Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005246.1 Kokia drynarioides strain JFW-HI SEQ_119144, 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: 8158
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:957 original size:106 final size:107
Alignment explanation
Indices: 763--964 Score: 289
Period size: 106 Copynumber: 1.9 Consensus size: 107
753 TCGTTAGACC
*
763 ACTAACCGTCATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTAGATAAAATTGAATTTT
1 ACTAACCGTCATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTAGATAAAATTGAATTGT
* * * **
828 ATTGGTGGTAGAGCTTGCGTGAATGAAAAGAATTATTAGTCA
66 ATTGGAGGTAAAGCTCGAATGAATGAAAAGAATTATTAGTCA
* * ** *
870 ACTAACTGTTATTTCAATGC-AAACGTGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAATTGT
1 ACTAACCGTCATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTAGATAAAATTGAATTGT
*
934 ATTGGAGGTAAAGGTCGAATGAATGAAAAGA
66 ATTGGAGGTAAAGCTCGAATGAATGAAAAGA
965 TTAAAAATCA
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
106 65 0.78
107 18 0.22
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (107 bp):
ACTAACCGTCATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTAGATAAAATTGAATTGT
ATTGGAGGTAAAGCTCGAATGAATGAAAAGAATTATTAGTCA
Found at i:1272 original size:19 final size:17
Alignment explanation
Indices: 1228--1286 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
1218 CCTCAACCTC
1228 TCTTTTTTTT-TT-T-T
1 TCTTTTTTTTCTTCTCT
1242 T-TTTTTTNTTCTTCTCTT
1 TCTTTTTT-TTCTTCTC-T
*
1260 TCCTTTTTTTTCTTTTCT
1 T-CTTTTTTTTCTTCTCT
1278 TCTTTTTTT
1 TCTTTTTTT
1287 AATTTATTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.16
14 3 0.08
15 2 0.05
16 1 0.03
17 8 0.22
18 4 0.11
19 7 0.19
20 6 0.16
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.83
Consensus pattern (17 bp):
TCTTTTTTTTCTTCTCT
Found at i:1281 original size:22 final size:22
Alignment explanation
Indices: 1241--1282 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1231 TTTTTTTTTT
*
1241 TTTTTTTTNTTCTTCTCTTTCC
1 TTTTTTTTCTTCTTCTCTTTCC
1263 TTTTTTTTCTT-TTCTTCTTT
1 TTTTTTTTCTTCTTC-TCTTT
1283 TTTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTTTTCTTCTTCTCTTTCC
Found at i:2169 original size:17 final size:15
Alignment explanation
Indices: 2149--2189 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
2139 TTCATCTTGC
2149 TTTCTTTTTTCTTCCTT
1 TTTCTTTTTTCTT-C-T
2166 TTTCTTTTTTTCTTCT
1 TTTC-TTTTTTCTTCT
2182 TTTCTTTT
1 TTTCTTTT
2190 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 5 0.22
18 9 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:2174 original size:18 final size:16
Alignment explanation
Indices: 2149--2189 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
2139 TTCATCTTGC
2149 TTTC-TTTTTTCTTCCTT
1 TTTCTTTTTTTCTT-C-T
2166 TTTCTTTTTTTCTTCT
1 TTTCTTTTTTTCTTCT
2182 TTTCTTTT
1 TTTCTTTT
2190 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTTTCTTCT
Found at i:2278 original size:19 final size:18
Alignment explanation
Indices: 2241--2282 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2231 CTTGACTTTC
2241 TTTCTCTTTTTTTCTTCT
1 TTTCTCTTTTTTTCTTCT
2259 TCTTCTCTTTTTTT-TATCT
1 T-TTCTCTTTTTTTCT-TCT
2278 TTTCT
1 TTTCT
2283 TTTAATGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTCTTTTTTTCTTCT
Found at i:6979 original size:30 final size:29
Alignment explanation
Indices: 6945--7236 Score: 247
Period size: 30 Copynumber: 9.9 Consensus size: 29
6935 AATTTCAAAA
*
6945 AAAGTTTAGGGGTAAAAATGTAATTTTAGG
1 AAAGTTTAGGGGTCAAAATGTAATTTT-GG
* * *
6975 AAAGTTT--GGGTTAAAATGTGATTTCGG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGG
*
7002 AGAAGTTT--GGGTCAAAATGTGATTTTTGG
1 A-AAGTTTAGGGGTCAAAATGT-AATTTTGG
* * *
7031 AATAG-TTAAGGGTTAAAATGTGATTTTGG
1 AA-AGTTTAGGGGTCAAAATGTAATTTTGG
* *
7060 AGAAGTTTAGGAGTTAAAATGTAATTTTGG
1 A-AAGTTTAGGGGTCAAAATGTAATTTTGG
**
7090 AAAAGTTTATTGGTCAAAATGTAATTTTGG
1 -AAAGTTTAGGGGTCAAAATGTAATTTTGG
** * *
7120 AAAAGTTTAAAGGTCAAAATATAATTTTGTA
1 -AAAGTTTAGGGGTCAAAATGTAATTTTG-G
* * * *
7151 AAAGTTTAAGGGTTTAAAATGAAATTTTAG
1 AAAGTTT-AGGGGTCAAAATGTAATTTTGG
7181 AGAAGTTT-GGGGTCAAAATGTAATTTTGG
1 A-AAGTTTAGGGGTCAAAATGTAATTTTGG
*
7210 AAAAG-TTAGGGGTCAAAATATAATTTT
1 -AAAGTTTAGGGGTCAAAATGTAATTTT
7237 CAAAGAAAAC
Statistics
Matches: 215, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.01
28 37 0.17
29 55 0.26
30 99 0.46
31 21 0.10
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTGG
Found at i:7111 original size:60 final size:60
Alignment explanation
Indices: 6946--7236 Score: 294
Period size: 60 Copynumber: 4.9 Consensus size: 60
6936 ATTTCAAAAA
* * * *
6946 AAGTTTAGGGGTAAAAATGTAATTTTAGG-AAAGTTT--GGGTTAAAATGTGATTTCGGAG
1 AAGTTTAGGAGTCAAAATGTAATTTT-GGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
* * *
7004 AAGTTT-GG-GTCAAAATGTGATTTTTGGAATAG-TTAAGGGTTAAAATGTGATTTTGGAG
1 AAGTTTAGGAGTCAAAATGT-AATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
* ** * *
7062 AAGTTTAGGAGTTAAAATGTAATTTTGGAAAAGTTTATTGGTCAAAATGTAATTTTGGAA
1 AAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
* * * * *
7122 AAGTTTA-AAGGTCAAAATATAATTTTGTAAAAGTTTAAGGGTTTAAAATGAAATTTTAGAG
1 AAGTTTAGGA-GTCAAAATGTAATTTTGGAAAAGTTTAAGGG-TTAAAATGTAATTTTGGAG
* * * *
7183 AAGTTT-GGGGTCAAAATGTAATTTTGGAAAAG-TTAGGGGTCAAAATATAATTTT
1 AAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTT
7237 CAAAGAAAAC
Statistics
Matches: 193, Mismatches: 30, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
56 13 0.07
57 10 0.05
58 45 0.23
59 20 0.10
60 84 0.44
61 21 0.11
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (60 bp):
AAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
Found at i:7123 original size:15 final size:15
Alignment explanation
Indices: 7075--7123 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
7065 TTTAGGAGTT
7075 AAAATGTAATTTTGG
1 AAAATGTAATTTTGG
7090 AAAA-GT--TTATTGG
1 AAAATGTAATT-TTGG
7103 TCAAAATGTAATTTTGG
1 --AAAATGTAATTTTGG
7120 AAAA
1 AAAA
7124 GTTTAAAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 2 0.07
15 12 0.43
16 2 0.07
17 4 0.14
18 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (15 bp):
AAAATGTAATTTTGG
Found at i:7502 original size:35 final size:35
Alignment explanation
Indices: 7456--7525 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
7446 TGATTCATTT
7456 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
1 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
7491 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
1 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
7526 AATCCTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (35 bp):
TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
Done.