Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019139.1 Corchorus olitorius cultivar O-4 contig19172, 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: 4927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:129 original size:51 final size:50
Alignment explanation
Indices: 28--130 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
18 GTTCTTCATA
* *
28 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
* * *
78 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGT
129 TT
1 TT
131 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
Found at i:2468 original size:331 final size:331
Alignment explanation
Indices: 1572--3550 Score: 2186
Period size: 331 Copynumber: 6.0 Consensus size: 331
1562 TTTTTGGCCA
* * * *
1572 CAATGCCAAAATGGTTGAAGGGCTTTTCAACG-CTTCTAATATC-TTTTTAAAATATTTTTTTGA
1 CAATGCCAAAAAGGTTGAAGGGC-TTTCCACGCCAT-TAATATCATTTTTTAAATATTTTTTTGA
* *
1635 ATTAATTTCTATTTAAATCGAAATAAGATTCAGATACTCGTAAAATCACAAACTTGAATCCAATG
64 ATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATG
* * * *
1700 TGGATGGGATTTGGCTGGATGAAGATAGATATTTCCAGGAGTCTGGGCGACAAAAAACATGCGAA
129 TGGATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCAAA
*
1765 ACTGAGTCGGGGTCCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGC
194 ACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGC
* * * ** * * *
1830 TAAAACTTTGCAAAAACTGATCTGAAAAAATTTTCCTCAATTTTTGGTCACAATACTCATAAAAA
259 TAAAACTTTGAAAAAATTGACCTG-AAAGTTTTTCCTCAATTTCTGGCCA-AATACTTAT-AAAA
* * *
1895 AATAGAAAATT
321 ATTATATAATT
* * * * ** * * * * * *
1906 CAACGCCAAAACGATGGAAGGATTTTTCACG-TATTTAATATCGTTTTTCT--GTTTTTTTTTCA
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCCA-TTAATATCATTTTT-TAAATATTTTTTT-G
* ** * * * * * * * *
1968 AATTTATTTCTCCTTAAATCGAAACAAGATTCAAATGCTTGCTAAAA-AAAATTCTTTAAAAATT
63 AATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCG-TAAAATCACATAC-TT--GAATC
* ** * * * * ** * * *
2032 CAATGTGGCTGCTA-TTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGCCGAAAATCA
124 CAATGTGGATGGGATTTTG-CTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACA
* * *
2096 TGCAAAACTGACTCGGGG-CCTCGGAACGCG---TTAGGCAAAAACCGTGATGGTTAATATC-CG
188 TGCAAAACTGAGTCGGGGTCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA-CACG
* * *
2156 ATTTCGGCTAAAATTTTGAAAAAATTGACCTGAAAGTTTTTACTCAATTTCTGGCCAAATACTTA
251 ATTTCAGCTAAAACTTTGAAAAAATTGACCTGAAAGTTTTTCCTCAATTTCTGGCCAAATACTTA
2221 TAAAAATTATATAATT
316 TAAAAATTATATAATT
*
2237 CAATGCCAAAAAGGTTGAAGGGCTTTCCACACCATTAATATCATTTTTTAAATATTTTTTTGAAT
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCCATTAATATCATTTTTTAAATATTTTTTTGAAT
2302 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
66 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
* * *
2367 GATGGGATTTTGCTGGATGAATATAGATATTTCAACGAGTCTGGGCGATAAAAAACATGCGAAAC
131 GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCAAAAC
* * * *
2432 TAAGTCGGGGTCCCGGAACGCGATTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAACAA
196 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTA
* ** *** * * * *
2497 AAACTTTGCAAAAACTT-ATATGAATAAAATTTCCTCAATTTTTGGCTACAATACTCATAAAAAA
261 AAACTTTG-AAAAAATTGACCTGAA-AGTTTTTCCTCAATTTCTGGCCA-AATACTTATAAAAAT
*
2561 TATAAAATT
323 TATATAATT
* * * ** * * * * * ** * *
2570 CAACGCCAAAAAGATGGAAGGATTTTTCACGTCTTTACTATCGTTTTTCT-TTTCTTTTTTTCAA
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCCATTAATATCATTTTT-TAAATATTTTTTT-GA
* * * * * * * *
2634 ATTTATTGCTCA-TTAAATAGAAACAAGATTCAGATGCTCGTTAAAA-AAAATCCTTAAATCCAA
64 ATTAATTTCT-ATTTAAATCGAAACAAGATTCAGATACTCG-TAAAATCACATACTTGAATCCAA
* ** * * * * ** * *
2697 TGTGGCTGCTA-TTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGTCAAAAATCATGC
127 TGTGGATGGGATTTTG-CTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGC
* *
2761 AAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTCGTAGC-CGATTT
191 AAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA-CACGATTT
* * * *
2825 CGGCTAAAATTTTGAAAAAATTGACCCGAAAGTTTTTCCTCAATTTCTTGCCAAATACTTATAAA
255 CAGCTAAAACTTTGAAAAAATTGACCTGAAAGTTTTTCCTCAATTTCTGGCCAAATACTTATAAA
*
2890 AATTAAATAATT
320 AATTATATAATT
* * **
2902 CAATGCCAAAAAGGTTGGAGGGCCTTCCACGCTTTTAATATCATTTTTTAAATATTTTTTTGAAT
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCCATTAATATCATTTTTTAAATATTTTTTTGAAT
2967 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
66 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
* *
3032 GATGGGATTTTGCTGGATAAATATAGATATTTCAAGGAGTCTGGGAGACAAAAAACATGCAAAAC
131 GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCAAAAC
*
3097 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTTGTACACGATTTCAGCTA
196 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTA
* * *
3162 AGATTTTGAAAAAATTGACCCGAAAGTTTTTCCTCAATTTCTGGCCAAATACTTATAAAAATTAT
261 AAACTTTGAAAAAATTGACCTGAAAGTTTTTCCTCAATTTCTGGCCAAATACTTATAAAAATTAT
3227 ATAATT
326 ATAATT
* * *
3233 CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCTACTAATATCATTTTTTAAATATTTTTTTGCAT
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCCATTAATATCATTTTTTAAATATTTTTTTGAAT
*
3298 TAATTTCTATTTAAATCGAAATAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
66 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
* * *
3363 GATGGGATTTTTCTGGATG-A-AT--ATA-TTCAAGGAGTCTGGGTGACAAAAAACATGCGAAAC
131 GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCAAAAC
* * * **
3423 TGAGTCGGGGTTCCGGAACGCGTTTTTAGCTAAAAACCGTTATGGTTAGTACACGATTTTGGCTA
196 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTA
* * * * ** * * *
3488 AAACTTTGCAAAAACTGATCTTAAAAAATTTTCCTCAATTTTTGACCACAATACTCATAAAAA
261 AAACTTTGAAAAAATTGA-CCTGAAAGTTTTTCCTCAATTTCTGGCCA-AATACTTATAAAAA
3551 AATTTAAAAT
Statistics
Matches: 1357, Mismatches: 250, Indels: 82
0.80 0.15 0.05
Matches are distributed among these distances:
326 106 0.08
327 25 0.02
328 85 0.06
329 8 0.01
330 17 0.01
331 501 0.37
332 109 0.08
333 135 0.10
334 279 0.21
335 15 0.01
336 5 0.00
337 72 0.05
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (331 bp):
CAATGCCAAAAAGGTTGAAGGGCTTTCCACGCCATTAATATCATTTTTTAAATATTTTTTTGAAT
TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCAAAAC
TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTA
AAACTTTGAAAAAATTGACCTGAAAGTTTTTCCTCAATTTCTGGCCAAATACTTATAAAAATTAT
ATAATT
Found at i:2842 original size:665 final size:664
Alignment explanation
Indices: 1572--3157 Score: 2583
Period size: 665 Copynumber: 2.4 Consensus size: 664
1562 TTTTTGGCCA
* * *
1572 CAATGCCAAAATGGTTGAAGGGCTTTTCA-ACGCTTCTAATATC-TTTTTAAAATATTTTTTTGA
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACAC-CTT-TAATATCATTTTTTAAATATTTTTTTGA
* *
1635 ATTAATTTCTATTTAAATCGAAATAAGATTCAGATACTCGTAAAATCACAAACTTGAATCCAATG
64 ATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATG
* * *
1700 TGGATGGGATTTGGCTGGATGAAGATAGATATTTCCAGGAGTCTGGGCGACAAAAAACATGCGAA
129 TGGATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAA
* *
1765 ACTGAGTCGGGGTCCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGC
194 ACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAAC
* *
1830 TAAAACTTTGCAAAAACTGATCTGAAAAAATTTTCCTCAATTTTTGGTCACAATACTCATAAAAA
259 AAAAACTTTGCAAAAACTGATATGAAAAAATTTTCCTCAATTTTTGGTCACAATACTCATAAAAA
*
1895 AATAGAAAATTCAACGCCAAAACGATGGAAGGATTTTTCACGTATTTAATATCGTTTTTCTGTTT
324 AATAGAAAATTCAACGCCAAAAAGATGGAAGGATTTTTCACGTATTTAATATCGTTTTTCTGTTT
* * * * *
1960 TTTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTCAAATGCTTGCTAAAAAAAATTCTTT
389 TTTTTTCAAATTTATTGCTCATTAAATAGAAACAAGATTCAAATGCTCGCTAAAAAAAATTCCTT
* *
2025 AAAAATTCAATGTGGCTGCTATTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGCCGA
454 -AAAATCCAATGTGGCTGCTATTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGCCAA
* * *
2090 AAATCATGCAAAACTGACTCGGGGCCTCGGAACGCGTTAGGCAAAAACCGTGATGGTTAATATCC
518 AAATCATGCAAAACTGACTCGGGGCCCCGGAACGCGTTAGCCAAAAACCGTGATGGTTAATAGCC
*
2155 GATTTCGGCTAAAATTTTGAAAAAATTGACCTGAAAGTTTTTACTCAATTTCTGGCCAAATACTT
583 GATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAGTTTTTACTCAATTTCTGGCCAAATACTT
*
2220 ATAAAAATTATATAATT
648 ATAAAAATTAAATAATT
*
2237 CAATGCCAAAAAGGTTGAAGGGCTTTCCACACCATTAATATCATTTTTTAAATATTTTTTTGAAT
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACACCTTTAATATCATTTTTTAAATATTTTTTTGAAT
2302 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
66 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
* *
2367 GATGGGATTTTGCTGGATGAATATAGATATTTCAACGAGTCTGGGCGATAAAAAACATGCGAAAC
131 GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAAAC
* *
2432 TAAGTCGGGGTCCCGGAACGCGATTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAACAA
196 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAACAA
*
2497 AAACTTTGCAAAAACTTATATGAATAAAA-TTTCCTCAATTTTTGG-CTACAATACTCAT-AAAA
261 AAACTTTGCAAAAACTGATATGAA-AAAATTTTCCTCAATTTTTGGTC-ACAATACTCATAAAAA
* * * *
2559 AATATAAAATTCAACGCCAAAAAGATGGAAGGATTTTTCACGTCTTTACTATCGTTTTTCTTTTC
324 AATAGAAAATTCAACGCCAAAAAGATGGAAGGATTTTTCACGTATTTAATATCGTTTTTCTGTT-
* *
2624 TTTTTTTCAAATTTATTGCTCATTAAATAGAAACAAGATTCAGATGCTCGTTAAAAAAAA-TCCT
388 TTTTTTTCAAATTTATTGCTCATTAAATAGAAACAAGATTCAAATGCTCGCTAAAAAAAATTCCT
*
2688 T-AAATCCAATGTGGCTGCTATTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGTCAA
453 TAAAATCCAATGTGGCTGCTATTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGCCAA
* **
2752 AAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTCGTA
518 AAATCATGCAAAACTGACTCGGGGCCCCGGAACGCG---TTAGCCAAAAACCGTGATGGTTAATA
* *
2817 GCCGATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAGTTTTTCCTCAATTTCTTGCCAAATA
580 GCCGATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAGTTTTTACTCAATTTCTGGCCAAATA
2882 CTTATAAAAATTAAATAATT
645 CTTATAAAAATTAAATAATT
* * * *
2902 CAATGCCAAAAAGGTTGGAGGGCCTTCCACGCTTTTAATATCATTTTTTAAATATTTTTTTGAAT
1 CAATGCCAAAAAGGTTGAAGGGCTTTCCACACCTTTAATATCATTTTTTAAATATTTTTTTGAAT
2967 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
66 TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
* * *
3032 GATGGGATTTTGCTGGATAAATATAGATATTTCAAGGAGTCTGGGAGACAAAAAACATGCAAAAC
131 GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAAAC
*
3097 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTTGTACACGATTTCA
196 TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCA
3158 GCTAAGATTT
Statistics
Matches: 857, Mismatches: 56, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
662 94 0.11
664 75 0.09
665 682 0.80
666 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (664 bp):
CAATGCCAAAAAGGTTGAAGGGCTTTCCACACCTTTAATATCATTTTTTAAATATTTTTTTGAAT
TAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTG
GATGGGATTTTGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAAAC
TGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAACAA
AAACTTTGCAAAAACTGATATGAAAAAATTTTCCTCAATTTTTGGTCACAATACTCATAAAAAAA
TAGAAAATTCAACGCCAAAAAGATGGAAGGATTTTTCACGTATTTAATATCGTTTTTCTGTTTTT
TTTTCAAATTTATTGCTCATTAAATAGAAACAAGATTCAAATGCTCGCTAAAAAAAATTCCTTAA
AATCCAATGTGGCTGCTATTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGCGCCAAAAA
TCATGCAAAACTGACTCGGGGCCCCGGAACGCGTTAGCCAAAAACCGTGATGGTTAATAGCCGAT
TTCGGCTAAAATTTTGAAAAAATTGACCCGAAAGTTTTTACTCAATTTCTGGCCAAATACTTATA
AAAATTAAATAATT
Done.