Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001833.1 Corchorus capsularis cultivar CVL-1 contig01834, 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, 883
Length: 1473
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Found at i:73 original size:22 final size:22
Alignment explanation
Indices: 48--144 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 22
38 TATTCATACG
48 AAATTATGATAATCTTCCTATT
1 AAATTATGATAATCTTCCTATT
*
70 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCTTC-CTATT
*
92 ---TT-TTATAA-CTTCCTTATT
1 AAATTATGATAATCTTCC-TATT
* * * *
110 AAATTTTGATAACCTTCCCATG
1 AAATTATGATAATCTTCCTATT
132 AAATTATGATAAT
1 AAATTATGATAAT
145 TACACTATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
17 1 0.02
18 11 0.19
19 2 0.03
21 4 0.07
22 36 0.61
23 5 0.08
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.44
Consensus pattern (22 bp):
AAATTATGATAATCTTCCTATT
Found at i:145 original size:62 final size:62
Alignment explanation
Indices: 47--198 Score: 241
Period size: 62 Copynumber: 2.5 Consensus size: 62
37 ATATTCATAC
* * * *
47 GAAATTATGATAATCTTCCTATTAAATTATGATAATTACACTATTTTTTATAACTTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
* * *
109 TAAATTTTGATAACCTTCCCATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
171 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
199 TAAATAAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 81 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.44
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
Found at i:193 original size:22 final size:21
Alignment explanation
Indices: 168--683 Score: 222
Period size: 22 Copynumber: 23.6 Consensus size: 21
158 ATGACGTCCT
168 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
** ** *
190 TATGAAATTTAAATAAAGATAC
1 TATGAAATTTTGAT-AACCTCC
* * **
212 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACC-TCC
** *
234 TAT-AAATTTTTTTTAACCTTTC
1 TATGAAA-TTTTGATAACC-TCC
*
256 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* *
278 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTC-C
* **
300 TATGATATTTTGATAATTTCC
1 TATGAAATTTTGATAACCTCC
* **
321 AAATGAAATTTTGATAATCAACAC
1 -TATGAAATTTTGATAA-CCTC-C
*
345 TAT-AAGATGTTGATAACCTCC
1 TATGAA-ATTTTGATAACCTCC
* * * *
366 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
389 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
410 ATATG-AATTGTCAGTAATCACAC
1 -TATGAAATTTTGA-TAACCTC-C
* * *
433 TTTGAAATTTTGATAATCGCAC
1 TATGAAATTTTGATAACCTC-C
*
455 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
477 TACGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACC-TCC
* *
500 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCT-CC
* *
523 TATAAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTC-C
*
545 TATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
*
562 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
583 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
605 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
627 TATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACCTCC
* *
649 TATAAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
671 TATGAAATTTTGA
1 TATGAAATTTTGA
684 AAACTGTCGT
Statistics
Matches: 367, Mismatches: 94, Indels: 66
0.70 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
21 21 0.06
22 264 0.72
23 66 0.18
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:1222 original size:22 final size:22
Alignment explanation
Indices: 1170--1290 Score: 120
Period size: 22 Copynumber: 5.5 Consensus size: 22
1160 GGTCACATTT
* * *
1170 TGAAAATTTAATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
1192 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
1214 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
1236 TGAAATTTTGATAATCC-CAT-TA
1 TGAAATTTTGATAA-CCTC-TCTA
* * *
1258 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
1280 TGAAATTTTGA
1 TGAAATTTTGA
1291 AATTGGACCA
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
21 2 0.02
22 76 0.94
23 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:1400 original size:38 final size:37
Alignment explanation
Indices: 1355--1441 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
1345 CCCAAATAGG
* * *
1355 ACGTTGGAGACGAAGACAAAAAATAAAATTAAATACA
1 ACGTTGGAAACAAAGACAAAAAACAAAATTAAATACA
* *
1392 ACGATTGGAAACAAAGACAAAAGACAAAATTAAATAGA
1 ACG-TTGGAAACAAAGACAAAAAACAAAATTAAATACA
1430 ACGTTGGAAACA
1 ACGTTGGAAACA
1442 GGAAATCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 12 0.27
38 32 0.73
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.15
Consensus pattern (37 bp):
ACGTTGGAAACAAAGACAAAAAACAAAATTAAATACA
Done.