Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024449.1 Corchorus olitorius cultivar O-4 contig24482, 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: 41525
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:1204 original size:29 final size:31
Alignment explanation
Indices: 1145--1213 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
1135 GCTAAATACT
* **
1145 CAAAA-AATCCCTTATGTTTCTCTTTTGGGA
1 CAAAATAATCCATTATGTTTCTCTTGGGGGA
1175 CAAAATAATCCATTATGTTT-T-TTGGGGGA
1 CAAAATAATCCATTATGTTTCTCTTGGGGGA
*
1204 CAAATTAATC
1 CAAAATAATC
1214 TCTTACATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.44
30 6 0.18
31 13 0.38
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (31 bp):
CAAAATAATCCATTATGTTTCTCTTGGGGGA
Found at i:2560 original size:21 final size:21
Alignment explanation
Indices: 2527--2577 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2517 TAGAAAGAAG
2527 GGGAAAAAAAGAAAAAGAAAA
1 GGGAAAAAAAGAAAAAGAAAA
* * *
2548 GGGAGAAAGAGAAAATGAAAA
1 GGGAAAAAAAGAAAAAGAAAA
*
2569 -TGAAAAAAA
1 GGGAAAAAAA
2578 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (21 bp):
GGGAAAAAAAGAAAAAGAAAA
Found at i:3441 original size:7 final size:7
Alignment explanation
Indices: 3430--3484 Score: 83
Period size: 7 Copynumber: 7.6 Consensus size: 7
3420 TGAAGAAGAG
3430 AAGAAAA
1 AAGAAAA
*
3437 GAGAAAA
1 AAGAAAA
3444 AAGAAAA
1 AAGAAAA
3451 AAGAAAGA
1 AAGAAA-A
3459 AAGAAAA
1 AAGAAAA
3466 AAGAAAGA
1 AAGAAA-A
3474 AAGAAAA
1 AAGAAAA
3481 AAGA
1 AAGA
3485 GTGAAACAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 30 0.68
8 14 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:3442 original size:29 final size:29
Alignment explanation
Indices: 3410--3484 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
3400 GGCCAAGGGT
** *
3410 GAAAGAAGAATGAAG-AAGAGAAGAAAAGA
1 GAAAGAAGAAAAAAGAAAGA-AAGAAAAAA
*
3439 GAAAAAAGAAAAAAGAAAGAAAGAAAAAA
1 GAAAGAAGAAAAAAGAAAGAAAGAAAAAA
3468 GAAAGAAAGAAAAAAGA
1 GAAAG-AAGAAAAAAGA
3485 GTGAAACAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (29 bp):
GAAAGAAGAAAAAAGAAAGAAAGAAAAAA
Found at i:3490 original size:15 final size:15
Alignment explanation
Indices: 3425--3484 Score: 95
Period size: 15 Copynumber: 4.0 Consensus size: 15
3415 AAGAATGAAG
*
3425 AAGAGAAGAAAAGAGA
1 AAGA-AAGAAAAAAGA
3441 AA-AAAGAAAAAAGA
1 AAGAAAGAAAAAAGA
3455 AAGAAAGAAAAAAGA
1 AAGAAAGAAAAAAGA
3470 AAGAAAGAAAAAAGA
1 AAGAAAGAAAAAAGA
3485 GTGAAACAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
14 12 0.29
15 28 0.67
16 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAAAAGA
Found at i:3685 original size:16 final size:15
Alignment explanation
Indices: 3652--3681 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3642 CACTTATTAG
3652 TTTTTTAATATTTTA
1 TTTTTTAATATTTTA
*
3667 TTTTTTATTATTTTA
1 TTTTTTAATATTTTA
3682 ATTTCCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTAATATTTTA
Found at i:3995 original size:30 final size:30
Alignment explanation
Indices: 3951--4009 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3941 AGACTTGTCT
3951 AATTTTATCCTTAATTGCTT-AAAACAATA
1 AATTTTATCCTTAATTGCTTGAAAACAATA
* *
3980 AATTTATATCTTTAATTGCTTGAAATCAAT
1 AATTT-TATCCTTAATTGCTTGAAAACAAT
4010 TTTATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 14 0.54
31 7 0.27
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (30 bp):
AATTTTATCCTTAATTGCTTGAAAACAATA
Found at i:11362 original size:32 final size:32
Alignment explanation
Indices: 11326--11389 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
11316 TCCTAATAAT
* **
11326 CAAGGAAATAAATTAAATTTAGGTTTAGCCCC
1 CAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
11358 CAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
1 CAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
11390 TAGTTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (32 bp):
CAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
Found at i:11943 original size:13 final size:13
Alignment explanation
Indices: 11925--11950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11915 TCTAAAAATA
11925 AAATAATTAATTT
1 AAATAATTAATTT
11938 AAATAATTAATTT
1 AAATAATTAATTT
11951 TAGCCTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAATTAATTT
Found at i:14550 original size:1 final size:1
Alignment explanation
Indices: 14544--14580 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
14534 TCTCTTTGTG
*
14544 TTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14581 CCCCTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:14563 original size:16 final size:16
Alignment explanation
Indices: 14538--14580 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
14528 GGGGAATCTC
*
14538 TTTGTGTTTTTTTTTT
1 TTTGTTTTTTTTTTTT
14554 TTTGTTTTTTTTTTTT
1 TTTGTTTTTTTTTTTT
14570 TTT-TTTTTTTT
1 TTTGTTTTTTTT
14581 CCCCTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (16 bp):
TTTGTTTTTTTTTTTT
Found at i:17014 original size:3 final size:3
Alignment explanation
Indices: 17006--17070 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
16996 TATTCTTTTC
17006 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17054 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
17071 TTAATATATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18094 original size:29 final size:30
Alignment explanation
Indices: 18055--18132 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 30
18045 CCTGATTTTA
*
18055 CAAA-TTCAGGGGGCAAAGTGG-CACAATTT
1 CAAAGTTCAGGGGGCAAACTGGCCA-AATTT
*
18084 -AAAGTTCAGGGGGCAATCTGGCCTAAATTT
1 CAAAGTTCAGGGGGCAAACTGGCC-AAATTT
18114 GCAAAGTTCAGGGGGCAAA
1 -CAAAGTTCAGGGGGCAAA
18133 AAGGCTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 3 0.07
29 15 0.37
30 6 0.15
31 1 0.02
32 16 0.39
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (30 bp):
CAAAGTTCAGGGGGCAAACTGGCCAAATTT
Found at i:21162 original size:30 final size:30
Alignment explanation
Indices: 21126--21186 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
21116 GCTTAAAATG
21126 CTTAGGCCGACACTTTCCCTTTCAAACCAT
1 CTTAGGCCGACACTTTCCCTTTCAAACCAT
*
21156 CTTAGGCCGATACTTTCCCTTTCAAACCAT
1 CTTAGGCCGACACTTTCCCTTTCAAACCAT
21186 C
1 C
21187 GGCCTAAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.10, T:0.31
Consensus pattern (30 bp):
CTTAGGCCGACACTTTCCCTTTCAAACCAT
Found at i:26016 original size:102 final size:102
Alignment explanation
Indices: 25840--26045 Score: 385
Period size: 102 Copynumber: 2.0 Consensus size: 102
25830 TCATGCCTAA
*
25840 AATAAACAATCATTTCTATCAAATCAATTATGGCCTGTCAAATTAGAAATCAGCAGTAAAAATCA
1 AATAAACAATCATTTCTATCAAATCAATTATGACCTGTCAAATTAGAAATCAGCAGTAAAAATCA
25905 TGGATTCCTTTACCATATAACAATATATGTGTATATT
66 TGGATTCCTTTACCATATAACAATATATGTGTATATT
*
25942 AATAAACAATCATTTCTATCAAATCAATTATGACCTGTCCAATTAGAAATCAGCAGTAAAAATCA
1 AATAAACAATCATTTCTATCAAATCAATTATGACCTGTCAAATTAGAAATCAGCAGTAAAAATCA
*
26007 TGGATTCCTTTACCGTATAACAATATATGTGTATATT
66 TGGATTCCTTTACCATATAACAATATATGTGTATATT
26044 AA
1 AA
26046 AATATGTTTC
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (102 bp):
AATAAACAATCATTTCTATCAAATCAATTATGACCTGTCAAATTAGAAATCAGCAGTAAAAATCA
TGGATTCCTTTACCATATAACAATATATGTGTATATT
Found at i:29062 original size:21 final size:21
Alignment explanation
Indices: 28999--29055 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
28989 TTGACATTGT
* *
28999 TTAGGTACTGTACAGATGAGA
1 TTAGGTACTGTACAGATCAAA
*
29020 TTA--CACTGTACAGATCAAA
1 TTAGGTACTGTACAGATCAAA
29039 TTAGGTACTGTACAGAT
1 TTAGGTACTGTACAGAT
29056 TATATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (21 bp):
TTAGGTACTGTACAGATCAAA
Found at i:30030 original size:14 final size:14
Alignment explanation
Indices: 30011--30037 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30001 TTTATCTAGT
30011 AATTCTTTTTTATC
1 AATTCTTTTTTATC
30025 AATTCTTTTTTAT
1 AATTCTTTTTTAT
30038 TTTATACTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTCTTTTTTATC
Found at i:30257 original size:36 final size:37
Alignment explanation
Indices: 30177--30257 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
30167 ACACTATTTC
* *
30177 AATCAAATAGTTGTGACAACAAAGTTGTTCAATATTGA
1 AATC-AATAGTTGTGACAACAAAGTTGCTCAATAGTGA
* * *
30215 ATTCAATAGTTGTGACAAC-GAGTTGCTCACTAGTGA
1 AATCAATAGTTGTGACAACAAAGTTGCTCAATAGTGA
30251 AATCAAT
1 AATCAAT
30258 TTTTTTGGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 19 0.51
37 15 0.41
38 3 0.08
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (37 bp):
AATCAATAGTTGTGACAACAAAGTTGCTCAATAGTGA
Found at i:30754 original size:35 final size:35
Alignment explanation
Indices: 30704--30795 Score: 102
Period size: 34 Copynumber: 2.7 Consensus size: 35
30694 CTTAAAAAGT
30704 TCAA-TAGCAACAAGCAAAACCAAACTAAAACCTA
1 TCAACTAGCAACAAGCAAAACCAAACTAAAACCTA
* * *
30738 -CAA-TAATGCAACAAGCAAATCC-AATTAAACCCTA
1 TCAACT-A-GCAACAAGCAAAACCAAACTAAAACCTA
*
30772 TCAACTAGCAGCAAGCAAAACCAA
1 TCAACTAGCAACAAGCAAAACCAA
30796 TTATGCTCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
33 4 0.08
34 24 0.50
35 19 0.40
36 1 0.02
ACGTcount: A:0.52, C:0.27, G:0.08, T:0.13
Consensus pattern (35 bp):
TCAACTAGCAACAAGCAAAACCAAACTAAAACCTA
Found at i:30819 original size:35 final size:35
Alignment explanation
Indices: 30749--30867 Score: 136
Period size: 35 Copynumber: 3.4 Consensus size: 35
30739 AATAATGCAA
* * *
30749 CAAGCAAATCCAATTAAAC-CCTATCAACTAGCAG
1 CAAGCAAAACCAATTATACTCCTATCAACTACCAG
* *
30783 CAAGCAAAACCAATTATGCTCCTATCAACCACCAG
1 CAAGCAAAACCAATTATACTCCTATCAACTACCAG
* *
30818 CAAGCAAAA-TAGATTATACTCCTA-AAATCTACCAG
1 CAAGCAAAACCA-ATTATACTCCTATCAA-CTACCAG
30853 CAAGCAAAACCAATT
1 CAAGCAAAACCAATT
30868 CAAACTATAC
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
34 19 0.27
35 51 0.72
36 1 0.01
ACGTcount: A:0.45, C:0.29, G:0.08, T:0.18
Consensus pattern (35 bp):
CAAGCAAAACCAATTATACTCCTATCAACTACCAG
Done.