Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020044.1 Corchorus olitorius cultivar O-4 contig20077, 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: 20691
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30
Found at i:1698 original size:22 final size:23
Alignment explanation
Indices: 1662--1707 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1652 TGTGATTTCA
*
1662 TTTTTATGAATGAAAATTACATT
1 TTTTTATGAAAGAAAATTACATT
*
1685 TTTTTA-GAAAGAAAATTATATT
1 TTTTTATGAAAGAAAATTACATT
1707 T
1 T
1708 AGGTCCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTTTATGAAAGAAAATTACATT
Found at i:5600 original size:72 final size:71
Alignment explanation
Indices: 5493--5626 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 71
5483 TTAATGAATG
*
5493 TGTGTATCCTGTTGATTTGTATTGGGAAAAGAAAAAAAACGTGCGATTGGTGTAGTCCTATCTTT
1 TGTGTATCCTGTTGATTTGTATTGGGAAAA-AAAAAAAACGTGCGATTGGTGTAGTCCCATCTTT
5558 TAATGGA
65 TAATGGA
* *
5565 TGTGTATCCTGTTCG-TTTGTATT-GGAAAACAAAAAAAACGTGCGGTTGGTGTGGTCCCATCT
1 TGTGTATCCTGTT-GATTTGTATTGGGAAAA-AAAAAAAACGTGCGATTGGTGTAGTCCCATCT
5627 CCTGTGAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
71 35 0.61
72 21 0.37
73 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (71 bp):
TGTGTATCCTGTTGATTTGTATTGGGAAAAAAAAAAAACGTGCGATTGGTGTAGTCCCATCTTTT
AATGGA
Found at i:7735 original size:2 final size:2
Alignment explanation
Indices: 7728--7757 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7718 AAATACTCAT
7728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7758 AAATTCAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15867 original size:332 final size:327
Alignment explanation
Indices: 14838--16130 Score: 1062
Period size: 316 Copynumber: 4.0 Consensus size: 327
14828 TTTTACGCTT
* * * * * *
14838 CTAATATCAG-TTTTCCTACTTTTTCTGAATTAATTTCTAATCAAATCGAAACAAGGCTT-AGAT
1 CTAATATC-GTTTTTCATATTTTTTCTGAATAAATTTCTAATTAAATCGAAACAA-GATTCAAAT
* * *
14901 GCTCGTAAAAATAAATCT-TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAAATAT-T
64 GCTCGTAAAAACAAAT-TATTAAATCCAATGTGGCTAAAATTTGATTAGATGAATAT-AATATCT
* ** * * * * *
14964 TCAAGGAGGCTTGGCGCAAAAAATCATGCAAAACTG-GCACG-GAGCCACGGAACGCGTTTTTAG
127 T-AAGGAGTCTTCACACCAAAAATCATGCAAAACTGAGC-CGAG-GCCCCGAAACACGTTTTTAG
* * * * * *
15027 CAAATAAACACCGTGATG----GTACACGATTTCGGCTAATATTTTGTAAAAATTGACCCGAAAT
189 C-CA-AAA-ACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCAAAAA
* * * * *
15088 ATTTTTCCTCAATTTTTTGGCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGA
251 ATATTTCCTCAATTTTTAGACAAAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGA
* *
15153 GGGGCTTTTCAC
316 AGGACTTTTCAC
* * * *
15165 GTTTCTAATATCG-TTTTCCTATTTTTTTCCT-AATTAATCTCTAATTAAATCGAAACATGATTT
1 ----CTAATATCGTTTTTCATA-TTTTTT-CTGAATAAATTTCTAATTAAATCGAAACAAGA-TT
* * * * * *
15228 CAGATGCTTGTAAAAAC--A--A-T-GA--C----T-GC---GATTTGGTTAGATGAATATTGAT
59 CAAATGCTCGTAAAAACAAATTATTAAATCCAATGTGGCTAAAATTTGATTAGATGAATA-TAAT
* * * * * *
15277 -TTTTCAAGGTGTC-TCGGCACCAAAAATCTTGCAAAACTGAACC-AGGCCCCGGAACGAC-TTT
123 ATCTT-AAGGAGTCTTC-ACACCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAAC-ACGTTT
* * * * *
15338 TTTGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
185 TTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCAAAA
* * * * * * * *
15403 GATATTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAATGCCTAAAATATTT
250 AATATTTCCTCAATTTTTAGACAAAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTG
*
15468 AAGGGCTTTTCAC
315 AAGGACTTTTCAC
15481 GCTTTTAATATCGTTTTTCATATTTTTTCTGAATAAATTTCTAATTAAATCGAAACAAGATTCAA
1 -C---TAATATCGTTTTTCATATTTTTTCTGAATAAATTTCTAATTAAATCGAAACAAGATTCAA
* *
15546 ATGCTCGTAAAAACAAATTATTAAATGCATTGTGGCTAAAAACTTT-ATTAGATGAATAT-ATAT
62 ATGCTCGTAAAAACAAATTATTAAATCCAATGTGGCT-AAAA-TTTGATTAGATGAATATAATAT
* * * * * * *
15609 GTTTCAAGGAGT-TTCGACGCCGAAAATCATTCAAAACTGAGCTGGGGGCCCGAAACACGTTTTT
125 -CTT-AAGGAGTCTTC-ACACCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACACGTTTTT
* * *
15673 AGCCAAAAACCGTGATGATTAGTACACGATTTTGGTTGAAATTTTGCAAAAAATGACCCAAAAAA
187 AGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCAAAAAA
* *
15738 -ATTTTCCTCAATTTTTTGAACAAAATAATCATAATATATATATATATAATTTAACGCCAAAAAG
252 TA-TTTCCTCAATTTTTAG-ACAAAATAATCATAA-A-A-A-ATATATAATTCAACGCCAAAAAG
*
15802 ATTGGAGGACTTTTCA-
311 ATTGAAGGACTTTTCAC
* * *
15818 C-AATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGC
1 CTAATATCGTTTTTCATATTTTTTCTGAATAAATTTCTAATTAAATCGAAACAAGATTCAAATGC
* * * *
15882 TCGTAAAAACAAATTCTTAAATCCAATGTGGGTGAGATTTGATTAGATGAATATGAATATCTTAA
66 TCGTAAAAACAAATTATTAAATCCAATGTGGCTAAAATTTGATTAGATGAATAT-AATATCTTAA
* * * *
15947 GGAGTCTTCACACTAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACGCTTTTTTCGCCAAAA
130 GGAGTCTTCACACCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACACGTTTTTAGCCAAAA
** * ** * * ** * *
16012 ACTATGATGGTTTTTACACGATTTCGACTAAAATTTTGTAAAAGTTGCCCCAAAAGATATTTCCT
195 ACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCAAAAAATATTTCCT
* * * *
16077 CAGTTTTT-GGCTAACATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT
260 CAATTTTTAGAC-AAAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATT
16131 CGTAAAAACA
Statistics
Matches: 793, Mismatches: 114, Indels: 115
0.78 0.11 0.11
Matches are distributed among these distances:
312 8 0.01
313 4 0.01
314 1 0.00
315 37 0.05
316 199 0.25
317 10 0.01
319 3 0.00
320 2 0.00
321 1 0.00
323 1 0.00
324 1 0.00
326 26 0.03
327 3 0.00
328 3 0.00
329 2 0.00
330 28 0.04
331 165 0.21
332 159 0.20
333 92 0.12
334 12 0.02
335 1 0.00
336 2 0.00
337 1 0.00
338 32 0.04
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (327 bp):
CTAATATCGTTTTTCATATTTTTTCTGAATAAATTTCTAATTAAATCGAAACAAGATTCAAATGC
TCGTAAAAACAAATTATTAAATCCAATGTGGCTAAAATTTGATTAGATGAATATAATATCTTAAG
GAGTCTTCACACCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACACGTTTTTAGCCAAAAA
CCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCAAAAAATATTTCCTC
AATTTTTAGACAAAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTC
AC
Found at i:16066 original size:331 final size:328
Alignment explanation
Indices: 15261--16130 Score: 988
Period size: 332 Copynumber: 2.6 Consensus size: 328
15251 TGCGATTTGG
** * * * * *
15261 TTAGATGAATAT-TGATTTTTCAAGGTGTCTCGGCACCAAAAATCTTGCAAAACTGAACC-AGGC
1 TTAGATGAATATAT-ATGCTTCAAGGAGTTTCGACACCAAAAATCATGCAAAACTGAGCCGAGGC
*
15324 CCCGGAACGACTTTTTTGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAA
65 CCCGAAACG-CTTTTTTGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAA
* * * *
15389 AAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAA
129 AAATTGACCCAAAAGATATTTCCTCAATTTTTTGACAAAATACTCATAAAAAATATATAATTCAA
* * * * *
15454 TGCCTAAAATATTTAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATAAAT
194 CGCCAAAAAGATTGAAGGACTTTTCAC-C---TAATATCGTTTTTCATATTTTTTCTGAATAAAT
* *
15519 TTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTATTAAATGCATTGTGGCTA
255 TTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTATTAAATCCAATGTGGCTA
15584 AAAACTTTA
320 AAAACTTTA
* * * * * * *
15593 TTAGATGAATATATATGTTTCAAGGAGTTTCGACGCCGAAAATCATTCAAAACTGAGCTGGGGGC
1 TTAGATGAATATATATGCTTCAAGGAGTTTCGACACCAAAAATCATGCAAAACTGAGCCGAGGCC
* * * * * * *
15658 CCGAAACACGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTTGGTTGAAATTTTGCAAA
66 CCGAAACGC-TTTTTTGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAA
* * *
15723 AAATGACCCAAAA-AAATTTTCCTCAATTTTTTGAACAAAATAATCATAATATATATATATATAA
130 AATTGACCCAAAAGATA-TTTCCTCAATTTTTTG-ACAAAATACTCATAA-A-A-A-ATATATAA
* * *
15787 TTTAACGCCAAAAAGATTGGAGGACTTTTCA-C-AATATCGTTTTTCATATTTTTTCTGAATTAA
189 TTCAACGCCAAAAAGATTGAAGGACTTTTCACCTAATATCGTTTTTCATATTTTTTCTGAATAAA
* * * *
15850 TTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGGT
254 TTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTATTAAATCCAATGTGGCT
* *
15915 -GAGA-TTTGA
319 AAAAACTTT-A
*
15924 TTAGATGAATATGAATAT-CTT-AAGGAGTCTTC-ACACTAAAAATCATGCAAAACTGAGCCGAG
1 TTAGATGAATAT--ATATGCTTCAAGGAGT-TTCGACACCAAAAATCATGCAAAACTGAGCCGAG
* * * * *
15986 GCCCCGAAACGCTTTTTTCGCCAAAAACTATGATGGTTTTTACACGATTTCGACTAAAATTTTGT
63 GCCCCGAAACGCTTTTTT-GCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGC
* * * * *
16051 AAAAGTTGCCCCAAAAGATATTTCCTC-AGTTTTTGGCTAACATACTCATAAAAAATATATAATT
127 AAAAATTGACCCAAAAGATATTTCCTCAATTTTTTGAC-AAAATACTCATAAAAAATATATAATT
16115 CAACGCCAAAAAGATT
191 CAACGCCAAAAAGATT
16131 CGTAAAAACA
Statistics
Matches: 450, Mismatches: 72, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
326 25 0.06
327 1 0.00
328 1 0.00
329 2 0.00
330 26 0.06
331 112 0.25
332 146 0.32
333 89 0.20
334 12 0.03
335 1 0.00
336 2 0.00
337 1 0.00
338 32 0.07
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
TTAGATGAATATATATGCTTCAAGGAGTTTCGACACCAAAAATCATGCAAAACTGAGCCGAGGCC
CCGAAACGCTTTTTTGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAA
ATTGACCCAAAAGATATTTCCTCAATTTTTTGACAAAATACTCATAAAAAATATATAATTCAACG
CCAAAAAGATTGAAGGACTTTTCACCTAATATCGTTTTTCATATTTTTTCTGAATAAATTTCTAA
TTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTATTAAATCCAATGTGGCTAAAAACT
TTA
Found at i:16870 original size:15 final size:16
Alignment explanation
Indices: 16852--16881 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16842 ATAAATAATA
16852 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
16867 ATATTATAATCTAAA
1 ATATTATAATCTAAA
16882 AATAATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:18003 original size:35 final size:35
Alignment explanation
Indices: 17951--18031 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
17941 GCTCTTAAGC
* * * *
17951 TCTCAAAACACCTTAATACCCTATTGAGTTCAGTA
1 TCTCCAAACACCATAATACCCTACTGACTTCAGTA
17986 TCTCCAAACACCATAATACCCTACTGACTTCAGTA
1 TCTCCAAACACCATAATACCCTACTGACTTCAGTA
18021 TCTCCAAACAC
1 TCTCCAAACAC
18032 GTTTAGACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.27
Consensus pattern (35 bp):
TCTCCAAACACCATAATACCCTACTGACTTCAGTA
Found at i:18049 original size:35 final size:35
Alignment explanation
Indices: 17951--18056 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 35
17941 GCTCTTAAGC
* * * *
17951 TCTCAAAACACCTTAATACCCTATTGAGTTCAGTA
1 TCTCCAAACACCATAAGACCCTATTGACTTCAGTA
* *
17986 TCTCCAAACACCATAATACCCTACTGACTTCAGTA
1 TCTCCAAACACCATAAGACCCTATTGACTTCAGTA
** * *
18021 TCTCCAAACACGTTTAGACCTTATTGACTTCAGTA
1 TCTCCAAACACCATAAGACCCTATTGACTTCAGTA
18056 T
1 T
18057 TGAAGAGAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 61 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.31
Consensus pattern (35 bp):
TCTCCAAACACCATAAGACCCTATTGACTTCAGTA
Done.