Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010516.1 Corchorus olitorius cultivar O-4 contig10548, 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: 3110
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:936 original size:39 final size:38
Alignment explanation
Indices: 893--1426 Score: 351
Period size: 39 Copynumber: 13.8 Consensus size: 38
883 GCCCCCATTC
893 AGAATTGTCATTTAAGTAAACCTGCTTAGGTCTATGTTT
1 AGAATT-TCATTTAAGTAAACCTGCTTAGGTCTATGTTT
*
932 AGAATTTCATTTAAGCAAACCTGCTTAGGTCTATGTTT
1 AGAATTTCATTTAAGTAAACCTGCTTAGGTCTATGTTT
*
970 AGAATTTCATTTAAGTAAACCTGCTTAGGTTCT-TGCTT
1 AGAATTTCATTTAAGTAAACCTGCTTAGG-TCTATGTTT
* * *
1008 AAAATTTCCGTTTAAGCAAACCTGCTTAGGTCCT-TGTTT
1 AGAATTT-CATTTAAGTAAACCTGCTTAGGT-CTATGTTT
* **
1047 AGAATTCCCGTTAAGTAAACCTGCTTAGGTCT-TCGTTT
1 AGAATTTCATTTAAGTAAACCTGCTTAGGTCTAT-GTTT
* *
1085 GGAAGTTTCGTTTAA-TCAAACCTGCTTAGGTTCTTATG--T
1 AGAA-TTTCATTTAAGT-AAACCTGCTTAGG-TC-TATGTTT
* * * *
1124 AGAATTCCCGTTTGAA-TGAACCTGCTTAGGTCTATGCTT
1 AGAATT-TCATTT-AAGTAAACCTGCTTAGGTCTATGTTT
** * *
1163 AGAATTTCGCTTAA-TCAAACCTGCTTAGGTCTACGCTT
1 AGAATTTCATTTAAGT-AAACCTGCTTAGGTCTATGTTT
* * ** *
1201 AGAGTTTTTATTTAA-TCAAACCTGCTTAGGTCCCTCTTT
1 AGA-ATTTCATTTAAGT-AAACCTGCTTAGGTCTATGTTT
* * * * *
1240 -GTAATCTTGC-CTT-AGAAAAACCTGTTTAGAGTCTCTGCTT
1 AG-AAT-TT-CATTTAAG-TAAACCTGCTTAG-GTCTATGTTT
* * * * ** * *
1280 AGAGCTTTGA-TCAAGTAAGCCTGCTTAGGTCCCTATAT
1 AGA-ATTTCATTTAAGTAAACCTGCTTAGGTCTATGTTT
* * *
1318 AGAGTTGCCATTTAAGTAAACCTGCTTAGGTCTATGTTC
1 AGAATT-TCATTTAAGTAAACCTGCTTAGGTCTATGTTT
* * *
1357 AGAATTTCGTTTAAGAAAACCTGCTTAGGTTCT-CGTTT
1 AGAATTTCATTTAAGTAAACCTGCTTAGG-TCTATGTTT
**
1395 AGAATTCTTGTTTAA-TCAAACCTGCTTAGGTC
1 AGAATT-TCATTTAAGT-AAACCTGCTTAGGTC
1427 CCCCCCCCTT
Statistics
Matches: 397, Mismatches: 68, Indels: 61
0.75 0.13 0.12
Matches are distributed among these distances:
37 12 0.03
38 173 0.44
39 190 0.48
40 17 0.04
41 4 0.01
42 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
AGAATTTCATTTAAGTAAACCTGCTTAGGTCTATGTTT
Found at i:1023 original size:77 final size:77
Alignment explanation
Indices: 893--1426 Score: 375
Period size: 77 Copynumber: 6.9 Consensus size: 77
883 GCCCCCATTC
* *
893 AGAATTGTCATTTAAGTAAACCTGCTTAGG-TCTATGTTTAGAATTT-CATTTAAGCAAACCTGC
1 AGAATT-TCATTTAAGTAAACCTGCTTAGGTTCT-TGCTTAGAATTTCCGTTTAAGCAAACCTGC
956 TTAGGTCTATGTTT
64 TTAGGTCTATGTTT
*
970 AGAATTTCATTTAAGTAAACCTGCTTAGGTTCTTGCTTAAAATTTCCGTTTAAGCAAACCTGCTT
1 AGAATTTCATTTAAGTAAACCTGCTTAGGTTCTTGCTTAGAATTTCCGTTTAAGCAAACCTGCTT
1035 AGGTCCT-TGTTT
66 AGGT-CTATGTTT
* ** * * *
1047 AGAATTCCCGTTAAGTAAACCTGCTTAGG-TCTTCGTTTGGAAGTTT-CGTTTAATCAAACCTGC
1 AGAATTTCATTTAAGTAAACCTGCTTAGGTTCTT-GCTTAGAA-TTTCCGTTTAAGCAAACCTGC
1110 TTAGGTTCTTATG--T
64 TTAGG-TC-TATGTTT
* * * * *
1124 AGAATTCCCGTTTGAA-TGAACCTGCTTAGG-TCTATGCTTAGAATTT-CGCTTAATCAAACCTG
1 AGAATT-TCATTT-AAGTAAACCTGCTTAGGTTCT-TGCTTAGAATTTCCGTTTAAGCAAACCTG
* *
1186 CTTAGGTCTACGCTT
63 CTTAGGTCTATGTTT
* * * * * *
1201 AGAGTTTTTATTTAA-TCAAACCTGCTTAGGTCCCT-CTTTGTAATCTTGCC--TT-AGAAAAAC
1 AGA-ATTTCATTTAAGT-AAACCTGCTTAGGTTCTTGCTTAG-AAT-TT-CCGTTTAAG-CAAAC
* * *
1261 CTGTTTAGAGTCTCTGCTT
60 CTGCTTAG-GTCTATGTTT
* * * * * * * * * * *
1280 AGAGCTTTGA-TCAAGTAAGCCTGCTTAGGTCCCT-ATATAGAGTTGCCATTTAAGTAAACCTGC
1 AGA-ATTTCATTTAAGTAAACCTGCTTAGGTTCTTGCT-TAGAATTTCCGTTTAAGCAAACCTGC
*
1343 TTAGGTCTATGTTC
64 TTAGGTCTATGTTT
* * * * * *
1357 AGAATTTCGTTTAAGAAAACCTGCTTAGGTTCTCGTTTAGAA-TTCTTGTTTAATCAAACCTGCT
1 AGAATTTCATTTAAGTAAACCTGCTTAGGTTCTTGCTTAGAATTTC-CGTTTAAGCAAACCTGCT
1421 TAGGTC
65 TAGGTC
1427 CCCCCCCCTT
Statistics
Matches: 368, Mismatches: 59, Indels: 60
0.76 0.12 0.12
Matches are distributed among these distances:
75 3 0.01
76 53 0.14
77 197 0.54
78 88 0.24
79 26 0.07
80 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (77 bp):
AGAATTTCATTTAAGTAAACCTGCTTAGGTTCTTGCTTAGAATTTCCGTTTAAGCAAACCTGCTT
AGGTCTATGTTT
Found at i:1154 original size:116 final size:114
Alignment explanation
Indices: 903--1231 Score: 368
Period size: 116 Copynumber: 2.8 Consensus size: 114
893 AGAATTGTCA
** *
903 TTTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTAAGCAAACCTGCTTAGGTCTAT-G
1 TTTAAG-AAACCTGCTTAGGTCTATGTTTAGAA-TTCCGTTAAGTAAACCTGCTTAGGTCT-TCG
* *
967 TTTAGAA-TTTCATTTAAGT-AAACCTGCTTAGGTTCTTGCTTAAAATTTCCG
63 TTTAGAAGTTTCATTTAA-TCAAACCTGCTTAGGTTCTTGATTAAAATTCCCG
1018 TTTAAGCAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCGTTAAGTAAACCTGCTTAGGTCTTCG
1 TTTAAG-AAACCTGCTTAGGT-CTATGTTTAGAATT-CCGTTAAGTAAACCTGCTTAGGTCTTCG
* * *
1082 TTTGGAAGTTTCGTTTAATCAAACCTGCTTAGGTTCTT-ATGTAGAATTCCCG
63 TTTAGAAGTTTCATTTAATCAAACCTGCTTAGGTTCTTGAT-TAAAATTCCCG
* * *
1134 TTTGAATG-AACCTGCTTAGGTCTATGCTTAGAATTTCGCTTAA-TCAAACCTGCTTAGGTCTAC
1 TTT-AA-GAAACCTGCTTAGGTCTATGTTTAGAATTCCG-TTAAGT-AAACCTGCTTAGGTCTTC
* *
1197 GCTTAG-AGTTTTTATTTAATCAAACCTGCTTAGGT
62 GTTTAGAAG-TTTCATTTAATCAAACCTGCTTAGGT
1232 CCCTCTTTGT
Statistics
Matches: 186, Mismatches: 16, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
114 3 0.02
115 67 0.36
116 113 0.61
117 2 0.01
118 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (114 bp):
TTTAAGAAACCTGCTTAGGTCTATGTTTAGAATTCCGTTAAGTAAACCTGCTTAGGTCTTCGTTT
AGAAGTTTCATTTAATCAAACCTGCTTAGGTTCTTGATTAAAATTCCCG
Found at i:1262 original size:116 final size:112
Alignment explanation
Indices: 910--1426 Score: 323
Period size: 116 Copynumber: 4.5 Consensus size: 112
900 TCATTTAAGT
* * * * *
910 AAACCTGCTTAGGTCTATGTTTAGAATTTCATTTAAGCAAACCTGCTTAGGTCTATGTTTAGAAT
1 AAACCTGCTTAGGTCTATGCTTAGAATTTCACTTAATCAAACCTGCTTAGGTCTACGTTTAGAGT
*
975 TTCATTTAAGT-AAACCTGCTTAGGT-TC-TTGCTTAAAATTTCCGTTTA-AGC
66 TTCATTTAA-TCAAACCTGCTTAGGTCTCTTTG--T--AATTTCCG-TTAGA-A
* * * *
1025 AAACCTGCTTAGGTCCT-TGTTTAGAA-TTCCCGTTAAGT-AAACCTGCTTAGGTCTTCGTTTGG
1 AAACCTGCTTAGGT-CTATGCTTAGAATTTCAC-TTAA-TCAAACCTGCTTAGGTCTACGTTTAG
* * *
1087 AAGTTTCGTTTAATCAAACCTGCTTAGGT-TCTTATGTAGAATTCCCGTTTGAA
63 -AGTTTCATTTAATCAAACCTGCTTAGGTCTCTT-TGT--AATTTCCGTTAGAA
* * *
1140 TGAACCTGCTTAGGTCTATGCTTAGAATTTCGCTTAATCAAACCTGCTTAGGTCTACGCTTAGAG
1 -AAACCTGCTTAGGTCTATGCTTAGAATTTCACTTAATCAAACCTGCTTAGGTCTACGTTTAGAG
*
1205 TTTTTATTTAATCAAACCTGCTTAGGTCCCTCTTTGTAATCTTGCC-TTAGAA
65 -TTTCATTTAATCAAACCTGCTTAGGT--CTCTTTGTAAT-TT-CCGTTAGAA
* * * * * * *
1257 AAACCTGTTTAGAGTCTCTGCTTAGAGCTTTGA-TCAAGT-AAGCCTGCTTAGGTCCCTA--TAT
1 AAACCTGCTTAG-GTCTATGCTTAGA-ATTTCACTTAA-TCAAACCTGCTTAGGT--CTACGTTT
* *
1318 AGAGTTGCCATTTAAGT-AAACCTGCTTAGGTCTATGTTCAG-AATTT-CGTTTA-AGA
61 AGAGTT-TCATTTAA-TCAAACCTGCTTAGGTCTCT-TT--GTAATTTCCG-TTAGA-A
* * ***
1373 AAACCTGCTTAGGTTCT-CGTTTAGAATTCTTGTTTAATCAAACCTGCTTAGGTC
1 AAACCTGCTTAGG-TCTATGCTTAGAATT-TCACTTAATCAAACCTGCTTAGGTC
1427 CCCCCCCCTT
Statistics
Matches: 324, Mismatches: 43, Indels: 71
0.74 0.10 0.16
Matches are distributed among these distances:
114 7 0.02
115 69 0.21
116 161 0.50
117 67 0.21
118 13 0.04
119 7 0.02
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (112 bp):
AAACCTGCTTAGGTCTATGCTTAGAATTTCACTTAATCAAACCTGCTTAGGTCTACGTTTAGAGT
TTCATTTAATCAAACCTGCTTAGGTCTCTTTGTAATTTCCGTTAGAA
Found at i:2186 original size:15 final size:15
Alignment explanation
Indices: 2166--2197 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2156 TTCAGCTCTC
2166 CTACACTCCATCAGA
1 CTACACTCCATCAGA
2181 CTACACTCCATCAGA
1 CTACACTCCATCAGA
2196 CT
1 CT
2198 GAACAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.41, G:0.06, T:0.22
Consensus pattern (15 bp):
CTACACTCCATCAGA
Found at i:2534 original size:10 final size:9
Alignment explanation
Indices: 2514--2553 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2504 AAACAGGAGG
2514 AAATACCAAA
1 AAATA-CAAA
*
2524 AGATACAAA
1 AAATACAAA
*
2533 AAAAACAAA
1 AAATACAAA
2542 AAATACAAA
1 AAATACAAA
2551 AAA
1 AAA
2554 AAGAGGGAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.78, C:0.12, G:0.03, T:0.07
Consensus pattern (9 bp):
AAATACAAA
Found at i:2541 original size:18 final size:18
Alignment explanation
Indices: 2520--2555 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2510 GAGGAAATAC
*
2520 CAAAAGATACAAAAAAAA
1 CAAAAAATACAAAAAAAA
2538 CAAAAAATACAAAAAAAA
1 CAAAAAATACAAAAAAAA
2556 GAGGGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.11, G:0.03, T:0.06
Consensus pattern (18 bp):
CAAAAAATACAAAAAAAA
Found at i:2554 original size:10 final size:10
Alignment explanation
Indices: 2514--2554 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2504 AAACAGGAGG
*
2514 AAATACCAAA
1 AAATACAAAA
*
2524 AGATACAAAA
1 AAATACAAAA
2534 AAA-AC-AAA
1 AAATACAAAA
2542 AAATACAAAA
1 AAATACAAAA
2552 AAA
1 AAA
2555 AGAGGGAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 6 0.23
9 4 0.15
10 16 0.62
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.07
Consensus pattern (10 bp):
AAATACAAAA
Done.