Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010706.1 Corchorus capsularis cultivar CVL-1 contig10727, 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: 41723
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1388 original size:2 final size:2
Alignment explanation
Indices: 1383--1411 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1373 TTTTCCAATT
1383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1412 TTGTACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2156 original size:20 final size:20
Alignment explanation
Indices: 2118--2158 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2108 AAACGAATAA
*
2118 TTAAACGTGTTAGTAGTGTT
1 TTAAACGTGTTAGCAGTGTT
* *
2138 TTAATCGTGTTAGCCGTGTT
1 TTAAACGTGTTAGCAGTGTT
2158 T
1 T
2159 GACACGGAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (20 bp):
TTAAACGTGTTAGCAGTGTT
Found at i:5050 original size:2 final size:2
Alignment explanation
Indices: 5043--5112 Score: 80
Period size: 2 Copynumber: 38.0 Consensus size: 2
5033 CTATTAAAAC
*
5043 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5084 AT CT -T AT AT -T A- AT AT A- AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5113 CTAAACCCCC
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
1 6 0.10
2 53 0.90
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7181 original size:84 final size:84
Alignment explanation
Indices: 7035--7198 Score: 292
Period size: 84 Copynumber: 2.0 Consensus size: 84
7025 CAAGAAATAC
* * *
7035 AGCAGTGACCTGAGCATCACTCCCTTTCTCAGTTTGCTCCTTATTTCTTTGGACATTAGACATGC
1 AGCACTGACCTGAGCATCACTCCCTTGCTCAGTTTGCTACTTATTTCTTTGGACATTAGACATGC
*
7100 ATCCACTTGACTGATCAAG
66 ATCCACTTGAATGATCAAG
7119 AGCACTGACCTGAGCATCACTCCCTTGCTCAGTTTGCTACTTATTTCTTTGGACATTAGACATGC
1 AGCACTGACCTGAGCATCACTCCCTTGCTCAGTTTGCTACTTATTTCTTTGGACATTAGACATGC
7184 ATCCACTTGAATGAT
66 ATCCACTTGAATGAT
7199 TACTTGCAGC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (84 bp):
AGCACTGACCTGAGCATCACTCCCTTGCTCAGTTTGCTACTTATTTCTTTGGACATTAGACATGC
ATCCACTTGAATGATCAAG
Found at i:12319 original size:48 final size:48
Alignment explanation
Indices: 12248--12342 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
12238 AACTCGAGTT
*
12248 CATTGTGAATGAAGAAAGCTATTACTTACACAACTTTACCTTATAATC
1 CATTGTGAATGAAGAAAGCTATTACTTACACAACTTTACCTAATAATC
* * *
12296 CATTGTGAATGGAGAAAGCTATTATTTACATAACTTTACCTAATAAT
1 CATTGTGAATGAAGAAAGCTATTACTTACACAACTTTACCTAATAAT
12343 GGACTGACCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (48 bp):
CATTGTGAATGAAGAAAGCTATTACTTACACAACTTTACCTAATAATC
Found at i:16447 original size:24 final size:24
Alignment explanation
Indices: 16415--16461 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
16405 ATTCTCTGGC
* *
16415 ATCCTCACTTTAGTATGTACTAAG
1 ATCCTCACTTTAGAATGGACTAAG
16439 ATCCTCACTTTAGAATGGACTAA
1 ATCCTCACTTTAGAATGGACTAA
16462 ATATGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (24 bp):
ATCCTCACTTTAGAATGGACTAAG
Found at i:19903 original size:5 final size:5
Alignment explanation
Indices: 19893--19919 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19883 TTAGATTTAT
19893 ATTAC ATTAC ATTAC ATTAC ATTAC AT
1 ATTAC ATTAC ATTAC ATTAC ATTAC AT
19920 ACAGAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAC
Found at i:21025 original size:23 final size:23
Alignment explanation
Indices: 20995--21038 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
20985 TAAAAAAAGA
20995 TTTTTTTTCTTTTTTGAATTGAT
1 TTTTTTTTCTTTTTTGAATTGAT
21018 TTTTTTTTCTTTTTTGAATTG
1 TTTTTTTTCTTTTTTGAATTG
21039 GGACCAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTTTTTTCTTTTTTGAATTGAT
Found at i:23184 original size:3 final size:3
Alignment explanation
Indices: 23176--23201 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23166 TTCGTTGTCC
23176 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
23202 GGGGAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:27357 original size:16 final size:16
Alignment explanation
Indices: 27313--27386 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
27303 AAACAATTAT
27313 ATATTATATATATAAC
1 ATATTATATATATAAC
* *
27329 ATCTTATAAATATAAC
1 ATATTATATATATAAC
*
27345 -TATTAT-TATAT-AT
1 ATATTATATATATAAC
27358 ATA-TATATATAATAA-
1 ATATTATATAT-ATAAC
27373 ATATT-TAATATATA
1 ATATTAT-ATATATA
27387 TTAAAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 4 0.09
14 9 0.19
15 14 0.30
16 20 0.43
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTATATATATAAC
Found at i:27385 original size:18 final size:17
Alignment explanation
Indices: 27362--27397 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
27352 ATATATATAT
27362 ATATATAATAAATATTTA
1 ATATATAATAAA-ATTTA
*
27380 ATATATATTAAAATTTA
1 ATATATAATAAAATTTA
27397 A
1 A
27398 CCTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATAATAAAATTTA
Found at i:27833 original size:46 final size:46
Alignment explanation
Indices: 27782--27871 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
27772 TGGCCCTGTC
*
27782 GATTTATTTGCAGATCTGGGATTTGTTTATTTTTCAAGGATAGTTT
1 GATTTATTTGCAGATCTGGGATTTCTTTATTTTTCAAGGATAGTTT
*
27828 GATTTATTTGCAGATCTGGGTTTTCTTTATTTTTCAAGGATAGT
1 GATTTATTTGCAGATCTGGGATTTCTTTATTTTTCAAGGATAGT
27872 GATGGGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (46 bp):
GATTTATTTGCAGATCTGGGATTTCTTTATTTTTCAAGGATAGTTT
Found at i:27850 original size:23 final size:23
Alignment explanation
Indices: 27782--27859 Score: 56
Period size: 23 Copynumber: 3.4 Consensus size: 23
27772 TGGCCCTGTC
27782 GATTTATTTGCAGATCTGGGATTT
1 GATTTATTTGCAGATCTGGG-TTT
* *
27806 G-TTTATTTTTCAAGGA--T-AGTTT
1 GATTTA-TTTGC-A-GATCTGGGTTT
27828 GATTTATTTGCAGATCTGGGTTT
1 GATTTATTTGCAGATCTGGGTTT
**
27851 TCTTTATTT
1 GATTTATTT
27860 TTCAAGGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 15
0.66 0.10 0.24
Matches are distributed among these distances:
20 2 0.05
21 1 0.02
22 9 0.22
23 20 0.49
24 6 0.15
25 1 0.02
26 2 0.05
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.53
Consensus pattern (23 bp):
GATTTATTTGCAGATCTGGGTTT
Found at i:29422 original size:15 final size:15
Alignment explanation
Indices: 29402--29432 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29392 GCCAGTAGCT
29402 TAGAATAATAGAACA
1 TAGAATAATAGAACA
*
29417 TAGAATACTAGAACA
1 TAGAATAATAGAACA
29432 T
1 T
29433 CCCATTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.23
Consensus pattern (15 bp):
TAGAATAATAGAACA
Found at i:32747 original size:3 final size:3
Alignment explanation
Indices: 32733--32808 Score: 143
Period size: 3 Copynumber: 25.0 Consensus size: 3
32723 GGAATTAGGG
32733 TTC TTCC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
32779 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
32809 ATCTACTCAT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:41489 original size:3 final size:3
Alignment explanation
Indices: 41476--41506 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
41466 TTATTTAGCC
41476 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
41507 TATATATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Done.