Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008681.1 Corchorus capsularis cultivar CVL-1 contig08702, 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: 30112
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:73 original size:49 final size:49
Alignment explanation
Indices: 1--205 Score: 311
Period size: 49 Copynumber: 4.2 Consensus size: 49
* *
1 CGGAAGTCACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
1 CGGAAGGCACTTATTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
50 CGGAAGGCACTTATTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
1 CGGAAGGCACTTATTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
*
99 CGGAAGGCACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
1 CGGAAGGCACTTATTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
** * * * * *
148 CGGAAGGCACCAATTTTTATTTGTTTTTTCCTAAAACGCCCCTTCCCGGA
1 CGGAAGGCACTTATTTTTATCTGCTATTTCCCAAAATG-CCCTTCCCGGA
198 CGGAAGGC
1 CGGAAGGC
206 GTCGCTTTTT
Statistics
Matches: 144, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 125 0.87
50 19 0.13
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.32
Consensus pattern (49 bp):
CGGAAGGCACTTATTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGA
Found at i:1673 original size:13 final size:13
Alignment explanation
Indices: 1651--1690 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1641 CAGAGAATAT
1651 TATCAACAGAAGA
1 TATCAACAGAAGA
*
1664 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
1677 TTTCAACTGAAGA
1 TATCAACAGAAGA
1690 T
1 T
1691 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:1703 original size:11 final size:11
Alignment explanation
Indices: 1683--1713 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1673 AAGATTTCAA
1683 CTGAAGATTAT
1 CTGAAGATTAT
*
1694 CTGGAGATTAT
1 CTGAAGATTAT
1705 CTGAAGATT
1 CTGAAGATT
1714 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:2444 original size:6 final size:6
Alignment explanation
Indices: 2429--2474 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
2419 TGGACGATTC
* * *
2429 CGGTTT CGGTTA CGGTTA CGGTTA CGGTT- CGGTTC CGATTA CGGTT
1 CGGTTA CGGTTA CGGTTA CGGTTA CGGTTA CGGTTA CGGTTA CGGTT
2475 CCATATATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.11, C:0.20, G:0.33, T:0.37
Consensus pattern (6 bp):
CGGTTA
Found at i:2470 original size:17 final size:17
Alignment explanation
Indices: 2435--2475 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2425 ATTCCGGTTT
*
2435 CGGTTACGGTTACGGTTA
1 CGGTT-CGGTTACGATTA
*
2453 CGGTTCGGTTCCGATTA
1 CGGTTCGGTTACGATTA
2470 CGGTTC
1 CGGTTC
2476 CATATATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.12, C:0.22, G:0.32, T:0.34
Consensus pattern (17 bp):
CGGTTCGGTTACGATTA
Found at i:3334 original size:3 final size:3
Alignment explanation
Indices: 3326--3368 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3316 ATATAACTTG
3326 TTA TTA TTA TTA TTA -TA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3369 CTAGAATTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3772 original size:11 final size:11
Alignment explanation
Indices: 3758--3795 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3748 ATTCATAACA
3758 AATTTATAATT
1 AATTTATAATT
3769 AATTTATAATT
1 AATTTATAATT
3780 -ATTTGATAATT
1 AATTT-ATAATT
*
3791 TATTT
1 AATTT
3796 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:14449 original size:2 final size:2
Alignment explanation
Indices: 14442--14467 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14432 AAGTACTTGA
14442 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
14468 AATTTTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17840 original size:20 final size:21
Alignment explanation
Indices: 17799--17841 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
17789 AACATAGCAC
*
17799 TAATTAGACATGGAAAATGGG
1 TAATTAGACATGGAAAAGGGG
17820 TAATTAGACAT-GAAAAGGGG
1 TAATTAGACATGGAAAAGGGG
17840 TA
1 TA
17842 CTTCCCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (21 bp):
TAATTAGACATGGAAAAGGGG
Found at i:20644 original size:102 final size:102
Alignment explanation
Indices: 20468--20672 Score: 392
Period size: 102 Copynumber: 2.0 Consensus size: 102
20458 AGGATAGAAA
20468 TAGATCGGTTTCAAGTAAATCTGGTGGCTAGAATCGGAGATCTGGGTAACTTTTAGATTGGGGAA
1 TAGATCGGTTTCAAGTAAATCTGGTGGCTAGAATCGGAGATCTGGGTAACTTTTAGATTGGGGAA
*
20533 AAATGACTTTTGGGGCTTTTGGGTTTACTGTTTTTTT
66 AAATGACTTTTGGGGCTTTTGGGTTTACAGTTTTTTT
20570 TAGATCGGTTTCAAGTAAATCTGGTGGCTAGAATCGGAGATCTGGGTAACTTTTAGATTGGGGAA
1 TAGATCGGTTTCAAGTAAATCTGGTGGCTAGAATCGGAGATCTGGGTAACTTTTAGATTGGGGAA
*
20635 AAGTGACTTTTGGGGCTTTTGGGTTTACAGTTTTTTT
66 AAATGACTTTTGGGGCTTTTGGGTTTACAGTTTTTTT
20672 T
1 T
20673 TTGAAATTGA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (102 bp):
TAGATCGGTTTCAAGTAAATCTGGTGGCTAGAATCGGAGATCTGGGTAACTTTTAGATTGGGGAA
AAATGACTTTTGGGGCTTTTGGGTTTACAGTTTTTTT
Found at i:21588 original size:19 final size:18
Alignment explanation
Indices: 21564--21603 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21554 TTGAAGATTT
*
21564 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
21583 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
21601 ATT
1 ATT
21604 ATCTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:26954 original size:10 final size:10
Alignment explanation
Indices: 26939--26981 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
26929 CCGACACCAA
26939 GCCATGCCCG
1 GCCATGCCCG
26949 GCCATGTCCGCG
1 GCCATG-CC-CG
*
26961 CACCATGCCCG
1 -GCCATGCCCG
26972 GCCATGCCCG
1 GCCATGCCCG
26982 TCCAATGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 15 0.54
11 4 0.14
12 4 0.14
13 5 0.18
ACGTcount: A:0.12, C:0.49, G:0.28, T:0.12
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:28434 original size:33 final size:33
Alignment explanation
Indices: 28363--28481 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
28353 AAAGGATCGT
* * *
28363 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCGT
1 GTGGCCGGTTGTGGCCGGACATGTCC-ATGTCGC
* * *
28396 TTGGCCGGTTGTAGCCGGCCATGTCCATGTCGC
1 GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
28429 GTGGCCGG-TGATGGCCGGACATGTCCATGTCGC
1 GTGGCCGGTTG-TGGCCGGACATGTCCATGTCGC
28462 GTGGCCGGTCTTGTGGCCGG
1 GTGGCCGG--TTGTGGCCGG
28482 TGTTGCGCGG
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.04
33 61 0.84
35 7 0.10
36 2 0.03
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.24
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
Done.