Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020324.1 Corchorus olitorius cultivar O-4 contig20357, 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: 8381
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1781 original size:2 final size:2
Alignment explanation
Indices: 1774--1849 Score: 58
Period size: 2 Copynumber: 41.5 Consensus size: 2
1764 AAATGAAATA
* *
1774 AT AT AT AT A- AT -T AT AT AT -T AT TT AT AT AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1812 TT CT -T AT AT AT A- AT AT AT AT AT AC AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1850 AAAAATAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
1 7 0.12
2 52 0.88
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1812 original size:20 final size:20
Alignment explanation
Indices: 1777--1833 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
1767 TGAAATAATA
*
1777 TATATAATTA-TATATTAT-T
1 TATATAAATATTATATT-TCT
1796 TATATAAATATTATATTTCT
1 TATATAAATATTATATTTCT
1816 TATATATAATATATATAT
1 TATATA-AATAT-TATAT
1834 ACATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 10 0.30
20 13 0.39
21 5 0.15
22 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATAAATATTATATTTCT
Found at i:3635 original size:20 final size:20
Alignment explanation
Indices: 3610--3680 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
3600 TAGTAATAAT
3610 CTAATAATAATTGTTTTAAA
1 CTAATAATAATTGTTTTAAA
* *
3630 CTAATAGACTAATCAGTGGTATTAAT
1 CTAATA-A-TAAT---T-GTTTTAAA
*
3656 CT-ATAACAATTGTTTTAAA
1 CTAATAATAATTGTTTTAAA
3675 CTAATA
1 CTAATA
3681 GACTAATCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
19 8 0.21
20 10 0.26
21 1 0.03
22 4 0.10
23 3 0.08
24 1 0.03
25 4 0.10
26 8 0.21
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (20 bp):
CTAATAATAATTGTTTTAAA
Found at i:3671 original size:45 final size:46
Alignment explanation
Indices: 3606--3693 Score: 160
Period size: 45 Copynumber: 1.9 Consensus size: 46
3596 CTATTAGTAA
*
3606 TAATCTAATAATAATTGTTTTAAACTAATAGACTAATCAGTGGTAT
1 TAATCTAATAACAATTGTTTTAAACTAATAGACTAATCAGTGGTAT
3652 TAATCT-ATAACAATTGTTTTAAACTAATAGACTAATCAGTGG
1 TAATCTAATAACAATTGTTTTAAACTAATAGACTAATCAGTGG
3694 AAACACTCGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 35 0.85
46 6 0.15
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (46 bp):
TAATCTAATAACAATTGTTTTAAACTAATAGACTAATCAGTGGTAT
Found at i:4715 original size:213 final size:212
Alignment explanation
Indices: 4324--4890 Score: 876
Period size: 213 Copynumber: 2.7 Consensus size: 212
4314 AATTTCAATA
* *
4324 CCACTAAACCCCTGT--CCCTTATTTAGATGTGAATGTAAGTCCCTCATCCTTCACATGTTTTCT
1 CCACTAAACCCCTGTCCCCCTTACTTAGATGTGAATGTAAGTCTCTCATCCTTCACATGTTTTCT
* *
4387 ATTTTTTCTTGTTTATTATTTATAATTTTAACACTAACGATAAATTTTTTAGGTTTGCTAGTTAA
66 ATTTTTGCTTGTTTATTATTTATAATTTTAACACTAACGATAAATTTTTTAGGTTTGCTGGTTAA
*
4452 GCATGAGCTATTATGGTGCTTTCATGGAAGAGAAGGTTTTGTCACGTACCTTCAGTCTAGAGGCG
131 GCATGAGCTATTATGGTGCTTTCATGGAAGAGAAGGTCTTGTCACGTACCTTCAGTCTAGAGGCG
4517 CATGAATGGCTAGCTCT
196 CATGAATGGCTAGCTCT
*
4534 CACACTAAACCCCCGTCCCCCTTACTTAGATGTGAATGTAAGTCTCTCATCCTTCACATGTTTTC
1 C-CACTAAACCCCTGTCCCCCTTACTTAGATGTGAATGTAAGTCTCTCATCCTTCACATGTTTTC
*
4599 TATTTTTGCTTGTTTATTATTTATAATTTTAACACTAACGATAAATTTTTTAGGTTTCCTGGTTA
65 TATTTTTGCTTGTTTATTATTTATAATTTTAACACTAACGATAAATTTTTTAGGTTTGCTGGTTA
* *
4664 AGCATGAGCTATTATGGTGATTTCATGGAAGAGAAGGTCTTGTCCCGTACCTTCAGTCTAGAGGC
130 AGCATGAGCTATTATGGTGCTTTCATGGAAGAGAAGGTCTTGTCACGTACCTTCAGTCTAGAGGC
4729 GCATGAATGGCTAGCTCT
195 GCATGAATGGCTAGCTCT
*
4747 CCTACTAAACCCTTGTCCCCCTTACTTAGATGTGAATGTAAGTCTCTCA----TC-C-----TTC
1 CC-ACTAAACCCCTGTCCCCCTTACTTAGATGTGAATGTAAGTCTCTCATCCTTCACATGTTTTC
* * * *
4802 TATTTTTGCTTATTT-TT-TTT-TAATTTTAACACTAACAATAATTTTTTTAGGATTGCTGGTTA
65 TATTTTTGCTTGTTTATTATTTATAATTTTAACACTAACGATAAATTTTTTAGGTTTGCTGGTTA
*
4864 AGCATGAGCTATTATGGGGCTTTCATG
130 AGCATGAGCTATTATGGTGCTTTCATG
4891 CAAGGGGAGG
Statistics
Matches: 335, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
200 63 0.19
201 3 0.01
202 2 0.01
203 17 0.05
208 1 0.00
209 2 0.01
210 1 0.00
211 13 0.04
212 1 0.00
213 232 0.69
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (212 bp):
CCACTAAACCCCTGTCCCCCTTACTTAGATGTGAATGTAAGTCTCTCATCCTTCACATGTTTTCT
ATTTTTGCTTGTTTATTATTTATAATTTTAACACTAACGATAAATTTTTTAGGTTTGCTGGTTAA
GCATGAGCTATTATGGTGCTTTCATGGAAGAGAAGGTCTTGTCACGTACCTTCAGTCTAGAGGCG
CATGAATGGCTAGCTCT
Found at i:6404 original size:26 final size:27
Alignment explanation
Indices: 6351--6417 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
6341 ACGTAAAAAC
* *
6351 AAAAAAT-ATAATAACAAAATTATCCA
1 AAAAAATAATAATAACAAAACTATACA
6377 AAAAAATAATAATAAC-AAACTATACA
1 AAAAAATAATAATAACAAAACTATACA
* *
6403 AACAAATAAAAATAA
1 AAAAAATAATAATAA
6418 GCCAAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 28 0.78
27 8 0.22
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.19
Consensus pattern (27 bp):
AAAAAATAATAATAACAAAACTATACA
Done.