Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020395.1 Corchorus olitorius cultivar O-4 contig20428, 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: 20238
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:1473 original size:334 final size:331
Alignment explanation
Indices: 383--1724 Score: 1196
Period size: 334 Copynumber: 4.0 Consensus size: 331
373 ACAATGGTTA
* * * *
383 AGATTTGGTTA-ACTGAATATAGATATTTCAAGGAGTCTC-AATGCCAAAAATCATTCAAAACAG
1 AGATTTGATTAGA-TGAATATAGATATTTCAAGGAGTCTCGGA-GCCAAAAATCATGCAAAACTG
* * * * * * *
446 AAAT-GAGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G---TTACATGATTTCGGCTAAA
64 -AGTCGGGTCCCGGAACGTGTTTTTACCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAA
* * * * * * * * *
506 ATTTTGTAAAAATTGACCCGAAAGATATTACCTCGATTTTTAGCCATAATAATAATAAAGAATAT
128 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATAT
* *
571 ATAATTCAACGTCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTC
193 ATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTTAATATCGTTTTTCTTATTTTTTC
* * * * * *
636 TAAAATAATTTCTAATTAAATCGAAA-AATGATTCAGATGCTCGTTAAAAATAATAAAAAATAAA
257 TAAATTAATTTCTAATTAAATAGAAACAA-AATTCAGATGCTTGGT----A-AA-AACAAAT---
* * * *
700 ATCTTACATGCAATTTGGCTA
312 -TCTTAAATCCAATGTGGCTG
* * * **
721 AGATTTTATTAGATGAATATAGTTATTTCAAGGAGTGTC-GACGTAAAAAATCATGCAAAACTGA
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGA-GCCAAAAATCATGCAAAACTGA
* * * * * * **
785 G-CTGGTGCGCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTTTGCTAAA
65 GTCGGGT-C-CCGGAACGTGTTTTTACCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAA
* * * * * * * *
849 ATTCTGCAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTGGATAAAATACTTC-TAATATATA
128 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATAC-TCATAAAAAATA
* * * * *
913 TATAATTTAATGGCAAAAAGATTG--GAG-----GAC-TTTTAATATTGTTTTTCTTA-TTTTTC
192 TATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTTAATATCGTTTTTCTTATTTTTTC
* * * *
969 TATATTAATTTCTAATTAAATCA-AAACAAGATTAAGATGCTT-GTAAAAACAAATTTTTAAATC
257 TAAATTAATTTCTAATTAAAT-AGAAACAAAATTCAGATGCTTGGTAAAAACAAATTCTTAAATC
*
1032 CAATGTGACTG
321 CAATGTGGCTG
* ** * *
1043 AGATTTGATTAGATGAATATAAATATCCCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAG
* * * * * *
1108 TCGGGGCCACAGAAAGCT-TTTTTATCCAAAAATTGTGATGGTTATTACACGATATCGGCTAAAA
66 TCGGGTCC-CGGAACG-TGTTTTTACCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAA
* *
1172 TTTTGTAAAAATTGACCCGAAAGATATTTCCTAAATTTTTGGCTAAAATACTCATAAAAAATATA
129 TTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATA
* * * *
1237 TAACTCAATGCCAAAAAAATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTATTTTTT-T
194 TAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTT-TAATATCGTTTTTCTTATTTTTTCT
* * * *
1301 CAAATTAATTTCTAATTAAATAGCAACAAAATTCAGATG-TTGGTAAAGACAAATCCTTAAATCT
258 -AAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTTGGTAAAAACAAATTCTTAAATCC
*
1365 AATGTGGGGGTG
322 AATGT--GGCTG
* * * *
1377 AGATTTGATTAGATGAATATAGATATTTTAAGTAGTCTCGGAGCCAGAAATCATGCAAAATTGAG
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAG
* * ** * *
1442 TCGGGTCCTCGGAACGTGTTTTTACCCAAAAATCGTGATAGTTTGTTA-GTGATTTCAGCTACAA
66 TCGGGTCC-CGGAACGTGTTTTTACCCAAAAATCGTGAT-GGTTATTACACGATTTCGGCTAAAA
* * *
1506 TTTTGCAAAAATTGACACGAAAGAT-TTCTTCTCAATTTTTGGCTAAAATCCTCAT-AAAAATAT
129 TTTTGCAAAAATTGACCCGAAAGATATT-TCCTCAATTTTTGGCTAAAATACTCATAAAAAATAT
* * * *
1569 ATAATTCAACGCCAAAAAGATTGGAA-GACTTTTTACACTTTTAATATCGTATTTTTTTATTTTT
193 ATAATTCAACGCCAAAAAGATT-GAAGGGCTTTTGAC-GTTTTAATATCGT-TTTTCTTATTTTT
* * * * *
1633 TCTAAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGC-TCGTAAAAACAAATTCTTAAAT
255 TCTAAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTTGGTAAAAACAAATTCTTAAAT
**
1697 CCAATGTTACTG
320 CCAATGTGGCTG
*
1709 AGATTTGGTTAGATGA
1 AGATTTGATTAGATGA
1725 TGTAAAGTAT
Statistics
Matches: 812, Mismatches: 153, Indels: 84
0.77 0.15 0.08
Matches are distributed among these distances:
321 3 0.00
322 181 0.22
323 4 0.00
324 2 0.00
326 6 0.01
327 2 0.00
328 1 0.00
329 3 0.00
330 3 0.00
331 19 0.02
332 78 0.10
333 86 0.11
334 244 0.30
335 7 0.01
336 3 0.00
337 2 0.00
338 52 0.06
339 31 0.04
340 1 0.00
341 2 0.00
343 81 0.10
344 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (331 bp):
AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAG
TCGGGTCCCGGAACGTGTTTTTACCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAATT
TTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATA
ATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTTAATATCGTTTTTCTTATTTTTTCTAAA
TTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTTGGTAAAAACAAATTCTTAAATCCAATG
TGGCTG
Found at i:2100 original size:15 final size:17
Alignment explanation
Indices: 2077--2120 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
2067 TGACTATAAA
2077 AAATAATATTATAAT-T
1 AAATAATATTATAATCT
2093 AAAT-ATATTATAATCT
1 AAATAATATTATAATCT
2109 AAA-AATAATTAT
1 AAATAAT-ATTAT
2121 TAGAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.40
16 10 0.40
17 5 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAATATTATAATCT
Found at i:10747 original size:13 final size:13
Alignment explanation
Indices: 10729--10755 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10719 CAGTTCATCC
10729 GGAGACTTTAAAT
1 GGAGACTTTAAAT
10742 GGAGACTTTAAAT
1 GGAGACTTTAAAT
10755 G
1 G
10756 AATCAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (13 bp):
GGAGACTTTAAAT
Found at i:20215 original size:2 final size:2
Alignment explanation
Indices: 20208--20238 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20198 GATTAGATGG
20208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.