Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011239.1 Corchorus olitorius cultivar O-4 contig11272, 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: 29567
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1699 original size:11 final size:11
Alignment explanation
Indices: 1683--1717 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1673 TTTTTCTGTT
1683 TTTTGTTTTTG
1 TTTTGTTTTTG
*
1694 TTTTGTTTTCG
1 TTTTGTTTTTG
1705 TTTTGTTTTTG
1 TTTTGTTTTTG
1716 TT
1 TT
1718 GCGTTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:3030 original size:2 final size:2
Alignment explanation
Indices: 3023--3056 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3013 TACCTACAAA
3023 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3057 TCATACAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4494 original size:25 final size:25
Alignment explanation
Indices: 4459--4516 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
4449 AGATTCAAAA
*
4459 TCTATAGAAACATGAAAA-GATGTATT
1 TCTAT-GAAACATAAAAATG-TGTATT
*
4485 TCTATGAAACATAAAAATGTGTCTT
1 TCTATGAAACATAAAAATGTGTATT
4510 TCTATGA
1 TCTATGA
4517 GAGATTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (25 bp):
TCTATGAAACATAAAAATGTGTATT
Found at i:6041 original size:31 final size:31
Alignment explanation
Indices: 6006--6068 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
5996 AAGAAACTTG
* *
6006 ATGATCTTGGTTTCAAAGTTGAGTTTGATTC
1 ATGATCATGATTTCAAAGTTGAGTTTGATTC
6037 ATGATCATGATTTCAAAGTTGAGTTTGATTC
1 ATGATCATGATTTCAAAGTTGAGTTTGATTC
6068 A
1 A
6069 CAAAAAGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (31 bp):
ATGATCATGATTTCAAAGTTGAGTTTGATTC
Found at i:7914 original size:15 final size:15
Alignment explanation
Indices: 7894--7955 Score: 81
Period size: 15 Copynumber: 4.0 Consensus size: 15
7884 ATATCTTATC
7894 TTATTACTATTACTA
1 TTATTACTATTACTA
7909 TTATTACTATTACTA
1 TTATTACTATTACTA
7924 TTACTATTACTA-TACTA
1 -T--TATTACTATTACTA
*
7941 TTACTACTATTACTA
1 TTATTACTATTACTA
7956 CTATCTTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 7 0.17
15 20 0.48
16 2 0.05
17 5 0.12
18 8 0.19
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTACTATTACTA
Found at i:7955 original size:6 final size:6
Alignment explanation
Indices: 7895--7946 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
7885 TATCTTATCT
7895 TATTAC TATTAC TA-T-- TATTAC TATTAC TATTAC TATTAC TA-TAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
7939 TATTAC TA
1 TATTAC TA
7947 CTATTACTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 6 0.14
6 33 0.79
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAC
Found at i:7956 original size:9 final size:9
Alignment explanation
Indices: 7898--7959 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
7888 CTTATCTTAT
7898 TACTATTAC
1 TACTATTAC
*
7907 TATTATTAC
1 TACTATTAC
* * *
7916 TATTACTAT
1 TACTATTAC
7925 TACTATTAC
1 TACTATTAC
7934 TATACTATTAC
1 --TACTATTAC
7945 TACTATTAC
1 TACTATTAC
7954 TACTAT
1 TACTAT
7960 CTTATAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
9 36 0.80
11 9 0.20
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (9 bp):
TACTATTAC
Found at i:9796 original size:21 final size:21
Alignment explanation
Indices: 9770--9812 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9760 TCCTTCAATC
9770 ATGGCATTTGAGATGTGAAGA
1 ATGGCATTTGAGATGTGAAGA
9791 ATGGCATTTGAGATGTGAAGA
1 ATGGCATTTGAGATGTGAAGA
9812 A
1 A
9813 AGTAAGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (21 bp):
ATGGCATTTGAGATGTGAAGA
Found at i:22724 original size:19 final size:19
Alignment explanation
Indices: 22690--22730 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
22680 AATCTTCTCC
22690 AATTAGAGCTAATTGCAACA
1 AATTAGAGCTAATTGCAA-A
*
22710 AATTAGATC-AATTGCAAA
1 AATTAGAGCTAATTGCAAA
22728 AAT
1 AAT
22731 CAAAAACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (19 bp):
AATTAGAGCTAATTGCAAA
Found at i:25261 original size:3 final size:3
Alignment explanation
Indices: 25253--25287 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
25243 GTACTAGTAT
25253 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT
25288 GATAGTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 26 0.87
4 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25467 original size:22 final size:21
Alignment explanation
Indices: 25442--25561 Score: 78
Period size: 22 Copynumber: 5.5 Consensus size: 21
25432 AGAACCTATA
*
25442 TATGAAACTTTGTTAACTTCCC
1 TATGAAATTTTGTTAACTT-CC
*
25464 TATGAAATTTTGTTAGGCTTCC
1 TATGAAATTTTGTTA-ACTTCC
* **
25486 TATGAAATTTTGATAACCTTAA
1 TATGAAATTTTGTTAA-CTTCC
* * **
25508 TATTAAATTTTGATAACCACC
1 TATGAAATTTTGTTAACTTCC
* * *
25529 ATACGAAATTTTGATAACATCC
1 -TATGAAATTTTGTTAACTTCC
*
25551 TTATAAAATTT
1 -TATGAAATTT
25562 CAATAACATC
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.01
22 73 0.95
23 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGTTAACTTCC
Done.