Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016436.1 Corchorus capsularis cultivar CVL-1 contig16457, 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: 25052
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1394 original size:33 final size:33
Alignment explanation
Indices: 1298--1394 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
1288 GTGTTTTAGA
* *
1298 TGTTGTTTGCGATGATACTAAATCTAATTTGAG
1 TGTTGTTTGCGATGAAACTAAATCTATTTTGAG
* *
1331 AGTTGTTTGCGATGACACTAAATCTATTTTGAG
1 TGTTGTTTGCGATGAAACTAAATCTATTTTGAG
* * *
1364 TGTTGTTTGTGATGAAACAAAATCTGTTTTG
1 TGTTGTTTGCGATGAAACTAAATCTATTTTG
1395 GATGCTAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (33 bp):
TGTTGTTTGCGATGAAACTAAATCTATTTTGAG
Found at i:1456 original size:33 final size:33
Alignment explanation
Indices: 1419--1494 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
1409 TGAAAACAAA
1419 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1452 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1485 TCTGTTTTGG
1 TCTGTTTTGG
1495 GTGAAAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:3319 original size:18 final size:18
Alignment explanation
Indices: 3278--3379 Score: 61
Period size: 18 Copynumber: 5.8 Consensus size: 18
3268 ACCGACTGCC
*
3278 TAATATATATAATATTTT
1 TAATATATATAATATATT
*
3296 TAATATATATATTTATATT
1 TAATATATATA-ATATATT
*
3315 T-ATATA-AT--TATGTT
1 TAATATATATAATATATT
* *
3329 AATAATATATATAATAAATG
1 --TAATATATATAATATATT
* *
3349 AAATATATAT-ATATATC
1 TAATATATATAATATATT
* *
3366 TGAGATATATAATA
1 TAATATATATAATA
3380 CATATGATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
14 5 0.08
16 1 0.02
17 19 0.30
18 30 0.47
19 6 0.09
20 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (18 bp):
TAATATATATAATATATT
Found at i:7598 original size:16 final size:16
Alignment explanation
Indices: 7577--7620 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
7567 TGAATTTTGA
*
7577 TGGTATATATTGTTGC
1 TGGTATATATTGCTGC
7593 TGGTATATAATATTGCTGC
1 TGG--TAT-ATATTGCTGC
7612 TGGTATATA
1 TGGTATATA
7621 ATATTGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 6 0.25
17 3 0.12
18 3 0.12
19 12 0.50
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (16 bp):
TGGTATATATTGCTGC
Found at i:7607 original size:19 final size:19
Alignment explanation
Indices: 7583--7629 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
7573 TTGATGGTAT
7583 ATATTGTTGCTGGTATATA
1 ATATTGTTGCTGGTATATA
*
7602 ATATTGCTGCTGGTATATA
1 ATATTGTTGCTGGTATATA
7621 ATATTGTTG
1 ATATTGTTG
7630 TTGCTTGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (19 bp):
ATATTGTTGCTGGTATATA
Found at i:8527 original size:22 final size:22
Alignment explanation
Indices: 8491--8534 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8481 AATTTCAGGA
*
8491 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
8513 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
8535 GCACAGGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:8569 original size:51 final size:52
Alignment explanation
Indices: 8486--8587 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 52
8476 ACAAGAATTT
8486 CAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCA
1 CAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCA
*
8538 CAGGACAA-TTCGGCCCAGAACTTGTAT-AACTTCGGGACAGAATTTGTTGC
1 CAGGACAACTTCGGCCCAGAACTTGT-TCAACTTCGGGACAGAAGTTGTTGC
8588 GGGAAAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
51 39 0.81
52 9 0.19
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (52 bp):
CAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCA
Found at i:11111 original size:19 final size:18
Alignment explanation
Indices: 11073--11112 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
11063 TTCTTAAAAT
*
11073 AATTCTTCAATGATCTTC
1 AATTCTTCAATGACCTTC
*
11091 AATTCTTCAAATTACCTTC
1 AATTCTTC-AATGACCTTC
11110 AAT
1 AAT
11113 AAGTCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (18 bp):
AATTCTTCAATGACCTTC
Found at i:14994 original size:21 final size:21
Alignment explanation
Indices: 14969--15046 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 21
14959 AGATACCGTC
14969 ATTTAGTGTTAAACCCATTAG
1 ATTTAGTGTTAAACCCATTAG
* ** ***
14990 ATTTAGTTTAGATAAAAGCAACCG
1 ATTTAG--T-GTTAAACCCATTAG
15014 -TTTAGTGTTAAACCCATTAG
1 ATTTAGTGTTAAACCCATTAG
15034 ATTTAGT-TTAAAC
1 ATTTAGTGTTAAAC
15047 TAGAGATACC
Statistics
Matches: 41, Mismatches: 12, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
20 14 0.34
21 13 0.32
23 6 0.15
24 8 0.20
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (21 bp):
ATTTAGTGTTAAACCCATTAG
Found at i:15058 original size:44 final size:43
Alignment explanation
Indices: 14956--15058 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 43
14946 AATTTTGGGT
*
14956 TAGAGATACCGTCATTTAGTGTTAAACCCATTAGATTTAGTTTAGA
1 TAGAGATACCG---TTTAGTGTTAAACCCATTAGATTTAGTTTAAA
*
15002 TAAAAGCA-ACCGTTTAGTGTTAAACCCATTAGATTTAGTTTAAA
1 T-AGAG-ATACCGTTTAGTGTTAAACCCATTAGATTTAGTTTAAA
15046 CTAGAGATACCGT
1 -TAGAGATACCGT
15059 CGTTTGACGG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
43 1 0.02
44 39 0.78
45 1 0.02
46 1 0.02
47 7 0.14
48 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (43 bp):
TAGAGATACCGTTTAGTGTTAAACCCATTAGATTTAGTTTAAA
Found at i:16231 original size:17 final size:17
Alignment explanation
Indices: 16206--16239 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16196 AATTATGCAA
16206 ATCCCACTTATGCATTG
1 ATCCCACTTATGCATTG
*
16223 ATCCTACTTATGCATTG
1 ATCCCACTTATGCATTG
16240 TCTAACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (17 bp):
ATCCCACTTATGCATTG
Found at i:17710 original size:19 final size:20
Alignment explanation
Indices: 17667--17713 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
17657 TTAAAAACTA
*
17667 AAATTAAAGAAATAAGGACT
1 AAATTGAAGAAATAAGGACT
* *
17687 AAATTGAAGCAATAAGG-TT
1 AAATTGAAGAAATAAGGACT
17706 AAATTGAA
1 AAATTGAA
17714 AGAATTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (20 bp):
AAATTGAAGAAATAAGGACT
Found at i:21487 original size:17 final size:17
Alignment explanation
Indices: 21462--21495 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21452 AATTATGCAA
21462 ATCCCACTTATGCATTG
1 ATCCCACTTATGCATTG
*
21479 ATCCTACTTATGCATTG
1 ATCCCACTTATGCATTG
21496 TCTAACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (17 bp):
ATCCCACTTATGCATTG
Done.