Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020393.1 Corchorus olitorius cultivar O-4 contig20426, 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: 7356
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:6455 original size:323 final size:315
Alignment explanation
Indices: 5590--7356 Score: 1430
Period size: 323 Copynumber: 5.5 Consensus size: 315
5580 TTATGTCAAG
* * *
5590 AAAATTCTTTT-CTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAATGTCAAAAAG
1 AAAATT-TTTTCCTCAATTTTTTGCCACAATACTCAT-AAAAATATATAATTCAACGCCAAAAAG
*
5654 ATTGAAGAGTTTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAAT
64 ATTGAAG-G--GTTTTCACGCTTCTAATATCGTTTTT-CA-TTTTTTTCCGAATTAATTTCTAAT
* * * *
5719 TAAATCGAAACAAGATTCAGATGCATGCTTGTAAAAA-AAAT-GTTATATCGAATGTGACTGAGA
124 TAAATCGAAACAAGATTCAGATGC-T--TCGTAAAAACAAATCCTTAAATC-AATGTGGCTGAGA
* * * *
5782 TTTGATTCA-ATGAATATTGGTATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAACA
185 TTTG-GT-AGATGAATATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCA
* * * *
5846 GGGGCCTCGGAACGCGTTTTTAGCCAAATACCATGATGAGTAATCGATTTCGGCTAAAATTTTGC
247 GGGGCC-CGAAACGCGTTTTTAGCCAAAAACC--G-T--G--AT-GATTTAGG-TAAGATTTTGC
*
5911 AAAAACTGACCTGA
302 AAAAACTGACCCGA
* * * *
5925 AAAATTTTTAT--TCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCGACG-CAAAAAA
1 AAAATTTTT-TCCTCAATTTTTTGCCACAATACTCA-TAAAAATATATAATTCAACGCCAAAAAG
* * * *
5987 ATTGATGGGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCC-ATCTTTATTTGTAATTAAA
64 ATTGAAGGGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCGA-ATTAATTTCTAATTAAA
* * * *
6051 TCGAAACAAAATTCAGATGC-TCGTAAAAACAAATCTTTAAATCAATTGTGGCTTA-CTTTGGTT
128 TCGAAACAAGATTCAGATGCTTCGTAAAAACAAATCCTTAAATCAA-TGTGGCTGAGATTTGG-T
* * *
6114 AGATGAATATCA-ATATTTCAAGGAGTCTTTCTGCCAAAAATTATGCAAAACTGAGCTAGAGTCC
191 AGATGAATAT-AGATATTTCAAGGAGTCTTTC-GCCAAAAATCATGCAAAACTGAGC-AGGGGCC
* * *
6178 CGAAACGCGTTTTTAGTCAAAAACCGTGATGGTTTAGGTACACGATTTCGGCTAAAAACTGACCC
253 CGAAACGCGTTTTTAGCCAAAAACCGTGATGATTTAGGTA-A-GATTT-TGC-AAAAACTGACCC
6243 GA
314 GA
* * * *
6245 AAAGTTGTAT-CTCAAATTTTTTTGCCACAATACTCA-AAAAATATATAATTCAACGCCAAAAAT
1 AAAATTTTTTCCTC-AA-TTTTTTGCCACAATACTCATAAAAATATATAATTCAACGCCAAAAAG
* * * * *
6308 ATTGATGGGTTTTCACGCTTCTAATATTGTTTTTCCTTTTTTTTTCCAAATTAAGTTCTAATTAA
64 ATTGAAGGGTTTTCACGCTTCTAATATCGTTTTT-C-ATTTTTTTCCGAATTAATTTCTAATTAA
* * *
6373 ATCGAAACAAGATTTAGAT-CTTCGTAAAAACAAATCCTTATATGCAATGTGGCTAAGATTTGGT
127 ATCGAAACAAGATTCAGATGCTTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAGATTTGGT
* * * * * *
6437 CGATGAATAAAGATATTTCAGGGAGTCTTTGCGCAAAAAATCATGTAAAATTGAGTC-GGGGCTC
191 AGATGAATATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAG-CAGGGGC-C
* ** *
6501 CAAAACATGTTTTTAGCCAAAAACC--------CTA---AAG-TTTTGCAAAAACTGACCCGA
253 CGAAACGCGTTTTTAGCCAAAAACCGTGATGATTTAGGTAAGATTTTGCAAAAACTGACCCGA
* * * * *
6552 AAAATTTTTTGCTCAATTTTTTGCCACAATACTCATAGAATATATATAATTAAAAGCCAAGAAGA
1 AAAATTTTTTCCTCAATTTTTTGCCACAATACTCATA-AAAATATATAATTCAACGCCAAAAAGA
* * * * * * * *
6617 TTGGAGGACTCTTCACGTTTTTAAATATCGTTTTTCATATTTTTCTGAATTAACTTCTAATTAAA
65 TTGAAGG-GTTTTCACGCTTCT-AATATCGTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAA
* * * * *
6682 TCGAAATAAGATTCTGATACTT-GTAAAAACAAATCCTTAAATTCAATGTGCCTGAGATTTGATT
128 TCGAAACAAGATTCAGATGCTTCGTAAAAACAAATCCTTAAA-TCAATGTGGCTGAGATTTG-GT
* * ** * * * * *
6746 AGATGAATATAGATATTCCACGGAGTCTCAACGTCAAAAATCAAGCAAAACTAAGCCGGGGTCTC
191 AGATGAATATAGATATTTCAAGGAGTCT-TTCGCCAAAAATCATGCAAAACTGAGCAGGGG-CCC
* * * *
6811 GAAACGCATTTTTAGCCAAAAACCGTGACATGATTTCGGCTAAAATTTTGCAAAAAATGACCCGA
254 GAAACGCGTTTTTAGCCAAAAACCGTG--ATGATTTAGG-TAAGATTTTGCAAAAACTGACCCGA
* ** * * * * *
6876 AAAA-TTTTTCCGTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATGCTAAGAAG
1 AAAATTTTTTCC-TCAATTTTTTGCCACAATACTCATAAAA-ATATATAATTCAACGCCAAAAAG
** * *
6940 ATTGGAAGACTTTTCACACTT-TCAATATCATTTTTCATATTTTTT--GAATTAATTTCTAATTA
64 ATT-GAAGGGTTTTCACGCTTCT-AATATCGTTTTTCAT-TTTTTTCCGAATTAATTTCTAATTA
* * * *
7002 AATCGAAACAAGATTCAGATGC-TCTTAAAAACAAATTCTTAAATCCAATGTAGCTGATATTTGG
126 AATCGAAACAAGATTCAGATGCTTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAGATTTGG
* * * * * * *
7066 TTAGATGAATATGGATATCTCAAAGAGTCTTGACGCCAAAAATCATGCAAAACTTAAC-CGGGCC
190 -TAGATGAATATAGATATTTCAAGGAGTCTT-TCGCCAAAAATCATGCAAAACTGAGCAGGGGCC
* * *
7130 TTGGAACGCGTTTTTAGCCAAAACCCGTGATGATTATTACACGATTTCGGCT-AGAATTTTGCAA
253 -CGAAACGCGTTTTTAGCCAAAAACCGTGATGA-T-TT-----A----GG-TAAG-ATTTTGCAA
* **
7194 AAATTGACTTG-
304 AAACTGACCCGA
* * *
7205 AAAATTATTTCCTCAATTTTTAGCCACAATACTCATAAAAATTATATAATTCAACGCCAATAAGA
1 AAAATTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAA-TATATAATTCAACGCCAAAAAGA
* *
7270 TTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCGAATTAATTTCTAATTAA
65 TTGAAGGG-TTTTCACGCTTCTAATATCGTTTTT-C-ATTTTTTTCCGAATTAATTTCTAATTAA
* *
7335 ATTGAAACATA-ATTTAGATGCT
127 ATCGAAACA-AGATTCAGATGCT
Statistics
Matches: 1167, Mismatches: 179, Indels: 174
0.77 0.12 0.11
Matches are distributed among these distances:
306 19 0.02
307 24 0.02
308 106 0.09
309 86 0.07
310 13 0.01
311 1 0.00
312 1 0.00
315 2 0.00
316 2 0.00
317 7 0.01
318 6 0.01
319 8 0.01
320 42 0.04
321 72 0.06
322 138 0.12
323 159 0.14
324 102 0.09
325 83 0.07
326 18 0.02
327 1 0.00
328 47 0.04
329 72 0.06
330 59 0.05
331 2 0.00
332 36 0.03
333 13 0.01
334 41 0.04
335 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (315 bp):
AAAATTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAATATATAATTCAACGCCAAAAAGAT
TGAAGGGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCG
AAACAAGATTCAGATGCTTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAGATTTGGTAGATG
AATATAGATATTTCAAGGAGTCTTTCGCCAAAAATCATGCAAAACTGAGCAGGGGCCCGAAACGC
GTTTTTAGCCAAAAACCGTGATGATTTAGGTAAGATTTTGCAAAAACTGACCCGA
Found at i:7119 original size:322 final size:324
Alignment explanation
Indices: 6526--7356 Score: 898
Period size: 322 Copynumber: 2.5 Consensus size: 324
6516 GCCAAAAACC
* * * * *
6526 CTAAAGTTTTGCAAAAACTGACCCGAAAAATTTTT-TGCTCAATTTTTTGCCACAATACTCATAG
1 CTAAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCG-TCAATTTTTAGCCACAATACTCATAA
* * ** *
6590 AATATATATAATTAAAAGCCAAGAAGATTGGAGGACTCTTCACGTTTTTAAATATCGTTTTTCAT
65 AATATATATAATTAAAAGCCAAGAAGATTGGAAGACTTTTCAC-ACTTTCAATATCGTTTTTCAT
* * * *
6655 ATTTTTCTGAATTAACTTCTAATTAAATCGAAATAAGATTCTGATACTTGTAAAAACAAATCCTT
129 ATTTTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATCCTT
* ** *
6720 AAATTCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTCCACGGAGTCTCAACGTCAAAA
193 AAATCCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTCCAAAGAGTCTCAACGCCAAAA
* *
6785 ATCAAGCAAAAC-TAAGCCGGGGTCTCGAAACGCATTTTTAGCCAAAAACC-G-TG-ACATGATT
258 ATCAAGCAAAACTTAA-CC-GGGCCTCGAAACGCATTTTTAGCCAAAAACCGGATGTACACGATT
6846 TCGG
321 TCGG
* ** *
6850 CTAAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCGTCAATTTTTGGATAAAATACTCATAAA
1 CTAAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCGTCAATTTTTAGCCACAATACTCATAAA
* * * *
6915 ATATATATAATTTAATGCTAAGAAGATTGGAAGACTTTTCACACTTTCAATATCATTTTTCATAT
66 ATATATATAATTAAAAGCCAAGAAGATTGGAAGACTTTTCACACTTTCAATATCGTTTTTCATAT
*
6980 TTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCT-TAAAAACAAATTCTTAA
131 TTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT-TGTAAAAACAAATCCTTAA
* * * **
7044 ATCCAATGTAG-CTGATATTTGGTTAGATGAATATGGATA-TCTCAAAGAGTCTTGACGCCAAAA
195 ATCCAATGT-GCCTGAGATTTGATTAGATGAATATAGATATTC-CAAAGAGTCTCAACGCCAAAA
* * * * *
7107 ATCATGCAAAACTTAACCGGGCCTTGGAACGCGTTTTTAGCCAAAACCCGTGATGATTATTACAC
258 ATCAAGCAAAACTTAACCGGGCCTCGAAACGCATTTTTAGCCAAAAACCG-GATG-----TACAC
7172 GATTTCGG
317 GATTTCGG
* * **
7180 CTAGAATTTTGCAAAAATTGACTTG-AAAATTATTTCC-TCAATTTTTAGCCACAATACTCATAA
1 CTAAAATTTTGCAAAAAATGACCCGAAAAATT-TTTCCGTCAATTTTTAGCCACAATACTCATAA
* * * * **
7243 AA-ATTATATAATTCAACGCCAATAAGATT-GAAGGGCTTTTCATGC-TTCTAATATCGTTTTTC
65 AATA-TATATAATTAAAAGCCAAGAAGATTGGAA-GACTTTTCACACTTTC-AATATCGTTTTTC
* * *
7305 CTATTATTTTCCGAATTAATTTCTAATTAAATTGAAACATA-ATTTAGATGCT
127 ATATT-TTTT--GAATTAATTTCTAATTAAATCGAAACA-AGATTCAGATGCT
Statistics
Matches: 428, Mismatches: 57, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
321 28 0.07
322 115 0.27
323 29 0.07
324 94 0.22
325 1 0.00
328 7 0.02
329 76 0.18
330 41 0.10
332 36 0.08
333 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (324 bp):
CTAAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCGTCAATTTTTAGCCACAATACTCATAAA
ATATATATAATTAAAAGCCAAGAAGATTGGAAGACTTTTCACACTTTCAATATCGTTTTTCATAT
TTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATCCTTAAA
TCCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTCCAAAGAGTCTCAACGCCAAAAATC
AAGCAAAACTTAACCGGGCCTCGAAACGCATTTTTAGCCAAAAACCGGATGTACACGATTTCGG
Done.