Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002615.1 Corchorus olitorius cultivar O-4 contig02617, 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: 2034
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:1294 original size:600 final size:605
Alignment explanation
Indices: 599--1726 Score: 1508
Period size: 600 Copynumber: 1.9 Consensus size: 605
589 CATCATAGTA
* * * *
599 TTTCGCTAAAAACGCGTTTTGAGGCCCCGGATCAGTTTTGGATGATTTTTGGCAGAAATACTCCT
1 TTTCGCTAAAAACACGTTTTGAGGCCCCGGATCAATTTTGCATGATTTTTGGCAGAAACACTCCT
*
664 CAAAATATCTATATTCATATATCTGAATCTCAACCACATTGGATTTAAGGATTTGATTTTACGAG
66 CAAAATATCTATATTCATATATCTGAATCTCAACCACATTGGATTTAAGGATTTCATTTTACGAG
* * * * *
729 TATTTAAATCTTGTTTCGATTTAATTGGAAATAAAATCGGGAAAAAAATGTAAAAA-TGATATTA
131 CATCTAAATCTTGTTTCGATTTAATTAGAAATAAAATC-AGAAAAAAATGGAAAAACT-ATATTA
* * * *
793 GAAGCGTGAAAAACCCTTTATTTTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGCA
194 GAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTGTGGCA
* *
858 CAAAAATTTAGAAAAAAACTTTCGGGTCAATTTTTAGCCGAAATC-GTAC-A-GT-TTTTCGCTA
259 AAAAAATTTAGAAAAAAACTTTCGGGTCAATTTTTAGCCGAAATCAGTACTACATATTTTCGCTA
* * * *
919 AAAACG-TGTTTCGGGGCGCCGACATAGTTTTGCA-AGATTTT-G-GGAA-AACTTCTTGAAATA
324 AAAA-GACGTTTCGGGGCCCCGACATAGATTTGCATA-ATTTTCGAAGAAGAACTTCTTGAAATA
* *
979 TCTATATTCCTCTACCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTCGTACGTGCATCTGA
387 TCTATATTCATCTACCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTCGTACGAGCATCTGA
* * * * **
1044 ATCTTTTTTCGATTTAATTTGTAATAAATTTGAAAAAAAAATGGAAAAACGATATTAGAATCGTG
452 ATCTTGTTTCGATTTAATTAGAAATAAATTCG-AAAAAAAATACAAAAACGATATTAGAATCGTG
1109 AAAACCCCTTCCAATTTTTTTGGCAATGAATTATATATTTTTTATGATTATTTTGGCAAAAAATT
516 AAAACCCCTTCCAATTTTTTTGGCAATGAATTATATATTTTTTATGATTATTTTGGCAAAAAATT
1174 TTGAAAAAAAATTTTCGGGTCAGTT
581 TTGAAAAAAAATTTTCGGGTCAGTT
*
1199 TTTCGCTAAAAACACGTTTTG-GGACCCTGGAT-ATATTTTGCATGATTTTTGGCAGAAACACTC
1 TTTCGCTAAAAACACGTTTTGAGG-CCCCGGATCA-ATTTTGCATGATTTTTGGCAGAAACACTC
** * * * *
1262 CTTGAAATATCTATATTCATCTAT-TCGAATCTCATCCACATTGGATTTAAGGATTTCTTTTTAT
64 CTCAAAATATCTATATTCATATATCT-GAATCTCAACCACATTGGATTTAAGGATTTCATTTTAC
* * * * *
1326 GTGCATCTGAATCTTGTTTCTATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACTTTATT
128 GAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAAATCAGAAAAAAATGGAAAAACTATATT
1391 AGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTGTGGC
193 AGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTGTGGC
* *
1456 AAAAAAATTTAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCATGTACGTTACATCACAAC
258 AAAAAAATTTAGAAAAAAACTTTCGGGTCAATTTTTAGCCGAAATCA-GTAC--TACAT----A-
* * *
1521 TTTTCGCTAAAAAGACGTTTCGGGGCCCCGACTTAGATTTGTATAATTTTCGCAAGAAGGACTTC
315 TTTTCGCTAAAAAGACGTTTCGGGGCCCCGACATAGATTTGCATAATTTTCG-AAGAAGAACTTC
* * ** * ** *
1586 TTGAAATATCTATATTCATCTACTCGAATCTCTTCCACTTTGGATTTAAGGATTTGTTTTTATGA
379 TTGAAATATCTATATTCATCTACCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTCGTACGA
* * *
1651 GCTTCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATACAAAAATGATATTAG
444 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATACAAAAACGATATTAG
1716 AATCGTGAAAA
509 AATCGTGAAAA
1727 AAAAACCCTT
Statistics
Matches: 450, Mismatches: 56, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
599 127 0.28
600 143 0.32
601 4 0.01
604 1 0.00
605 1 0.00
610 1 0.00
611 41 0.09
612 2 0.00
614 35 0.08
615 95 0.21
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (605 bp):
TTTCGCTAAAAACACGTTTTGAGGCCCCGGATCAATTTTGCATGATTTTTGGCAGAAACACTCCT
CAAAATATCTATATTCATATATCTGAATCTCAACCACATTGGATTTAAGGATTTCATTTTACGAG
CATCTAAATCTTGTTTCGATTTAATTAGAAATAAAATCAGAAAAAAATGGAAAAACTATATTAGA
AGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTGTGGCAAA
AAAATTTAGAAAAAAACTTTCGGGTCAATTTTTAGCCGAAATCAGTACTACATATTTTCGCTAAA
AAGACGTTTCGGGGCCCCGACATAGATTTGCATAATTTTCGAAGAAGAACTTCTTGAAATATCTA
TATTCATCTACCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTCGTACGAGCATCTGAATCT
TGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATACAAAAACGATATTAGAATCGTGAAAAC
CCCTTCCAATTTTTTTGGCAATGAATTATATATTTTTTATGATTATTTTGGCAAAAAATTTTGAA
AAAAAATTTTCGGGTCAGTT
Found at i:1832 original size:921 final size:906
Alignment explanation
Indices: 1--2034 Score: 2391
Period size: 921 Copynumber: 2.2 Consensus size: 906
* * * *
1 ACGTGTTTCGGGGCCCCGACTAGATTTTGCATGATTTTCGGAAGAAAGACTCCTTAAAATATATA
1 ACGTGTTTCGGGGCCCCGACTAG-TTTTGCAAGATTTTCGG--GAAA-ACTTCTTGAAATATCTA
* *
66 CATTCATCTACCCGAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCT
62 AATTCATCTACCCGAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCT
* * * * *
131 TGTTTCAATTTAGTTTAAAATAAATTCAGAAAAAATGG-AAAATGATATTAGAATCTTGAAAAAC
127 TGTTTCGATTTAATTTGAAATAAATT-AAAAAAAATGGAAAAACGATATTAGAATCTTGAAAAAC
** *
195 CCTTCAATTTTTTTGGCGTTGAATTATATATTTTTAAAGAGTATTTTGGCAAAAAATTTAGGAAA
191 CCTTCAATTTTTTTGGCAATGAATTATATATTTTTAAAGAGTATTTTGGCAAAAAATTTAGAAAA
* * * * *
260 TAGTGTACCATCACAGTTTTTCGCTAAAAACGCATTTTGGGGCCCTAGATCAGTTTTGCATGATT
256 AAATGTACCAT-ACAGTTTTTCGCTAAAAACACATTTTGGGACCCTAGATCAATTTTGCATGATT
325 TTTGGAAGAAACACTCCTTGAAATATCTATATTCATCTATCCGAATCTCAGCCACATTAGATTTA
320 TTTGGAAGAAACACTCCTTGAAATATCTATATTCATCTATCCGAATCTCAGCCACATTAGATTTA
* *
390 AGAATTTCTTTTTACGAGTATCTGAATCTTGGTTCGATTCAATTAGAAATAAATTCGGAAAAAAA
385 AGAATTTCTTTTTACGAGCATCTGAATCTTGGTTCGATTCAATTAGAAATAAATTCAGAAAAAAA
* *
455 TGGAAAACGATAATAGAATCGTAAAAAAACCCTTCACTTTTTTTGGCGTTGAACTATATATTTTT
450 TGGAAAACGATAATAGAAGCGTAAAAAAACCCTTCAATTTTTTTGGCGTTGAACTATATATTTTT
* ** * * *
520 GATGACTATTTTGGAAAAAAAATTGAAAAATTTTTTCGGGTTAGTTTGTAGCTGAAATCGTGTAC
515 GATGACTATTGTGGAAAAAAAATTGAAAAAAATTTTCGGGTCAGTTTGTAGCCGAAATCATGTAC
* * * * * *
585 TAACCATCATAGTATTTCGCTAAAAACGCGTTTTGAGGCCCCGGATCAGTTTTGGATGATTTTTG
580 TAACCATCAAACTATTTCGCTAAAAACGCGTTTCGAGGCCCCGGATCAGATTTGGATGAATTTTC
*
650 GCAGAAATACTCCTCAAAATATCTATATTCATATATCTGAATCTCAACCACATTGGATTTAAGGA
645 GCAGAAAGACTCCTCAAAATATCTATATTCATATATCTGAATCTCAACCACATTGGATTTAAGGA
* * **
715 TTTGATTTTACGAGTATTTAAATCTTGTTTCGATTTAATTGGAAATAAAATCGGGAAAAAAATGT
710 TTTGATTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATAAAATCGGGAAAAAAATAC
******
780 AAAAATGATATTAGAAGCGTGAAAAACCCTTTATTTTTTTTGGTGTTGAATTATATATTTTTTAT
775 AAAAATGATATTAGAAGCGTGAAAAA--C---A-----TAAACCCTTGAATTATATATTTTTTAT
* ** *
845 GAGTATTGTGGCACAAAAATTTAGAAAAAAACTTTCGGGTCAATTTTTAGCCGAAATCGTACAGT
830 GAGTATTGTGGCACAAAAAATTAGAAAAAAAAATTCGGGTCAATTTTTAGCCAAAATCGTACAGT
910 TTTTCGCTAAAA
895 TTTTCGCTAAAA
* *
922 ACGTGTTTCGGGGCGCCGACATAGTTTTGCAAGATTTT-GGGAAAACTTCTTGAAATATCTATAT
1 ACGTGTTTCGGGGCCCCGAC-TAGTTTTGCAAGATTTTCGGGAAAACTTCTTGAAATATCTAAAT
* * ** * * *
986 TCCTCTACCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTCGTACGTGCATCTGAATCTTTT
65 TCATCTACCCGAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * *
1051 TTCGATTTAATTTGTAATAAATTTGAAAAAAAAATGGAAAAACGATATTAGAATCGTGAAAACCC
130 TTCGATTTAATTTGAAATAAA-TT--AAAAAAAATGGAAAAACGATATTAGAATCTTGAAAAACC
* * * *
1116 CTTCCAATTTTTTTGGCAATGAATTATATATTTTTTATGATTATTTTGGCAAAAAATTTTGAAAA
192 CTT-CAATTTTTTTGGCAATGAATTATATATTTTTAAAGAGTATTTTGGCAAAAAATTTAG-AAA
* * ** * *
1181 AAAATTTTCGGGT-CAGTTTTTCGCTAAAAACACGTTTTGGGACCCTGGAT-ATATTTTGCATGA
255 AAAATGTAC-CATACAGTTTTTCGCTAAAAACACATTTTGGGACCCTAGATCA-ATTTTGCATGA
* * * *
1244 TTTTTGGCAGAAACACTCCTTGAAATATCTATATTCATCTATTCGAATCTCATCCACATTGGATT
318 TTTTTGGAAGAAACACTCCTTGAAATATCTATATTCATCTATCCGAATCTCAGCCACATTAGATT
* * * * * *
1309 TAAGGATTTCTTTTTATGTGCATCTGAATCTTGTTTCTATTTAATTAGAAATAAATTCAGAAAAA
383 TAAGAATTTCTTTTTACGAGCATCTGAATCTTGGTTCGATTCAATTAGAAATAAATTCAGAAAAA
** * * *
1374 AATGGAAAAACTTTATTAGAAGCGT-GAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATT
448 AATGG-AAAACGATAATAGAAGCGTAAAAAAACCCTTCAATTTTTTTGGCGTTGAACTATATATT
* * *
1438 TGTT-ATGAGTATTGTGGCAAAAAAATTTAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATC
512 T-TTGATGACTATTGTGG-AAAAAAAATT-GAAAAAAATTTTCGGGTCAGTTTGTAGCCGAAATC
* * * *
1502 ATGTACGTTA-CATCACAACT-TTTCGCTAAAAA-GACGTTTCGGGGCCCC-GACTTAGATTTGT
574 ATGTAC-TAACCATCA-AACTATTTCGCTAAAAACG-CGTTTCGAGGCCCCGGA-TCAGATTTGG
* * ** * ** *
1563 AT-AATTTTCGCAAGAAGGACTTCTTGAAATATCTATATTCATCTA-CTCGAATCTCTTCCACTT
635 ATGAATTTTCGC-AGAAAGACTCCTCAAAATATCTATATTCATATATCT-GAATCTCAACCACAT
* * * *
1626 TGGATTTAAGGATTTGTTTTTATGAGCT-TCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
698 TGGATTTAAGGATTTGATTTTACGAG-TATCTAAATCTTGTTTCGATTTAATTAGAAATAAAATC
*
1690 -GGAAAAAAATACAAAAATGATATTAGAATCGTGAAAAA-A-AAACCCTT-AATTATAT-TATTT
762 GGGAAAAAAATACAAAAATGATATTAGAAGCGTGAAAAACATAAACCCTTGAATTATATAT-TTT
* *
1750 TTATGATTATTTTGGCA-AAAAAATTAGAAAAAAAAAATTCGGGTCAATTTTTAGCCAAAATCAT
826 TTATGAGTATTGTGGCACAAAAAATTAG-AAAAAAAAATTCGGGTCAATTTTTAGCCAAAATC--
1814 GTACTAACCATCACAGTTTTTCGCTAAAA
888 G---------T-ACAGTTTTTCGCTAAAA
* * * *
1843 ACGCGTTTCGGGGCCCCGACTCAGTTTTGTATA-ATTTTCGCAAGAAGGACTAT-TTGAAATATC
1 ACGTGTTTCGGGGCCCCGACT-AGTTTTGCA-AGATTTTCG--GGAA-AACT-TCTTGAAATATC
1906 TAAATTCATCTACCCGAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAAT
60 TAAATTCATCTACCCGAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAAT
* *
1971 CTTGTTTCGATTTAATTTGAAATAAATTCAGAAAAATGGAAAAACGATATTAGAATCTTGAAAA
125 CTTGTTTCGATTTAATTTGAAATAAATTAAAAAAAATGGAAAAACGATATTAGAATCTTGAAAA
Statistics
Matches: 947, Mismatches: 126, Indels: 79
0.82 0.11 0.07
Matches are distributed among these distances:
908 10 0.01
909 57 0.06
910 2 0.00
911 1 0.00
916 1 0.00
917 90 0.10
918 6 0.01
919 10 0.01
920 32 0.03
921 345 0.36
922 118 0.12
923 169 0.18
924 10 0.01
925 95 0.10
926 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (906 bp):
ACGTGTTTCGGGGCCCCGACTAGTTTTGCAAGATTTTCGGGAAAACTTCTTGAAATATCTAAATT
CATCTACCCGAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
TCGATTTAATTTGAAATAAATTAAAAAAAATGGAAAAACGATATTAGAATCTTGAAAAACCCTTC
AATTTTTTTGGCAATGAATTATATATTTTTAAAGAGTATTTTGGCAAAAAATTTAGAAAAAAATG
TACCATACAGTTTTTCGCTAAAAACACATTTTGGGACCCTAGATCAATTTTGCATGATTTTTGGA
AGAAACACTCCTTGAAATATCTATATTCATCTATCCGAATCTCAGCCACATTAGATTTAAGAATT
TCTTTTTACGAGCATCTGAATCTTGGTTCGATTCAATTAGAAATAAATTCAGAAAAAAATGGAAA
ACGATAATAGAAGCGTAAAAAAACCCTTCAATTTTTTTGGCGTTGAACTATATATTTTTGATGAC
TATTGTGGAAAAAAAATTGAAAAAAATTTTCGGGTCAGTTTGTAGCCGAAATCATGTACTAACCA
TCAAACTATTTCGCTAAAAACGCGTTTCGAGGCCCCGGATCAGATTTGGATGAATTTTCGCAGAA
AGACTCCTCAAAATATCTATATTCATATATCTGAATCTCAACCACATTGGATTTAAGGATTTGAT
TTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATAAAATCGGGAAAAAAATACAAAAAT
GATATTAGAAGCGTGAAAAACATAAACCCTTGAATTATATATTTTTTATGAGTATTGTGGCACAA
AAAATTAGAAAAAAAAATTCGGGTCAATTTTTAGCCAAAATCGTACAGTTTTTCGCTAAAA
Found at i:1995 original size:310 final size:308
Alignment explanation
Indices: 1427--2034 Score: 893
Period size: 310 Copynumber: 2.0 Consensus size: 308
1417 TTTGGCGTTG
** *
1427 AATTATATATTTGTTATGAGTATTGTGGCAAAAAAATTTAGAAAAAAATTTTCGGGTCAGTTTTT
1 AATTATATATTTGTTATGAGTATTGTGGCAAAAAAATTTAGAAAAAAAAATTCGGGTCAATTTTT
* * *
1492 AGCCGAAATCATGTACGTTACATCACAACTTTTCGCTAAAAAGACGTTTCGGGGCCCCGACTTAG
66 AGCCAAAATCATGTACGTAACATCACAACTTTTCGCTAAAAAGACGTTTCGGGGCCCCGACTCAG
* * **
1557 ATTTGTATAATTTTCGCAAGAAGGACTTCTTGAAATATCTATATTCATCTACTCGAATCTCTTCC
131 ATTTGTATAATTTTCGCAAGAAGGACTTCTTGAAATATCTAAATTCATCTACCCGAATCTCAGCC
* * * *
1622 ACTTTGGATTTAAGGATTTGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATAAA
196 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAA
*
1687 TTCGGAAAAAAATACAAAAATGATATTAGAATCGTGAAAAAAAAACCCTT
261 TTC--AAAAAAATACAAAAACGATATTAGAATCGTGAAAAAAAAACCCTT
* *
1737 AATTATATTATTT-TTATGATTATTTTGGCAAAAAAA-TTAGAAAAAAAAAATTCGGGTCAATTT
1 AATTATA-TATTTGTTATGAGTATTGTGGCAAAAAAATTTAG-AAAAAAAAATTCGGGTCAATTT
**
1800 TTAGCCAAAATCATGTAC-TAACCATCACAGTTTTTCGCTAAAAACG-CGTTTCGGGGCCCCGAC
64 TTAGCCAAAATCATGTACGTAA-CATCACAACTTTTCGCTAAAAA-GACGTTTCGGGGCCCCGAC
*
1863 TCAGTTTTGTATAATTTTCGCAAGAAGGACTAT-TTGAAATATCTAAATTCATCTACCCGAATCT
127 TCAGATTTGTATAATTTTCGCAAGAAGGACT-TCTTGAAATATCTAAATTCATCTACCCGAATCT
*
1927 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTTGAA
191 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
* ** *
1992 ATAAATTCAGAAAAATGGAAAAACGATATTAGAATCTTGAAAA
256 ATAAATTCAAAAAAATACAAAAACGATATTAGAATCGTGAAAA
Statistics
Matches: 268, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
308 30 0.11
309 6 0.02
310 225 0.84
311 7 0.03
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (308 bp):
AATTATATATTTGTTATGAGTATTGTGGCAAAAAAATTTAGAAAAAAAAATTCGGGTCAATTTTT
AGCCAAAATCATGTACGTAACATCACAACTTTTCGCTAAAAAGACGTTTCGGGGCCCCGACTCAG
ATTTGTATAATTTTCGCAAGAAGGACTTCTTGAAATATCTAAATTCATCTACCCGAATCTCAGCC
ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAA
TTCAAAAAAATACAAAAACGATATTAGAATCGTGAAAAAAAAACCCTT
Done.