Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012426.1 Kokia drynarioides strain JFW-HI SEQ_127430, 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: 120760
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:1525 original size:25 final size:24
Alignment explanation
Indices: 1478--1526 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1468 AATCTATTAA
*
1478 TTTAAATCAATATTTCAATTAATT
1 TTTAAATCAATAATTCAATTAATT
*
1502 TTTAATTCAATCAATTCAATTAATT
1 TTTAAATCAAT-AATTCAATTAATT
1527 AATGTAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAAATCAATAATTCAATTAATT
Found at i:2914 original size:19 final size:18
Alignment explanation
Indices: 2892--2927 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2882 TACCAACTTT
*
2892 AAAAATTATCTTAAACCTA
1 AAAAAATAT-TTAAACCTA
2911 AAAAAATATTTAAACCT
1 AAAAAATATTTAAACCT
2928 CGATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATATTTAAACCTA
Found at i:6087 original size:20 final size:19
Alignment explanation
Indices: 6057--6108 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
6047 GTGTTTTAGT
6057 ATTTGAAATTTTAGAT-TAA
1 ATTT-AAATTTTAGATATAA
*
6076 GATTTAAGATTTAAGATATAA
1 -ATTTAA-ATTTTAGATATAA
6097 ATTTAAATTTTA
1 ATTTAAATTTTA
6109 TTTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (19 bp):
ATTTAAATTTTAGATATAA
Found at i:16661 original size:15 final size:15
Alignment explanation
Indices: 16634--16679 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
16624 ATCTTAATTT
16634 ATTTATTTATACTTC
1 ATTTATTTATACTTC
16649 ATTT-TTTAGTACTT-
1 ATTTATTTA-TACTTC
16663 ATTTATTTATACTTC
1 ATTTATTTATACTTC
16678 AT
1 AT
16680 AATCTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.61
Consensus pattern (15 bp):
ATTTATTTATACTTC
Found at i:16666 original size:14 final size:14
Alignment explanation
Indices: 16632--16676 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
16622 TAATCTTAAT
16632 TTATTTATTTATAC
1 TTATTTATTTATAC
16646 TTCATTT-TTTAGTAC
1 TT-ATTTATTTA-TAC
16661 TTATTTATTTATAC
1 TTATTTATTTATAC
16675 TT
1 TT
16677 CATAATCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTATTTATAC
Found at i:22658 original size:16 final size:16
Alignment explanation
Indices: 22637--22670 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22627 ATTGAATTTT
**
22637 TTTGTTTTTTATTTGA
1 TTTGTTTTGGATTTGA
22653 TTTGTTTTGGATTTGA
1 TTTGTTTTGGATTTGA
22669 TT
1 TT
22671 ATGGACGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (16 bp):
TTTGTTTTGGATTTGA
Found at i:25175 original size:22 final size:23
Alignment explanation
Indices: 25150--25196 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
25140 GCAATATAAG
25150 AAAAAATAAAAG-AAAGAGAATT
1 AAAAAATAAAAGAAAAGAGAATT
*
25172 -AAAAATAAAAGAAAATAGAATT
1 AAAAAATAAAAGAAAAGAGAATT
25194 AAA
1 AAA
25197 CAAAATAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 9 0.41
23 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAAAATAAAAGAAAAGAGAATT
Found at i:25206 original size:22 final size:22
Alignment explanation
Indices: 25151--25210 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
25141 CAATATAAGA
*
25151 AAAAATAAAAG-AAAGAGAATT
1 AAAAATAAAAGAAAATAGAATT
25172 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
25194 AAACAA-AATAGAAAATA
1 AAA-AATAAAAGAAAATA
25211 AGGAAGTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 22 0.63
23 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:26035 original size:19 final size:19
Alignment explanation
Indices: 26011--26053 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
26001 AAACATAAAT
26011 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
26030 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
26049 TAAAT
1 TAAAT
26054 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:38283 original size:14 final size:14
Alignment explanation
Indices: 38264--38292 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38254 GATTGATTGG
38264 TGATGAACAATGGA
1 TGATGAACAATGGA
38278 TGATGAACAATGGA
1 TGATGAACAATGGA
38292 T
1 T
38293 TCGTTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.28, T:0.24
Consensus pattern (14 bp):
TGATGAACAATGGA
Found at i:52403 original size:16 final size:17
Alignment explanation
Indices: 52382--52414 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52372 ATAATTTTAT
*
52382 TTTTATTAATT-TAAAA
1 TTTTATAAATTATAAAA
52398 TTTTATAAATTATAAAA
1 TTTTATAAATTATAAAA
52415 AAAAACAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTATAAATTATAAAA
Found at i:55118 original size:117 final size:118
Alignment explanation
Indices: 54960--55216 Score: 399
Period size: 118 Copynumber: 2.2 Consensus size: 118
54950 AATGATCAAA
* * * *
54960 ACGTAAATTTATTAATAATTTAGTAACATTTTAAGTGTAATTTACCTTAAAAATAATTTAGGAAA
1 ACGTAAATTTATTAATAATTTAATAACATTTTAAATATAATTTACCTTAAAAACAATTTAGGAAA
*
55025 TGT-AGAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATT
66 TGTAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATT
** *
55077 ACGTAAATTTATTAATAATTTAATAATTTTTTAAATATAATTTACCTTGAAAACAATTTAGGAAA
1 ACGTAAATTTATTAATAATTTAATAACATTTTAAATATAATTTACCTTAAAAACAATTTAGGAAA
* *
55142 TGTAAAAAAAGATATTTAAATTATCGGATTTAGTAACCTTTAAGTGTAATTTT
66 TGTAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATT
* *
55195 ACGTAAATTTAGTAATAGTTTA
1 ACGTAAATTTATTAATAATTTA
55217 CCAAATTTTT
Statistics
Matches: 127, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
117 61 0.48
118 66 0.52
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (118 bp):
ACGTAAATTTATTAATAATTTAATAACATTTTAAATATAATTTACCTTAAAAACAATTTAGGAAA
TGTAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATT
Found at i:66440 original size:15 final size:15
Alignment explanation
Indices: 66404--66446 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
66394 ATAATAAAAA
66404 TATAATTTTATCATTTT
1 TATAA-TTTAT-ATTTT
*
66421 AATAATTTATATTTT
1 TATAATTTATATTTT
66436 TATAATTTATA
1 TATAATTTATA
66447 AATGATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.62
16 5 0.21
17 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATAATTTATATTTT
Found at i:76454 original size:181 final size:180
Alignment explanation
Indices: 75846--76563 Score: 788
Period size: 182 Copynumber: 4.0 Consensus size: 180
75836 ACTATGAATT
* * * * *
75846 AAGTATCACGTGTTGTAATCAGGCTTCGGTTAGTTTAGTTTCTTTTTAGGAAGCAATTTGAAATT
1 AAGTATTACATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTTTA-GAAGCAA-TTGCAATT
* * * ** ** * *
75911 CATCAAGAGGATGCAAATTGCA-CTTAATATTAAGCTTGGTGGAGTGTTAGAAAT-TGAGTTAAA
64 AATCAAGAAGCTGTGAATTGCAGC-TAATATTAAGCTTAATGGAGTGTTAAAAATCAG-GTTAAA
** * ** * *
75974 TTGACAAAAATAATCTGTTTATGTATATATTTGTCTTAGAAAGGGAGAAAGTTG
127 TTGATGAAAATAGTCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
* * * *
76028 AAGTATCACTTGATGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTCTTAGAAGCAACTTGCAATC
1 AAGTATTACATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTT-TTAGAAGCAA-TTGCAATT
*
76093 AATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGATTAAATT
64 AATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGGTTAAATT
* * * * *
76158 GATGAAAATAGTCCATTTATGTTTACATTTGTCTCAG--GA-GAG-GA-TTC
129 GATGAAAATAGTCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
* ** * *
76205 AAGTATCTA-ATGTTGTAACCAGGCTTGGGTCAGTTTAGTTTCTTTTTCAGTAACCAATTGCTAT
1 AAGTAT-TACATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTTT-AG-AAGCAATTGCAAT
* * * * ** * *
76269 TAATCAAGAAGCTCTGAATTGCAGCT-ATAGTAAGCTTAACGGAGGGTTAAATTTCGGGTTAATT
63 TAATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGGTTAAAT
* **
76333 TGATGAAAATAGTCCATTCATGTATATATGCGTCTCAGAAAAGGAGAAAGTTG
128 TGATGAAAATAGTCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
*
76386 AAGTATTACATGTTGTAATCAGGCTTCAGTCAGTTAAGTTTCTATTTTAGAAGCATATTGCAATT
1 AAGTATTACATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCT-TTTTAGAAGCA-ATTGCAATT
*
76451 AATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGGTTAAGTT
64 AATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGGTTAAATT
* * * * *
76516 GATGAAAGTAATCCATTTATGTATTTGTTTGTGTCAGAAAAGGAGAAA
129 GATGAAAATAGTCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAA
76564 AGTAATGGAA
Statistics
Matches: 444, Mismatches: 77, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
176 65 0.15
177 71 0.16
178 8 0.02
179 6 0.01
180 7 0.02
181 72 0.16
182 210 0.47
183 5 0.01
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (180 bp):
AAGTATTACATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTTTAGAAGCAATTGCAATTAA
TCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGGTTAAATTGA
TGAAAATAGTCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
Found at i:78478 original size:50 final size:50
Alignment explanation
Indices: 78403--78499 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
78393 ATCAATGAAG
*
78403 ATCAACCAAACTGTTATTTTGGTGATAATAACGGTATCATGGAAGGCTTC
1 ATCAACCAAACTGTTATTTTGGTGATAATAACAGTATCATGGAAGGCTTC
*
78453 ATCAACCAAACTGTTATTTTGGTGATAGTAACAGTATCATGGAAGGC
1 ATCAACCAAACTGTTATTTTGGTGATAATAACAGTATCATGGAAGGC
78500 ATTGTCTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (50 bp):
ATCAACCAAACTGTTATTTTGGTGATAATAACAGTATCATGGAAGGCTTC
Found at i:85183 original size:53 final size:53
Alignment explanation
Indices: 85103--85215 Score: 199
Period size: 53 Copynumber: 2.1 Consensus size: 53
85093 GCACTTGAAC
*
85103 TCACATTATCTTGCATTAACAACAATACTAAAGTCATTCGAACTAAAATTCAA
1 TCACATTATCTTGCATTAACAACAATACTAAAGTCAATCGAACTAAAATTCAA
*
85156 TCACATTATCTTGCATTAACAACAATACTCAAGTCAATCGAACTAAAATTCAA
1 TCACATTATCTTGCATTAACAACAATACTAAAGTCAATCGAACTAAAATTCAA
85209 TCTACAT
1 TC-ACAT
85216 GATAATAACA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 53 0.93
54 4 0.07
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.30
Consensus pattern (53 bp):
TCACATTATCTTGCATTAACAACAATACTAAAGTCAATCGAACTAAAATTCAA
Found at i:85447 original size:2 final size:2
Alignment explanation
Indices: 85442--85480 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
85432 AGGTGTGTGA
85442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85481 CCTCTAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94065 original size:15 final size:15
Alignment explanation
Indices: 94042--94084 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
94032 ATTTAAATTC
94042 CTTAATTTTTCAACA
1 CTTAATTTTTCAACA
* *
94057 CTTATTTTTTTAACA
1 CTTAATTTTTCAACA
*
94072 CTTAATATTTCAA
1 CTTAATTTTTCAA
94085 TTTATCAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (15 bp):
CTTAATTTTTCAACA
Found at i:97253 original size:10 final size:10
Alignment explanation
Indices: 97238--97262 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
97228 ATATAAATCG
97238 AAATACATTA
1 AAATACATTA
97248 AAATACATTA
1 AAATACATTA
97258 AAATA
1 AAATA
97263 ACTGATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATACATTA
Found at i:113431 original size:16 final size:16
Alignment explanation
Indices: 113410--113440 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
113400 GATACACCAT
113410 CAAACGAGCTCAAGCA
1 CAAACGAGCTCAAGCA
113426 CAAACGAGCTCAAGC
1 CAAACGAGCTCAAGC
113441 TTAAATACCA
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:0.42, C:0.32, G:0.19, T:0.06
Consensus pattern (16 bp):
CAAACGAGCTCAAGCA
Found at i:120708 original size:2 final size:2
Alignment explanation
Indices: 120701--120736 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
120691 CATTAAAATA
120701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120737 TTGCATTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.