Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011167.1 Corchorus capsularis cultivar CVL-1 contig11188, 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: 10677
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6338 original size:22 final size:22
Alignment explanation
Indices: 6296--6339 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6286 TATTTATATG
* *
6296 AAATTATGATAATTTCCTTATT
1 AAATTATGATAATTACATTATT
*
6318 AAATTATGATGATTACATTATT
1 AAATTATGATAATTACATTATT
6340 TTTTATGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
AAATTATGATAATTACATTATT
Found at i:6652 original size:22 final size:22
Alignment explanation
Indices: 6354--6821 Score: 130
Period size: 22 Copynumber: 21.8 Consensus size: 22
6344 ATGAGATCCT
* *
6354 TATGAAATTTTGATAAACTTCC
1 TATGAAATTTTGATAACCTCCC
* * *
6376 TATGAAATTTTAATAACGAT-AC
1 TATGAAATTTTGATAAC-CTCCC
* * * ***
6398 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCCC
* * ** * *
6420 TATTAATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTCCC
* *
6442 TATGAAAATTTGTTAACCT-CC
1 TATGAAATTTTGATAACCTCCC
* * **
6463 TAAGGAATTTTGA-ACACCTCAT
1 TATGAAATTTTGATA-ACCTCCC
* * *
6485 TTTGAAA-TTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCCC
* * *
6507 TATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * * **
6529 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCC
* * * *
6551 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * *
6573 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAACCTCCC
* * * *
6595 TCTAAAATTTTGAT-A-CACAC
1 TATGAAATTTTGATAACCTCCC
* * **
6615 TATGAAATTGTAATAACCTCGT
1 TATGAAATTTTGATAACCTCCC
* *
6637 TATGAAATTTTGATAAACATTCC
1 TATGAAATTTTGAT-AACCTCCC
* *
6660 TATAAAATTTTGATAAACTTCCC
1 TATGAAATTTTGAT-AACCTCCC
* *
6683 TATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCC
*
6705 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTCCC
* *
6722 TA-CAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCTCCC
* ** **
6743 TATG--ATTTT-TTTGCCTCAT
1 TATGAAATTTTGATAACCTCCC
* *
6762 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
*
6784 TATGAAATTTTGAT---CTACAC
1 TATGAAATTTTGATAACCT-CCC
6804 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
6822 CTCTTATAAT
Statistics
Matches: 320, Mismatches: 99, Indels: 53
0.68 0.21 0.11
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
19 10 0.03
20 37 0.12
21 37 0.12
22 169 0.53
23 54 0.17
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:6667 original size:23 final size:23
Alignment explanation
Indices: 6641--6720 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
6631 CCTCGTTATG
6641 AAATTTTGATAAACATT-CCTATA
1 AAATTTTGATAAAC-TTCCCTATA
6664 AAATTTTGATAAACTTCCCTATA
1 AAATTTTGATAAACTTCCCTATA
* * *
6687 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAACTTCCCTATA
*
6709 AAATCTTGATAA
1 AAATTTTGATAA
6721 CTACAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.39
23 31 0.61
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACTTCCCTATA
Found at i:6832 original size:20 final size:20
Alignment explanation
Indices: 6809--6878 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
6799 TACACTATGA
6809 AATTTTGATAACCCTCTTAT
1 AATTTTGATAACCCTCTTAT
* *** * *
6829 AATTTTGAAAACTAAACTAAAA
1 AATTTTGATAAC-CCTCT-TAT
6851 AATTTTGATAACCCTCTTAT
1 AATTTTGATAACCCTCTTAT
6871 AATTTTGA
1 AATTTTGA
6879 AAACTAAACT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
20 20 0.56
21 4 0.11
22 12 0.33
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (20 bp):
AATTTTGATAACCCTCTTAT
Found at i:6854 original size:42 final size:42
Alignment explanation
Indices: 6808--6905 Score: 196
Period size: 42 Copynumber: 2.3 Consensus size: 42
6798 CTACACTATG
6808 AAATTTTGATAACCCTCTTATAATTTTGAAAACTAAACTAAA
1 AAATTTTGATAACCCTCTTATAATTTTGAAAACTAAACTAAA
6850 AAATTTTGATAACCCTCTTATAATTTTGAAAACTAAACTAAA
1 AAATTTTGATAACCCTCTTATAATTTTGAAAACTAAACTAAA
6892 AAATTTTGATAACC
1 AAATTTTGATAACC
6906 TTCATATGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (42 bp):
AAATTTTGATAACCCTCTTATAATTTTGAAAACTAAACTAAA
Found at i:6857 original size:22 final size:22
Alignment explanation
Indices: 6829--6900 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
6819 ACCCTCTTAT
6829 AATTTTGAAAACTAAACTAAAA
1 AATTTTGAAAACTAAACTAAAA
* *** * *
6851 AATTTTGATAAC-CCTCT-TAT
1 AATTTTGAAAACTAAACTAAAA
6871 AATTTTGAAAACTAAACTAAAA
1 AATTTTGAAAACTAAACTAAAA
6893 AATTTTGA
1 AATTTTGA
6901 TAACCTTCAT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
20 12 0.33
21 4 0.11
22 20 0.56
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.35
Consensus pattern (22 bp):
AATTTTGAAAACTAAACTAAAA
Found at i:7151 original size:22 final size:22
Alignment explanation
Indices: 7116--7197 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
7106 TTGACCCCTC
7116 TATGAAA-TTTGATAATAACAT
1 TATGAAATTTTGATAATAACAT
* **
7137 TATGTAATTTTGATAACCTTGC-T
1 TATGAAATTTTGATAA--TAACAT
* *
7160 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAATAACAT
7181 TATGAAATTTTGATAAT
1 TATGAAATTTTGATAAT
7198 CTTCCTATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.02
21 7 0.15
22 35 0.74
23 2 0.04
24 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATAACAT
Found at i:7205 original size:22 final size:22
Alignment explanation
Indices: 7137--7550 Score: 203
Period size: 22 Copynumber: 18.6 Consensus size: 22
7127 ATAATAACAT
* *
7137 TATGTAATTTTGATAACCTTGC
1 TATGAAATTTTGATAACCTTCC
* **
7159 TTTGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAACCTTC-C
*
7181 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTCC
* *
7203 TAT-AAATTTTAATAATCCGATCTC
1 TATGAAATTTTGATAA-CC-TTC-C
* *
7227 TATAAAATTTCGATAATCAC-T-C
1 TATGAAATTTTGATAA-C-CTTCC
* *
7249 TGTGAGA-TTTGATAACCTT-C
1 TATGAAATTTTGATAACCTTCC
* * *
7269 TATCAATTTTTGGT-A-C-TCC
1 TATGAAATTTTGATAACCTTCC
* *
7288 TCATGAAATTGAGACTTTTATAACCTTCA
1 T-ATGAAA-T-----TTTGATAACCTTCC
*
7317 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTCC
* * *
7339 TATAAAATTGTGATAACC-ACAC
1 TATGAAATTTTGATAACCTTC-C
**
7361 TATGAAATTTCAATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *
7383 TAAGAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACCT--TCC
* *
7407 TATGAAATTTTGGTAACAC--AC
1 TATGAAATTTTGATAAC-CTTCC
*
7428 TATGAAATTTTGATTACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
7450 CATGAAATTTTG-TAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* *
7470 ATATGAAATTTTGGTAACC-ACAC
1 -TATGAAATTTTGATAACCTTC-C
*
7493 TATGGAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
7514 TCATGAAATTATAATGACCATCT
1 T-ATGAAATTTTGATAACCTTCC
7537 TATGAAATTTTGAT
1 TATGAAATTTTGAT
7551 TACAACATAG
Statistics
Matches: 297, Mismatches: 62, Indels: 66
0.70 0.15 0.16
Matches are distributed among these distances:
18 1 0.00
19 4 0.01
20 17 0.06
21 56 0.19
22 157 0.53
23 10 0.03
24 22 0.07
25 13 0.04
26 5 0.02
27 2 0.01
28 7 0.02
29 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Done.