAAAAATTGGCTAGAAATAGT-TTTCCTC
124 ---T-GAT-A-TTACACGATTTCGGCTAAAATTTTGCAAAAA-T-GCCAGAAAGA-TATTTCCTC
* * * *
1546 AATTTTTAT-CTAAAATAATCATAAAAAATATATAATTCAACT-CCAAAAATATTGGAGGACTTT
180 AATTTTT-TGCT-AAATACTCATAAAAAATATATAATTCAA-TGCCAAAAAGATTGAAGGGCTTT
* * *
1609 TCACGCTTTTAATGTCGTTTTTCATATTTTTATGAATTAATTTCTAATTAAATTGAAACAAGATT
242 TCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
*
1674 CAGATGCTCGTAATAAC
307 CAGATGCTCGTAAAAAC
** * * * *
1691 AAATATTTAAATGCAATGTGGCTGAGATTTGATTAAATGAATATATATACATTTCAAGGAGGCTC
1 AAATCCTTAAATGCAATGTGGTTGATATTTGATTAGATGAATATAGAT--ATTTCAAGGA-G-TC
** * * * * * *
1756 GACGCCAAAAATCATACAAAACTGA-GTCGGGGCCCCGAAACGCTTTTTTAACAAAAAACCGTGA
62 TTCGCCAAAAATCATGCAAAACTGACCT-GGGG--CCGGAACGCGTTTTTAGCCAAAAACCGTGA
* * * * *
1820 TG-TA-T--ACGATTTCGCCTAAAATTTTGTAAAAAATAAG-CAGAAAAATTTTTCCTCATTTTT
124 TGATATTACACGATTTCGGCTAAAATTTTG-CAAAAAT--GCCAGAAAGATATTTCCTCAATTTT
* * * ** * *
1880 TTGCTAAAATACTCATGAAATATATATAATTTAATGCCAAAAAGATTGGTGGACTTTTGACGCTT
186 TTGCT-AAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTT
* *
1945 TTCATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGC
250 TTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
2010 TCGTAAAAAC
314 TCGTAAAAAC
* * *
2020 AAATCCTTAAATGCAATGTGGTTGATATTTGATTAGATGAATATGGATATCTCAAGTAGTC-TCG
1 AAATCCTTAAATGCAATGTGGTTGATATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTCG
* *
2084 CCAAAAATCATGCAAAATTGACCTGAGGCCGTGCAACGCGCATTTTTAGCCAAAAACCGTGATGA
66 CCAAAAATCATGCAAAACTGACCTGGGGCCG-G-AACGCG--TTTTTAGCCAAAAACCGTGATG-
**
2149 TATTATTACACGATTTCGGCTAAAATTTTGCAAAAATGGTCTGGAAAGATATTTCCTCAATTTTT
126 -A-TATTACACGATTTCGGCTAAAATTTTGCAAAAAT-G-CCAGAAAGATATTTCCTCAATTTTT
* ** * * * *
2214 TGCTAAATTA-TCATAAAAAATATATAATTCAACGCCAAAATTATTGAAGGGTTTTTTATGCTTC
187 TGCTAAA-TACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTT
* * * *
2278 TAATATCGTTTTTCTTACTTTTTCGGAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCT
251 TAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
*
2343 CGTAAAAAA
315 CGTAAAAAC
* * *
2352 AAATCCTTAAATCCAATGTGGTTGATATTTGATTAGATGAATATAGATAATTGAAGGAGTCTTGA
1 AAATCCTTAAATGCAATGTGGTTGATATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT--
* * * ****
2417 CGCCAAAAATCATGCAATATTGACCCGGGGTCCCGGAACGCGTTTTTAGCCAAACAAAAAAG-TG
64 CGCCAAAAATCATGCAAAACTGACCTGGGG--CCGGAACGCGTTTTTAGCCAAA-AACCGTGATG
* * * * * *
2481 ACATTACACGATTTCGGCTAATATTTTGCAAAAAATGACCCA-AAATATTTTTCCTCAATATTTA
126 ATATTACACGATTTCGGCTAAAATTTTGC-AAAAATG--CCAGAAAGATATTTCCTCAATTTTTT
* * * *
2545 GCCACAATACTTATAAAAAATATATAATTCAATTCCAAAAAGATTGAAGGGCTTTTCACGCTTCT
188 GCTA-AATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTT
* * * * *
2610 AATATCGTTTTTTGTATTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGC
252 AATATCG-TTTTT-CA-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
*
2675 T--T-ATAA-
314 TCGTAAAAAC
* *
2681 AAA--C---AATG--GT-TGG--G--ATTTGGTTAGATG-ATATAGATATTTCAAGGAGTCTTGG
1 AAATCCTTAAATGCAATGTGGTTGATATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT--
* ** * *
2733 CGCCAAAAAATCATTCAAAACTGAAATGGGTCCCGGAATGCGTTTTTAGCCAAAAACCGTGATGA
64 CGCC-AAAAATCATGCAAAACTGACCTGGG-GCCGGAACGCGTTTTTAGCCAAAAACCGTGATGA
* * * * *
2798 TTATTACATGATTTCGGCTAAAATTTTGAAAAAATTTACCCGAAAGATATTTCCTCAATTTTTAG
127 -TATTACACGATTTCGGCTAAAATTTTGCAAAAA--TGCCAGAAAGATATTTCCTCAATTTTTTG
* * * * *
2863 CCATAATACTCAGAAAAAATACATAATTCAATGCTAAAAAGATTGAAGGGCTTTTGACGCTTTTA
189 CTA-AATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTA
* *
2928 ATATCGTTTTTCATAATTTTCTGAGTTAAGTTT-TAATTAAAT
253 ATATCGTTTTTCATATTTTTCTGAATTAA-TTTCTAATTAAAT
2970 TAAATATTTC
Statistics
Matches: 1062, Mismatches: 167, Indels: 122
0.79 0.12 0.09
Matches are distributed among these distances:
314 20 0.02
315 7 0.01
316 62 0.06
317 138 0.13
318 1 0.00
319 1 0.00
321 3 0.00
322 4 0.00
324 32 0.03
325 3 0.00
326 21 0.02
327 12 0.01
328 107 0.10
329 102 0.10
330 56 0.05
331 67 0.06
332 177 0.17
333 103 0.10
334 5 0.00
335 34 0.03
336 38 0.04
337 5 0.00
338 57 0.05
339 2 0.00
340 4 0.00
341 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (323 bp):
AAATCCTTAAATGCAATGTGGTTGATATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTCG
CCAAAAATCATGCAAAACTGACCTGGGGCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATATT
ACACGATTTCGGCTAAAATTTTGCAAAAATGCCAGAAAGATATTTCCTCAATTTTTTGCTAAATA
CTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTT
TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
Found at i:3491 original size:70 final size:70
Alignment explanation
Indices: 3347--3549 Score: 238
Period size: 66 Copynumber: 2.9 Consensus size: 70
3337 TTTATATAAC
* * *
3347 AAATTAAAATC-CGATAAACGATACAAGTTTAGAAGTAAAAGTC-TTAATAACAATAACAGACAA
1 AAATTAAAATCACGATAAA--AT-TAAGTTTGGAAGTAAAAGTCTTTAATAACAATAAAAGACAA
** * *
3410 ATGAGAGG
63 ACAACACG
*
3418 AAATTAAAATCACGATAAAATTAAGTTTGGAAGTAAAAGTCTTTAATAAGAATAAAAGACAAACA
1 AAATTAAAATCACGATAAAATTAAGTTTGGAAGTAAAAGTCTTTAATAACAATAAAAGACAAACA
3483 ACACG
66 ACACG
* * *
3488 AAATTAAAATTAGGAT---A-TAAATTTGGAAGTAAAAGTCTTTAATAACAATAAAAGACAAACA
1 AAATTAAAATCACGATAAAATTAAGTTTGGAAGTAAAAGTCTTTAATAACAATAAAAGACAAACA
3549 A
66 A
3550 TAAACTAAAG
Statistics
Matches: 118, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
66 43 0.36
67 1 0.01
69 18 0.15
70 38 0.32
71 11 0.09
72 7 0.06
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.23
Consensus pattern (70 bp):
AAATTAAAATCACGATAAAATTAAGTTTGGAAGTAAAAGTCTTTAATAACAATAAAAGACAAACA
ACACG
Done.