Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012685.1 Corchorus olitorius cultivar O-4 contig12718, 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: 6818
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1206 original size:205 final size:198
Alignment explanation
Indices: 828--1235 Score: 681
Period size: 205 Copynumber: 2.0 Consensus size: 198
818 GCTTAATAAC
828 TTTATAAATGGTGAATGTTATTAGTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATAAATGGTGAATGTTATTAGTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
893 GATACAACACATTATTATTATTATATATAACTATACCAAAAGTAGTTGAACATTAGTGGTTGATT
66 GATACAACACATTACTATTATTATATAGAACTATACCAAAAGTAGTTGAACATTAGTGGTTGATT
*
958 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
131 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCCA
1023 TTTA
195 TTTA
* *
1027 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATAAATGGTGAATGTTATT-AGTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
1092 AGATACAACACATTACTATTATGTATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
65 AGATACAACACATTACTATTAT-TATATAGAACTATACC----AAAAGTAGTTGAACATTAGTGG
* *
1157 TTGATTTATTATATTAAATTAGATCAATGTCAAACAAAATTTGAAAATTATAAAAGATATTAAGA
125 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
1222 TCCCATTTA
190 TCCCATTTA
1231 TTTAT
1 TTTAT
1236 TATTAAGGAA
Statistics
Matches: 195, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
199 21 0.11
200 62 0.32
201 15 0.08
204 17 0.09
205 80 0.41
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (198 bp):
TTTATAAATGGTGAATGTTATTAGTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATTATATAGAACTATACCAAAAGTAGTTGAACATTAGTGGTTGATT
TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCCAT
TTA
Found at i:1399 original size:39 final size:40
Alignment explanation
Indices: 1345--1425 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
1335 ATGCCTAAGA
*
1345 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
1384 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
1424 AT
1 AT
1426 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2211 original size:38 final size:38
Alignment explanation
Indices: 2169--2245 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2159 ATGAAAAAAG
* *
2169 TTATATATTTATCAAAAAATTTAAAACCATTTATTATA
1 TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
2207 TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
1 TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
2245 T
1 T
2246 CATTTGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (38 bp):
TTATATATTTACCAAAAAATTTAAAACCATTCATTATA
Found at i:3160 original size:22 final size:22
Alignment explanation
Indices: 3112--3171 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
3102 GCTCCAACAT
**
3112 AGAAA-TTTGAATAACCACACTG
1 AGAAATTTTG-ATAACCACACAA
*
3134 TGAAATTTTGATAACCACACAA
1 AGAAATTTTGATAACCACACAA
3156 AGAAATTTTGATAACC
1 AGAAATTTTGATAACC
3172 TTAGTGTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (22 bp):
AGAAATTTTGATAACCACACAA
Found at i:3471 original size:22 final size:22
Alignment explanation
Indices: 3443--3635 Score: 142
Period size: 22 Copynumber: 8.8 Consensus size: 22
3433 ATTTCCTCCC
*
3443 TATGAAATTTTGTTAACCTTCT
1 TATGAAATTTTGATAACCTTCT
* * *
3465 TATGAAATTTTGGTAACC-ACAC
1 TATGAAATTTTGATAACCTTC-T
* * *
3487 TATAAAATTTTGATAACTTTCG
1 TATGAAATTTTGATAACCTTCT
* * *
3509 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCT
* * *
3531 TAAGAAATTTGGATAACCTTTT
1 TATGAAATTTTGATAACCTTCT
* *
3553 TATGAAATCTTGGTAACC-TCT
1 TATGAAATTTTGATAACCTTCT
*
3574 ATGTGAAATTTTGATAA-CTATAC-
1 -TATGAAATTTTGATAACCT-T-CT
* *
3597 TATGAAGTTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCT
* *
3619 TACGAAATTTTGTTAAC
1 TATGAAATTTTGATAAC
3636 AATACTATTA
Statistics
Matches: 131, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
21 5 0.04
22 121 0.92
23 4 0.03
24 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:3571 original size:44 final size:44
Alignment explanation
Indices: 3437--3635 Score: 161
Period size: 44 Copynumber: 4.5 Consensus size: 44
3427 TGATAAATTT
* * *
3437 CCTCCCTATGAAATTTTGTTAACCTTCTTATGAAATTTTGGTAA
1 CCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGGTAA
* * * *
3481 CCACACTATA-AAATTTTGATAA-CTTTCGTATGAAATTTTGTTAA
1 CCTCCCTA-AGAAATTTTGATAACCTTT-TTATGAAATTTTGGTAA
* *
3525 CCTCCCTAAGAAATTTGGATAACCTTTTTATGAAATCTTGGTAA
1 CCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGGTAA
** ** ** * *
3569 CCTCTATGTGAAATTTTGATAA-CTATACTATGAAGTTTTGATAA
1 CCTCCCTAAGAAATTTTGATAACCT-TTTTATGAAATTTTGGTAA
* * * *
3613 CCTTCATACGAAATTTTGTTAAC
1 CCTCCCTAAGAAATTTTGATAAC
3636 AATACTATTA
Statistics
Matches: 121, Mismatches: 28, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
43 6 0.05
44 111 0.92
45 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (44 bp):
CCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGGTAA
Found at i:3586 original size:88 final size:88
Alignment explanation
Indices: 3437--3615 Score: 227
Period size: 88 Copynumber: 2.0 Consensus size: 88
3427 TGATAAATTT
* * * *
3437 CCTCCCTATGAAATTTTGTTAACCTTCTTATGAAATTTTGGTAACCACACTATAAAATTTTGATA
1 CCTCCCTAAGAAATTTGGATAACCTTCTTATGAAATCTTGGTAACCACACTATAAAATTTTGATA
* *
3502 ACT-TTCGTATGAAATTTTGTTAA
66 ACTATAC-TATGAAATTTTGATAA
* * * *
3525 CCTCCCTAAGAAATTTGGATAACCTTTTTATGAAATCTTGGTAACCTCTA-TGTGAAATTTTGAT
1 CCTCCCTAAGAAATTTGGATAACCTTCTTATGAAATCTTGGTAACCAC-ACTATAAAATTTTGAT
*
3589 AACTATACTATGAAGTTTTGATAA
65 AACTATACTATGAAATTTTGATAA
3613 CCT
1 CCT
3616 TCATACGAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
88 75 0.96
89 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (88 bp):
CCTCCCTAAGAAATTTGGATAACCTTCTTATGAAATCTTGGTAACCACACTATAAAATTTTGATA
ACTATACTATGAAATTTTGATAA
Found at i:3674 original size:44 final size:44
Alignment explanation
Indices: 3491--3661 Score: 114
Period size: 44 Copynumber: 3.9 Consensus size: 44
3481 CCACACTATA
* * * * * * *
3491 AAATTTTGATAAC-TTTCGTATGAAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACAATAC-TATGAAATTTGGATAACCTTCATACG
* ** ** **
3535 AAATTTGGATAACCTTTTTATGAAATCTTGG-TAACC-TCTATGTG
1 AAATTTTGATAACAATACTATGAAAT-TTGGATAACCTTC-ATACG
* * *
3579 AAATTTTGATAACTATACTATGAAGTTTTGATAACCTTCATACG
1 AAATTTTGATAACAATACTATGAAATTTGGATAACCTTCATACG
* * *
3623 AAATTTTGTTAACAATACTATTAAATTTGGATAGCCTTC
1 AAATTTTGATAACAATACTATGAAATTTGGATAACCTTC
3662 CTATGTAATT
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
43 4 0.04
44 88 0.88
45 8 0.08
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAACAATACTATGAAATTTGGATAACCTTCATACG
Done.