Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014999.1 Corchorus olitorius cultivar O-4 contig15032, 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: 7687
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:748 original size:35 final size:36
Alignment explanation
Indices: 698--1495 Score: 936
Period size: 35 Copynumber: 22.9 Consensus size: 36
688 GCCCACCGAG
* *
698 TTCA-TTTTGAAGATGCTACATCGAGTCATCCGAGA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
733 -TCATTTTTGAAGATGCTACACCGAGTCATCTGA-A
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* * *
767 TTCGTTTTTGAAGATGCTACACTGAGTCACCTGA-A
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* * *
802 TTCGTTTTTTGAAGATGCTACACTGAGTCACCTGA-A
1 TTC-ATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* *
838 TTCCTCTTTGAAGATGCTACACCGAGTCATCTG-GA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
873 CTT-ATTTTTGAAGATGCTACACCGAGTCATCTG-GA
1 -TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
908 CTT-ATTTTTGAAGATGCTACACCGAGTCATCTG-GA
1 -TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* * *
943 CTT-ATTTATGAGGATGCTACACTGAGTCATCTG-GA
1 -TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* ** *
978 TTTACCTTTGAAGATGCTACACCGAGTCATCTGGGA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
1014 -TCATTTTTGAAGATGCTACACCGAGTCATCTGA-A
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
*
1048 TTCATGTTTGAAGATGCTACACCGAGTCATCTGAGA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
1084 -TCATTTTTGAAGATGCTACACCGAGTCATCTGA-A
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
** *
1118 TTCAACTTTGAGGATGCTACACCGAGTCATCTGAG-
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* * *
1153 TTCAATTTTGAAGATGCTCCGCCGAGTCATCTGAG-
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* * *
1188 TTCAATTTTGAAGATGTTGCACC--GTCATCTG-GA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* *
1221 TTCAATTTTGAAGATGCTACACCGAGTTATCTG-GA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
** * * *
1256 TTCAACTTTGAAGATGCTGCATCGAGTCATCCGAGA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
*
1292 -TCATTTTTGAAGATGCTACACCGAGTTATCTG-GA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
** *
1326 TTCAACTTTGAGGATGCTACACCGAGTCATCTGAG-
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
*
1361 GTCATTTTTGAAGATGCTACACC-AGTCATCT--GA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
* * * *
1394 TTCATCTTTGAAAATGCTGCACCGAGTCATCCGAGA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
1430 -TCATTTTTGAAGATGCTACACCGAGTCATCTG-GA
1 TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
** *
1464 TTCAACTTTGAGGATGCTACACCGAGTCATCT
1 TTCATTTTTGAAGATGCTACACCGAGTCATCT
1496 AAGAAGCTGG
Statistics
Matches: 671, Mismatches: 70, Indels: 44
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.00
33 48 0.07
34 27 0.04
35 550 0.82
36 44 0.07
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (36 bp):
TTCATTTTTGAAGATGCTACACCGAGTCATCTGAGA
Found at i:1591 original size:50 final size:50
Alignment explanation
Indices: 1513--1696 Score: 289
Period size: 50 Copynumber: 3.7 Consensus size: 50
1503 TGGTAATGTA
* * *
1513 TCGTATGG-AACGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGAC
1 TCGTATGGAAACG-AGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
* *
1563 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGCTGAAAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
*
1613 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATCGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
*
1663 TCGTATGGAAACGAGTTTGACTTGTGGAAAAGCC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1697 AAACATTCGG
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 120 0.97
51 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (50 bp):
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
Found at i:2352 original size:50 final size:50
Alignment explanation
Indices: 2298--2445 Score: 190
Period size: 50 Copynumber: 3.0 Consensus size: 50
2288 CTTAAATGCC
* * *
2298 CTTTGAAAAACGAATTTTGATATTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAACGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTA
* * *
2348 CTTTGAAAAGCGAATTTTAATCTT-GAGCTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAACGAATTTTGATCTTGGA-CTCACAAATGGAAAGCAATCTTA
* * * *
2398 TTTTGAAAAACGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCT
1 CTTTGAAAAACGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCT
2446 AGTTATAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 80 0.96
51 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAACGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTA
Found at i:3042 original size:6 final size:6
Alignment explanation
Indices: 3031--3074 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
3021 ATCAATTCTC
3031 TTTTGA TTTTGA TTTTGA -TTTGA -TTTGA TTTTTGA TTTT-A TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTT
3075 TTCTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.42
6 16 0.44
7 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:3054 original size:17 final size:18
Alignment explanation
Indices: 3032--3074 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
3022 TCAATTCTCT
3032 TTTGATTTTGA-TTTTGA
1 TTTGATTTTGATTTTTGA
3049 TTTGA-TTTGATTTTTGA
1 TTTGATTTTGATTTTTGA
*
3066 TTTTATTTT
1 TTTGATTTT
3075 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 15 0.65
18 3 0.13
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (18 bp):
TTTGATTTTGATTTTTGA
Found at i:3536 original size:22 final size:21
Alignment explanation
Indices: 3496--3539 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
3486 TCTAAGTGCC
3496 TTTATTTTCCTTTTTTCATTT
1 TTTATTTTCCTTTTTTCATTT
3517 TTTATTTT-CTTCATTTTCATTT
1 TTTATTTTCCTT--TTTTCATTT
3539 T
1 T
3540 CATTTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTCCTTTTTTCATTT
Found at i:3538 original size:15 final size:15
Alignment explanation
Indices: 3499--3540 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3489 AAGTGCCTTT
*
3499 ATTTTCCTTTT-TTC
1 ATTTTCATTTTCTTC
*
3513 ATTTTTTATTTTCTTC
1 A-TTTTCATTTTCTTC
3529 ATTTTCATTTTC
1 ATTTTCATTTTC
3541 ATTTTCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCATTTTCTTC
Found at i:4690 original size:42 final size:42
Alignment explanation
Indices: 4644--4726 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
4634 GATCTATGCC
* * *
4644 TGAACACATATACAAAGGAATGAATAATGCCTGATGGATGTG
1 TGAACACATATACAAAGGAATGAACAATGCATGAAGGATGTG
* * *
4686 TGAACATATATACAAAGGCATGGACAATGCATGAAGGATGT
1 TGAACACATATACAAAGGAATGAACAATGCATGAAGGATGT
4727 ATGATCTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (42 bp):
TGAACACATATACAAAGGAATGAACAATGCATGAAGGATGTG
Done.