Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009656.1 Corchorus olitorius cultivar O-4 contig09688, 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: 2627
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1381 original size:650 final size:650
Alignment explanation
Indices: 4--1443 Score: 1506
Period size: 650 Copynumber: 2.2 Consensus size: 650
1 AAT
* * * * *
4 ATTTTACCTCAATTTTTGGCCAAAATACTCGTCAAAAATATATAATTCAACGCAAAAAAGCTTAA
1 ATTTT-CCTCAATTTTTGGCC-AAATACTCATAAAAAATATATAATTCAACGCCAAAAAGTTTGA
* * * **
69 AGGGCTTTTCAA-GCTTCTAATATCGTTGTTCCAAATTGTTTCCTA--AATTAATTT-TTAATTA
64 AGGGATTTT-AACGTTTCTAATATCGTTTTTCC--ATTGTTTTTTACTAATTAATTTCTT-ATTA
* * * * * *
130 AATCGAAACAAGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTTAT
125 AATCGAAAAAAGAATCAGAAGCTCGTAAAAACATATCCTTAAATCCAATGAGGCGGAGATTTGAT
* *
195 TAGTTGAATATAGATATGTTAAGGACTCTCGACGCCAAAAGTCAAGAAAATTGAGCCGTGGCCTC
190 TAGATGAATATAGATATGTTAAGGACTCTCGA---CAAAAG-C------A-TGAGCCGTGGCCAC
* *
260 GGAACGCGTTTTTAGCCAAAAACTGTGATGATTAGAACACGATTTCGACTAAAATTTTACAAAAA
244 AGAACGCATTTTTAGCCAAAAACTGTGATG---AGAACACGATTTCGACTAAAATTTTACAAAAA
* * * * *
325 TTGACCTGGAATATTTTTCCTCAATTTTTGACCAAAATACTAATAACAATATACAATTCAACGCC
306 TTGACCTCGAATATTTTTCCACAATTTTTGACCAAAATACTAAAAAAAATATACAATTAAACGCC
* * *
390 AAAAATATTGAAGATATCTTAACGCTTCTAATATCTTGTTCCCTATTTTTTCCTAAATTAATTTA
371 AAAAATATTGAAGAGATCTTAACGCTTCTAATATCTTGTTCACTATTTTTTACTAAATTAATTTA
* * * *
455 TGATTAAAACGAAACAAGATTCATATGCTCGTAAAAACAAATCCTCTAATCTAATATGGCTGAGA
436 TGATTAAAACGAAACAAGAATCAGAAGCTCGTAAAAACAAATCCTCTAATCCAATATGGCTGAGA
* * * * * * * *
520 ATTGGTTAGATGAATATATATATTACAACGACTCTTGGCTCCAAAAATCATGCAAAACTGAGCCG
501 ATTGGTTAGATAAATATAGATATTACAACGACTCTCGGCGCAAAAAAACAGGAAAAACTGAGCCG
* *
585 GTGCCCCGAAACACTAGGCTTTCACCAAAAACCGTGAGGGTTAGCACACGATTTCGGCTAAAATT
566 GTGCCCCGAAACAC-A-GCTTTCACCAAAAACCGTGAGGGATAGCACACGATTTCGGCAAAAATT
* * *
650 TTGCAAAAATTGACTCGAATTT
629 TTGCAAAAATTGACCCGAAATA
* * *
672 TTTTTTCTCAATTTTTGAG-CACAATACTCATAAGAAAATATATAATTCAACGTCAAAAAGTTTG
1 ATTTTCCTCAATTTTTG-GCCA-AATACTCATAA-AAAATATATAATTCAACGCCAAAAAGTTTG
736 AAGGGATTTTAACGTTTCTAATATCGTTTTTCCATTGTTTTTTACTAATTAATTTCTTATTAAAT
63 AAGGGATTTTAACGTTTCTAATATCGTTTTTCCATTGTTTTTTACTAATTAATTTCTTATTAAAT
* *
801 CGAAAAAAGAATCAGAAGCTCGTAAAAATATATCCTTAAATCCAATGAGGCGGAGATTTGATTTG
128 CGAAAAAAGAATCAGAAGCTCGTAAAAACATATCCTTAAATCCAATGAGGCGGAGATTTGATTAG
* ** *
866 ATGAATATAGATAT-TTCAAGGAGTCT-GA-AAAA-C-TGAGTTGTGGCCACAGAATGCATTTTT
193 ATGAATATAGATATGTT-AAGGACTCTCGACAAAAGCATGAGCCGTGGCCACAGAACGCATTTTT
* * *
926 AGCCAAAAA-TCGTGATG-G-ACACGATTTCGGCTAAAATTTTTCCAAAATTGACC-CGAATTAT
257 AGCCAAAAACT-GTGATGAGAACACGATTTCGACTAAAATTTTACAAAAATTGACCTCGAA-TAT
** ** *
987 TTTTCCACAATTTTTGGGCACGATACTCACAAAAAAATATATAATTAAACGCCAAAAAGT-TTGA
320 TTTTCCACAATTTTTGACCAAAATACT-A-AAAAAAATATACAATTAAACGCCAAAAA-TATTGA
* * * * * * *
1051 AGGGCTTTTAACGTTTCTAATATCGTTTTTCTATTGTTTTTTACT-AATTAATTCT-TGATTAAA
382 AGAGATCTTAACGCTTCTAATATC-TTGTTC-ACTATTTTTTACTAAATTAATT-TATGATTAAA
* * * * * *
1114 TCGAAACAAGAATCAGAAGCTCGTAAAAATATATCCT-TAAATCCAATGTGGCTGAGATTTGATT
444 ACGAAACAAGAATCAGAAGCTCGTAAAAACAAATCCTCT-AATCCAATATGGCTGAGAATTG-GT
* *
1178 TA-ATAAATATAGATATTTA-ATA-GAGTCTCGGCGCTAAAAAAAGAGGAAAAACTGAGCC-GTG
507 TAGATAAATATAGATA-TTACA-ACGACTCTCGGCGC-AAAAAAACAGGAAAAACTGAGCCGGT-
* * * * * * *
1239 GCCCTGGAACGC-GTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCAAAAATTTTG
568 GCCCCGAAACACAGCTTTCA-CCAAAAACCGTGAGGGATAGCACACGATTTCGGCAAAAATTTTG
1303 CAAAAATTGACCCGAAATA
632 CAAAAATTGACCCGAAATA
* *
1322 ATTTTCCTCAATTTTTGGCCGAAATACTCTTAAATAAATATATAATTCAATGCCAAAAAGTTTGA
1 ATTTTCCTCAATTTTTGGCC-AAATACTCATAAA-AAATATATAATTCAACGCCAAAAAGTTTGA
* * * * *
1387 AGGGGTTTTAACGTTTCAAATATCG-TTTTCCAATGTTTTTTGCTAATTAATTCCTTA
64 AGGGATTTTAACGTTTCTAATATCGTTTTTCCATTGTTTTTTACTAATTAATTTCTTA
1444 AACCCTATAT
Statistics
Matches: 652, Mismatches: 94, Indels: 71
0.80 0.12 0.09
Matches are distributed among these distances:
647 3 0.00
648 57 0.09
649 38 0.06
650 181 0.28
651 96 0.15
652 45 0.07
653 36 0.06
661 1 0.00
663 4 0.01
666 10 0.02
667 27 0.04
668 152 0.23
669 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (650 bp):
ATTTTCCTCAATTTTTGGCCAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGTTTGAAG
GGATTTTAACGTTTCTAATATCGTTTTTCCATTGTTTTTTACTAATTAATTTCTTATTAAATCGA
AAAAAGAATCAGAAGCTCGTAAAAACATATCCTTAAATCCAATGAGGCGGAGATTTGATTAGATG
AATATAGATATGTTAAGGACTCTCGACAAAAGCATGAGCCGTGGCCACAGAACGCATTTTTAGCC
AAAAACTGTGATGAGAACACGATTTCGACTAAAATTTTACAAAAATTGACCTCGAATATTTTTCC
ACAATTTTTGACCAAAATACTAAAAAAAATATACAATTAAACGCCAAAAATATTGAAGAGATCTT
AACGCTTCTAATATCTTGTTCACTATTTTTTACTAAATTAATTTATGATTAAAACGAAACAAGAA
TCAGAAGCTCGTAAAAACAAATCCTCTAATCCAATATGGCTGAGAATTGGTTAGATAAATATAGA
TATTACAACGACTCTCGGCGCAAAAAAACAGGAAAAACTGAGCCGGTGCCCCGAAACACAGCTTT
CACCAAAAACCGTGAGGGATAGCACACGATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAATA
Found at i:2031 original size:314 final size:317
Alignment explanation
Indices: 1533--2107 Score: 1014
Period size: 314 Copynumber: 1.8 Consensus size: 317
1523 CGATTTCGGC
* *
1533 TAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCGCAATTTTTGGCCGAAATACTCTAAAAAA
1 TAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCGCAATTTTTGGACGAAATACACTAAAAAA
* * **
1598 CATATATATTTCAATGCCAAAAAGTTTGAAGCGGTTTTAACGTTTCTAATATCGTTTTTCCAATG
66 CATATATAATTCAATGCCAAAAAGTTTGAAGCGGTTTTAACGTTTATAATATCGTTTCCCCAATG
1663 GTTTTTACTAATTAATTTCTGATTAAATCGAAACAAGAATCAGAAGCTCGTAAAAAATTTTCCTT
131 GTTTTTACTAATTAATTTCTGATTAAATCGAAACAAGAATCAGAAGCTCGTAAAAAATTTTCCTT
*
1728 AAATCCAATGGGTCTGAGATTTGATTTGATGAATATAAATATTTCAAGGA-GTCTCGGCGCCAAA
196 AAATCCAATGGGTCTGAGATTT-ATTTGATGAATATAAATATTTAAAGGACGTCTCGGCGCCAAA
1792 AAAGAGGAAAAATTGAGCCGTGGCCCCGGAACGCGTTTTTAGCTATAAAACTGTGATG
260 AAAGAGGAAAAATTGAGCCGTGGCCCCGGAACGCGTTTTTAGCTATAAAACTGTGATG
* * *
1850 TAAAATTTTGCAAAAATTGATCCGAAATAGTTTTCCTCAATTTTTGGACGAAATACACTAAAAAA
1 TAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCGCAATTTTTGGACGAAATACACTAAAAAA
1915 -ATATATAATTCAATGCCAAAAAGTTTGAAG-GGTTTTAACGTTTATAATATCGTTTCCCCAAT-
66 CATATATAATTCAATGCCAAAAAGTTTGAAGCGGTTTTAACGTTTATAATATCGTTTCCCCAATG
*
1977 GTTTTTACTAATTAATTTCTGATTAAATCGAAATAAGAATCAGAAGCTCGTAAAAAATTTTCCTT
131 GTTTTTACTAATTAATTTCTGATTAAATCGAAACAAGAATCAGAAGCTCGTAAAAAATTTTCCTT
2042 AAATCCAATGGGTCTGAGATTTATTTGATGAATATAAATATTTAAAGGACGTCTCGGCGCCAAAA
196 AAATCCAATGGGTCTGAGATTTATTTGATGAATATAAATATTTAAAGGACGTCTCGGCGCCAAAA
2107 A
261 A
2108 GAGCAGAAAG
Statistics
Matches: 246, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
313 26 0.11
314 102 0.41
315 29 0.12
316 29 0.12
317 60 0.24
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (317 bp):
TAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCGCAATTTTTGGACGAAATACACTAAAAAA
CATATATAATTCAATGCCAAAAAGTTTGAAGCGGTTTTAACGTTTATAATATCGTTTCCCCAATG
GTTTTTACTAATTAATTTCTGATTAAATCGAAACAAGAATCAGAAGCTCGTAAAAAATTTTCCTT
AAATCCAATGGGTCTGAGATTTATTTGATGAATATAAATATTTAAAGGACGTCTCGGCGCCAAAA
AAGAGGAAAAATTGAGCCGTGGCCCCGGAACGCGTTTTTAGCTATAAAACTGTGATG
Found at i:2181 original size:20 final size:21
Alignment explanation
Indices: 2138--2186 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
2128 GAAACCTTAG
*
2138 GAACCGGTCTGAGTTTGCTGT
1 GAACCGGTCTGAGTTTGCTAT
2159 GAACCGGTCTGA-TTTGAC-AT
1 GAACCGGTCTGAGTTTG-CTAT
2179 GAACCGGT
1 GAACCGGT
2187 TGGTCAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (21 bp):
GAACCGGTCTGAGTTTGCTAT
Done.