Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014909.1 Corchorus olitorius cultivar O-4 contig14942, 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: 46855
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1485 original size:639 final size:635
Alignment explanation
Indices: 264--1508 Score: 1487
Period size: 639 Copynumber: 1.9 Consensus size: 635
254 GTTGCCGAAA
* * * * *
264 TTTTTTCCCTCAATTTTGTGGCCAAAATACTTATATAAATATATAATTCAACGCGAAAAAGACTG
1 TTTTTTCCCTCAATTTTGTAGCCAAAATACTCATAAAAATAAATAATTCAACGCCAAAAAGACTG
*
329 AAGGGCTTTTCACACTTCTAATATCGTTTTCCTATTTTTTTAATCAATTTCTAATTAAATCGAAA
66 AAGGGCTTTTCACACTTCTAATATCGTTTTCCTATTTTTTTAATCAATTTATAATTAAATCGAAA
* * * * *
394 CAAGATTCAGATGCTCGTAAAAACAATTCCTTAAACCCCATGCGGCTGAGACTTGGTTAGATGAA
131 CAAGATTCAGATACTCGTAAAAACAAATCCTAAAACCCAATGCGGCTGAGACTTGGTTAGATAAA
* **
459 TATAGATATTTCAATGACTATTGGCGCAAAAAATCATACAAAATTGACCCGGGACCCTGGAACGC
196 TATAGATATATCAATGACTATTGGCGCAAAAAATCATACAAAATTGACCCGGGACCCCAGAACGC
* * * *
524 GTTTTAGCCAAAAATGGTAATGGTTATTACACGATTTTGGTTAAAATTTTAAAAAAATGACCAGA
261 GTTTTAGCCAAAAATGGTAATGATTAGTACACGATTTCGGCTAAAA-TTT-----AATGACCAGA
* * * * * *
589 AAAATTTTTCCTCAATTTTTAGTCACAATAGTTATAAAAATTATATAACTCAACGCAATAAAGAT
320 AAAATTTTTCCTCAATTTGTAGCCAAAATACTCATAAAAATTATATAACTCAACGCAATAAAGAC
* **
654 TTAATGGCTTTTCATTCTTCTAATATAGTTTTTTCTATATTAATTTCTAATTAAATCGAAACAAC
385 TGAATGGCTTTTCACACTTCTAATATAGTTTTTTCTATATTAATTTCTAATTAAATCGAAACAAC
* * * *
719 ATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATTTGGCAGAGATTTGGTTAGACAAATATA
450 ATTCAGATGCTCGTAAAAACAAATCCTTAAACCCAATGTGGCAGAGACTTGGTTAGACAAATATA
* *
784 GATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGCTGCCTCGGAACGCGTTG
515 GATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGCGGCCTCGAAACGCGTTG
849 TTAGCCAAAAACTGTGACGGTTAGTACACGATTTCAGCTAAAATTGACCCGGAATT
580 TTAGCCAAAAACTGTGACGGTTAGTACACGATTTCAGCTAAAATTGACCCGGAATT
* * *
905 TTTTTTTCCTCAATTTT-TAGCCAAAATACTCATAAAAATAAATAATTCAATGCCAAAAAGATTG
1 TTTTTTCCCTCAATTTTGTAGCCAAAATACTCATAAAAATAAATAATTCAACGCCAAAAAGACTG
* * *
969 AA-GGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCTAAATTAATTTATATTTAAAT
66 AAGGGCTTTTCACACTTCTAATATCG-TTTTCCTA--TTTTTT-T-AATCAATTTATAATTAAAT
* * * * * *
1033 CGAAACAGGATTGAGATACTCGTAAAAACAAATCCTAAAATCCAATGTGGTTGAGATTTGGTTAG
126 CGAAACAAGATTCAGATACTCGTAAAAACAAATCCTAAAACCCAATGCGGCTGAGACTTGGTTAG
* * * * * *
1098 ATAAATATAGATATATCAATGAGTCTTGGC-CCAAAAATCATCCAAAACTT-AGCTGAGG-CCCC
191 ATAAATATAGATATATCAATGACTATTGGCGCAAAAAATCATACAAAA-TTGACCCG-GGACCCC
*
1160 AGAACGCGTTTTTAGCCAAAAACT-GTCATGATTAGTACACGATTTCGGCTAAAA-TT-A-G-CC
254 AGAACGCG-TTTTAGCCAAAAA-TGGTAATGATTAGTACACGATTTCGGCTAAAATTTAATGACC
* * * * *
1220 TG-AAAGTTTTCTCCTCAATTTGTGGCCAAAATACTCATATAAA-TATATAACTCAATGCTAA-A
317 AGAAAAATTTT-TCCTCAATTTGTAGCCAAAATACTCATAAAAATTATATAACTCAACGC-AATA
* * * * *
1282 AAGACTGAATGGCTTTTCACAGTTCTAATTTTGTTTTTCCTTTTTTTTAATTAATTTCTAATTAA
380 AAGACTGAATGGCTTTTCACACTTCTAATATAG---TT--TTTTCTAT-ATTAATTTCTAATTAA
* * * * *
1347 ATCGAAACAAGATTCAGATGCTCGTAAAAGCAATTCCTTAAACCCCATGTGGCTGAGACTTGGTT
439 ATCGAAACAACATTCAGATGCTCGTAAAAACAAATCCTTAAACCCAATGTGGCAGAGACTTGGTT
** * * *
1412 AGATGAATATAGATATTTCAAGGAGTTTTGGCGCCAAAAATCATGCAAAACTG-TTC-CGGAACC
504 AGACAAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGCGG--CC
*
1475 -CTGAAACGCGTTTTTAGCCAAAAACTGTGACGGT
567 TC-GAAACGCGTTGTTAGCCAAAAACTGTGACGGT
1509 CTGTCAAGAG
Statistics
Matches: 511, Mismatches: 73, Indels: 42
0.82 0.12 0.07
Matches are distributed among these distances:
633 48 0.09
634 30 0.06
635 1 0.00
636 3 0.01
637 2 0.00
638 9 0.02
639 175 0.34
640 50 0.10
641 16 0.03
642 8 0.02
643 29 0.06
644 139 0.27
645 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (635 bp):
TTTTTTCCCTCAATTTTGTAGCCAAAATACTCATAAAAATAAATAATTCAACGCCAAAAAGACTG
AAGGGCTTTTCACACTTCTAATATCGTTTTCCTATTTTTTTAATCAATTTATAATTAAATCGAAA
CAAGATTCAGATACTCGTAAAAACAAATCCTAAAACCCAATGCGGCTGAGACTTGGTTAGATAAA
TATAGATATATCAATGACTATTGGCGCAAAAAATCATACAAAATTGACCCGGGACCCCAGAACGC
GTTTTAGCCAAAAATGGTAATGATTAGTACACGATTTCGGCTAAAATTTAATGACCAGAAAAATT
TTTCCTCAATTTGTAGCCAAAATACTCATAAAAATTATATAACTCAACGCAATAAAGACTGAATG
GCTTTTCACACTTCTAATATAGTTTTTTCTATATTAATTTCTAATTAAATCGAAACAACATTCAG
ATGCTCGTAAAAACAAATCCTTAAACCCAATGTGGCAGAGACTTGGTTAGACAAATATAGATATT
TCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTCGCGGCCTCGAAACGCGTTGTTAGCC
AAAAACTGTGACGGTTAGTACACGATTTCAGCTAAAATTGACCCGGAATT
Found at i:1747 original size:77 final size:77
Alignment explanation
Indices: 1625--1788 Score: 269
Period size: 80 Copynumber: 2.1 Consensus size: 77
1615 ACCCGAAATT
*
1625 TTTTGGATGAATTATTATGGCCTTGTTCTTCTGACCCATTTTGCATTTTG-T-TTTGGTCTTAAA
1 TTTTGGATGAATTATTATGGCCTTGTTCTTCTGACCCATTTTGCATTTTGCTATGTGGTCTTAAA
1688 ATGATCCATATG
66 ATGATCCATATG
1700 TTTTGGATGAATTATTATGGCCTTGTTTTCTTCTGACCCATTTTGCATTTTGCCTATGTGGTCTT
1 TTTTGGATGAATTATTATGGCCTTG--TTCTTCTGACCCATTTTGCATTTTG-CTATGTGGTCTT
*
1765 ACAATGATCCATATG
63 AAAATGATCCATATG
1780 TTTTGGATG
1 TTTTGGATG
1789 GGCTTATTCT
Statistics
Matches: 82, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
75 25 0.30
77 25 0.30
79 1 0.01
80 31 0.38
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (77 bp):
TTTTGGATGAATTATTATGGCCTTGTTCTTCTGACCCATTTTGCATTTTGCTATGTGGTCTTAAA
ATGATCCATATG
Found at i:3251 original size:14 final size:14
Alignment explanation
Indices: 3232--3259 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3222 CAAAAAGGAC
3232 GTGTCAATATGTAA
1 GTGTCAATATGTAA
3246 GTGTCAATATGTAA
1 GTGTCAATATGTAA
3260 ATGTACGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GTGTCAATATGTAA
Found at i:10351 original size:17 final size:17
Alignment explanation
Indices: 10305--10357 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
10295 ATCTATGCAT
*
10305 TTATTATTCTTATTATA
1 TTATAATTCTTATTATA
* *
10322 TTATAATTATTATTATC
1 TTATAATTCTTATTATA
10339 TTAT-ATATCTTATATATA
1 TTATAAT-TCTTAT-TATA
10357 T
1 T
10358 ACAATATAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.07
17 23 0.79
18 4 0.14
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATAATTCTTATTATA
Found at i:24091 original size:76 final size:76
Alignment explanation
Indices: 23937--24084 Score: 208
Period size: 76 Copynumber: 1.9 Consensus size: 76
23927 GAAAGCTCTC
* * *
23937 TCCGACTGATCCTGAGTCGAGCTGCATTGAACCAATATAAAAAATCTCTCTCCGACTAATCCTGA
1 TCCGACTAATCCTGAGTCAAGCTACATTGAACCAATATAAAAAATCTCTCTCCGACTAATCCTGA
*
24002 GTCAAGCCACG
66 ATCAAGCCACG
* * **
24013 TCCGACTAATCTTGAGTCAAGCTACATTGAACCAATATGGAAAAA-CTCTCTTTGACTAATCCTG
1 TCCGACTAATCCTGAGTCAAGCTACATTGAACCAATAT-AAAAAATCTCTCTCCGACTAATCCTG
24077 AATCAAGC
65 AATCAAGC
24085 GGCGTCCAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 58 0.92
77 5 0.08
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (76 bp):
TCCGACTAATCCTGAGTCAAGCTACATTGAACCAATATAAAAAATCTCTCTCCGACTAATCCTGA
ATCAAGCCACG
Done.