Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021211.1 Corchorus olitorius cultivar O-4 contig21244, 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: 28231
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:2610 original size:27 final size:29
Alignment explanation
Indices: 2564--2641 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
2554 ATGTGAACTT
**
2564 AAAATGACCAAAATAACCCT-GA-ACATG
1 AAAATGACCAAAATGCCCCTAGATACATG
* * * *
2591 CAAATGACTAAAATGCCCCTAGATTCTTG
1 AAAATGACCAAAATGCCCCTAGATACATG
2620 AAAATGACCAAAATGCCCCTAG
1 AAAATGACCAAAATGCCCCTAG
2642 GTGATCCTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 16 0.39
28 2 0.05
29 23 0.56
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTAGATACATG
Found at i:2952 original size:21 final size:22
Alignment explanation
Indices: 2928--2983 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
2918 GTTGCTGCAT
*
2928 ACTTTCAATCGATTGACA-TTC
1 ACTTTCAATCGATTGAAATTTC
*
2949 AC-TTCAATCGACTGAAATTTC
1 ACTTTCAATCGATTGAAATTTC
*
2970 A-TTTCAATTGATTG
1 ACTTTCAATCGATTG
2984 TACAATTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (22 bp):
ACTTTCAATCGATTGAAATTTC
Found at i:5892 original size:14 final size:14
Alignment explanation
Indices: 5870--5899 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5860 ATATACCACG
*
5870 AAGGCAAAAAAAAA
1 AAGGAAAAAAAAAA
5884 AAGGAAAAAAAAAA
1 AAGGAAAAAAAAAA
5898 AA
1 AA
5900 AAACAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (14 bp):
AAGGAAAAAAAAAA
Found at i:5893 original size:13 final size:14
Alignment explanation
Indices: 5870--5898 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5860 ATATACCACG
5870 AAGGCAAAAAAAAA
1 AAGGCAAAAAAAAA
5884 AAGG-AAAAAAAAA
1 AAGGCAAAAAAAAA
5897 AA
1 AA
5899 AAAACAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (14 bp):
AAGGCAAAAAAAAA
Found at i:7642 original size:21 final size:21
Alignment explanation
Indices: 7612--7666 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
7602 ATTGGCATAG
* *
7612 TTTAGATTTAATTTACTTTGC-
1 TTTATATTTAATTTA-ATTGCT
* *
7633 TTTATTTTTAGTTTAATTGCT
1 TTTATATTTAATTTAATTGCT
7654 TTTATATTTAATT
1 TTTATATTTAATT
7667 GTTTTAATCC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTATATTTAATTTAATTGCT
Found at i:8172 original size:50 final size:49
Alignment explanation
Indices: 8097--8246 Score: 194
Period size: 50 Copynumber: 3.0 Consensus size: 49
8087 AGGAGTCTTG
*
8097 ATAATTACCATAATTATCTCTAATATATAAAGATAATATGGTTAATAAAT
1 ATAATCACCAT-ATTATCTCTAATATATAAAGATAATATGGTTAATAAAT
* * *
8147 ATAATCACCATCATTATTTCTAATATAGATAGATAATATGGTTAAT-AAT
1 ATAATCACCAT-ATTATCTCTAATATATAAAGATAATATGGTTAATAAAT
* *
8196 ATAATCACCATAGTTATCTCTAATATATATATGGTTAATATGGTTAATAAA
1 ATAATCACCATA-TTATCTCTAATATATA-A-AGATAATATGGTTAATAAA
8247 GCTAACAAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
48 1 0.01
49 28 0.33
50 41 0.48
51 14 0.16
52 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (49 bp):
ATAATCACCATATTATCTCTAATATATAAAGATAATATGGTTAATAAAT
Found at i:10080 original size:182 final size:183
Alignment explanation
Indices: 9854--10208 Score: 532
Period size: 182 Copynumber: 1.9 Consensus size: 183
9844 GTACAAATGG
*
9854 AAATCTATCATAAAAAAGACAGAACAAATAGGCAATAAAATGCGAAAAACAAATGAACCATGCAT
1 AAATCCATCATAAAAAAGACAGAACAAATAGGCAATAAAATGCGAAAAACAAATGAACCATGCAT
* *
9919 AAAAAAGTTAACCCGCAAAGAGAAGAAAC-AAAAAGATACTTGAAATCAGTTACATAGTTGTCAT
66 AAAAAAGTTAACCCACAAAGAGAAGAAACAAAAAAGATACTTGAAATCAGTTACATAGTTATCAT
9983 CAGTCAGTCCCTTTGTGGTGATCAAAATTCTCGTTGATGGATAGCATAGATGA
131 CAGTCAGTCCCTTTGTGGTGATCAAAATTCTCGTTGATGGATAGCATAGATGA
* * ** *
10036 AAATCCATCATAAAAAAGACATAATAAATAGGCAATGGAATGCGAAAAACAAATGAGCCATGCAT
1 AAATCCATCATAAAAAAGACAGAACAAATAGGCAATAAAATGCGAAAAACAAATGAACCATGCAT
* ** * *
10101 AAAAAATTTAACCCACGTAGAGAAGAAACAAAAAAAAGATGCTTGAAATGAGTTACATAGTTATC
66 AAAAAAGTTAACCCACAAAGAGAAGAAAC--AAAAAAGATACTTGAAATCAGTTACATAGTTATC
** **
10166 ATCAGTGTGTCCCTTTGTGGTGATCAAGCTTCTCGTTGATGGA
129 ATCAGTCAGTCCCTTTGTGGTGATCAAAATTCTCGTTGATGGA
10209 CAACTTTGGA
Statistics
Matches: 153, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
182 84 0.55
185 69 0.45
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (183 bp):
AAATCCATCATAAAAAAGACAGAACAAATAGGCAATAAAATGCGAAAAACAAATGAACCATGCAT
AAAAAAGTTAACCCACAAAGAGAAGAAACAAAAAAGATACTTGAAATCAGTTACATAGTTATCAT
CAGTCAGTCCCTTTGTGGTGATCAAAATTCTCGTTGATGGATAGCATAGATGA
Found at i:10601 original size:158 final size:158
Alignment explanation
Indices: 10313--10609 Score: 468
Period size: 158 Copynumber: 1.9 Consensus size: 158
10303 GGGGGCACCA
* * *
10313 CAAAAACGTTAATACTTACGTTAGACAAAGCTTGGCTGACGACGTTTTTACCACAACCAAGAATT
1 CAAAAACGTTAATACTTACATCAAACAAAGCTTGGCTGACGACGTTTTTACCACAACCAAGAATT
* * *
10378 GATAACAAATTGATAAGCCAATCACATCCTTCAAAAGAAAATTTAATCAAACTCAATCACCAATG
66 GAAAACAAATTGATAAGCAAATCACATCCTTCAAAAGAAAATATAATCAAACTCAATCACCAATG
10443 AAACTCACCTAGCCTGTTAGCAAAAAAG
131 AAACTCACCTAGCCTGTTAGCAAAAAAG
* * * *
10471 CAAAAATGTTAATACTTACATCAAACAGAGCTTGGCTGATGATGTTTTTACCACAACCAAGAATT
1 CAAAAACGTTAATACTTACATCAAACAAAGCTTGGCTGACGACGTTTTTACCACAACCAAGAATT
* * *
10536 GAAAACAAATTGATTAGCAAATCACATCCTTCAAAAGAATATATACTCAAACTCAATCACCAATG
66 GAAAACAAATTGATAAGCAAATCACATCCTTCAAAAGAAAATATAATCAAACTCAATCACCAATG
*
10601 AGACTCACC
131 AAACTCACC
10610 CACCCTCTAT
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 125 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (158 bp):
CAAAAACGTTAATACTTACATCAAACAAAGCTTGGCTGACGACGTTTTTACCACAACCAAGAATT
GAAAACAAATTGATAAGCAAATCACATCCTTCAAAAGAAAATATAATCAAACTCAATCACCAATG
AAACTCACCTAGCCTGTTAGCAAAAAAG
Found at i:10867 original size:22 final size:22
Alignment explanation
Indices: 10835--10891 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
10825 TAGGAAGTCG
10835 ATCACCAATGAGACTCACCTCA
1 ATCACCAATGAGACTCACCTCA
*
10857 ATCACCTATGAGACTCACCTCA
1 ATCACCAATGAGACTCACCTCA
10879 ATCACCAATGAGA
1 ATCACCAATGAGA
10892 ATCAGCTGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.33, G:0.11, T:0.19
Consensus pattern (22 bp):
ATCACCAATGAGACTCACCTCA
Found at i:14419 original size:24 final size:24
Alignment explanation
Indices: 14391--14437 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14381 GGGAGAGAGG
*
14391 TTATGGGGTGAGGAGAGAGGGAGA
1 TTATGGAGTGAGGAGAGAGGGAGA
* *
14415 TTATGGAGTGAGGCGAGATGGAG
1 TTATGGAGTGAGGAGAGAGGGAG
14438 TTCTGTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.51, T:0.19
Consensus pattern (24 bp):
TTATGGAGTGAGGAGAGAGGGAGA
Found at i:23608 original size:29 final size:28
Alignment explanation
Indices: 23554--23610 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
23544 TCCTTCTATG
** *
23554 TTTTTTTGTGTTGTTTTCTTTCTTCTTC
1 TTTTTTTGTGTTGTTTTCGGTATTCTTC
*
23582 TTTTTTTGTGTTTTTTTCGGGTATTCTTC
1 TTTTTTTGTGTTGTTTTC-GGTATTCTTC
23611 CTGTATTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.02, C:0.12, G:0.14, T:0.72
Consensus pattern (28 bp):
TTTTTTTGTGTTGTTTTCGGTATTCTTC
Found at i:24294 original size:15 final size:16
Alignment explanation
Indices: 24270--24309 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
24260 AGAGGTTGAA
*
24270 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
24285 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
24301 AGAAAACAA
1 AGAAAACAA
24310 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:25094 original size:11 final size:12
Alignment explanation
Indices: 25068--25094 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25058 CCCTTAGCCT
25068 AAAACTAGAAGA
1 AAAACTAGAAGA
25080 AAAACTAGAAGA
1 AAAACTAGAAGA
25092 AAA
1 AAA
25095 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAACTAGAAGA
Done.