Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013133.1 Corchorus capsularis cultivar CVL-1 contig13154, 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: 25425
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:221 original size:33 final size:34
Alignment explanation
Indices: 143--288 Score: 185
Period size: 33 Copynumber: 4.4 Consensus size: 34
133 TAGACAAAGG
* *
143 GTCGCGTGGCCGGTTG-TGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCC-AT
** * *
176 GTCGTTTAGCCGGTTG-TAGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT
*
209 GTCGCGTGGCCGG-TGATGGTCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT
242 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT
275 GTCGCGTGGCCGGT
1 GTCGCGTGGCCGGT
289 GTTGCGCGGC
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
32 3 0.03
33 95 0.97
ACGTcount: A:0.10, C:0.26, G:0.40, T:0.23
Consensus pattern (34 bp):
GTCGCGTGGCCGGTTGATGGCCGGACATGTCCAT
Found at i:409 original size:30 final size:30
Alignment explanation
Indices: 373--433 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
363 TCTACATGAT
373 CTTCATTGGCTCCAATGTGTTCTTCTAAGC
1 CTTCATTGGCTCCAATGTGTTCTTCTAAGC
403 CTTCATTGGCTCCAATGTGTTCTTCTAAGC
1 CTTCATTGGCTCCAATGTGTTCTTCTAAGC
433 C
1 C
434 ATGATAAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.39
Consensus pattern (30 bp):
CTTCATTGGCTCCAATGTGTTCTTCTAAGC
Found at i:9753 original size:81 final size:81
Alignment explanation
Indices: 9659--9822 Score: 310
Period size: 81 Copynumber: 2.0 Consensus size: 81
9649 GCAGCCTATC
*
9659 TATACTAACTAAAAATAAAACCCTAATTCTAAGAAAAACTTAAATTATTTGACGGCCAAAACATA
1 TATACTAACTAAAAATAAAACCCTAATTCTAAGAAAAACTAAAATTATTTGACGGCCAAAACATA
9724 AAACCTAAAAAGCCCA
66 AAACCTAAAAAGCCCA
*
9740 TATACTAACTAAAAATAAAACCTTAATTCTAAGAAAAACTAAAATTATTTGACGGCCAAAACATA
1 TATACTAACTAAAAATAAAACCCTAATTCTAAGAAAAACTAAAATTATTTGACGGCCAAAACATA
9805 AAACCTAAAAAGCCCA
66 AAACCTAAAAAGCCCA
9821 TA
1 TA
9823 AAAGCCCATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (81 bp):
TATACTAACTAAAAATAAAACCCTAATTCTAAGAAAAACTAAAATTATTTGACGGCCAAAACATA
AAACCTAAAAAGCCCA
Found at i:23889 original size:70 final size:70
Alignment explanation
Indices: 23649--23895 Score: 370
Period size: 71 Copynumber: 3.5 Consensus size: 70
23639 GATCAACTGG
* * *
23649 AAACAACTGATGAAAAACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
1 AAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTAGATAAA
23714 CTTG-
66 CTTGA
* * * *
23718 AAACAACTGAAGAAAGATCGCCCTGGGTCGACTGAATCGATAATTCTGACATAAACTTCGAATAA
1 AAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTAG-ATAA
23783 ACTTGA
65 ACTTGA
* * *
23789 AAACAACTAAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTAGATAAA
1 AAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTAGATAAA
23854 CTTGA
66 CTTGA
* *
23859 AAACAATTGAAGAAAGACCACCCTGGGTCGACCGAAT
1 AAACAACTGAAGAAAGACCACCCTGGGTCGACTGAAT
23896 TGCATTGAAG
Statistics
Matches: 160, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
69 54 0.34
70 51 0.32
71 55 0.34
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (70 bp):
AAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTAGATAAA
CTTGA
Found at i:25013 original size:5 final size:5
Alignment explanation
Indices: 25012--25045 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
25002 CATTTTTCTT
25012 TTTTC TTTTC TTTTC TTTTC TTTCTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC TTTT
25046 TTTCAATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:25032 original size:15 final size:15
Alignment explanation
Indices: 25010--25049 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
25000 TTCATTTTTC
25010 TTTTTTCTTT-TCTT
1 TTTTTTCTTTCTCTT
25024 TTCTTTTCTTTCTCTT
1 TT-TTTTCTTTCTCTT
25040 TTTTTT-TTTC
1 TTTTTTCTTTC
25050 AATGCACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.25
15 12 0.50
16 6 0.25
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTCTCTT
Done.