Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010483.1 Corchorus capsularis cultivar CVL-1 contig10504, 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: 12633
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1264 original size:52 final size:52
Alignment explanation
Indices: 1203--1345 Score: 268
Period size: 52 Copynumber: 2.8 Consensus size: 52
1193 AAAAATTTTT
1203 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
1 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
1255 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
1 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
* *
1307 CATCAAGTTTTCAAAGTGTTCAATTTAAGTCTTTTCAAA
1 CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAA
1346 ACATTCAAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (52 bp):
CATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
Found at i:5650 original size:13 final size:14
Alignment explanation
Indices: 5621--5657 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5611 AGAGTCATGA
5621 TTTTCAAAAATGTT
1 TTTTCAAAAATGTT
*
5635 TTTTCAAGAATG-T
1 TTTTCAAAAATGTT
5648 TTTTCAAAAA
1 TTTTCAAAAA
5658 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (14 bp):
TTTTCAAAAATGTT
Found at i:5986 original size:6 final size:6
Alignment explanation
Indices: 5971--6003 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5961 TGCAAAAAAA
*
5971 AAAATC -AAATC AAAATC AAGATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
6004 AAATGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.67, C:0.15, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:7305 original size:16 final size:16
Alignment explanation
Indices: 7284--7314 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7274 TTTCAATTAA
*
7284 CTTCAATTCTTCAATC
1 CTTCAATGCTTCAATC
7300 CTTCAATGCTTCAAT
1 CTTCAATGCTTCAAT
7315 TTATATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (16 bp):
CTTCAATGCTTCAATC
Found at i:7356 original size:8 final size:8
Alignment explanation
Indices: 7334--7580 Score: 124
Period size: 8 Copynumber: 32.0 Consensus size: 8
7324 AATAATCTTT
7334 TTCTTCAA
1 TTCTTCAA
* *
7342 CTATTCAA
1 TTCTTCAA
*
7350 TGCTTCAA
1 TTCTTCAA
* *
7358 ATCTTCCA
1 TTCTTCAA
*
7366 TTATTCAA
1 TTCTTCAA
7374 TTCTTCAA
1 TTCTTCAA
*
7382 TACTTCAA
1 TTCTTCAA
7390 -T-TT--A
1 TTCTTCAA
7394 TCTCTTCAA
1 T-TCTTCAA
* *
7403 CTCTTTAA
1 TTCTTCAA
* *
7411 CTATTCAA
1 TTCTTCAA
* *
7419 CTCTTTAA
1 TTCTTCAA
* *
7427 CTATTCAA
1 TTCTTCAA
**
7435 CACTTCAA
1 TTCTTCAA
7443 -T-TT--A
1 TTCTTCAA
7447 TCTCTTCAA
1 T-TCTTCAA
* *
7456 CTCTTTAA
1 TTCTTCAA
*
7464 TTATTCAA
1 TTCTTCAA
7472 TTCTTCAA
1 TTCTTCAA
7480 TTCTTCAA
1 TTCTTCAA
7488 TTCTTCAA
1 TTCTTCAA
7496 TTCTTCAA
1 TTCTTCAA
*
7504 TACTTCAA
1 TTCTTCAA
*
7512 -T-TT-AT
1 TTCTTCAA
7517 TTCTTCAA
1 TTCTTCAA
7525 TTCTTCAA
1 TTCTTCAA
* *
7533 TTATT-TA
1 TTCTTCAA
7540 TTGCTTCAA
1 TT-CTTCAA
*
7549 TTTTTCAA
1 TTCTTCAA
7557 TTAC-TCAA
1 TT-CTTCAA
* *
7565 TGCTTCTA
1 TTCTTCAA
7573 TTCTTCAA
1 TTCTTCAA
7581 ATTCACTTCA
Statistics
Matches: 177, Mismatches: 45, Indels: 34
0.69 0.18 0.13
Matches are distributed among these distances:
4 2 0.01
5 1 0.01
6 9 0.05
7 10 0.06
8 150 0.85
9 5 0.03
ACGTcount: A:0.28, C:0.23, G:0.01, T:0.48
Consensus pattern (8 bp):
TTCTTCAA
Found at i:7434 original size:53 final size:53
Alignment explanation
Indices: 7377--7497 Score: 179
Period size: 53 Copynumber: 2.3 Consensus size: 53
7367 TATTCAATTC
*
7377 TTCAATACTTCAATTTATCTCTTCAACTCTTTAACTATTCAACTCTTTAACTA
1 TTCAATACTTCAATTTATCTCTTCAACTCTTTAACTATTCAACTCTTCAACTA
* * * * *
7430 TTCAACACTTCAATTTATCTCTTCAACTCTTTAATTATTCAATTCTTCAATTC
1 TTCAATACTTCAATTTATCTCTTCAACTCTTTAACTATTCAACTCTTCAACTA
*
7483 TTCAATTCTTCAATT
1 TTCAATACTTCAATT
7498 CTTCAATACT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (53 bp):
TTCAATACTTCAATTTATCTCTTCAACTCTTTAACTATTCAACTCTTCAACTA
Found at i:7547 original size:37 final size:37
Alignment explanation
Indices: 7480--7551 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
7470 AATTCTTCAA
*
7480 TTCTTCAATTCTTCAATTCTTCAATACTTCAATTTAT
1 TTCTTCAATTCTTCAATTATTCAATACTTCAATTTAT
* * *
7517 TTCTTCAATTCTTCAATTATTTATTGCTTCAATTT
1 TTCTTCAATTCTTCAATTATTCAATACTTCAATTT
7552 TTCAATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.01, T:0.54
Consensus pattern (37 bp):
TTCTTCAATTCTTCAATTATTCAATACTTCAATTTAT
Found at i:7654 original size:50 final size:50
Alignment explanation
Indices: 7586--7682 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
7576 TTCAAATTCA
* * *
7586 CTTCAATGACCCAGGGTGGTCTTTCTT-CGTTTCTTTAATTATTCAATTTG
1 CTTCAATGACACAGGGTGGTCTTTCTTCCG-TTCCTCAATTATTCAATTTG
* *
7636 CTTCAATGATACATGGTGGTCTTTCTTCCGTTCCTCAATTATTCAAT
1 CTTCAATGACACAGGGTGGTCTTTCTTCCGTTCCTCAATTATTCAAT
7683 GCATCGATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 39 0.95
51 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (50 bp):
CTTCAATGACACAGGGTGGTCTTTCTTCCGTTCCTCAATTATTCAATTTG
Found at i:7748 original size:64 final size:64
Alignment explanation
Indices: 7670--7789 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
7660 CTTCCGTTCC
7670 TCAATTATTCAATGCATCGATTCCAA-ATCTTCAAGGCTTCAATTTCAATTCTTCAATGTTTCTT
1 TCAATTATTCAATGCATCGATTCCAATAT-TTCAAGGCTTCAATTTCAATTCTTCAATGTTTCTT
* * * * * *
7734 TCAATTCTTTAATGCTTCGATTTCAATATTTCAATGTTTCAATTTCAATTCTTCAA
1 TCAATTATTCAATGCATCGATTCCAATATTTCAAGGCTTCAATTTCAATTCTTCAA
7790 ATTCCAAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
64 47 0.96
65 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (64 bp):
TCAATTATTCAATGCATCGATTCCAATATTTCAAGGCTTCAATTTCAATTCTTCAATGTTTCTT
Found at i:7760 original size:22 final size:22
Alignment explanation
Indices: 7670--7789 Score: 120
Period size: 22 Copynumber: 5.5 Consensus size: 22
7660 CTTCCGTTCC
* * *
7670 TCAATTATTCAATGCATCGATT
1 TCAATTCTTCAATGCTTCAATT
* * *
7692 CCAAATCTTCAAGGCTTCAATT
1 TCAATTCTTCAATGCTTCAATT
*
7714 TCAATTCTTCAATGTTTC--TT
1 TCAATTCTTCAATGCTTCAATT
* *
7734 TCAATTCTTTAATGCTTCGATT
1 TCAATTCTTCAATGCTTCAATT
*
7756 TCAATAT-TTCAATGTTTCAATT
1 TCAAT-TCTTCAATGCTTCAATT
7778 TCAATTCTTCAA
1 TCAATTCTTCAA
7790 ATTCCAAATG
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 18 0.23
21 1 0.01
22 59 0.75
23 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (22 bp):
TCAATTCTTCAATGCTTCAATT
Found at i:7760 original size:42 final size:43
Alignment explanation
Indices: 7705--7786 Score: 123
Period size: 42 Copynumber: 1.9 Consensus size: 43
7695 AATCTTCAAG
7705 GCTTCAATTTCAAT-TCTTCAATGTTTC-TTTCAATTCTTTAAT
1 GCTTCAATTTCAATAT-TTCAATGTTTCATTTCAATTCTTTAAT
*
7747 GCTTCGATTTCAATATTTCAATGTTTCAATTTCAATTCTT
1 GCTTCAATTTCAATATTTCAATGTTTC-ATTTCAATTCTT
7787 CAAATTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 24 0.67
43 1 0.03
44 11 0.31
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
GCTTCAATTTCAATATTTCAATGTTTCATTTCAATTCTTTAAT
Found at i:7803 original size:22 final size:23
Alignment explanation
Indices: 7778--7820 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
7768 TGTTTCAATT
*
7778 TCAATTCTTCAA-ATTCCAAATG
1 TCAATGCTTCAATATTCCAAATG
*
7800 TCAATGCTTCAATATTTCAAA
1 TCAATGCTTCAATATTCCAAA
7821 ACTTCAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TCAATGCTTCAATATTCCAAATG
Found at i:7818 original size:8 final size:8
Alignment explanation
Indices: 7753--7832 Score: 53
Period size: 8 Copynumber: 10.5 Consensus size: 8
7743 TAATGCTTCG
7753 ATTTCAAT
1 ATTTCAAT
7761 ATTTCAAT
1 ATTTCAAT
*
7769 GTTTC-A-
1 ATTTCAAT
7775 ATTTCAAT
1 ATTTCAAT
7783 -TCTTCAA-
1 AT-TTCAAT
*
7790 ATTCCAA-
1 ATTTCAAT
*
7797 ATGTCAAT
1 ATTTCAAT
**
7805 GCTTCAAT
1 ATTTCAAT
*
7813 ATTTCAAA
1 ATTTCAAT
*
7821 ACTTCAAT
1 ATTTCAAT
7829 ATTT
1 ATTT
7833 TAATTATTCA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
6 4 0.08
7 12 0.23
8 37 0.70
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (8 bp):
ATTTCAAT
Found at i:7959 original size:8 final size:8
Alignment explanation
Indices: 7946--8071 Score: 55
Period size: 8 Copynumber: 16.9 Consensus size: 8
7936 TTTCTACAAT
7946 TTCAATTC
1 TTCAATTC
7954 TTCAATATTC
1 TTC-A-ATTC
*
7964 TTCAAATGC
1 TTC-AATTC
7973 TTCAA-T-
1 TTCAATTC
7979 TTCAATTC
1 TTCAATTC
* *
7987 TCCAATGC
1 TTCAATTC
7995 TTCAATTC
1 TTCAATTC
8003 --CAA-T-
1 TTCAATTC
8007 TTC-ATT-
1 TTCAATTC
8013 TTCAATGT-
1 TTCAAT-TC
*
8021 TTCCA-T-
1 TTCAATTC
8027 TTCAATTC
1 TTCAATTC
*
8035 TTCAATGC
1 TTCAATTC
8043 TTC-A--C
1 TTCAATTC
8048 TTGCAATTC
1 TT-CAATTC
8057 TTCAATTC
1 TTCAATTC
*
8065 CTCAATT
1 TTCAATT
8072 TATTTTCGAT
Statistics
Matches: 93, Mismatches: 10, Indels: 30
0.70 0.08 0.23
Matches are distributed among these distances:
5 5 0.05
6 19 0.20
7 6 0.06
8 44 0.47
9 10 0.11
10 9 0.10
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (8 bp):
TTCAATTC
Found at i:7959 original size:14 final size:14
Alignment explanation
Indices: 7937--8063 Score: 50
Period size: 14 Copynumber: 8.7 Consensus size: 14
7927 AGGGTGGTCT
*
7937 TTCTACAATTTCAA
1 TTCTTCAATTTCAA
7951 TTCTTCAATATTCTTCAAA
1 TTCTTC-A-A-T-TTC-AA
*
7970 TGCTTCAATTTCAA
1 TTCTTCAATTTCAA
*
7984 TTCTCCAATGCTTCAA
1 TTCTTCAAT--TTCAA
8000 TTC--CAATTTC-A
1 TTCTTCAATTTCAA
*
8011 TT-TTCAATGTTTCCA
1 TTCTTCAA--TTTCAA
8026 -T-TTCAATTCTTCAA
1 TTCTTCAA-T-TTCAA
* * *
8040 TGCTTCACTTGCAA
1 TTCTTCAATTTCAA
8054 TTCTTCAATT
1 TTCTTCAATT
8064 CCTCAATTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
11 3 0.03
12 6 0.07
13 1 0.01
14 44 0.51
15 6 0.07
16 14 0.16
17 2 0.02
18 4 0.05
19 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.46
Consensus pattern (14 bp):
TTCTTCAATTTCAA
Found at i:8040 original size:22 final size:22
Alignment explanation
Indices: 7960--8062 Score: 91
Period size: 22 Copynumber: 4.5 Consensus size: 22
7950 ATTCTTCAAT
*
7960 ATTCTTCAAATGCTTCAATTTCA
1 ATTCTTC-AATGCTTCCATTTCA
* * *
7983 ATTCTCCAATGCTTCAATTCCA
1 ATTCTTCAATGCTTCCATTTCA
*
8005 ATTTCATTTTCAATGTTTCCATTTCA
1 A-TTC---TTCAATGCTTCCATTTCA
*
8031 ATTCTTCAATGCTT-CACTTGCA
1 ATTCTTCAATGCTTCCA-TTTCA
8053 ATTCTTCAAT
1 ATTCTTCAAT
8063 TCCTCAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.03
22 38 0.57
23 9 0.13
25 3 0.04
26 15 0.22
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTCTTCAATGCTTCCATTTCA
Found at i:9079 original size:42 final size:42
Alignment explanation
Indices: 8991--9091 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
8981 AAGGGTAAAG
* * * * *
8991 TGGCCGGTTGTGGTCGGATGGTCCGTGCGTTGGCCCGTGTGA
1 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGGCCCATGTCA
* *
9033 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGTCTCATG-CA
1 TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGGCCCATGTCA
**
9074 TTGGCCGGTCATGGCCGG
1 -TGGCCGGTTGTGGCCGG
9092 TTGCTCCATG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.07, C:0.25, G:0.43, T:0.26
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATGGCCCGTGCGATGGCCCATGTCA
Done.