Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013742.1 Corchorus capsularis cultivar CVL-1 contig13763, 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: 11985
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3626 original size:34 final size:34
Alignment explanation
Indices: 3583--3652 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3573 TCGTATAACG
3583 TAAAATAAAAATTCAAAATAAAATTCCTCTCTTT
1 TAAAATAAAAATTCAAAATAAAATTCCTCTCTTT
3617 TAAAATAAAAATTCAAAATAAAATTCCTCTCTTT
1 TAAAATAAAAATTCAAAATAAAATTCCTCTCTTT
3651 TA
1 TA
3653 TTCGTATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAAATAAAAATTCAAAATAAAATTCCTCTCTTT
Found at i:6247 original size:36 final size:36
Alignment explanation
Indices: 6207--6278 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
6197 ATGAAGGTAA
6207 ACAGAGAGTCACCTTCTTTAGCTTCATCTTCATCAG
1 ACAGAGAGTCACCTTCTTTAGCTTCATCTTCATCAG
*
6243 ACAGAGAGTCACCTTCTTTAGCTTCATTTTCATCAG
1 ACAGAGAGTCACCTTCTTTAGCTTCATCTTCATCAG
6279 TCTCCTCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (36 bp):
ACAGAGAGTCACCTTCTTTAGCTTCATCTTCATCAG
Found at i:9526 original size:26 final size:27
Alignment explanation
Indices: 9466--9540 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
9456 TAGATAAGGA
9466 AAAAAAAAAAGAAATAAAAGTATCTCC
1 AAAAAAAAAAGAAATAAAAGTATCTCC
9493 AAAAAAAAAAGAAATAAAAGTATCTCC
1 AAAAAAAAAAGAAATAAAAGTATCTCC
** *
9520 -ACGAAAAAAGAAAAAAAAGTA
1 AAAAAAAAAAGAAATAAAAGTA
9541 GGGGAGAGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 18 0.40
27 27 0.60
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.12
Consensus pattern (27 bp):
AAAAAAAAAAGAAATAAAAGTATCTCC
Found at i:9750 original size:3 final size:3
Alignment explanation
Indices: 9742--9771 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9732 TTCATTTTTA
9742 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9772 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11068 original size:60 final size:61
Alignment explanation
Indices: 10950--11068 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 61
10940 ATTGACATGG
*
10950 TTAGAATTGATGAAATTCATTAGAGGTATCGGATTTGAGACTCTTCATCCTTAACCATCGA
1 TTAGAATTGATGAAATTCATTAGAGGTATCGGATTTGAAACTCTTCATCCTTAACCATCGA
*
11011 TTAGAATTGTTGAAATTCATTAGAGGTAT-GGATTTGAAACTCTTCATCCTTAACCATC
1 TTAGAATTGATGAAATTCATTAGAGGTATCGGATTTGAAACTCTTCATCCTTAACCATC
11069 AATAATACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 28 0.50
61 28 0.50
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (61 bp):
TTAGAATTGATGAAATTCATTAGAGGTATCGGATTTGAAACTCTTCATCCTTAACCATCGA
Found at i:11299 original size:8 final size:8
Alignment explanation
Indices: 11280--11313 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
11270 AAATACCGCC
11280 CTAATAAAA
1 CTAAT-AAA
11289 CTAATAAA
1 CTAATAAA
11297 CTAATAAA
1 CTAATAAA
*
11305 CTATTAAA
1 CTAATAAA
11313 C
1 C
11314 AATCAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (8 bp):
CTAATAAA
Found at i:11383 original size:22 final size:23
Alignment explanation
Indices: 11348--11394 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
11338 GTAGTTAATC
*
11348 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
11370 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
11393 AT
1 AT
11395 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:11406 original size:22 final size:22
Alignment explanation
Indices: 11359--11408 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
11349 TAAATTAACT
*
11359 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
11381 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
11403 AATTAA
1 AATTAA
11409 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:11409 original size:15 final size:15
Alignment explanation
Indices: 11372--11410 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11362 TAAAACTAAT
*
11372 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
11387 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
11402 AAATTAATT
1 AAACTAATT
11411 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Found at i:11505 original size:32 final size:32
Alignment explanation
Indices: 11425--11516 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 32
11415 AATAAAAAAT
*
11425 TGGCTATGCCGCCCAATTTGGGCGGCATGCCCA
1 TGGC-ATGCCGCCCATTTTGGGCGGCATGCCCA
* * *
11458 TGGCCTTGCCGCCCATTTTGGGTGGCTTGCCCA
1 TGG-CATGCCGCCCATTTTGGGCGGCATGCCCA
11491 TGGCATGCCGCCCATTTTGGGCGGCA
1 TGGCATGCCGCCCATTTTGGGCGGCA
11517 CAGTCCTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 20 0.39
33 30 0.59
34 1 0.02
ACGTcount: A:0.11, C:0.33, G:0.32, T:0.25
Consensus pattern (32 bp):
TGGCATGCCGCCCATTTTGGGCGGCATGCCCA
Found at i:11855 original size:70 final size:71
Alignment explanation
Indices: 11742--11954 Score: 403
Period size: 70 Copynumber: 3.0 Consensus size: 71
11732 TACTAGTATC
11742 TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCATAAAAAATCGGCTAAATACCC-AAAAA
1 TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCATAAAAAATCGGCTAAATACCCAAAAAA
11806 ATCCCT
66 ATCCCT
11812 TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCATAAAAAATCGGCTAAATACCCAAAAAA
1 TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCATAAAAAATCGGCTAAATACCCAAAAAA
11877 ATCCC-
66 ATCCCT
11882 TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCATAAAAAAATCGGCTAAATACCCAAAAA
1 TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCAT-AAAAAATCGGCTAAATACCCAAAAA
11947 AATCCCT
65 AATCCCT
11954 T
1 T
11955 ATGTTTTGCT
Statistics
Matches: 140, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
70 98 0.70
71 41 0.29
72 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (71 bp):
TTTTATCGAGTGAATAAGGAATTGGTTTATTTACACCATAAAAAATCGGCTAAATACCCAAAAAA
ATCCCT
Done.