Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012651.1 Corchorus olitorius cultivar O-4 contig12684, 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: 17242
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:716 original size:317 final size:321
Alignment explanation
Indices: 1--1272 Score: 1768
Period size: 319 Copynumber: 4.0 Consensus size: 321
*
1 TGGTTAATACACAATTTCGGCTAAAAAACTGACCCGACAAAATTTTCCCTTCAATTTTTTATCAC
1 TGGTTAATACACAATTTCGGCT-AAAAACTGACCCGA-AAAATTTTCCC-TCAATTTTTTGTCAC
* * * *
66 AACATTACAGAAAACATATTTAATTCAACGCCAAGAATATTGACGGCTTTTTCACACTTCTAATA
63 AACATT-CAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACACTTCTAATA
* *
131 TCGTTTT-CCATTTTTTTTCCTGATTAATTTCTAAATAAAACGAATCAAGATTCAGATGCTCGTA
127 TCGTTTTCCCA-TTTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTCAGATGCTCGTA
*
195 ATAACAAATCCTTAAATCTCATCTGGCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGT
191 AT-A-AAATCCTTAAATCTCATATGGCTGAGATTTCATTAGATGAATATAGATATTTC-AGGAGT
* * * * *
260 CTTTACG-CAAAAATTCATTCAAATCTAAGTCGGCACCCTGGAACGCGTTTTTAGCC-AAAAAAC
253 CTTTACGCCAAAAA-TCATGCAAAACTGAGCCGGCACCCCGGAACGCGTTTTTAGCCAAAAAAAC
323 CGTGA
317 CGTGA
*
328 TGG-T--TACACGATTTCGGCTAAAAACTGACCCGAAAAATTTTCCCTCAATTTTTTGTCACAAC
1 TGGTTAATACACAATTTCGGCTAAAAACTGACCCGAAAAATTTTCCCTCAATTTTTTGTCACAAC
* *
390 ATTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACTCTTCTAATATCAT
66 ATTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACACTTCTAATATCGT
455 TTTCCCA-TTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTCAGATGCTCGTAAT-AA
131 TTTCCCATTTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTCAGATGCTCGTAATAAA
* ** * *
518 ATCCTTAAATCCCATATTACTGATATTTCATTAGATGAATATAGATATTTC-GAAGT-TTTACGC
196 ATCCTTAAATCTCATATGGCTGAGATTTCATTAGATGAATATAGATATTTCAGGAGTCTTTACGC
* * *
581 CAAAAATCATGCAAAACTGAGCCAGCACTCTGGAACGCGTTTTTAGCCAAAAAAACCGTGA
261 CAAAAATCATGCAAAACTGAGCCGGCACCCCGGAACGCGTTTTTAGCCAAAAAAACCGTGA
* *
642 TGGTTAATACACAATTTTGGTTAAAAACTGACCCGAAAAATTTTCCCTCAATTTTTTGTCACAAC
1 TGGTTAATACACAATTTCGGCTAAAAACTGACCCGAAAAATTTTCCCTCAATTTTTTGTCACAAC
707 ATTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACACTTCTAATATCGT
66 ATTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACACTTCTAATATCG-
* * * *
772 TTTTTCCATTTTTTTCCAAATTAATATCTAAATAAAACGAAACAAGATTCAGATACTCGTAATAA
130 TTTTCCCATTTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTCAGATGCTCGTAAT-A
*
837 CAAATCCATAAATCTCATATGGCTGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTTT
194 -AAATCCTTAAATCTCATATGGCTGAGATTTCATTAGATGAATATAGATATTTC-AGGAGTCTTT
* * ** ** *
902 ATGTCAAAAATCATGCAAAACTGAGATGGCGTCCCAGAACGCGTTTTTAGCCAAAAAAA-C---A
257 ACGCCAAAAATCATGCAAAACTGAGCCGGCACCCCGGAACGCGTTTTTAGCCAAAAAAACCGTGA
* * * * *
963 ---TTACATACACGATTTTGGCTAAAATCTGACCCGAAAAAATTTCCTTCAATTTTTTGTCACAA
1 TGGTTA-ATACACAATTTCGGCTAAAAACTGACCCGAAAAATTTTCCCTCAATTTTTTGTCACAA
*
1025 CATTCAGAAAAAATATATAATTCAACGCCAAGTATATTGAAGGGTTTTTCACACTTCTAATATCG
65 CATTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACACTTCTAATATCG
* *
1090 TTTTCTCATTTTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTTAGATGCTCGTAGTA
130 TTTTCCCA-TTTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTCAGATGCTCGTA--A
* * * * *
1155 AAAAATCCTTAAATCTCATATGGCTGAGATTTCATTAGATCAATATAAATATATTTTAAGGAGTT
192 TAAAATCCTTAAATCTCATATGGCTGAGATTTCATTAGATGAATAT--AGATA-TTTCAGGAGTC
* *
1220 TTTACGCTAAAAATCATGCAAAACTGAGCCGGCACCCCGGAACGCATTTTTAG
254 TTTACGCCAAAAATCATGCAAAACTGAGCCGGCACCCCGGAACGCGTTTTTAG
1273 TGGTTTAGCC
Statistics
Matches: 850, Mismatches: 74, Indels: 48
0.87 0.08 0.05
Matches are distributed among these distances:
313 42 0.05
314 25 0.03
315 1 0.00
316 48 0.06
317 117 0.14
318 16 0.02
319 311 0.37
320 60 0.07
321 79 0.09
322 62 0.07
323 14 0.02
324 19 0.02
325 52 0.06
326 1 0.00
327 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (321 bp):
TGGTTAATACACAATTTCGGCTAAAAACTGACCCGAAAAATTTTCCCTCAATTTTTTGTCACAAC
ATTCAGAAAAAATATATAATTCAACGCCAAGAATATTGAAGGGTTTTTCACACTTCTAATATCGT
TTTCCCATTTTTTTCCTAATTAATTTCTAAATAAAACGAAACAAGATTCAGATGCTCGTAATAAA
ATCCTTAAATCTCATATGGCTGAGATTTCATTAGATGAATATAGATATTTCAGGAGTCTTTACGC
CAAAAATCATGCAAAACTGAGCCGGCACCCCGGAACGCGTTTTTAGCCAAAAAAACCGTGA
Found at i:1389 original size:21 final size:19
Alignment explanation
Indices: 1364--1421 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
1354 GTTGTTCTAA
*
1364 TAATCTCATATGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
1385 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
1404 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
1422 TGCTAATGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:1557 original size:17 final size:17
Alignment explanation
Indices: 1535--1571 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1525 TTGATAATCC
1535 TGTCTAGGGTTCTTGCT
1 TGTCTAGGGTTCTTGCT
1552 TGTCTAGGGTTCTTGCT
1 TGTCTAGGGTTCTTGCT
1569 TGT
1 TGT
1572 AAGCAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (17 bp):
TGTCTAGGGTTCTTGCT
Found at i:2409 original size:12 final size:12
Alignment explanation
Indices: 2394--2418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2384 TCTATACTCA
2394 CTTTCTTCTCCT
1 CTTTCTTCTCCT
2406 CTTTCTTCTCCT
1 CTTTCTTCTCCT
2418 C
1 C
2419 AGCAGCAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTTCTTCTCCT
Found at i:4988 original size:18 final size:18
Alignment explanation
Indices: 4965--5007 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
4955 TAATCCAGTT
4965 GTTGCTGTTGTTGTCGTC
1 GTTGCTGTTGTTGTCGTC
4983 GTTGCTGTTGTTGTCGTC
1 GTTGCTGTTGTTGTCGTC
*
5001 ATTGCTG
1 GTTGCTG
5008 CTGGTGGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.16, G:0.33, T:0.49
Consensus pattern (18 bp):
GTTGCTGTTGTTGTCGTC
Found at i:10821 original size:15 final size:15
Alignment explanation
Indices: 10803--10836 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10793 AAAGGGAAAA
10803 AAAGAAAA-GAAATGG
1 AAAGAAAAGGAAA-GG
10818 AAAGAAAAGGAAAGG
1 AAAGAAAAGGAAAGG
10833 AAAG
1 AAAG
10837 GCGTGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
AAAGAAAAGGAAAGG
Found at i:11597 original size:28 final size:27
Alignment explanation
Indices: 11524--11598 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
11514 TATAACAACT
* *
11524 AAAATCATACCAAAATTTACGGCCAAAA
1 AAAATCATACCAAAA-TTATGACCAAAA
11552 AAAATCATACCAAAATTATGTACCAAAA
1 AAAATCATACCAAAATTATG-ACCAAAA
*
11580 GAAATCATACCAAAATTAT
1 AAAATCATACCAAAATTAT
11599 ATGTTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 4 0.09
28 39 0.91
ACGTcount: A:0.55, C:0.19, G:0.05, T:0.21
Consensus pattern (27 bp):
AAAATCATACCAAAATTATGACCAAAA
Done.