Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013634.1 Corchorus olitorius cultivar O-4 contig13667, 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: 16830
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Found at i:5427 original size:26 final size:27
Alignment explanation
Indices: 5390--5441 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5380 ACGGGAGTAG
5390 TGGACAAATAG-TATTTGATGATGTAC
1 TGGACAAATAGTTATTTGATGATGTAC
* *
5416 TGGACAAGTAGTTATTTGGTGATGTA
1 TGGACAAATAGTTATTTGATGATGTA
5442 ATTAAGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.37
Consensus pattern (27 bp):
TGGACAAATAGTTATTTGATGATGTAC
Found at i:13093 original size:1 final size:1
Alignment explanation
Indices: 13087--13111 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
13077 AGGGGAATTT
13087 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
13112 CTAAGACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13160 original size:40 final size:41
Alignment explanation
Indices: 13102--13215 Score: 176
Period size: 42 Copynumber: 2.8 Consensus size: 41
13092 AAAAAAAAAA
*
13102 AAAAAAAAAACTAAGACCTAAAATAGAAAGAGGTC-GAAATG
1 AAAAAAAAAACT-TGACCTAAAATAGAAAGAGGTCGGAAATG
*
13143 AAAAAAAAAACTTGACCTAAAACAGAAAGAGGTCGGAAATG
1 AAAAAAAAAACTTGACCTAAAATAGAAAGAGGTCGGAAATG
*
13184 AAAAGAAAAAACTTGGCCTAAAATAGAAAGAG
1 AAAA-AAAAAACTTGACCTAAAATAGAAAGAG
13216 TTCTTAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
40 20 0.30
41 22 0.33
42 25 0.37
ACGTcount: A:0.59, C:0.11, G:0.18, T:0.12
Consensus pattern (41 bp):
AAAAAAAAAACTTGACCTAAAATAGAAAGAGGTCGGAAATG
Found at i:14417 original size:117 final size:116
Alignment explanation
Indices: 14127--14583 Score: 383
Period size: 117 Copynumber: 3.9 Consensus size: 116
14117 TCTTGTCTTG
* * * * ** *
14127 TTTTTAAAATCCTGCTCGAGGTTTCTGGTCGAGAGATTTC-AATCCAAA-ATCTTGTCTCATTTT
1 TTTTAAAAATCCTGTTCGAGGTCTCTGGTCGAGAG-TTTCTATTTAAAATATCTTGTTTCA--TT
* * * * * * * *
14190 TAAATCCTGCTCGAGGTCTTTGGTCAAGAGTTTTCAATTT-AAA-ATCTTGTCTT-G
63 AAAATCATGTTCGAGGTCTCTAGTCGAGAGTTTT--GTTTCAAATATCTTGT-TTCA
** * * *
14244 TTTTAAAAA-CCTACTCGAGGTCTTTGGTCGAGAGTTTTCAATTTCAAATATCTTGTTTCATTAA
1 TTTTAAAAATCCTGTTCGAGGTCTCTGGTCGAGAG-TTTCTATTTAAAATATCTTGTTTCATTAA
* *
14308 AATCTTGTTCGAGGTCTCTAGTCGAGAGTTTTTGTTTCAAGTATCTTGTTTCA
65 AATCATGTTCGAGGTCTCTAGTCGAGAG-TTTTGTTTCAAATATCTTGTTTCA
* *
14361 TTTTAAAAATCCTGTTCGAGGTCTCTAGTCGAGAGTTTCTGTTTAAAATATCTTGTTTCATTTTA
1 TTTTAAAAATCCTGTTCGAGGTCTCTGGTCGAGAGTTTCTATTTAAAATATCTTGTTTCA--TTA
* * * * *
14426 AAATCCTGTTCAAGGTCTCTAGTCGAGAGATCTATTTCAAATATCTTGTTTCA
64 AAATCATGTTCGAGGTCTCTAGTCGAGAGTTTTGTTTCAAATATCTTGTTTCA
* * * * * *
14479 TTTT-AAAATCATGTTTGAGGTCGCTGGTCGAGAGTTACTATTTCAAAA-ATATTGTTTCGTTTT
1 TTTTAAAAATCCTGTTCGAGGTCTCTGGTCGAGAGTTTCTATTT-AAAATATCTTGTTTC--ATT
* * *
14542 TAAATCATGTTTGAGGTCTCT-GTTCGAGAATTTTGTTTCAAA
63 AAAATCATGTTCGAGGTCTCTAG-TCGAGAGTTTTGTTTCAAA
14584 AAGCCCCGCT
Statistics
Matches: 281, Mismatches: 46, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
115 3 0.01
116 57 0.20
117 132 0.47
118 59 0.21
119 30 0.11
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (116 bp):
TTTTAAAAATCCTGTTCGAGGTCTCTGGTCGAGAGTTTCTATTTAAAATATCTTGTTTCATTAAA
ATCATGTTCGAGGTCTCTAGTCGAGAGTTTTGTTTCAAATATCTTGTTTCA
Found at i:14549 original size:59 final size:59
Alignment explanation
Indices: 14128--14583 Score: 401
Period size: 58 Copynumber: 7.8 Consensus size: 59
14118 CTTGTCTTGT
* * * * * * *
14128 TTTTAAAATCCTGCTCGAGGTTTCTGGTCGAGAGATTTC-AATCCAAA-ATCTTGTCTCA
1 TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAG-TTTCTATTTCAAATATCTTGTTTCA
* * * * * * * *
14186 TTTTTAAATCCTGCTCGAGGTCTTTGGTCAAGAGTTTTCAATTT-AAA-ATCTTGTCTT-G
1 TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAG-TTTCTATTTCAAATATCTTGT-TTCA
* * ** * * *
14244 TTTTAAAAACCTACTCGAGGTCTTTGGTCGAGAGTTTTCAATTTCAAATATCTTGTTTCA
1 TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAG-TTTCTATTTCAAATATCTTGTTTCA
* * * *
14304 --TTAAAATCTTGTTCGAGGTCTCTAGTCGAGAGTTTTTGTTTCAAGTATCTTGTTTCA
1 TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAGTTTCTATTTCAAATATCTTGTTTCA
* * *
14361 TTTTAAAAATCCTGTTCGAGGTCTCTAGTCGAGAGTTTCTGTTTAAAATATCTTGTTTCA
1 TTTT-AAAATCATGTTCGAGGTCTCTAGTCGAGAGTTTCTATTTCAAATATCTTGTTTCA
* * *
14421 TTTTAAAATCCTGTTCAAGGTCTCTAGTCGAGAG-ATCTATTTCAAATATCTTGTTTCA
1 TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAGTTTCTATTTCAAATATCTTGTTTCA
* * * * * * *
14479 TTTTAAAATCATGTTTGAGGTCGCTGGTCGAGAGTTACTATTTCAAAAATATTGTTTCG
1 TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAGTTTCTATTTCAAATATCTTGTTTCA
* * * *
14538 TTTTTAAATCATGTTTGAGGTCTCT-GTTCGAGAATTT-TGTTTCAAA
1 TTTTAAAATCATGTTCGAGGTCTCTAG-TCGAGAGTTTCTATTTCAAA
14584 AAGCCCCGCT
Statistics
Matches: 341, Mismatches: 47, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
57 21 0.06
58 169 0.50
59 89 0.26
60 62 0.18
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (59 bp):
TTTTAAAATCATGTTCGAGGTCTCTAGTCGAGAGTTTCTATTTCAAATATCTTGTTTCA
Found at i:14920 original size:15 final size:15
Alignment explanation
Indices: 14902--14946 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
14892 CTTTCATTCG
14902 TATTAATCACATTAA
1 TATTAATCACATTAA
14917 TATTAATCACATTAA
1 TATTAATCACATTAA
14932 TATTAATCACATTAA
1 TATTAATCACATTAA
14947 GAACATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTAATCACATTAA
Found at i:15208 original size:15 final size:15
Alignment explanation
Indices: 15188--15217 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15178 TACAAATGTC
*
15188 CAAAGAAAGAAAAAA
1 CAAAGAAACAAAAAA
15203 CAAAGAAACAAAAAA
1 CAAAGAAACAAAAAA
15218 AGAGGGTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (15 bp):
CAAAGAAACAAAAAA
Done.