Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010103.1 Corchorus olitorius cultivar O-4 contig10135, 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: 2581
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:812 original size:333 final size:333
Alignment explanation
Indices: 23--2199 Score: 3080
Period size: 333 Copynumber: 6.6 Consensus size: 333
13 ATATATATAT
* *
23 ATATATAAATCATCGCCAAAAAGATTGAAAGGTTTTTCACGCTTCGAAGATCGTTTTTCTTATGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
* * *
88 TTTTCCGAATTACTTTTTCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAA-AAATTATTT
66 TTTTCCGAATTA-ATTTTCAATTAATTCGAAACTGGATTCTGATGCTCGTAAAAATAAA-TCTTT
* * *
152 AATTCTTATGTTGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGACGCCAAAA
129 AAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAA
* * * * * * *
217 ATCATACAAAACTGAGTCGGGGCCCTGGAATGCGTTTTTAGCCGAAAACTGTGA-CG-TA-TAC-
194 ATTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACA
*
278 -GATTTCGGTCAACATTTT-CTAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAAT
259 TGATTTCGGTCAAGATTTTGC-AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAAT
341 ACTCATAAAAA
323 ACTCATAAAAA
* * * *
352 TTATATAAATAATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGATGATCGTTTTTCCTATGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
* * *
417 TTTTCCGAATTAATTTCCAATTAAATT-GAAACTGGATTCAGATGCTCGTAAAAATTAATCTTTA
66 TTTTCCGAATTAATTTTCAATT-AATTCGAAACTGGATTCTGATGCTCGTAAAAATAAATCTTTA
* * *
481 AATCTTATGTGGCCGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGACTTGGCGGCAAAAA
130 AATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAAA
* * *
546 TTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGTCGAAAATAGTGATGGTTTGCACAT
195 TTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACAT
*
611 GATTTTGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATAC
260 GATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATAC
676 TCATAAAAA
325 TCATAAAAA
* * * * **
685 ATATATAAATCATCGCCAAAAAGATTGAAGGATGTTTCACGCTTTGAAGATCGTTTTTCTTGGGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
* *
750 TTTTCCGAATTACTTTTTCAATTAATTCGAAACTGGATTCTGATGCTCGTAAAAA-AAATCTTTT
66 TTTTCCGAATTA-ATTTTCAATTAATTCGAAACTGGATTCTGATGCTCGTAAAAATAAATCTTTA
* ** * ** * *
814 ATTCTTATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTTGGTGCCGAAAA
130 AATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAAA
*** * * *
879 TTATACAAAACTGAGGTAGGGTCCCGGAACGCGTTTTTAGCCGAAAACTA-TGTTGGTTAGTACA
195 TTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAAC-AGTGATGGTTAGCACA
* * * *
943 CGATTTCGGTCAACATTTTGCAAAAATTGACCCGAATGATTTTCCCTCAATTTTTGGCAAAAATA
259 TGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATA
1008 CTCATAAAAA
324 CTCATAAAAA
* ** *
1018 ATATATAAATCATTGCCAAAAAGATTGAAGGGTTTTTCACGCTTAAAAGATCGTTTTTCCTATGT
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
* *
1083 TTTTCCGAATTAA-ATTCTAATTAAATCGAAACTGGATTCTGATGCTCGT-AAAATCAAATCTTT
66 TTTTCCGAATTAATTTTC-AATTAATTCGAAACTGGATTCTGATGCTCGTAAAAAT-AAATCTTT
* * * **
1146 AAATCTTATGTGGCTGAGATTTGGGTAGATAAATATAGAAATTCAAAGGAGTCTTAACGCCAAAA
129 AAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAA
* *
1211 ATTATACAAAACTGAGCCGGGGCACCGGAACGCGTTTTTAGCCGAAAACAGTGATGATTAGCACA
194 ATTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACA
*
1276 CGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCT-AATTTTTTGGCCAAAAT
259 TGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAA-TTTTTGGCCAAAAT
1340 ACTCATAAAAA
323 ACTCATAAAAA
* * * *
1351 ATATATAAATCATAGCCATAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCATTTTTCCTAAGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
*
1416 TTTTCCGAATTAATTTCCAATTAAATT-GAAACT-GATTTCTGATGCTCGTAAAAATAAATCTTT
66 TTTTCCGAATTAATTTTCAATT-AATTCGAAACTGGA-TTCTGATGCTCGTAAAAATAAATCTTT
* *
1479 AAATCTTATGTGGCTAAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGTGCCAAAA
129 AAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAA
* ** * *
1544 ATCATACAAAACTGAGCATGGTCCCCAGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACA
194 ATTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACA
*
1609 TGATTTTGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATA
259 TGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATA
1674 CTCAT-AAAA
324 CTCATAAAAA
*
1683 ATATAT-AAGCAATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATG
1 ATATATAAATC-ATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATG
* * *
1747 TTTTTCCGAATTAATTTCCAATTAAATT-GACACTGGATTCTGATGCTCGTAAAAATAAATCTTT
65 CTTTTCCGAATTAATTTTCAATT-AATTCGAAACTGGATTCTGATGCTCGTAAAAATAAATCTTT
* *
1811 AAATCTTATGTGGCTAAGATTTGGGTAAATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAA
129 AAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAA
* * *
1876 ATTATACAAAACTGAGCCTGGGCCCCGGAACGCGTTTTTAGCCGAAAACATTAATGGTTAGCACA
194 ATTATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACA
* * *
1941 TGATTTAGGTCAAGGTTTTGCAAAAATTGACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATA
259 TGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATA
2006 CTCATAAAAA
324 CTCATAAAAA
* * * * * * *
2016 ATATACAAATCATCGCCTAAAAGTTTGAAGGATTTTTAACGCTTGGAAGATCGTTTTTCCTGTGC
1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
* * * *
2081 TTTTCCGAATGAA-TTTCAAATTAA-ACTGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTT
66 TTTTCCGAATTAATTTTC-AATTAATTC-GAAACTGGATTCTGATGCTCGTAAAAATAAATCTTT
* * * * *
2144 AAATCTTATGTGGCTGAGATTTGGGAAGATAAATACAGATATTTCAAGGAGTCTTG
129 AAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTG
2200 ACGCTGTTTT
Statistics
Matches: 1649, Mismatches: 171, Indels: 52
0.88 0.09 0.03
Matches are distributed among these distances:
328 144 0.09
329 77 0.05
330 1 0.00
331 12 0.01
332 347 0.21
333 1017 0.62
334 51 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (333 bp):
ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTATGC
TTTTCCGAATTAATTTTCAATTAATTCGAAACTGGATTCTGATGCTCGTAAAAATAAATCTTTAA
ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGACATTCCAAGGAGTCTTGGCGCCAAAAAT
TATACAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACAGTGATGGTTAGCACATG
ATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACT
CATAAAAA
Done.