Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015308.1 Kokia drynarioides strain JFW-HI SEQ_130353, 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: 468748
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 814 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:406081 original size:19 final size:19
Alignment explanation
Indices: 406057--406095 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
406047 TAGTTGGGGG
406057 TAATTAGCGATTTAATTGA
1 TAATTAGCGATTTAATTGA
*
406076 TAATTAGGGATTTAATTGA
1 TAATTAGCGATTTAATTGA
406095 T
1 T
406096 TATAGGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (19 bp):
TAATTAGCGATTTAATTGA
Found at i:407872 original size:20 final size:21
Alignment explanation
Indices: 407835--407874 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
407825 AATTGTCTTT
407835 TTTGTCGCGACACGACTCCTG
1 TTTGTCGCGACACGACTCCTG
*
407856 TTTGTCGCGA-TCGACTCCT
1 TTTGTCGCGACACGACTCCT
407875 AAATGCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.12, C:0.33, G:0.23, T:0.33
Consensus pattern (21 bp):
TTTGTCGCGACACGACTCCTG
Found at i:420873 original size:36 final size:36
Alignment explanation
Indices: 420815--420948 Score: 173
Period size: 36 Copynumber: 3.8 Consensus size: 36
420805 TGGTAAGAGG
* * *
420815 CATGACCTTTGGGTTAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
420851 CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
* * * *
420887 CATG-CCTTTGGGTCAACAGAGAGTGAAATGACCAT
1 CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
*
420922 TATGACCTTT-AGGTCAACAGGGAGTAA
1 CATGACCTTTGA-GTCAACAGGGAGTAA
420949 GCATGACCTT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
35 30 0.35
36 55 0.65
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (36 bp):
CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
Found at i:420938 original size:71 final size:72
Alignment explanation
Indices: 420815--420948 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 72
420805 TGGTAAGAGG
* * * *
420815 CATGACCTTTGGGTTAATAGGGAGTAAAATGAGCATCATGACCTTTGAGTCAACAGGGAGTAAAA
1 CATGACCTTTGGGTCAACAGAGAGTAAAATGACCATCATGACCTTTGAGTCAACAGGGAGTAAAA
420880 TGAGCAT
66 TGAGCAT
* *
420887 CATG-CCTTTGGGTCAACAGAGAGTGAAATGACCATTATGACCTTT-AGGTCAACAGGGAGTAA
1 CATGACCTTTGGGTCAACAGAGAGTAAAATGACCATCATGACCTTTGA-GTCAACAGGGAGTAA
420949 GCATGACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
70 1 0.02
71 50 0.91
72 4 0.07
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (72 bp):
CATGACCTTTGGGTCAACAGAGAGTAAAATGACCATCATGACCTTTGAGTCAACAGGGAGTAAAA
TGAGCAT
Found at i:420964 original size:28 final size:28
Alignment explanation
Indices: 420923--420976 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
420913 AATGACCATT
420923 ATGACCTTTAGGTCAACAGGGAGTAAGC
1 ATGACCTTTAGGTCAACAGGGAGTAAGC
*
420951 ATGACCTTTGGGTCAACAGGGAGTAA
1 ATGACCTTTAGGTCAACAGGGAGTAA
420977 ATCGGTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (28 bp):
ATGACCTTTAGGTCAACAGGGAGTAAGC
Found at i:421644 original size:21 final size:22
Alignment explanation
Indices: 421606--421668 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
421596 TTTTAGTACT
* *
421606 GGTAGAAGCATG-ATTTGTTTC
1 GGTAGAAGCTTGCACTTGTTTC
* *
421627 GGTATAAGCTT-CACTTGTATC
1 GGTAGAAGCTTGCACTTGTTTC
*
421648 GGTAGAAGTTTGCAC-TGTTTC
1 GGTAGAAGCTTGCACTTGTTTC
421669 ATGAATTGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.38
Consensus pattern (22 bp):
GGTAGAAGCTTGCACTTGTTTC
Found at i:426407 original size:11 final size:12
Alignment explanation
Indices: 426389--426419 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
426379 GTCGGTTCGA
426389 TCAAAAAATTCT
1 TCAAAAAATTCT
426401 T-AAAAAATTCT
1 TCAAAAAATTCT
426412 TCAAAAAA
1 TCAAAAAA
426420 ATATTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (12 bp):
TCAAAAAATTCT
Found at i:426638 original size:30 final size:30
Alignment explanation
Indices: 426590--426658 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
426580 TAGATCTCCC
* *
426590 AATCTTCATAGTATTCATCTTCATCAA-TAT
1 AATCCTCATAGTATTCATCATCAT-AACTAT
*
426620 CATCCTCATAG-ATGTCATCATCATAACTAT
1 AATCCTCATAGTAT-TCATCATCATAACTAT
426650 AATCCTCAT
1 AATCCTCAT
426659 TTGAATAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (30 bp):
AATCCTCATAGTATTCATCATCATAACTAT
Found at i:432122 original size:31 final size:31
Alignment explanation
Indices: 432084--432142 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
432074 ATAGTAAACA
432084 TTTTTTTTCTTCTTT-TC-TTTTCTCTTTTCTT
1 TTTTTTTTCTT-TTTCTCATTTTC-CTTTTCTT
432115 TTTTTTTTCTTTTTCTCATTTTCCTTTT
1 TTTTTTTTCTTTTTCTCATTTTCCTTTT
432143 TCAAGTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 3 0.12
31 18 0.69
32 5 0.19
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (31 bp):
TTTTTTTTCTTTTTCTCATTTTCCTTTTCTT
Found at i:432128 original size:24 final size:24
Alignment explanation
Indices: 432096--432143 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
432086 TTTTTTCTTC
*
432096 TTTTCTTTTCTC-TTTTCTTTTTT
1 TTTTCTTTTCTCATTTTCCTTTTT
432119 TTTTCTTTTTCTCATTTTCCTTTTT
1 TTTTC-TTTTCTCATTTTCCTTTTT
432144 CAAGTGACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 7 0.32
25 10 0.45
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTCTTTTCTCATTTTCCTTTTT
Found at i:432136 original size:17 final size:17
Alignment explanation
Indices: 432087--432136 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 17
432077 GTAAACATTT
432087 TTTTTCTTCTTTTCTTTTC
1 TTTTTC-TCTTTT-TTTTC
*
432106 TCTTTTCTTTTTTTTTTC
1 T-TTTTCTCTTTTTTTTC
432124 TTTTTCTCATTTT
1 TTTTTCTC-TTTT
432137 CCTTTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 6 0.22
20 5 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTCTTTTTTTTC
Found at i:444284 original size:37 final size:37
Alignment explanation
Indices: 444228--444410 Score: 190
Period size: 37 Copynumber: 4.9 Consensus size: 37
444218 CATCTAAATA
*** * * *
444228 TTCAGGCTATGTAATTAGTACGCTCTGTGCTGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
** *
444265 TTCAGGCTAAT-TGCCTAGTAGGCTTTGTGCTAGTGTA
1 TTCAGGCT-ATGTGCCTAGTAGGCTTTGTGCCGGTGTT
* * *
444302 TTCAAGCTATGTGCCTAGTAGGCTTCGTTCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
444339 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGT-T
* * * *
444377 TT-GGGCTATGTGCCTAGCAGACTTTGTGTCGGTG
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
444411 ATCCAAGAAT
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
36 2 0.02
37 116 0.94
38 5 0.04
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.38
Consensus pattern (37 bp):
TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
Found at i:450271 original size:28 final size:28
Alignment explanation
Indices: 450239--450311 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
450229 CTTTCCGACA
450239 CTGTTAAAGGAAGCCTTTGAGACTGATT
1 CTGTTAAAGGAAGCCTTTGAGACTGATT
* *
450267 CTGTTAAAGGAAGCCTTTGTGGCTGATT
1 CTGTTAAAGGAAGCCTTTGAGACTGATT
450295 CTGTTAAAGGAAGCCTT
1 CTGTTAAAGGAAGCCTT
450312 CATGGCTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (28 bp):
CTGTTAAAGGAAGCCTTTGAGACTGATT
Found at i:450405 original size:27 final size:27
Alignment explanation
Indices: 450375--450429 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
450365 ATGTGCCATG
* *
450375 TTTGTAAAGGGCGCCTTTGAGGCTATC
1 TTTGTAAAGGACGCCTCTGAGGCTATC
* * *
450402 TTTGTTAATGACGCCTCTGTGGCTATC
1 TTTGTAAAGGACGCCTCTGAGGCTATC
450429 T
1 T
450430 ATGTTGAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.38
Consensus pattern (27 bp):
TTTGTAAAGGACGCCTCTGAGGCTATC
Found at i:466202 original size:49 final size:49
Alignment explanation
Indices: 466092--466202 Score: 150
Period size: 49 Copynumber: 2.3 Consensus size: 49
466082 CACCGACTCT
* ** *
466092 AAAGCCTGTTAAACCGTAGCTTGAGTTATTTCATCACCACACCAGCTCA
1 AAAGCCTGCTAAGTCGTAGCTTGAGTTATCTCATCACCACACCAGCTCA
***
466141 AAAGCCTGCTAAGTCGTAGCTTGAGTTATCTCATCATTTCACCAGCTCA
1 AAAGCCTGCTAAGTCGTAGCTTGAGTTATCTCATCACCACACCAGCTCA
*
466190 AAAGCCTTCTAAG
1 AAAGCCTGCTAAG
466203 CCAAAGTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (49 bp):
AAAGCCTGCTAAGTCGTAGCTTGAGTTATCTCATCACCACACCAGCTCA
Done.