Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016194.1 Corchorus olitorius cultivar O-4 contig16227, 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: 11467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:6037 original size:18 final size:19
Alignment explanation
Indices: 6003--6039 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5993 GAAGTTCGTG
6003 TTTGAAGACAAATTGAAGA
1 TTTGAAGACAAATTGAAGA
*
6022 TTTGAAGAC-CATTGAAGA
1 TTTGAAGACAAATTGAAGA
6040 ATAATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (19 bp):
TTTGAAGACAAATTGAAGA
Found at i:8134 original size:327 final size:318
Alignment explanation
Indices: 7536--8382 Score: 1185
Period size: 327 Copynumber: 2.6 Consensus size: 318
7526 ACGACCAATC
* * *
7536 AACTGACTTGAAAAATTTCTTCTCAAATTTTTGCCACAATATTCAGAGAAAAATATATAATTCAA
1 AACTGAC-TCAAAAATTT-TTCTCAATTTTTTGCCACAATACTCAGA-AAAAATATATAATTCAA
* * *
7601 CGCCAAAAAGATTGACAGGCTTTTCACGCTGCTAATATCTTTTTTCCATTTTTTTCGAAATAATT
63 CGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTAATT
* * * *
7666 TCTAATTAAATCGAAGCAAGATTGAGATGGTCAATAAAACAATTCCTTATATCCAATATTGCTGA
128 TCTAATTAAATCGAAACAAGATTGAGATGCTC-ATAAAACAAATCCTTATATCCAATATGGCTGA
7731 GATTTGTTTCGATGAATATAAATATTTCAAGGAGTCTTTGCGTCAAAAATCATGCAAAATTGAGA
192 GATTTGTTTCGATGAATATAAATATTTCAAGGAGTCTTTGCGTCAAAAATCATGCAAAATTGAGA
* * * *
7796 CGGGGCTCCGGAACGTGTTTTTAGCCAAAAAAAACCCGTGATGGTTAGTATTACGATTTCGGCTA
257 CGGGGCTCCGGAACGCGTTTTTAGCC---AAAAA-CCGTGATAGTTAGTA-CACGACTTCGGCTA
7861 AA
317 AA
* * *
7863 AACTGACTCAAAAAGTATTTTCTCAATTTTTTACCACAATACTCCGAAAAAATATGTAATTCAAC
1 AACTGACTCAAAAA-T-TTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC
* *
7928 GCCAAAAAGATTGACAAGCTTTTCACACTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATT
64 GCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTT-CGAATTAATT
* * * *
7993 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAATACAAATCCTTCTATCCAATGTGGCTGA
128 TCTAATTAAATCGAAACAAGATTGAGATGCTCATAAA-ACAAATCCTTATATCCAATATGGCTGA
* *
8058 GATTTGATTT-GATGAATATAGATATTTCAAGGAGTCTTTGCG-CTAAAAATCATGTAAAATTGA
192 GATTTG-TTTCGATGAATATAAATATTTCAAGGAGTCTTTGCGTC-AAAAATCATGCAAAATTGA
* * *
8121 GTCGGGTCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACACGACTTCGGCTAAA
255 GACGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGACTTCGGCTAAA
* * *
8185 AACTGACTCGAAAATTTTATACTCAATTTTTTGCCATAATACACAGAAAAAATATATAATTCAAC
1 AACTGACTCAAAAATTTT-T-CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC
* * *
8250 GCCAAAAAGATAGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTT
64 GCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTAATTT
* * *
8315 CTAATTAAATCTAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTATATCCAATATGGCGGAG
129 CTAATTAAATCGAAACAAGATTGAGATGCTC-ATAAAACAAATCCTTATATCCAATATGGCTGAG
8380 ATT
193 ATT
8383 AGAGCTGTCA
Statistics
Matches: 465, Mismatches: 46, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
320 3 0.01
321 70 0.15
322 118 0.25
323 13 0.03
324 5 0.01
326 78 0.17
327 173 0.37
328 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (318 bp):
AACTGACTCAAAAATTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC
CAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTAATTTCT
AATTAAATCGAAACAAGATTGAGATGCTCATAAAACAAATCCTTATATCCAATATGGCTGAGATT
TGTTTCGATGAATATAAATATTTCAAGGAGTCTTTGCGTCAAAAATCATGCAAAATTGAGACGGG
GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGACTTCGGCTAAA
Found at i:8507 original size:16 final size:16
Alignment explanation
Indices: 8486--8529 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
8476 CCCGACCCGA
* *
8486 ACCCGAGGCCGAAATT
1 ACCCGAGCCCGAAAAT
8502 ACCCGAGCCCGAAAAT
1 ACCCGAGCCCGAAAAT
*
8518 ACCCGAACCCGA
1 ACCCGAGCCCGA
8530 CCCGAGACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.34, C:0.39, G:0.20, T:0.07
Consensus pattern (16 bp):
ACCCGAGCCCGAAAAT
Found at i:9067 original size:31 final size:31
Alignment explanation
Indices: 8996--9067 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
8986 GTCTATTAGC
*
8996 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
9027 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
9057 GTTTTAATTTG
1 -TTTTAATTTG
9068 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:9357 original size:13 final size:12
Alignment explanation
Indices: 9321--9367 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
9311 TCAATCTTTA
*
9321 TATATATTGATAA
1 TATATATT-ATAT
*
9334 TA-ATGTTATAT
1 TATATATTATAT
9345 TATATTATTATAT
1 TATA-TATTATAT
9358 TATATATTAT
1 TATATATTAT
9368 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:9584 original size:16 final size:16
Alignment explanation
Indices: 9535--9607 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
9525 CTACTCGAGA
*
9535 CCGAACCGGAAAATAC
1 CCGAACCCGAAAATAC
* *
9551 CCAAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
9567 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
9583 CCGAACCCGAAAA-AGC
1 CCGAACCCGAAAATA-C
9599 CCGAACCCG
1 CCGAACCCG
9608 CCCGAGCACA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 4 0.09
16 40 0.85
17 3 0.06
ACGTcount: A:0.40, C:0.40, G:0.16, T:0.04
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:9602 original size:32 final size:32
Alignment explanation
Indices: 9535--9607 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
9525 CTACTCGAGA
* *
9535 CCGAACCGGAAAATACCCAAACCCGACATAAC
1 CCGAACCCGAAAATACCCAAACCCGACAAAAC
* *
9567 CCGAGCCCGAAAATACCCGAACCCGA-AAAAGC
1 CCGAACCCGAAAATACCCAAACCCGACAAAA-C
9599 CCGAACCCG
1 CCGAACCCG
9608 CCCGAGCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.40, C:0.40, G:0.16, T:0.04
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCAAACCCGACAAAAC
Found at i:10241 original size:323 final size:321
Alignment explanation
Indices: 9635--10994 Score: 1932
Period size: 321 Copynumber: 4.2 Consensus size: 321
9625 GCCAGCTCTA
* * * * * * * *
9635 GCTGAGATTTGGTTCAATTAATATAGATACTGCAAGGAGTTTTTGCGCCAATAATCATGCCAAAT
1 GCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
* * * *
9700 TGAGCCGCGGCTCCGGAACGCGTGTTTAGCCAAAAACTCGTGATGGTTAGTACACGATTTCGGCT
66 TGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAAC-CGTGAAGGTTAGTACACGATTTCGGCT
9765 AAAAACTGACCCGAAAAGTATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
130 AAAAACTGACCCGAAAAGTATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
9830 AACGCCAAAAAGATTGAC-GGTCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTA
195 AACGCCAAAAAGATTGACAGG-CTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTA
* * *
9894 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAACAAATCCTTATATCCAATATG
259 ATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATT
* **
9957 GCTGAAATTTGATTCGATGAATATAGATATTTC-AGGCAGTCTTTGCGTTAAAAATCATGCAAAA
1 GCTGAGATTTGATTCGATGAATATAGATATTTCAAGG-AGTCTTTGCGCCAAAAATCATGCAAAA
10021 TTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAAGGTTAGTACACGATTTCGGCT
65 TTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAAGGTTAGTACACGATTTCGGCT
* ** * * *
10086 AAAAACTTACTTGAAAAAT-TTCTTCTCAAATTTTTGCCACAATATTCAGAAAAAAAATATATAA
130 AAAAACTGACCCGAAAAGTATT-TTCTCAATTTTTTGCCACAATACTCAG--AAAAAATATATAA
*
10150 TTCAACGCCAAAAAGATTGACAGGCTTTTCACG-TTGCTAATATCGTTTTTCCATTTTTTTCGAA
192 TTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTT-CTAATATCGTTTTTCCATTTTTTCCGAA
* * *
10214 ATAATTTCTAATTAAATTGAAACAAGATTGAGATGCTC-AATAAAACAATTCCTTATATCCAATA
256 TTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAA-AAAACAAATCCTTATATCCAATA
10278 TT
320 TT
* * * *
10280 GCTGAGATTTGCTTCGATGAATATAAATATTTCAATGAGTCTTTGCGTCAAAAATCATGCAAAAT
1 GCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
* * * *
10345 TGAGACGGGGCTCCGGAACGCGTTTTTAGCCAAAAAAAAACCCGTGATGGGTA-T-TACGATTTC
66 TGAGTCGGGGCTCCGGAACGCGTTTTTAGCC----AAAAA-CCGTGAAGGTTAGTACACGATTTC
* * *
10408 GGCTAAAAACTGACTCGAAAAGTATTTTCTCAATTTTTTACCACAATACTCAGAAAAAATATGTA
126 GGCTAAAAACTGACCCGAAAAGTATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATA
* * *
10473 ATTCAACGCCAAAAAGATTGACAAGCTTTTCACACTTCTAATATCATTTTTCCATTTTTTTCCGA
191 ATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGA
* *
10538 ATTAATTTCTAATTAAATCGAAACAAGATTTAGTTGCTC-ATAAAAACAAATCCTTATATCCAAT
255 ATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGA-AAAAACAAATCCTTATATCCAAT
* *
10602 GTA
319 ATT
* * * *
10605 GATGAGATTTGATTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCTAAAAATCATGTAAAAT
1 GCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
10670 TGAGTCGGGG-TCCGGAACGCGTTTTTAGCCAAAAACCGTGATA-GTTAGTACACGATTTCGGCT
66 TGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGA-AGGTTAGTACACGATTTCGGCT
* * *
10733 AAAAACTTACCCGAAAA-TTTTATTCTCAATTTTTTTGCCACAATACACAGAAAAAATATATAAT
130 AAAAACTGACCCGAAAAGTATT-TTCTCAA-TTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * *
10797 TCAACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAATATTGTTTTTCCATTTTTTCCGAATT
193 TCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATT
*
10862 AATTTCTAATTATATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATT
258 AATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATT
* * * *
10926 GCTGAGCTTTGGTTCGATGAATATAGATATTTCACGGAGTCTTTACGCCAAAAATCATGCAAAAT
1 GCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
10991 TGAG
66 TGAG
10995 ACGAGACCCC
Statistics
Matches: 923, Mismatches: 92, Indels: 47
0.87 0.09 0.04
Matches are distributed among these distances:
319 9 0.01
320 11 0.01
321 234 0.25
322 165 0.18
323 215 0.23
324 83 0.09
325 135 0.15
326 53 0.06
327 8 0.01
328 10 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (321 bp):
GCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
TGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAAGGTTAGTACACGATTTCGGCTA
AAAACTGACCCGAAAAGTATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCA
ACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAAT
TTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATT
Found at i:11258 original size:289 final size:289
Alignment explanation
Indices: 10723--11286 Score: 895
Period size: 288 Copynumber: 2.0 Consensus size: 289
10713 GTTAGTACAC
* *
10723 GATTTCGGCTAAAAACTTACCCGAAAATTTTATTCTCAATTTTTTTGCCACAATACACAGAAAAA
1 GATTTCGGCTAAAAACTGACCCGAAAATATTATTCTCAATTTTTTTGCCACAATACACAGAAAAA
*
10788 ATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAATATTGTTTTTCCATTTT
66 ATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTT
* *
10853 TTCCGAATTAATTTCTAATTATATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATAT
131 TTCCGAATTAATTTCTAATTATATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTAAAT
* * *
10918 CCAATATTGCTGAGCTTTGGTTCGATGAATATAGATATTTCACGGAGTCTTTACGCCAAAAATCA
196 CCAATATTGCTGAGATTTGGTTCGATGAATATAAATATTTCAAGGAGTCTTTACGCCAAAAATCA
10983 TGCAAAATTGAGACGAGACCCCGCAACAA
261 TGCAAAATTGAGACGAGACCCCGCAACAA
* * *
11012 GATTTCGGGC-AAAAACTGACTCGAAAAGTATT-TTGTCAA-TTTTTTGCCACAATACTCAGAAA
1 GATTTC-GGCTAAAAACTGACCCGAAAA-TATTATTCTCAATTTTTTTGCCACAATACACAGAAA
* * *
11074 TAATATATAATTCAACGCCAAAAAGATAT-ACGGGCTTTTCACGCTTCTAGTATCGTTTTTCCAT
64 AAATATATAATTCAACGCCAAAAAGAT-TGACGGGATTTTCACGCTTCTAATATCGTTTTTCCAT
* *
11138 TTTTTTCGAATTAATTTCTAATTGA-ATCGAAACAAGATTGAGATGCTCAAAAAAAACAATTCCT
128 TTTTTCCGAATTAATTTCTAATT-ATATCGAAACAAGATTGAGATGCTC-AAAAAAACAAATCCT
*
11202 TAAATCCAATATTGCTGAGATTTGGTTCGATGAATATAAATATTTCAAGGAGTCTTTGCGCCAAA
191 TAAATCCAATATTGCTGAGATTTGGTTCGATGAATATAAATATTTCAAGGAGTCTTTACGCCAAA
11267 AATCATGCAAAATTGAGACG
256 AATCATGCAAAATTGAGACG
11287 GGGCTTCGGA
Statistics
Matches: 253, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
288 125 0.49
289 122 0.48
290 6 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (289 bp):
GATTTCGGCTAAAAACTGACCCGAAAATATTATTCTCAATTTTTTTGCCACAATACACAGAAAAA
ATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTT
TTCCGAATTAATTTCTAATTATATCGAAACAAGATTGAGATGCTCAAAAAAACAAATCCTTAAAT
CCAATATTGCTGAGATTTGGTTCGATGAATATAAATATTTCAAGGAGTCTTTACGCCAAAAATCA
TGCAAAATTGAGACGAGACCCCGCAACAA
Done.