Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016618.1 Corchorus olitorius cultivar O-4 contig16651, 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: 4301
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:912 original size:11 final size:11
Alignment explanation
Indices: 898--935 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
888 ATTCATAACA
898 AATTTATAATT
1 AATTTATAATT
909 AATTTATAATT
1 AATTTATAATT
920 -ATTTGATAATT
1 AATTT-ATAATT
*
931 TATTT
1 AATTT
936 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:1128 original size:7 final size:7
Alignment explanation
Indices: 1096--1213 Score: 54
Period size: 7 Copynumber: 16.6 Consensus size: 7
1086 ATAGTAGGTT
1096 TAATTAA
1 TAATTAA
1103 TAAATTAAA
1 T-AATT-AA
1112 TAA-TAA
1 TAATTAA
1118 -AATTAA
1 TAATTAA
*
1124 TAATTAT
1 TAATTAA
1131 TAATT-A
1 TAATTAA
*
1137 TAACTCTTA
1 TAA-T-TAA
1146 -AATT-A
1 TAATTAA
1151 TGAA-TAA
1 T-AATTAA
1158 -AA-TAA
1 TAATTAA
1163 TAATTAA
1 TAATTAA
1170 TAATTAA
1 TAATTAA
1177 TAACCCTTAA
1 TAA---TTAA
1187 TAATCCTAA
1 TAAT--TAA
*
1196 TACTTAA
1 TAATTAA
*
1203 TACTTAA
1 TAATTAA
1210 TAAT
1 TAAT
1214 CCCAACTCTT
Statistics
Matches: 90, Mismatches: 4, Indels: 34
0.70 0.03 0.27
Matches are distributed among these distances:
5 8 0.09
6 12 0.13
7 44 0.49
8 9 0.10
9 10 0.11
10 7 0.08
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.39
Consensus pattern (7 bp):
TAATTAA
Found at i:1406 original size:21 final size:22
Alignment explanation
Indices: 1382--1428 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1372 GTCATGATCT
*
1382 GGTCACGACCATGCCAT-GTCC
1 GGTCACGACCACGCCATGGTCC
* *
1403 GGTCGCGATCACGCCATGGTCC
1 GGTCACGACCACGCCATGGTCC
1425 GGTC
1 GGTC
1429 TCGATCTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.15, C:0.36, G:0.30, T:0.19
Consensus pattern (22 bp):
GGTCACGACCACGCCATGGTCC
Found at i:1427 original size:22 final size:21
Alignment explanation
Indices: 1394--1434 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1384 TCACGACCAT
1394 GCCATGTCCGGTCGCGATCAC
1 GCCATGTCCGGTCGCGATCAC
*
1415 GCCATGGTCCGGTCTCGATC
1 GCCAT-GTCCGGTCGCGATC
1435 TGGTCGCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.37, G:0.29, T:0.22
Consensus pattern (21 bp):
GCCATGTCCGGTCGCGATCAC
Found at i:1454 original size:33 final size:33
Alignment explanation
Indices: 1403--1470 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
1393 TGCCATGTCC
* * *
1403 GGTCGCGATCACGCCATGGTCCGGTCTCGATCT
1 GGTCGCGACCACGCCATGGTCCGATCGCGATCT
* *
1436 GGTCGCGACCGCGGCATGGTCCGATCGCGATCT
1 GGTCGCGACCACGCCATGGTCCGATCGCGATCT
1469 GG
1 GG
1471 GCACAACACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.35, T:0.21
Consensus pattern (33 bp):
GGTCGCGACCACGCCATGGTCCGATCGCGATCT
Found at i:2540 original size:47 final size:48
Alignment explanation
Indices: 2488--2621 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 48
2478 TACATGCCTA
* * * *
2488 AAAATTTTGATAATCGCACTATCAAATTGTGATAACCTTC-TC-TTAAT
1 AAAATTTTGATAATCACACTATGAAATTTTAATAACCTTCGTCATT-AT
* *
2535 AAAATTTTGATAACCACACTATGAAATTTTAATAACC-ACGTCATTAT
1 AAAATTTTGATAATCACACTATGAAATTTTAATAACCTTCGTCATTAT
*
2582 AAAATTTTGATAATCAAACTATGAAATTTTAATAACCTTC
1 AAAATTTTGATAATCACACTATGAAATTTTAATAACCTTC
2622 CTATGAATTC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.01
47 71 0.95
48 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.37
Consensus pattern (48 bp):
AAAATTTTGATAATCACACTATGAAATTTTAATAACCTTCGTCATTAT
Found at i:2594 original size:25 final size:22
Alignment explanation
Indices: 2488--2618 Score: 91
Period size: 22 Copynumber: 5.7 Consensus size: 22
2478 TACATGCCTA
* *
2488 AAAATTTTGATAATCGCACTAT
1 AAAATTTTGATAACCACACTAT
* * * *
2510 CAAATTGTGATAACCTTCTCTTAAT
1 AAAATTTTGATAACC-ACAC-T-AT
2535 AAAATTTTGATAACCACACTAT
1 AAAATTTTGATAACCACACTAT
* * *
2557 GAAATTTTAATAACCACGTCATTAT
1 AAAATTTTGATAACCA---CACTAT
* *
2582 AAAATTTTGATAATCAAACTAT
1 AAAATTTTGATAACCACACTAT
* *
2604 GAAATTTTAATAACC
1 AAAATTTTGATAACC
2619 TTCCTATGAA
Statistics
Matches: 83, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
22 44 0.53
23 3 0.04
24 3 0.04
25 33 0.40
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAATTTTGATAACCACACTAT
Done.