Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017115.1 Corchorus olitorius cultivar O-4 contig17148, 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: 10841
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1338 original size:22 final size:22
Alignment explanation
Indices: 1312--1353 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1302 GAAGTTTCAA
* *
1312 TGATTGTTCTAAAAAATATAAG
1 TGATTATTCGAAAAAATATAAG
*
1334 TGATTATTCGAAAAACTATA
1 TGATTATTCGAAAAAATATA
1354 TTATTATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (22 bp):
TGATTATTCGAAAAAATATAAG
Found at i:2755 original size:15 final size:14
Alignment explanation
Indices: 2721--2769 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
2711 ATACATACCA
*
2721 TTAATAATAATTAT
1 TTAATAATAATAAT
2735 TATAATAATAATAAGT
1 T-TAATAATAATAA-T
*
2751 TTAATAATTATAAT
1 TTAATAATAATAAT
2765 ATTAA
1 -TTAA
2770 GATGTTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TTAATAATAATAAT
Found at i:2764 original size:9 final size:9
Alignment explanation
Indices: 2724--2765 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2714 CATACCATTA
2724 ATAATAATT
1 ATAATAATT
* *
2733 ATTATAATA
1 ATAATAATT
2742 ATAATAAGTT
1 ATAATAA-TT
2752 -TAATAATT
1 ATAATAATT
2760 ATAATA
1 ATAATA
2766 TTAAGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:2776 original size:24 final size:24
Alignment explanation
Indices: 2728--2778 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2718 CCATTAATAA
* *
2728 TAATTATTATAATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
2752 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
2776 TAA
1 TAA
2779 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:6306 original size:16 final size:16
Alignment explanation
Indices: 6285--6317 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6275 AACATGCATA
6285 TATATGTAATTAGGGG
1 TATATGTAATTAGGGG
6301 TATATGTAATTAGGGG
1 TATATGTAATTAGGGG
6317 T
1 T
6318 GTAAGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (16 bp):
TATATGTAATTAGGGG
Found at i:7813 original size:161 final size:156
Alignment explanation
Indices: 7498--7816 Score: 460
Period size: 161 Copynumber: 2.0 Consensus size: 156
7488 ATAATTTTTA
* * *
7498 AAACGGTAACATAAACCATAAATATTAATTATTAAAAGTTTTGATTTTTTTTTTTTGAAAAATTT
1 AAACGGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTAATTTTTTTTTTTTGAAAAATTT
* * *
7563 AATAGATCATTCATTCACTACTTTTATTTTGCTCTGTTAGCTTAAATCACCTTATTCCATTCATT
66 AATAGATCATTCATTCACTACTTTTATTTTGATCGGTTAACTTAAATCACCTTATTCCATTCATT
7628 ATTATGCATAAAATTGGTAGTGTAAT
131 ATTATGCATAAAATTGGTAGTGTAAT
**
7654 AAACGGTAACAGAAACAATAAATATTAATTATTAAATTTTTTTTTAAGTTTTGATTTTTTTTGAA
1 AAACGGTAACAGAAACAATAAATATTAATTATTAAA---AGTTTTAA-TTTT--TTTTTTTTGAA
* * * *
7719 AAATTTAATAGATCATTCATTCACTACTTTTA-TTTGATCGGTTAATTTAAATCACTTTCTTTCA
60 AAATTTAATAGATCATTCATTCACTACTTTTATTTTGATCGGTTAACTTAAATCACCTTATTCCA
*
7783 TTCTTTATTATGCATAAAATTGGTAGTGTAAT
125 TTCATTATTATGCATAAAATTGGTAGTGTAAT
7815 AA
1 AA
7817 TAAAAATTAA
Statistics
Matches: 144, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
156 34 0.24
159 5 0.03
160 4 0.03
161 58 0.40
162 43 0.30
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (156 bp):
AAACGGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTAATTTTTTTTTTTTGAAAAATTT
AATAGATCATTCATTCACTACTTTTATTTTGATCGGTTAACTTAAATCACCTTATTCCATTCATT
ATTATGCATAAAATTGGTAGTGTAAT
Found at i:8164 original size:22 final size:22
Alignment explanation
Indices: 8134--8175 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8124 AAGATAATAA
* *
8134 TATAGTTTTTAGAATAATCACT
1 TATACTTTTTAGAACAATCACT
8156 TATACTTTTTAGAACAATCA
1 TATACTTTTTAGAACAATCA
8176 TTGAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAGAACAATCACT
Found at i:8187 original size:23 final size:22
Alignment explanation
Indices: 8139--8187 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
8129 AATAATATAG
* *
8139 TTTTTAGAATAATCACTTATAC
1 TTTTTAGAACAATCACTTAAAC
8161 TTTTTAGAACAATCA-TTGAAAC
1 TTTTTAGAACAATCACTT-AAAC
8183 TTTTT
1 TTTTT
8188 TAGTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (22 bp):
TTTTTAGAACAATCACTTAAAC
Done.