Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020509.1 Corchorus olitorius cultivar O-4 contig20542, 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: 4823
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Found at i:347 original size:154 final size:153
Alignment explanation
Indices: 1--1072 Score: 1475
Period size: 154 Copynumber: 6.9 Consensus size: 153
* *
1 CTCACTAAAATGATTATAGTTAGGCGATAAACAATAGG-AAGAAAAGCATTGAGGTTTGCCAAAT
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAAT
* *
65 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGTCCCATAATTAACAAGTGTTCCAAAT
65 CGAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGG-CCCA-AAATAACAAGTGTTCCAAAT
130 GAGTTAAAAACTTCACAGTGGACTAAT
127 GAGTTAAAAACTTCACAGTGGACTAAT
* * *
157 TTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCTAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* * * ** *
222 GAAGACGATTCAGAACAGAACTAATGGGTCCCGAAAGGCCCAAAATAACAAGAGAACCAATTGAG
66 GAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * *
287 TAAAAAACTTCATAGTGGACTTAT
130 TTAAAAACTTCACAGTGGACTAAT
* *
311 CTCACCAAAATGGTTATAGTTGGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
*
376 GAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
66 GAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
**
441 TTAAAAACTTCACAACGGACTAAT
130 TTAAAAACTTCACAGTGGACTAAT
* * *
465 CTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAGAAAAGCATTGAGATTTGCTAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* *
530 GAAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAATTGA
66 G-AAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
* *
595 GCTAAAAACTTCACAGTGGACAAAT
129 GTTAAAAACTTCACAGTGGACTAAT
*
620 CTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* ** ** * *
685 GAAGACAATTCAAAACGGAACTAATGGGCCTTGATCGGCACAAAATAACAAGTGTTCAAAATGA-
66 GAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * *
749 TCTAAAAACGTCACAATTGACTAAT
130 T-TAAAAACTTCACAGTGGACTAAT
* * * * *
774 CTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAGGAAAGCATCG-GGAATCGCCAAAT
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAAT
* * * *
838 TGAAGACGATTCAAAACGGAAATAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGA
65 CGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
* *
903 GCTAAAAACTTCACAGTGGACAAAT
129 GTTAAAAACTTCACAGTGGACTAAT
928 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* * * * * * * * * *
993 GAATACAATTCAAAACGAAATAAAGGGCCTCGATAGGCACAGAATAACAAGTGTTCCGAATGAGC
66 GAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGT
1058 TAAAAACTTCACAGT
131 TAAAAACTTCACAGT
1073 TGATACGGGG
Statistics
Matches: 808, Mismatches: 99, Indels: 21
0.87 0.11 0.02
Matches are distributed among these distances:
153 59 0.07
154 508 0.63
155 149 0.18
156 91 0.11
157 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
GAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGT
TAAAAACTTCACAGTGGACTAAT
Found at i:978 original size:463 final size:461
Alignment explanation
Indices: 1--1072 Score: 1506
Period size: 463 Copynumber: 2.3 Consensus size: 461
* *
1 CTCACTAAAATGATTATAGTTAGGCGATAAACAATAGG-AAGAAAAGCATTGAGGTTTGCCAAAT
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAAT
** * *
65 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGTCCCATAATTAACAAGTGTTCCAAAT
65 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG-CCCA-AAATAACAAGTGTTCC-AAT
* * *
130 GAGTTAAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
127 GAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * *
195 AAGAAAAGAATTGAGGTTTGCTAAATCGAAGACGATTCAGAACAGAACTAATGGGTCCCGAAAGG
192 AAGAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACAGAACTAATGGGTCCCGAAAGG
* * * * * * * *
260 CCCAAAATAACAAGAGAACCAATTGAGTAAAAAACTTCATAGTGGACTTATCTCACCAAAATGGT
257 CACAAAATAACAAGAGAACAAAATGAGTAAAAAACGTCACAATGGACTAATCTCACCAAAATGAT
* * * *
325 TATAGTTGGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
322 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATCGCCAAATCGAAGACGATTCAAA
** * * *
390 ACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACA
387 ACGGAAATAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
*
455 ACGGACTAAT
452 ACGGACAAAT
* * *
465 CTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAGAAAAGCATTGAGATTTGCTAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
530 GAAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAATTGA
66 G-AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA-TGA
*
595 GCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAA
129 GCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * **
660 GAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGG-CCTTGATCGGC
194 GAAAAGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACAGAACTAATGGGTCC-CGAAAGGC
* ** * *
724 ACAAAATAACAAGTGTTCAAAATGA-TCTAAAAACGTCACAATTGACTAATCTCACCAAAATGAT
258 ACAAAATAACAAGAGAACAAAATGAGT-AAAAAACGTCACAATGGACTAATCTCACCAAAATGAT
* * *
788 TATAGTTAGGCCATAAAGAATGGAAAGGAAAGCATCG-GGAATCGCCAAATTGAAGACGATTCAA
322 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGG-ATCGCCAAATCGAAGACGATTCAA
*
852 AACGGAAATAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCAC
386 AACGGAAATAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
**
917 AGTGGACAAAT
451 AACGGACAAAT
928 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* * * * * * *
993 GAATACAATTCAAAAC-GAAATAAAGGGCCTCGATAGGCACAGAATAACAAGTGTTCCGAATGAG
66 GAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC-AATGAG
1057 CTAAAAACTTCACAGT
130 CTAAAAACTTCACAGT
1073 TGATACGGGG
Statistics
Matches: 541, Mismatches: 60, Indels: 17
0.88 0.10 0.03
Matches are distributed among these distances:
461 56 0.10
462 22 0.04
463 367 0.68
464 62 0.11
465 34 0.06
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (461 bp):
CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
GAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAATGAGC
TAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
AAAGAATTGAGGTTTGCCAAATCGAAGACAATTCAAAACAGAACTAATGGGTCCCGAAAGGCACA
AAATAACAAGAGAACAAAATGAGTAAAAAACGTCACAATGGACTAATCTCACCAAAATGATTATA
GTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATCGCCAAATCGAAGACGATTCAAAACGG
AAATAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAACGG
ACAAAT
Found at i:1003 original size:308 final size:308
Alignment explanation
Indices: 1--1070 Score: 1565
Period size: 309 Copynumber: 3.5 Consensus size: 308
* *
1 CTCACTAAAATGATTATAGTTAGGCGATAAACAATAGG-AAGAAAAGCATTGAGGTTTGCCAAAT
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAAT
* ** * *
65 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGTCCCATAATTAACAAGTGTTCCAAAT
65 CGAAGACAATTCAAAACGGAACTAATGGGCCCCGAAAGG-CACA-AAATAACAAGTGTTCCAAAT
* * *
130 GAGTTAAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
128 GAGTTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGA
* * * *
195 AAGAAAAGAATTGAGG-TTTGCTAAATCGAAGACGATTCAGAACAGAACTAATGGGTCCCGAAAG
193 AAGAAAAGCATTG-GGATTTGCTAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAG
* ** * **
259 GCCCAAAATAACAAGAGAACCAATTGAG-TAAAAAACTTCATAGTGGACTTAT
257 GCCCAAAATAACAAGTGTTCCAATTGAGCT-AAAAACTTCACAGTGGACAAAT
* *
311 CTCACCAAAATGGTTATAGTTGGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* ** *
376 GAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
66 GAAGACAATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAG
*
441 TTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAG
131 TTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAG
* *
506 AAAAGCATTGAGATTTGCTAAATCGAAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
196 AAAAGCATTGGGATTTGCTAAATCG-AAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCC
571 CAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAAT
260 CAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAAT
*
620 CTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
** ** *
685 GAAGACAATTCAAAACGGAACTAATGGGCCTTGATCGGCACAAAATAACAAGTGTTCAAAATGA-
66 GAAGACAATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAG
* *
749 TCTAAAAACGTCACAATTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAA
131 T-TAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAA
* * * * * * * *
814 GGAAAGCATCGGGAATCGCCAAATTGAAGACGATTCAAAACGGAAATAATGGACCCCGAAAGGCC
195 GAAAAGCATTGGGATTTGCTAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCC
879 CAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAAT
260 CAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAAT
928 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
1 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* * * * * * *
993 GAATACAATTCAAAAC-GAAATAAAGGGCCTCGATAGGCACAGAATAACAAGTGTTCCGAATGAG
66 GAAGACAATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAG
*
1057 CTAAAAACTTCACA
131 TTAAAAACTTCACA
1071 GTTGATACGG
Statistics
Matches: 697, Mismatches: 57, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
307 53 0.08
308 269 0.39
309 278 0.40
310 97 0.14
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (308 bp):
CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
GAAGACAATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAG
TTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAGAATGGAAAG
AAAAGCATTGGGATTTGCTAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCC
AAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACAAAT
Found at i:2657 original size:30 final size:30
Alignment explanation
Indices: 2621--2975 Score: 368
Period size: 30 Copynumber: 11.6 Consensus size: 30
2611 TCTAAATGAT
*
2621 ACCAGAAGTTGTCATGATCTTGCGATTGAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
** *
2651 ACCAGAAGTTGTCATGGCCTTGAAATTGAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
**
2681 ACCAGAAGTTGTCATGGCCTTGCAATTGAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
**
2711 ACCAGAAGTTGTCATGGCCTTGCAATTGAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
* * *
2741 ACCAGAAGCTGTCATGATGTTGCAATTAAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
* *
2771 ACTAGAAGTTGTCATGATGTTGCAATTGAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
* *
2801 ACCAGAAGCTGTCATGATCTTGCAATTGAT
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
** * * * *
2831 ACTTGAAGATGTCATAATTTTATTCAATTGAC
1 ACCAGAAGTTGTCATGA-TCT-TGCAATTGAC
* * * *
2863 ACCAGAAGTTGTCATGATAAATTTCCTATAGAC
1 ACCAGAAGTTGTCATGAT---CTTGCAATTGAC
** * * * *
2896 ACTTGAAGATGTCATAATTTTACTCAATTGAC
1 ACCAGAAGTTGTCATGATCTT--GCAATTGAC
2928 ACCAGAAGTTGTCATGATCTTGCAATTGAC
1 ACCAGAAGTTGTCATGATCTTGCAATTGAC
2958 ACCAGAAGTTGTCATGAT
1 ACCAGAAGTTGTCATGAT
2976 TTTACCTTTC
Statistics
Matches: 274, Mismatches: 44, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
30 205 0.75
31 3 0.01
32 43 0.16
33 21 0.08
34 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (30 bp):
ACCAGAAGTTGTCATGATCTTGCAATTGAC
Found at i:2860 original size:32 final size:32
Alignment explanation
Indices: 2823--2929 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
2813 CATGATCTTG
*
2823 CAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
** * ** *
2855 CAATTGACACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACTTGAAGATGTCAT-A-ATTTTATT
* * *
2888 CTATAGACACTTGAAGATGTCATAATTTTACT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
2920 CAATTGACAC
1 CAATTGACAC
2930 CAGAAGTTGT
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
31 3 0.06
32 28 0.52
33 20 0.37
34 3 0.06
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (32 bp):
CAATTGACACTTGAAGATGTCATAATTTTATT
Found at i:2923 original size:65 final size:62
Alignment explanation
Indices: 2733--3008 Score: 252
Period size: 65 Copynumber: 4.4 Consensus size: 62
2723 CATGGCCTTG
* * * * * * * *
2733 CAATTGACACCAGAAGCTGTCATGATGTTGCAATTA-ACACTAGAAGTTGTCATGATGTT--G
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAA-TAGACACTTGAAGATGTCATAATTTTACT
* * * * *
2793 CAATTGACACCAGAAGCTGTCATGATCTTGCAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTACT
* *
2855 CAATTGACACCAGAAGTTGTCATGATAAATTTCCTATAGACACTTGAAGATGTCATAATTTTACT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATAATTTTACT
* * ** * *
2920 CAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATTTTACCTTT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTA-C--T
* *
2985 CAAAATGACACAAGAAGTTGTCAT
1 C-AATTGACACCAGAAGTTGTCAT
3009 ATGCACTATT
Statistics
Matches: 181, Mismatches: 25, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
59 1 0.01
60 50 0.28
62 51 0.28
63 1 0.01
65 58 0.32
66 20 0.11
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (62 bp):
CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTACT
Done.