Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012198.1 Kokia drynarioides strain JFW-HI SEQ_127199, 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: 8017
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:2004 original size:87 final size:87
Alignment explanation
Indices: 1913--2104 Score: 339
Period size: 87 Copynumber: 2.2 Consensus size: 87
1903 TGGATACCGG
1913 GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAATTCGGGGTCAAA
1 GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAATTCGGGGTCAAA
*
1978 AATGAAATTTTTTGACATCCAA
66 AACGAAATTTTTTGACATCCAA
* **
2000 GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAGTTCGGGGTTGAA
1 GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAATTCGGGGTCAAA
*
2065 AACGAAATTTTTTTACATCCAA
66 AACGAAATTTTTTGACATCCAA
2087 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
2105 TGGAAAATCG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 100 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.32
Consensus pattern (87 bp):
GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAATTCGGGGTCAAA
AACGAAATTTTTTGACATCCAA
Found at i:2054 original size:29 final size:29
Alignment explanation
Indices: 1917--2046 Score: 92
Period size: 29 Copynumber: 4.5 Consensus size: 29
1907 TACCGGGGGT
1917 AAAATGGTAATTTTAGATAGTTAGGGCAC
1 AAAATGGTAATTTTAGATAGTTAGGGCAC
* * *
1946 AAAATGGTAATTTTGGGA-AATTCGGGGTCA-
1 AAAATGGTAATTTT-AGATAGTT-AGGG-CAC
* * * * *
1976 AAAAT-GAAATTTTTTGACA-TCCAAGGG--T
1 AAAATGGTAA-TTTTAGATAGT--TAGGGCAC
2004 AAAATGGTAATTTTAGATAGTTAGGGCAC
1 AAAATGGTAATTTTAGATAGTTAGGGCAC
2033 AAAATGGTAATTTT
1 AAAATGGTAATTTT
2047 GGGAAGTTCG
Statistics
Matches: 77, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
27 4 0.05
28 12 0.16
29 41 0.53
30 18 0.23
31 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTAGATAGTTAGGGCAC
Found at i:2123 original size:29 final size:29
Alignment explanation
Indices: 2086--2312 Score: 180
Period size: 29 Copynumber: 7.8 Consensus size: 29
2076 TTTACATCCA
*
2086 AGGGTAAAATGGTAATTTTTGGAAAATCG
1 AGGGTAAAATGGTAATTTTTGGAAAATTG
** **
2115 AGGCCAAAAATGG-AATTTTTGGAAGTTTG
1 AGG-GTAAAATGGTAATTTTTGGAAAATTG
2144 AGGGTAAAATGGTAATTTTTGGAAAAATTG
1 AGGGTAAAATGGTAATTTTTGG-AAAATTG
* * *
2174 A-GATCAAAAATGG-AATTTTTGG-AAGTTT
1 AGGGT--AAAATGGTAATTTTTGGAAAATTG
* *
2202 AGGGGTAAAATGTTAATTTTTGGAGAAATCG
1 A-GGGTAAAATGGTAATTTTTGGA-AAATTG
* * * * *
2233 AGGTTAAAAAGGGAATTTTT-GAAAGTTTA
1 AGGGTAAAATGGTAATTTTTGGAAA-ATTG
*
2262 AGGGTAAAATGGTAATTTTTGGAAAATCG
1 AGGGTAAAATGGTAATTTTTGGAAAATTG
* *
2291 -GGGCAAAATTG-AATTTTTGGAA
1 AGGGTAAAATGGTAATTTTTGGAA
2313 GTTCGAAGGT
Statistics
Matches: 154, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
27 11 0.07
28 29 0.19
29 60 0.39
30 43 0.28
31 11 0.07
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTGGAAAATTG
Found at i:2123 original size:87 final size:87
Alignment explanation
Indices: 1913--2141 Score: 300
Period size: 87 Copynumber: 2.6 Consensus size: 87
1903 TGGATACCGG
* * * *
1913 GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAATTCGGGGTCAAA
1 GGGTAAAATGGTAATTTTAGAAAATGAGGGCACAAAATGGTAATTTTGGGAAGTTCGGGGTCAAA
*
1978 AATGAAATTTTTTGACATCCAA
66 AACGAAATTTTTTGACATCCAA
* * * **
2000 GGGTAAAATGGTAATTTTAGATAGTTAGGGCACAAAATGGTAATTTTGGGAAGTTCGGGGTTGAA
1 GGGTAAAATGGTAATTTTAGAAAATGAGGGCACAAAATGGTAATTTTGGGAAGTTCGGGGTCAAA
*
2065 AACGAAATTTTTTTACATCCAA
66 AACGAAATTTTTTGACATCCAA
* * *
2087 GGGTAAAATGGTAATTTTTGGAAAATCGAGGCCA-AAAATGG-AATTTTTGGAAGTT
1 GGGTAAAATGGTAA-TTTTAGAAAAT-GAGGGCACAAAATGGTAATTTTGGGAAGTT
2142 TGAGGGTAAA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
87 109 0.84
88 15 0.12
89 5 0.04
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (87 bp):
GGGTAAAATGGTAATTTTAGAAAATGAGGGCACAAAATGGTAATTTTGGGAAGTTCGGGGTCAAA
AACGAAATTTTTTGACATCCAA
Found at i:2132 original size:58 final size:58
Alignment explanation
Indices: 2085--2315 Score: 331
Period size: 59 Copynumber: 4.0 Consensus size: 58
2075 TTTTACATCC
*
2085 AAGGGTAAAATGGTAATTTTTGGAAAATCGAGGCCAAAAATGGAATTTTTGGAAGTTT
1 AAGGGTAAAATGGTAATTTTTGGAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTT
* * *
2143 GAGGGTAAAATGGTAATTTTTGGAAAAATTGAGATCAAAAATGGAATTTTTGGAAGTTT
1 AAGGGTAAAATGGTAATTTTTGG-AAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTT
* * * * *
2202 AGGGGTAAAATGTTAATTTTTGGAGAAATCGAGGTTAAAAAGGGAATTTTTGAAAGTTT
1 AAGGGTAAAATGGTAATTTTTGGA-AAATCGAGGTCAAAAATGGAATTTTTGGAAGTTT
* *
2261 AAGGGTAAAATGGTAATTTTTGGAAAATCG-GGGC-AAAATTGAATTTTTGGAAGTT
1 AAGGGTAAAATGGTAATTTTTGGAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTT
2316 CGAAGGTTAA
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
56 18 0.12
57 2 0.01
58 29 0.19
59 103 0.68
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (58 bp):
AAGGGTAAAATGGTAATTTTTGGAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTT
Found at i:4260 original size:6 final size:6
Alignment explanation
Indices: 4236--4315 Score: 58
Period size: 6 Copynumber: 13.2 Consensus size: 6
4226 GTTTAAAATC
**
4236 ATTTCAA ATTT-A A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
* **
4283 ATAGATAA ATTTAA ATTTAA AAATAA ATTTAA A
1 AT--TTAA ATTTAA ATTTAA ATTTAA ATTTAA A
4316 ACCAATTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 7 0.12
6 35 0.61
7 8 0.14
8 4 0.07
9 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (6 bp):
ATTTAA
Found at i:4294 original size:21 final size:18
Alignment explanation
Indices: 4250--4315 Score: 80
Period size: 17 Copynumber: 3.6 Consensus size: 18
4240 CAAATTTAAT
*
4250 TAAATTTAAATTT-AAAG
1 TAAATTTAAATTTAAAAA
*
4267 CAAATTTAAATTTAAAATAGA
1 TAAATTTAAATTT-AAA-A-A
4288 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
4306 TAAATTTAAA
1 TAAATTTAAA
4316 ACCAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 12 0.29
18 11 0.26
19 3 0.07
20 4 0.10
21 12 0.29
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:4948 original size:48 final size:48
Alignment explanation
Indices: 4803--5088 Score: 224
Period size: 48 Copynumber: 5.9 Consensus size: 48
4793 AGGTTTGTCA
* * * *
4803 TTGCGACTTAAATCTTTCCCTTTGTGTTTTCATGGTACTGAATTCACCG
1 TTGCGACTTAAACCTTTCCC-TTGTGTCTTCATGGTACTGGATTCGCCG
*
4852 TTGCGACTTAAATCTTT-CCTT-T-TCCTTTCATGGTACTGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTGTGT-C-TTCATGGTACTGGATTCGCCG
* * *
4899 TTGCGGCTTAAACCTTTCCCATGTGTCTTCATGGTACTGGATTCACCG
1 TTGCGACTTAAACCTTTCCCTTGTGTCTTCATGGTACTGGATTCGCCG
* * ** * **
4947 TTGCGGCTTAAATCTTTCCCTTCACGTCTCTGA-GGTACTAGG-TTCGCTN
1 TTGCGACTTAAACCTTTCCCTT-GTGTCT-TCATGGTACT-GGATTCGCCG
* * * * *
4996 TTACGACTTAAACCTTTCCCTTTTGTGTCTTCAAGGTACAGGGTTGGCCG
1 TTGCGACTTAAACCTTTCCC--TTGTGTCTTCATGGTACTGGATTCGCCG
* * * * *
5046 TTGCGGCTTAAACATTT-CCTATGTGTGTTCGTGGTACTAGATT
1 TTGCGACTTAAACCTTTCCCT-TGTGTCTTCATGGTACTGGATT
5089 TGTTTGATAG
Statistics
Matches: 190, Mismatches: 34, Indels: 27
0.76 0.14 0.11
Matches are distributed among these distances:
45 1 0.01
46 1 0.01
47 37 0.19
48 61 0.32
49 56 0.29
50 32 0.17
51 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (48 bp):
TTGCGACTTAAACCTTTCCCTTGTGTCTTCATGGTACTGGATTCGCCG
Done.