Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014127.1 Corchorus capsularis cultivar CVL-1 contig14148, 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: 27224
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:809 original size:12 final size:13
Alignment explanation
Indices: 781--809 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
771 AGTTAACCCG
781 AAAACTCTTTTCA
1 AAAACTCTTTTCA
794 AAAACTCTTTTCA
1 AAAACTCTTTTCA
807 AAA
1 AAA
810 GTTTTGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACTCTTTTCA
Found at i:1118 original size:12 final size:12
Alignment explanation
Indices: 1091--1138 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
1081 TTTTTTGGTG
*
1091 ATTTTTTTGATAT
1 ATTTTTTTTAT-T
1104 ATTTTTTTTATT
1 ATTTTTTTTATT
1116 ATTTATTTTTTAATT
1 A-TT-TTTTTT-ATT
1131 ATTTTTTT
1 ATTTTTTT
1139 ATTTGATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 2 0.06
13 17 0.55
14 8 0.26
15 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (12 bp):
ATTTTTTTTATT
Found at i:1124 original size:28 final size:26
Alignment explanation
Indices: 1093--1167 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 26
1083 TTTTGGTGAT
*
1093 TTTTTTGATATATTTTTTTTATTATTTA
1 TTTTTTGATATATTTTTTTTA-T-TTGA
*
1121 TTTTTTAAT-TA-TTTTTTTATTTGA
1 TTTTTTGATATATTTTTTTTATTTGA
1145 TTTTTTGATTGATGATTTTTTTT
1 TTTTTTGA-T-AT-ATTTTTTTT
1168 TGAAAATTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 8 0.21
27 3 0.08
28 9 0.23
29 7 0.18
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.75
Consensus pattern (26 bp):
TTTTTTGATATATTTTTTTTATTTGA
Found at i:1150 original size:15 final size:13
Alignment explanation
Indices: 1092--1138 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1082 TTTTTGGTGA
*
1092 TTTTTTTGA-TAT
1 TTTTTTTTATTAT
1104 ATTTTTTTTATTAT
1 -TTTTTTTTATTAT
1118 TTATTTTTTAATTAT
1 TT-TTTTTT-ATTAT
1133 TTTTTT
1 TTTTTT
1139 ATTTGATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.33
14 13 0.43
15 7 0.23
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTTTTATTAT
Found at i:1467 original size:14 final size:15
Alignment explanation
Indices: 1450--1489 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
1440 TCAAAAACCG
1450 TTTTTGAAAAACATTT
1 TTTTTGAAAAACA-TT
*
1466 TTTTTGAAAATCA-T
1 TTTTTGAAAAACATT
1480 TTTTTGAAAA
1 TTTTTGAAAA
1490 CCATGACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
16 12 0.52
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTTTGAAAAACATT
Found at i:1471 original size:16 final size:16
Alignment explanation
Indices: 1450--1484 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1440 TCAAAAACCG
1450 TTTTTGAAAAACATTT
1 TTTTTGAAAAACATTT
*
1466 TTTTTGAAAATCATTT
1 TTTTTGAAAAACATTT
1482 TTT
1 TTT
1485 GAAAACCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTTTGAAAAACATTT
Found at i:7236 original size:6 final size:6
Alignment explanation
Indices: 7225--7274 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
7215 TATCTAATGT
*
7225 GTGTAA GTGTAA --GTAA GTGTAA CTGTAA GTGTAA GTGTAA GTGTAA
1 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA
7271 GTGT
1 GTGT
7275 GTGATTTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 4 0.10
6 36 0.90
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (6 bp):
GTGTAA
Found at i:21059 original size:19 final size:18
Alignment explanation
Indices: 21035--21070 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21025 TGAAGATTTC
21035 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
21054 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
21071 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.