Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021569.1 Corchorus olitorius cultivar O-4 contig21602, 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: 13317
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1390 original size:2 final size:2
Alignment explanation
Indices: 1383--1416 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1373 TACTTTCATT
1383 TA TA 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 TA TA
1417 ACACAACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7387 original size:40 final size:40
Alignment explanation
Indices: 7342--7422 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
7332 ATTGTTTGCC
*
7342 TAATGCCAATGTCTGTTTTATTCTGAAACTTTGTTTATCA
1 TAATGCCAATGTCTGTTTTATTCTGAAACTTTGTCTATCA
*
7382 TAATGCTAATGTCTGTTTTATTCTGAAACTTTGTCTATCA
1 TAATGCCAATGTCTGTTTTATTCTGAAACTTTGTCTATCA
7422 T
1 T
7423 TATCTTCTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (40 bp):
TAATGCCAATGTCTGTTTTATTCTGAAACTTTGTCTATCA
Found at i:8130 original size:20 final size:21
Alignment explanation
Indices: 8095--8135 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
8085 ATGAACAAAG
*
8095 ATAGATAAATAGCACAGGGCT
1 ATAGAGAAATAGCACAGGGCT
8116 ATAGAGAAA-AGCACAGGGCT
1 ATAGAGAAATAGCACAGGGCT
8136 TTGGTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.15
Consensus pattern (21 bp):
ATAGAGAAATAGCACAGGGCT
Found at i:8748 original size:15 final size:16
Alignment explanation
Indices: 8728--8764 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
8718 TTGAAGGATA
8728 TTTAAG-AATGTATTT
1 TTTAAGTAATGTATTT
*
8743 TTTAAGTAATTTATTT
1 TTTAAGTAATGTATTT
8759 TTTAAG
1 TTTAAG
8765 GATATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTAAGTAATGTATTT
Found at i:8772 original size:15 final size:15
Alignment explanation
Indices: 8728--8772 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
8718 TTGAAGGATA
*
8728 TTTAAGAATGTATTT
1 TTTAAGAATATATTT
*
8743 TTTAAGTAATTTATTT
1 TTTAAG-AATATATTT
*
8759 TTTAAGGATATATT
1 TTTAAGAATATATT
8773 ATGATGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (15 bp):
TTTAAGAATATATTT
Found at i:8841 original size:18 final size:19
Alignment explanation
Indices: 8804--8842 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
8794 TTATGTTTGG
*
8804 AAACAAGTATACACATACA
1 AAACAAATATACACATACA
*
8823 AAACAAATA-ACAGATACA
1 AAACAAATATACACATACA
8841 AA
1 AA
8843 CAGATTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.64, C:0.18, G:0.05, T:0.13
Consensus pattern (19 bp):
AAACAAATATACACATACA
Found at i:9951 original size:41 final size:41
Alignment explanation
Indices: 9864--10192 Score: 414
Period size: 41 Copynumber: 7.8 Consensus size: 41
9854 CAATAGCCAA
* * * *
9864 AAAGTCCCCAAACACATATATAACACTGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-T-C
*
9907 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
9948 AAAGTCCCCAAACACATATATAACACATGA--CAACTCTACTA-C
1 AAAGTCCCCAAACACATATATAACACA-GAGGC-A-TCTA-TATC
*
9990 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
*
10031 AAAGTCCCCAAACACATATATAACACAGGGGCAAATCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC--ATCTATAT-C
* *
10074 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
* *
10115 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-T-C
*
10158 AAAAGTCCTCAAACACATATATAACACAGAGGCAT
1 -AAAGTCCCCAAACACATATATAACACAGAGGCAT
10193 TTCTCCTTAT
Statistics
Matches: 254, Mismatches: 18, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
40 3 0.01
41 106 0.42
42 38 0.15
43 75 0.30
44 32 0.13
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
Found at i:9959 original size:84 final size:84
Alignment explanation
Indices: 9864--10192 Score: 561
Period size: 84 Copynumber: 3.9 Consensus size: 84
9854 CAATAGCCAA
* * *
9864 AAAGTCCCCAAACACATATATAACACTGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
9929 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
* * *
9948 AAAGTCCCCAAACACATATATAACACA-TGACAACTCTACTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
10012 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
10031 AAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
10096 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
*
10115 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
10180 AACACAGAGGCAT
65 AACACAGAGGCAT
10193 TTCTCCTTAT
Statistics
Matches: 230, Mismatches: 13, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
83 78 0.34
84 118 0.51
85 34 0.15
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:10140 original size:167 final size:169
Alignment explanation
Indices: 9864--10192 Score: 563
Period size: 167 Copynumber: 2.0 Consensus size: 169
9854 CAATAGCCAA
* ** *
9864 AAAGTCCCCAAACACATATATAACACTGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTCAAACACATATATA
*
9929 ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACA-TGACAACTCTACTAC-AA
66 ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGGGACAACTCTACTACAAA
9992 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
131 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
10031 AAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTCAAACACATATATA
* * * *
10096 ACACAGAGGCATTTATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAA
66 ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGGGACAACTCTACTACAAA
10161 AGTCCTCAAACACATATATAACACAGAGGCAT
131 AGTCCTCAAACACATATATAACACAGAGGCAT
10193 TTCTCCTTAT
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
167 106 0.70
168 11 0.07
169 34 0.23
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (169 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAAATCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGGGACAACTCTACTACAAA
AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
Done.