Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004369.1 Corchorus capsularis cultivar CVL-1 contig04377, 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, 792
Length: 1320
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Found at i:774 original size:19 final size:18
Alignment explanation
Indices: 735--774 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
725 GTCCTTTCCC
**
735 TTTTTTTATCATTTTTTT
1 TTTTTTTATCATTTTCAT
753 TTTTTTTAATCATTTTCAT
1 TTTTTTT-ATCATTTTCAT
772 TTT
1 TTT
775 CCTCCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTATCATTTTCAT
Found at i:1079 original size:30 final size:30
Alignment explanation
Indices: 1045--1296 Score: 195
Period size: 30 Copynumber: 8.4 Consensus size: 30
1035 TTTGATTTCA
1045 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
1075 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
**
1105 TTCTATTTCATTATATGGTATTATGTAATT
1 TTCTATTTCATTATATGGTATTACATAATT
* * *
1135 TT-GATTTCATTCTAT-G--TT-CATTATT
1 TTCTATTTCATTATATGGTATTACATAATT
** * * * * *
1160 ATGGTATTACATAATTTTG-ATT---TCA--
1 -TTCTATTTCATTATATGGTATTACATAATT
1185 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
1215 TTCTATGTTCATTTATATGGTATTTACATAATTTGT
1 TTCTAT-TTCA-TTATATGGTA-TTACATAA--T-T
*
1251 CATTCTTATGTTCATTATATGATATTACATAATT
1 --TTC-TAT-TTCATTATATGGTATTACATAATT
1285 TT-TGATTTCATT
1 TTCT-ATTTCATT
1297 CTATTTCATT
Statistics
Matches: 180, Mismatches: 22, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
24 12 0.07
25 7 0.04
26 3 0.02
27 10 0.06
28 4 0.02
29 13 0.07
30 73 0.41
31 6 0.03
32 12 0.07
33 8 0.04
34 1 0.01
35 2 0.01
36 1 0.01
37 8 0.04
38 12 0.07
39 8 0.04
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (30 bp):
TTCTATTTCATTATATGGTATTACATAATT
Found at i:1126 original size:15 final size:15
Alignment explanation
Indices: 1048--1126 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
1038 GATTTCATTC
1048 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
1063 TATTACATAATTTTC
1 TATTTCATTATATGG
1078 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
1093 TATTACATAATTTTC
1 TATTTCATTATATGG
1108 TATTTCATTATATGG
1 TATTTCATTATATGG
1123 TATT
1 TATT
1127 ATGTAATTTT
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (15 bp):
TATTTCATTATATGG
Found at i:1168 original size:41 final size:39
Alignment explanation
Indices: 1105--1318 Score: 225
Period size: 41 Copynumber: 5.6 Consensus size: 39
1095 TTACATAATT
**
1105 TTCTATTTCATTATATGGTATTATGTAATTTTGATTTCA
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
1144 TTCTATGTTCATTATTATGGTATTACATAATTTTGATTTCA
1 TTCTAT-TTCATTA-TATGGTATTACATAATTTTGATTTCA
* * *
1185 TTCTATTTCATTATATGGTATTACATAATTTT-CTAT-G
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
1222 TTC-A--T--TTATATGGTATTTACATAA-TTTG---TCA
1 TTCTATTTCATTATATGGTA-TTACATAATTTTGATTTCA
*
1253 TTCTTATGTTCATTATATGATATTACATAATTTTTGATTTCA
1 TTC-TAT-TTCATTATATGGTATTACATAA-TTTTGATTTCA
1295 TTCTATTTCATTTATATGGGTATT
1 TTCTATTTCA-TTATAT-GGTATT
1319 TT
Statistics
Matches: 148, Mismatches: 8, Indels: 35
0.77 0.04 0.18
Matches are distributed among these distances:
30 1 0.01
31 3 0.02
32 13 0.09
33 9 0.06
34 1 0.01
36 2 0.01
37 11 0.07
38 11 0.07
39 29 0.20
40 18 0.12
41 39 0.26
42 11 0.07
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (39 bp):
TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
Found at i:1261 original size:110 final size:108
Alignment explanation
Indices: 1075--1318 Score: 359
Period size: 110 Copynumber: 2.2 Consensus size: 108
1065 TTACATAATT
**
1075 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTATGTAATTTTGAT
1 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTACATAATTTTG--
*
1140 TTCATTCTATGTTCATTATTATGGTATTACATAA-TTTTGATTTCA
64 TTCATTCTATGTTCATTA-TATGATATTACATAATTTTTGATTTCA
1185 TTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTTATATGGTATTTACATAA-TTT
1 TTCTATTTCATTATATGGTATTACATAATTTTCTAT-TTCA-TTATATGGTA-TTACATAATTTT
1249 G-TCATTCTTATGTTCATTATATGATATTACATAATTTTTGATTTCA
63 GTTCATTC-TATGTTCATTATATGATATTACATAATTTTTGATTTCA
1295 TTCTATTTCATTTATATGGGTATT
1 TTCTATTTCA-TTATAT-GGTATT
1319 TT
Statistics
Matches: 124, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
109 20 0.16
110 68 0.55
111 10 0.08
112 20 0.16
113 6 0.05
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (108 bp):
TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTACATAATTTTGTT
CATTCTATGTTCATTATATGATATTACATAATTTTTGATTTCA
Found at i:1296 original size:140 final size:139
Alignment explanation
Indices: 1025--1284 Score: 368
Period size: 140 Copynumber: 1.9 Consensus size: 139
1015 CATAATTACA
1025 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATA
1 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATA
* * ** *
1090 TGGTATTACATAATTTTCTATTTCATTATATGGTATTATGTAATTTTGATTTCATTCTATGTTCA
66 TGGTATTACATAATTTTCTATTTCA-TATATGGTATTATATAATATTGACATAATTCTATGTTCA
1155 TTATTATGGT
130 TTATTATGGT
1165 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTTA
1 ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTAT-TTCA-TTA
* *
1230 TATGGTATTTACATAATTTGTC-A-TTC-T-TATGTTCATTATATGATATT-ACATAATT
64 TATGGTA-TTACATAATTT-TCTATTTCATATATGGT-ATTATATAATATTGACATAATT
1285 TTTGATTTCA
Statistics
Matches: 108, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
139 10 0.09
140 67 0.62
141 4 0.04
142 13 0.12
143 12 0.11
144 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (139 bp):
ATTACATAATTTTGATTTCATTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATA
TGGTATTACATAATTTTCTATTTCATATATGGTATTATATAATATTGACATAATTCTATGTTCAT
TATTATGGT
Done.