Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011114.1 Corchorus capsularis cultivar CVL-1 contig11135, 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: 61074
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1105 original size:17 final size:18
Alignment explanation
Indices: 1066--1099 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1056 GAATATTGTT
*
1066 TTAAAAACATTAAAGAAC
1 TTAAAAACATGAAAGAAC
1084 TTAAAAA-ATGAAAGAA
1 TTAAAAACATGAAAGAA
1100 TGTAAAGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (18 bp):
TTAAAAACATGAAAGAAC
Found at i:1226 original size:2 final size:2
Alignment explanation
Indices: 1219--1249 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1209 TAAATTAATA
1219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1250 GTTCCAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5524 original size:30 final size:31
Alignment explanation
Indices: 5446--5527 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
5436 TCTTTGGCTT
* *
5446 AATGCACAATTTGCACCCTAAACTGTAAGCA
1 AATGGACAATTTGCACCCTAAACTATAAGCA
*
5477 AATGGACAATTTGCACCCTAAACTATAA-CT
1 AATGGACAATTTGCACCCTAAACTATAAGCA
* * *
5507 TATGGCCAATATGCACCCTAA
1 AATGGACAATTTGCACCCTAA
5528 TTGGACGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 19 0.42
31 26 0.58
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (31 bp):
AATGGACAATTTGCACCCTAAACTATAAGCA
Found at i:16875 original size:56 final size:56
Alignment explanation
Indices: 16803--16914 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
16793 TGGTATTCAT
16803 TCATACTAGTGATTGTATCATTAGAGCTAGGAAAACATAAATAGATTTATATACAA
1 TCATACTAGTGATTGTATCATTAGAGCTAGGAAAACATAAATAGATTTATATACAA
16859 TCATACTAGTGATTGTATCATTAGAGCTAGGAAAACATAAATAGATTTATATACAA
1 TCATACTAGTGATTGTATCATTAGAGCTAGGAAAACATAAATAGATTTATATACAA
16915 GGTTGTATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (56 bp):
TCATACTAGTGATTGTATCATTAGAGCTAGGAAAACATAAATAGATTTATATACAA
Found at i:30120 original size:7 final size:7
Alignment explanation
Indices: 30108--30147 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
30098 CTCTCTCTGA
30108 TGAGAAG
1 TGAGAAG
30115 TGAGAAG
1 TGAGAAG
30122 TGAGAAG
1 TGAGAAG
*
30129 TGAGAAC
1 TGAGAAG
*
30136 TGAGAAC
1 TGAGAAG
30143 TGAGA
1 TGAGA
30148 GAGGAGGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.42, C:0.05, G:0.38, T:0.15
Consensus pattern (7 bp):
TGAGAAG
Found at i:36670 original size:6 final size:6
Alignment explanation
Indices: 36656--36688 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
36646 GTAGAATTCC
36656 AAAAA- AAAAAG -AAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
36689 CAAACCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:48472 original size:85 final size:84
Alignment explanation
Indices: 48315--48487 Score: 328
Period size: 84 Copynumber: 2.0 Consensus size: 84
48305 CTTGCCGGTA
*
48315 TTTTACTTGCACTTACAATGCTATCAGATGTTGTATAAGATTCTCTATATAGTATAAGCCCTACA
1 TTTTACTTGCACTTACAATGCTATCAGATGTTGTATAAGATTCTCTATATAGTATAAGCCCTAAA
48380 TTACTTCTCTTTAACTGCT
66 TTACTTCTCTTTAACTGCT
48399 TTTTACTTGCACTTACAATGCTATCAGATGTTGTATAAGATTCTCTAATATAGTATAAGCCCTAA
1 TTTTACTTGCACTTACAATGCTATCAGATGTTGTATAAGATTCTCT-ATATAGTATAAGCCCTAA
48464 ATTACTTCTCTTTAACTGCT
65 ATTACTTCTCTTTAACTGCT
48484 TTTT
1 TTTT
48488 TGCAGGGATG
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 46 0.53
85 41 0.47
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (84 bp):
TTTTACTTGCACTTACAATGCTATCAGATGTTGTATAAGATTCTCTATATAGTATAAGCCCTAAA
TTACTTCTCTTTAACTGCT
Found at i:59683 original size:35 final size:37
Alignment explanation
Indices: 59632--59702 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 37
59622 CTTACACTAT
*
59632 TAATCATTTTTTTTCTGATAATTCAAT-GATGCTTGC
1 TAATCATTTTCTTTCTGATAATTCAATAGATGCTTGC
*
59668 TAATC-TTTTCTTTCTGATAATTCCATAGATGCTTG
1 TAATCATTTTCTTTCTGATAATTCAATAGATGCTTG
59703 TTAAAAGCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 19 0.59
36 13 0.41
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.49
Consensus pattern (37 bp):
TAATCATTTTCTTTCTGATAATTCAATAGATGCTTGC
Found at i:60591 original size:40 final size:40
Alignment explanation
Indices: 60547--60628 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
60537 ACTTTTCAAT
60547 TCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAA
1 TCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAA
60587 TCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAA
1 TCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAA
60627 TC
1 TC
60629 ATTCAAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (40 bp):
TCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAA
Done.