Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015129.1 Corchorus olitorius cultivar O-4 contig15162, 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: 24600
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:696 original size:28 final size:28
Alignment explanation
Indices: 628--704 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
618 ACGTGAACTT
* * *
628 AAAATGACCAAAATACCCCCGAATGTGC
1 AAAATGACCAAAATGCCCCTGAATGTGA
656 AAAATGACCAAAATGCCCCTGAATGT-A
1 AAAATGACCAAAATGCCCCTGAATGTGA
*
683 AAAATGACTGAAAAATGCCCCT
1 AAAATGAC--CAAAATGCCCCT
705 ATGTGACTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 8 0.19
28 24 0.56
29 11 0.26
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATGTGA
Found at i:6526 original size:8 final size:8
Alignment explanation
Indices: 6511--6550 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
6501 TTCAATCTCG
6511 AATCTTCA
1 AATCTTCA
*
6519 AGTCTTCA
1 AATCTTCA
6527 AATCTTCA
1 AATCTTCA
*
6535 AGTCTTCA
1 AATCTTCA
6543 AATCTTCA
1 AATCTTCA
6551 CTCAAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (8 bp):
AATCTTCA
Found at i:6532 original size:16 final size:16
Alignment explanation
Indices: 6511--6550 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
6501 TTCAATCTCG
6511 AATCTTCAAGTCTTCA
1 AATCTTCAAGTCTTCA
6527 AATCTTCAAGTCTTCA
1 AATCTTCAAGTCTTCA
6543 AATCTTCA
1 AATCTTCA
6551 CTCAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (16 bp):
AATCTTCAAGTCTTCA
Found at i:8805 original size:32 final size:31
Alignment explanation
Indices: 8729--8838 Score: 87
Period size: 32 Copynumber: 3.4 Consensus size: 31
8719 GTGATTTAGG
* *
8729 AATAGGGGCGTTTTTAGCTGTAAACGCCGCTA
1 AATA-GGGCGTTTTTAGCTGAAAAAGCCGCTA
* * *
8761 AATAGAGACGTTTTTGGTTGAAAAAGCCGCTA
1 AATAG-GGCGTTTTTAGCTGAAAAAGCCGCTA
*** *
8793 AATATGGGCGTTTTTTTAT-AGAAACGCCGCTA
1 AATA-GGGCGTTTTTAGCTGA-AAAAGCCGCTA
8825 AATAGTGGCGTTTT
1 AATAG-GGCGTTTT
8839 GTTCAAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
31 3 0.05
32 60 0.94
33 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (31 bp):
AATAGGGCGTTTTTAGCTGAAAAAGCCGCTA
Found at i:8849 original size:64 final size:65
Alignment explanation
Indices: 8750--8870 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 65
8740 TTTTAGCTGT
*
8750 AAACGCCGCTAAATAGAGACGTTTTTGGTTGAAAAA-GCCGCTAAATATG-GGCGTTTTTTTATA
1 AAACGCCGCTAAATAGAGACGTTTTTGGTTAAAAAACGCCGCTAAAT-TGTGGCGTTTTTTTATA
8813 G
65 G
* * *
8814 AAACGCCGCTAAATAGTGGCG-TTTT-GTTCAAAAAAACGCCTCTAAATTGTGGCGTTT
1 AAACGCCGCTAAATAGAGACGTTTTTGGTT--AAAAAACGCCGCTAAATTGTGGCGTTT
8871 CAATTAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
62 3 0.06
63 4 0.08
64 26 0.53
65 16 0.33
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
AAACGCCGCTAAATAGAGACGTTTTTGGTTAAAAAACGCCGCTAAATTGTGGCGTTTTTTTATAG
Found at i:8859 original size:33 final size:32
Alignment explanation
Indices: 8750--8870 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 32
8740 TTTTAGCTGT
* * **
8750 AAACGCCGCTAAATAGAGACGTTTTTGGT-TGAA
1 AAACGCCGCTAAATAGTGGCGTTTTT--TCAAAA
* * *
8783 AAA-GCCGCTAAATA-TGGGCGTTTTTTTATAG
1 AAACGCCGCTAAATAGT-GGCGTTTTTTCAAAA
8814 AAACGCCGCTAAATAGTGGCGTTTTGTTCAAAA
1 AAACGCCGCTAAATAGTGGCGTTTT-TTCAAAA
* *
8847 AAACGCCTCTAAATTGTGGCGTTT
1 AAACGCCGCTAAATAGTGGCGTTT
8871 CAATTAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.01
31 4 0.05
32 38 0.52
33 30 0.41
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (32 bp):
AAACGCCGCTAAATAGTGGCGTTTTTTCAAAA
Found at i:8880 original size:33 final size:32
Alignment explanation
Indices: 8781--8885 Score: 83
Period size: 32 Copynumber: 3.3 Consensus size: 32
8771 TTTTTGGTTG
* *
8781 AAAAA-GCCGCTAAATA-TGGGCGTTT-TTTTA
1 AAAAACGCCGCTAAATAGT-GGCGTTTAATTCA
* **
8811 TAGAAACGCCGCTAAATAGTGGCGTTTTGTTCAA
1 -AAAAACGCCGCTAAATAGTGGCGTTTAATTC-A
* *
8845 AAAAACGCCTCTAAATTGTGGCGTTTCAATT-A
1 AAAAACGCCGCTAAATAGTGGCGTTT-AATTCA
8877 AAAAACGCC
1 AAAAACGCC
8886 CCTGTTTAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
31 4 0.07
32 28 0.46
33 26 0.43
34 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (32 bp):
AAAAACGCCGCTAAATAGTGGCGTTTAATTCA
Found at i:11980 original size:1 final size:1
Alignment explanation
Indices: 11974--12005 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
11964 TATATGTGTG
*
11974 TTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12006 AGACTTGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:11995 original size:16 final size:16
Alignment explanation
Indices: 11974--12004 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11964 TATATGTGTG
11974 TTTTTTTTTTTTTTTC
1 TTTTTTTTTTTTTTTC
11990 TTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTT
12005 TAGACTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTC
Found at i:12584 original size:31 final size:30
Alignment explanation
Indices: 12549--12607 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
12539 CATTTTTCCA
*
12549 ATTTAGGGGCATTTTCATACGAAACGCCATC
1 ATTTAGGGGCATTTT-ATAAGAAACGCCATC
* * *
12580 ATTTAGTGGCGTTTTTTAAGAAACGCCA
1 ATTTAGGGGCATTTTATAAGAAACGCCA
12608 CTATTCTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (30 bp):
ATTTAGGGGCATTTTATAAGAAACGCCATC
Found at i:14505 original size:64 final size:64
Alignment explanation
Indices: 14402--14557 Score: 258
Period size: 64 Copynumber: 2.4 Consensus size: 64
14392 TTGTTTAAAA
*
14402 TAATATATTGGGATAATACTGAATTAATAATATTTTAAAATATTTTTAATTTACTCAACCAAAC
1 TAATATATTGGGATAATACTGAATTAATAATATTTTAAAATATTTTTAATTCACTCAACCAAAC
* *
14466 TGATATATTGGGATAATACTGAATTAATAATATTTTAAAATATTTTTAATTCACTCACCCAAAC
1 TAATATATTGGGATAATACTGAATTAATAATATTTTAAAATATTTTTAATTCACTCAACCAAAC
* * *
14530 TAATACATTGGGATATTACTTAATTAAT
1 TAATATATTGGGATAATACTGAATTAAT
14558 GACTCTCTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 85 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (64 bp):
TAATATATTGGGATAATACTGAATTAATAATATTTTAAAATATTTTTAATTCACTCAACCAAAC
Found at i:21811 original size:15 final size:16
Alignment explanation
Indices: 21784--21813 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21774 CTTTGTTTTG
21784 TTTTCTAGTTTAATTA
1 TTTTCTAGTTTAATTA
21800 TTTTCT-GTTTAATT
1 TTTTCTAGTTTAATT
21814 GCTTTCTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTCTAGTTTAATTA
Found at i:22239 original size:30 final size:28
Alignment explanation
Indices: 22205--22268 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
22195 TGCGTTTTTG
22205 AAAAAAAAAAGATAGTTTTGCGTCATATA
1 AAAAAAAAAAGATAGTTTTGCGTCATA-A
* * **
22234 TAAAAAAAAACGTTTTTTTTGCGTCATAA
1 -AAAAAAAAAAGATAGTTTTGCGTCATAA
22263 AAAAAA
1 AAAAAA
22269 TTTTGCGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.20
29 1 0.03
30 23 0.77
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (28 bp):
AAAAAAAAAAGATAGTTTTGCGTCATAA
Done.