Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007301.1 Kokia drynarioides strain JFW-HI SEQ_121917, 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: 26166
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:227 original size:20 final size:18
Alignment explanation
Indices: 205--238 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
195 TTATTATTAT
205 TATTATT-ATAATATAAA
1 TATTATTAATAATATAAA
222 TATTATTAATAATATAA
1 TATTATTAATAATATAA
239 TAATCAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATTAATAATATAAA
Found at i:229 original size:3 final size:3
Alignment explanation
Indices: 173--213 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
163 ATTATTAAAA
* * *
173 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
214 AATATAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:229 original size:23 final size:24
Alignment explanation
Indices: 199--250 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
189 TTATTATTAT
* *
199 TATTATTATTATTATAAT-ATAAA
1 TATTATTAATAATATAATAATAAA
*
222 TATTATTAATAATATAATAATCAA
1 TATTATTAATAATATAATAATAAA
246 TATTA
1 TATTA
251 ACCTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATTAATAATATAATAATAAA
Found at i:889 original size:17 final size:17
Alignment explanation
Indices: 867--946 Score: 106
Period size: 17 Copynumber: 4.7 Consensus size: 17
857 TTGGACATTT
*
867 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
884 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
901 TACATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
918 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
935 TAAATTCAAATT
1 TAAATTTAAATT
947 CCAATAGGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:918 original size:7 final size:6
Alignment explanation
Indices: 865--946 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
855 AATTGGACAT
*
865 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TACA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * * * *
911 TTTAAA -ATAAA CTTAAT TTTAAA -ATAAA TTCAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
947 CCAATAGGCC
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
4 4 0.07
5 11 0.19
6 38 0.66
7 5 0.09
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:2143 original size:29 final size:29
Alignment explanation
Indices: 2096--2454 Score: 328
Period size: 29 Copynumber: 12.4 Consensus size: 29
2086 AAGGTCCCTA
* *
2096 AACTATCCAAAAATTCCATTTTTATCCTCG
1 AACT-TCCAAAAATCCCATTTTTACCCTCG
*
2126 AACTTCCAAAAATCCCATTTTTAACC-C-
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
2153 -A-----AAAACTTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
**
2176 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* *
2206 AACTACCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
2235 AATTTCCAAAAATCCCATTTTTGACCC-CAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTC-G
* *
2265 AACTTCCAAAAATCCCATTTTCACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
2294 AACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* *
2323 AAACTTCTAAAAATCCCATTTTTACCCTCCA
1 -AACTTCCAAAAATCCCATTTTTACCCT-CG
*** *
2354 AACTTCCAAAAATTAAAATTTTGACCC-CG
1 AACTTCCAAAAA-TCCCATTTTTACCCTCG
* *
2383 AAACTACCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATCCCATTTTTACCCTCG
* **
2413 AACTT-CAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
2442 AACTTCCAAAAAT
1 AACTTCCAAAAAT
2455 TATCATTTTA
Statistics
Matches: 270, Mismatches: 38, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
21 16 0.06
22 1 0.00
24 1 0.00
26 1 0.00
28 17 0.06
29 113 0.42
30 110 0.41
31 11 0.04
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTCG
Found at i:2156 original size:20 final size:21
Alignment explanation
Indices: 2131--2169 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2121 CCTCGAACTT
2131 CCAAAAA-TCCCATTTTTAAC
1 CCAAAAACTCCCATTTTTAAC
*
2151 CCAAAAACTTCCATTTTTA
1 CCAAAAACTCCCATTTTTA
2170 CCCTCGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (21 bp):
CCAAAAACTCCCATTTTTAAC
Found at i:2165 original size:50 final size:50
Alignment explanation
Indices: 2102--2319 Score: 222
Period size: 59 Copynumber: 4.0 Consensus size: 50
2092 CCTAAACTAT
* *
2102 CCAAAAA-TTCCATTTTTATCCTCGAACTTCCAAAAATCCCATTTTTAAC
1 CCAAAAACTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
2151 CCAAAAACTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
1 CCAAAAACTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
*
2201 CCTAAAACTACCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCATTTTTGAC
1 CC-AAAA--A-C-----TTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
* *
2260 CCCAAAACTTCCAAAAATCCCATTTTCACCCCCGAACTTCCAAAAATCCCATTTTTGAC
1 CCAAAAACTTCC----AT----TTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGAC
2319 C
1 C
2320 TCGAAACTTC
Statistics
Matches: 144, Mismatches: 6, Indels: 28
0.81 0.03 0.16
Matches are distributed among these distances:
49 7 0.05
50 46 0.32
51 4 0.03
53 1 0.01
54 3 0.02
55 1 0.01
56 1 0.01
58 7 0.05
59 74 0.51
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (50 bp):
CCAAAAACTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC
Found at i:2244 original size:59 final size:59
Alignment explanation
Indices: 2151--2455 Score: 398
Period size: 59 Copynumber: 5.2 Consensus size: 59
2141 CATTTTTAAC
*
2151 CCAAAAACTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTA
1 CCAAAAA-TTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTT
* *
2211 CCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTT
* * * *
2270 CCAAAAATCCCATTTTCACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACTT
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCT-AAAACTT
* * * *** * ** *
2329 CTAAAAATCCCATTTTTACCCTCCAAACTTCCAAAAATTAAAATTTTGACCCCGAAACTA
1 CCAAAAATTCCATTTTTACCCT-CGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTT
* *
2389 CCAAAAATTCCATTTTTACCCTCGAACTT-CAAAAATTCCATTTTTAACCCTAAAACTT
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTT
2447 CCAAAAATT
1 CCAAAAATT
2456 ATCATTTTAC
Statistics
Matches: 213, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
58 33 0.15
59 124 0.58
60 54 0.25
61 2 0.01
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (59 bp):
CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTT
Found at i:2455 original size:30 final size:29
Alignment explanation
Indices: 2151--2455 Score: 312
Period size: 30 Copynumber: 10.3 Consensus size: 29
2141 CATTTTTAAC
*
2151 CCAAAAACTTCCATTTTTACCCTCGAACTT
1 CCAAAAA-TTCCATTTTTACCCTCAAACTT
* * *
2181 CCAAAAATCCCATTTTTGACCCTAAAACTA
1 CCAAAAATTCCATTTTT-ACCCTCAAACTT
* *
2211 CCAAAAATTCCATTTTTACCCTCGAATTT
1 CCAAAAATTCCATTTTTACCCTCAAACTT
*
2240 CCAAAAATCCCATTTTTGACCC-CAAAACTT
1 CCAAAAATTCCATTTTT-ACCCTC-AAACTT
* * * *
2270 CCAAAAATCCCATTTTCACCCCCGAACTT
1 CCAAAAATTCCATTTTTACCCTCAAACTT
*
2299 CCAAAAATCCCATTTTTGA-CCTCGAAACTT
1 CCAAAAATTCCATTTTT-ACCCTC-AAACTT
* *
2329 CTAAAAATCCCATTTTTACCCTCCAAACTT
1 CCAAAAATTCCATTTTTACCCT-CAAACTT
** * *
2359 CCAAAAATTAAAATTTTGACCC-CGAAACTA
1 CCAAAAATT-CCATTTTTACCCTC-AAACTT
*
2389 CCAAAAATTCCATTTTTACCCTCGAACTT
1 CCAAAAATTCCATTTTTACCCTCAAACTT
*
2418 -CAAAAATTCCATTTTTAACCCTAAAACTT
1 CCAAAAATTCCATTTTT-ACCCTCAAACTT
2447 CCAAAAATT
1 CCAAAAATT
2456 ATCATTTTAC
Statistics
Matches: 231, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
28 16 0.07
29 87 0.38
30 118 0.51
31 10 0.04
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (29 bp):
CCAAAAATTCCATTTTTACCCTCAAACTT
Found at i:7019 original size:29 final size:29
Alignment explanation
Indices: 6955--7019 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
6945 GTTAAAAAAA
*
6955 TAATTTAAATTTAAAAGAAAATAGATTAT
1 TAATTTAAATTTAAAAAAAAATAGATTAT
**
6984 TTTTTTAAATTTAAGAAAAAAAT-G-TTAAT
1 TAATTTAAATTTAA-AAAAAAATAGATT-AT
7013 TAATTTA
1 TAATTTA
7020 GACATATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.07
29 20 0.69
30 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (29 bp):
TAATTTAAATTTAAAAAAAAATAGATTAT
Found at i:7361 original size:16 final size:17
Alignment explanation
Indices: 7329--7362 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7319 AAATGATTAT
*
7329 ATAAAAAATTTTAATAA
1 ATAAAAAATTGTAATAA
7346 ATAAAAAATTGT-ATAA
1 ATAAAAAATTGTAATAA
7362 A
1 A
7363 AGTACTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAAAAAATTGTAATAA
Found at i:7513 original size:17 final size:17
Alignment explanation
Indices: 7491--7551 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 17
7481 ATTATAAACC
7491 TAAATTTTAAATCAAAT
1 TAAATTTTAAATCAAAT
7508 TAAA-TTTAAAT-AAAT
1 TAAATTTTAAATCAAAT
7523 ATAAAATATATTAATATCATAAT
1 -T-AAAT-T-TTAA-ATCA-AAT
7546 TAAATT
1 TAAATT
7552 CAACTCCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
15 4 0.11
16 8 0.22
17 7 0.19
19 1 0.03
20 5 0.14
21 6 0.17
22 2 0.06
23 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTTAAATCAAAT
Found at i:17576 original size:24 final size:24
Alignment explanation
Indices: 17549--17606 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
17539 AGTTTTTATC
17549 TGCCTTTGTGGCACGTTTTTCCTT
1 TGCCTTTGTGGCACGTTTTTCCTT
* *
17573 TGCCTTTATGACACGTTTTTCCTT
1 TGCCTTTGTGGCACGTTTTTCCTT
17597 TGCC-TTGTGG
1 TGCCTTTGTGG
17607 TATGCTTCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.07, C:0.24, G:0.21, T:0.48
Consensus pattern (24 bp):
TGCCTTTGTGGCACGTTTTTCCTT
Found at i:23642 original size:25 final size:25
Alignment explanation
Indices: 23613--23738 Score: 174
Period size: 25 Copynumber: 5.3 Consensus size: 25
23603 AAGGTACATA
23613 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
23638 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
23663 AGTGCT--G-AGCAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
* *
23685 AGTG-T-TG-AACAAAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
*
23707 AGTGCTAGGTAACAGAAGCACACAC
1 AGTGCTGGGTAACAGAAGCACACAC
23732 AGTGCTG
1 AGTGCTG
23739 AACAGAAACG
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
21 1 0.01
22 36 0.40
23 2 0.02
24 1 0.01
25 51 0.56
ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13
Consensus pattern (25 bp):
AGTGCTGGGTAACAGAAGCACACAC
Found at i:23678 original size:22 final size:22
Alignment explanation
Indices: 23623--23745 Score: 165
Period size: 22 Copynumber: 5.3 Consensus size: 22
23613 AGTGCTGGGT
23623 AACAGAAGCACACACAGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
23647 TAACAGAAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
* *
23670 AGCAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
*
23692 AACAAAAGCACACACAGTGCTAGG
1 AACAGAAGCACACACAGTGCT--G
23716 TAACAGAAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
23739 AACAGAA
1 AACAGAA
23746 ACGCGCTAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
22 45 0.51
23 2 0.02
24 1 0.01
25 41 0.46
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:23741 original size:47 final size:46
Alignment explanation
Indices: 23613--23742 Score: 174
Period size: 47 Copynumber: 2.8 Consensus size: 46
23603 AAGGTACATA
*
23613 AGTGCTGGGTAACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACAC
1 AGTGCT-GGTAACAGAAGCACACACAGTGCT--G-AACAAAAGCACACAC
* *
23663 AGTGCT-G-AGCAGAAGCACACACAGTGTTGAACAAAAGCACACAC
1 AGTGCTGGTAACAGAAGCACACACAGTGCTGAACAAAAGCACACAC
23707 AGTGCTAGGTAACAGAAGCACACACAGTGCTGAACA
1 AGTGCT-GGTAACAGAAGCACACACAGTGCTGAACA
23743 GAAACGCGCT
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
44 20 0.28
45 1 0.01
46 1 0.01
47 43 0.60
48 1 0.01
50 6 0.08
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.12
Consensus pattern (46 bp):
AGTGCTGGTAACAGAAGCACACACAGTGCTGAACAAAAGCACACAC
Found at i:23957 original size:21 final size:21
Alignment explanation
Indices: 23931--23971 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23921 TGTCACCAAT
*
23931 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
23952 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
23972 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Done.