Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018681.1 Corchorus olitorius cultivar O-4 contig18714, 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: 30470
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:6628 original size:2 final size:2
Alignment explanation
Indices: 6621--6690 Score: 64
Period size: 2 Copynumber: 38.0 Consensus size: 2
6611 TCATTTCTTA
*
6621 AT AT AT AT AT AT AT AT A- AT -T AA AT AT AT -T AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6659 AT CAG AT AT AT AT -T A- AT AT AT AT AT AT A- AT AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6691 TTATTTAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
1 7 0.12
2 48 0.86
3 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6648 original size:14 final size:16
Alignment explanation
Indices: 6618--6686 Score: 75
Period size: 18 Copynumber: 4.0 Consensus size: 16
6608 CGATCATTTC
6618 TTAATATATATATATA
1 TTAATATATATATATA
*
6634 TATAATTAAATATATTATA
1 T-TAA-TATATATA-TATA
*
6653 TATAATATCAGATATATA
1 T-TAATAT-ATATATATA
6671 TTAATATATATATATA
1 TTAATATATATATATA
6687 ATATTTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.20
17 9 0.20
18 14 0.31
19 13 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (16 bp):
TTAATATATATATATA
Found at i:6699 original size:11 final size:13
Alignment explanation
Indices: 6618--6723 Score: 55
Period size: 14 Copynumber: 8.2 Consensus size: 13
6608 CGATCATTTC
6618 TTAATATATATA-
1 TTAATATATATAT
6630 -T-ATATATA-AT
1 TTAATATATATAT
*
6640 TAAATATATTATAT
1 TTAATATA-TATAT
*
6654 ATAATATCAGATATAT
1 TTAATAT---ATATAT
6670 ATTAATATATATAT
1 -TTAATATATATAT
*
6684 ATAATAT-T-TAT
1 TTAATATATATAT
* *
6695 TTAAT-TCTTTAT
1 TTAATATATATAT
*
6707 ATTATTATATATAT
1 -TTAATATATATAT
6721 TTA
1 TTA
6724 TAATAATTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 25
0.68 0.08 0.24
Matches are distributed among these distances:
9 1 0.01
10 8 0.11
11 9 0.12
12 9 0.12
13 15 0.21
14 18 0.25
16 5 0.07
17 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (13 bp):
TTAATATATATAT
Found at i:6714 original size:8 final size:9
Alignment explanation
Indices: 6621--6718 Score: 53
Period size: 10 Copynumber: 10.9 Consensus size: 9
6611 TCATTTCTTA
6621 ATATATATAT
1 ATATATAT-T
6631 ATATATAATT
1 ATATAT-ATT
*
6641 AAATATATT
1 ATATATATT
*
6650 ATATATAAT
1 ATATATATT
*
6659 ATCAGATA-T
1 AT-ATATATT
*
6668 ATAT-TAAT
1 ATATATATT
6676 ATATATA-T
1 ATATATATT
6684 ATA-ATATT
1 ATATATATT
*
6692 -TATTTAATT
1 ATATAT-ATT
* *
6701 CTTTATATT
1 ATATATATT
6710 ATTATATAT
1 A-TATATAT
6719 ATTTATAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
7 7 0.10
8 12 0.17
9 23 0.33
10 25 0.36
11 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (9 bp):
ATATATATT
Found at i:11782 original size:15 final size:15
Alignment explanation
Indices: 11759--11824 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
11749 TATCATCCGT
*
11759 AATATATCCTTCAAA
1 AATAAATCCTTCAAA
*
11774 AATAAATCCTTTAAA
1 AATAAATCCTTCAAA
* *
11789 AGATACATTCTT---A
1 A-ATAAATCCTTCAAA
11802 AAT--ATCCTTCAAA
1 AATAAATCCTTCAAA
11815 AATAAATCCT
1 AATAAATCCT
11825 AGTGATGCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
10 5 0.12
12 2 0.05
13 6 0.15
15 19 0.47
16 8 0.20
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAAATCCTTCAAA
Found at i:16334 original size:417 final size:417
Alignment explanation
Indices: 15558--16391 Score: 1535
Period size: 417 Copynumber: 2.0 Consensus size: 417
15548 GGTGCTATAA
15558 ATTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGC
1 ATTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGC
*
15623 CTCCTTTTGGCTTTTTTTTGTCTTTTCACACTTTTCGGATGACTAAAAAGGCCCTCGATAAATTT
66 CTCCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTCGGATGACTAAAAAGGCCCTCGATAAATTT
15688 CCTCCCTTCTTTTCCTGCTGCCCATTTTTGTAATTTACTATTTCTATATTTATGATCAAGTGTGT
131 CCTCCCTTCTTTTCCTGCTGCCCATTTTTGTAATTTACTATTTCTATATTTATGATCAAGTGTGT
*
15753 TTTAATTAATCACATAATATTAATTGTGTGTGGATATTAGGATTTATCGGTTCAACTCCTCTGCC
196 TTTAATTAATCAC--AATATTAATTGTGTGTGGATATTAGGATTTATCAGTTCAACTCCTCTGCC
*
15818 GGAATTCCAAAGGATTGGTGCTATAAATGTATCTGCAATAATGATTGATTCATGGGTAAACTATT
259 GGAATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGATTGATTCATGGGTAAACTATT
15883 GACATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAACA
324 GACATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAACA
15948 ATTCTCTAAATTGGTTTCACATGGACTCC
389 ATTCTCTAAATTGGTTTCACATGGACTCC
*
15977 ATTAGTATATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGC
1 ATTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGC
* *
16042 CTCCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTT
66 CTCCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTCGGATGACTAAAAAGGCCCTCGATAAATTT
*
16107 CCTCCCTTACTTTTCCTGCTGCCCATTTTTGTAATTTACTATTTCTATATTTATGATTAAGTGTG
131 CCTCCCTT-CTTTTCCTGCTGCCCATTTTTGTAATTTACTATTTCTATATTTATGATCAAGTGTG
16172 TTTTAATTAATCAC-ATATTAATTGTGTGTGGATATTAGGATTTATCAGTTCAACTCCTCTGCCG
195 TTTTAATTAATCACAATATTAATTGTGTGTGGATATTAGGATTTATCAGTTCAACTCCTCTGCCG
*
16236 GAATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGGTTGATTCATGGGTAAACTATTG
260 GAATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGATTGATTCATGGGTAAACTATTG
* * *
16301 ACATTCCAGTTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGGGTTTTTTCTTCCCTAACAT
325 ACATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAACAA
16366 TTCTCTAAATTGGTTTCACATGGACT
390 TTCTCTAAATTGGTTTCACATGGACT
16392 TTATTCTGTT
Statistics
Matches: 403, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
417 200 0.50
419 134 0.33
420 69 0.17
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (417 bp):
ATTAGTAAATATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGC
CTCCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTCGGATGACTAAAAAGGCCCTCGATAAATTT
CCTCCCTTCTTTTCCTGCTGCCCATTTTTGTAATTTACTATTTCTATATTTATGATCAAGTGTGT
TTTAATTAATCACAATATTAATTGTGTGTGGATATTAGGATTTATCAGTTCAACTCCTCTGCCGG
AATTCCAAAGGATTGGTGCTATAAATATATCTGCAATAATGATTGATTCATGGGTAAACTATTGA
CATTCCAATTCTGTTTTCCTTTCGTCTTCATTTTTATTTGGGTGAGTTTTTTCTTCCCTAACAAT
TCTCTAAATTGGTTTCACATGGACTCC
Found at i:28053 original size:15 final size:16
Alignment explanation
Indices: 28033--28070 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
28023 AGGTTGACAG
28033 AAAACAATTAAAC-AA
1 AAAACAATTAAACTAA
*
28048 AAAACAATTAAACTAG
1 AAAACAATTAAACTAA
28064 AAAACAA
1 AAAACAA
28071 AACAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAACAATTAAACTAA
Done.