Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012450.1 Corchorus olitorius cultivar O-4 contig12483, 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: 14912
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:754 original size:17 final size:16
Alignment explanation
Indices: 714--764 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
704 CATGTAATCT
*
714 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
730 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
747 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
764 T
1 T
765 GGGGAGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:1467 original size:10 final size:10
Alignment explanation
Indices: 1452--1479 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1442 CAAGAGTCCT
1452 TCCTTTCCCA
1 TCCTTTCCCA
1462 TCCTTTCCCA
1 TCCTTTCCCA
1472 TCCTTTCC
1 TCCTTTCC
1480 TGATCCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (10 bp):
TCCTTTCCCA
Found at i:2791 original size:30 final size:30
Alignment explanation
Indices: 2751--3273 Score: 652
Period size: 30 Copynumber: 17.7 Consensus size: 30
2741 ACTCTCTAAA
* *
2751 TGACATCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
2781 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
2811 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
2841 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
2871 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* * *
2901 TGACACCAGAAATTGTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* * *
2931 TGACACCAGAAGTTGTTATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* * *
2961 TGACACCAGAAGTTCTCATGGCCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
2991 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
3021 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
3051 TGACACCAGAAGTTGTCATGG-C---C--T
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
3075 TG---CCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* *
3102 TGACACCAAAAGTTATCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* * * *
3132 TGACACCAAAAGCTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* *
3162 TGACACCAAAAGTTGTCATGAG-GTTGCAAT
1 TGACACCAGAAGTTGTCATG-GTCTTGCAAT
* * *
3192 TGACACTAGAAGCTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
* ** * *
3222 TGACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCAT-GGTCT-TGCAAT
3254 TGACACCAGAAGTTGTCATG
1 TGACACCAGAAGTTGTCATG
3274 ATAAATTTGC
Statistics
Matches: 445, Mismatches: 35, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
21 16 0.04
22 1 0.00
24 2 0.00
25 1 0.00
26 1 0.00
27 3 0.01
29 1 0.00
30 395 0.89
31 2 0.00
32 23 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGGTCTTGCAAT
Found at i:3082 original size:21 final size:21
Alignment explanation
Indices: 3056--3098 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3046 GCAAATGACA
3056 CCAGAAGTTGTCATGGCCTTG
1 CCAGAAGTTGTCATGGCCTTG
*
3077 CCAGAAGTTGTCATGGTCTTG
1 CCAGAAGTTGTCATGGCCTTG
3098 C
1 C
3099 AATTGACACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (21 bp):
CCAGAAGTTGTCATGGCCTTG
Found at i:3106 original size:51 final size:51
Alignment explanation
Indices: 3026--3128 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
3016 GCAAATGACA
* *
3026 CCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTGTCATGGCCTTG
1 CCAGAAGTTGTCATGGTCTTGCAAATGACACCAAAAGTTATCATGGCCTTG
* *
3077 CCAGAAGTTGTCATGGTCTTGCAATTGACACCAAAAGTTATCATGGTCTTG
1 CCAGAAGTTGTCATGGTCTTGCAAATGACACCAAAAGTTATCATGGCCTTG
3128 C
1 C
3129 AATTGACACC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (51 bp):
CCAGAAGTTGTCATGGTCTTGCAAATGACACCAAAAGTTATCATGGCCTTG
Found at i:3160 original size:111 final size:111
Alignment explanation
Indices: 2966--3181 Score: 324
Period size: 111 Copynumber: 1.9 Consensus size: 111
2956 GCAAATGACA
* * *
2966 CCAGAAGTTCTCATGGCCTTGCAAATGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGA
1 CCAGAAGTTCTCATGGCCTTGCAAATGACACCAAAAGTTATCATGGTCTTGCAAATGACACCAAA
* * *
3031 AGTTGTCATGGTCTTGCAAATGACACCAGAAGTTGTCATGGCCTTG
66 AGCTGTCATGATCTTGCAAATGACACCAAAAGTTGTCATGGCCTTG
* * * *
3077 CCAGAAGTTGTCATGGTCTTGCAATTGACACCAAAAGTTATCATGGTCTTGCAATTGACACCAAA
1 CCAGAAGTTCTCATGGCCTTGCAAATGACACCAAAAGTTATCATGGTCTTGCAAATGACACCAAA
* *
3142 AGCTGTCATGATTTTGCAATTGACACCAAAAGTTGTCATG
66 AGCTGTCATGATCTTGCAAATGACACCAAAAGTTGTCATG
3182 AGGTTGCAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 93 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (111 bp):
CCAGAAGTTCTCATGGCCTTGCAAATGACACCAAAAGTTATCATGGTCTTGCAAATGACACCAAA
AGCTGTCATGATCTTGCAAATGACACCAAAAGTTGTCATGGCCTTG
Found at i:3190 original size:141 final size:141
Alignment explanation
Indices: 2936--3211 Score: 383
Period size: 141 Copynumber: 2.0 Consensus size: 141
2926 GCAAATGACA
* * * *
2936 CCAGAAGTTGTTATGGCCTTGCAAATGACACCAGAAGTTCTCATGGCCTTGCAAATGACACCAGA
1 CCAGAAGTTGTCATGGCCTTGCAAATGACACCAAAAGTTATCATGGCCTTGCAAATGACACCAAA
* * * *
3001 AGTTGTCATGGTCTTGCAAATGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTG
66 AGCTGTCATGATCTTGCAAATGACACCAAAAGTTGTCATGGTCTTGCAAATGACACCAGAAGCTG
3066 TCATGGCCTTG
131 TCATGGCCTTG
* * * *
3077 CCAGAAGTTGTCATGGTCTTGCAATTGACACCAAAAGTTATCATGGTCTTGCAATTGACACCAAA
1 CCAGAAGTTGTCATGGCCTTGCAAATGACACCAAAAGTTATCATGGCCTTGCAAATGACACCAAA
* * * * *
3142 AGCTGTCATGATTTTGCAATTGACACCAAAAGTTGTCATGAG-GTTGCAATTGACACTAGAAGCT
66 AGCTGTCATGATCTTGCAAATGACACCAAAAGTTGTCATG-GTCTTGCAAATGACACCAGAAGCT
3206 GTCATG
130 GTCATG
3212 ATCTTGCAAT
Statistics
Matches: 117, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
141 116 0.99
142 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (141 bp):
CCAGAAGTTGTCATGGCCTTGCAAATGACACCAAAAGTTATCATGGCCTTGCAAATGACACCAAA
AGCTGTCATGATCTTGCAAATGACACCAAAAGTTGTCATGGTCTTGCAAATGACACCAGAAGCTG
TCATGGCCTTG
Found at i:3311 original size:65 final size:63
Alignment explanation
Indices: 3188--3395 Score: 249
Period size: 65 Copynumber: 3.4 Consensus size: 63
3178 CATGAGGTTG
* * * * *
3188 CAATTGACACTAGAAGCTGTCATGAT--CTTGCAATTGACACCAT-AAGTTGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATAAATTGCAA-TGACA-CTTGAAGATGTCATAATTTTATT
3250 CAATTGACACCAGAAGTTGTCATGATAAATTTGCAATAGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATAAA-TTGCAAT-GACACTTGAAGATGTCATAATTTTATT
*
3315 CAATTGACACCAAAAGTTGTCATGATAAATT----T----CTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATAAATTGCAATGACACTTGAAGATGTCATAATTTTATT
3370 CAATTGACACCAGAAGTTGTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
3396 TTTACCTTTC
Statistics
Matches: 134, Mismatches: 7, Indels: 17
0.85 0.04 0.11
Matches are distributed among these distances:
55 48 0.36
60 1 0.01
62 24 0.18
64 5 0.04
65 56 0.42
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (63 bp):
CAATTGACACCAGAAGTTGTCATGATAAATTGCAATGACACTTGAAGATGTCATAATTTTATT
Found at i:3376 original size:55 final size:55
Alignment explanation
Indices: 3292--3395 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
3282 GCAATAGACA
3292 CTTGAAGATGTCATAATTTTATTCAATTGACACCAAAAGTTGTCATGATAAATTT
1 CTTGAAGATGTCATAATTTTATTCAATTGACACCAAAAGTTGTCATGATAAATTT
*
3347 CTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGAT
1 CTTGAAGATGTCATAATTTTATTCAATTGACACCAAAAGTTGTCATGAT
3396 TTTACCTTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (55 bp):
CTTGAAGATGTCATAATTTTATTCAATTGACACCAAAAGTTGTCATGATAAATTT
Done.