Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007018.1 Kokia drynarioides strain JFW-HI SEQ_121624, 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: 15456
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Found at i:1447 original size:49 final size:49
Alignment explanation
Indices: 1394--1742 Score: 189
Period size: 49 Copynumber: 7.1 Consensus size: 49
1384 TCAGAATCAT
*
1394 GAAGGGAAAAATTTAAGCTGCAACGGTAAATCTAGTACCACGAAGATAC
1 GAAGGGAAAAATTTAAGCTGCAACGGTGAATCTAGTACCACGAAGATAC
** * * *
1443 GAAGGGAAAGGTTTAAG-TCGCAACGGTGAACCTTGTACCTCAGAAGCAT--
1 GAAGGGAAAAATTTAAGCT-GCAACGGTGAATCTAGTACCAC-GAAG-ATAC
* * * *
1492 GAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAC
1 GAAGGGAAAAATTTAAGCTGCAACGGTGAATCTAGTACCACGAAGATAC
** * * * * *
1541 GAAGGGAAAGGTTTAAG-TCACAATGGTGAACCTTGTACCTTA-GAAGCGT--
1 GAAGGGAAAAATTTAAGCT-GCAACGGTGAATCTAGTACC--ACGAAG-ATAC
* * * * * * * *
1590 GAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCATGAAGACAC
1 GAAGGGAAAAATTTAAGCTGCAACGGTGAATCTAGTACCACGAAGATAC
** * * * * * *
1639 GAAGGGAAAGGTTTAAG-TCGCAATGGCGAACCTTA-TACCTC-AGAGACAT
1 GAAGGGAAAAATTTAAGCT-GCAACGGTGAATC-TAGTACCACGA-AGATAC
* * * *
1688 GAAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACC-CGAAGACAC
1 G-AAGGGAAAAATTTAAGCTGCAACGGTGAATCTAGTACCACGAAGATAC
1737 GAAGGG
1 GAAGGG
1743 GAAGGTTTAG
Statistics
Matches: 227, Mismatches: 52, Indels: 43
0.70 0.16 0.13
Matches are distributed among these distances:
47 3 0.01
48 15 0.07
49 166 0.73
50 39 0.17
51 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (49 bp):
GAAGGGAAAAATTTAAGCTGCAACGGTGAATCTAGTACCACGAAGATAC
Found at i:1508 original size:98 final size:98
Alignment explanation
Indices: 1329--1804 Score: 620
Period size: 98 Copynumber: 4.9 Consensus size: 98
1319 CTACAGGTCT
* * * ** * *
1329 CAGTACCACG-AGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTGCCTCAGAATCA
1 CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAGCA
* * **
1393 TGAAGGGAAAAATTTAAGCTGCAACGGTAAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
1426 TAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAGCA
*
1491 TGAAGGGAAATATTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
1524 CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCACAATGGTGAACCTTGTACCTTAGAAGCG
1 CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAGCA
*
1589 TGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
1622 CAATACCATGAAGACACGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAG-AGAC
1 CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAG-C
*
1686 ATGAAAGGGAAAGATTTAAGCCGCAACGGTGAATC
65 ATG-AAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
1721 CAGTACC-CGAAGACACGAAGGGGAAGGTTTAGGTCGCAATGGCT-AACCTTATACCTCAAAAGC
1 CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAATGG-TGAACCTTGTACCTCAGAAGC
*
1784 ATGAAAGGAAA-ATTTAAGCCG
65 ATGAAGGGAAAGATTTAAGCCG
1805 TAATGACGAA
Statistics
Matches: 339, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
96 10 0.03
97 18 0.05
98 274 0.81
99 37 0.11
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (98 bp):
CAGTACCACGAAGATACGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAGCA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:2241 original size:23 final size:23
Alignment explanation
Indices: 2215--2299 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
2205 CTAAACCCTT
2215 TTTAAATTT-ATTGTAAGATTAAA
1 TTTAAATTTAATT-TAAGATTAAA
*
2238 TTTAAATTTAATTTAAGTTTAAA
1 TTTAAATTTAATTTAAGATTAAA
** *
2261 TTTATCTTTGAATTTAA-ATTTAA
1 TTTAAATTT-AATTTAAGATTAAA
*
2284 TTTAAGTTTAAATTTA
1 TTTAAATTT-AATTTA
2300 TCTTTGAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
23 42 0.81
24 10 0.19
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (23 bp):
TTTAAATTTAATTTAAGATTAAA
Found at i:2242 original size:6 final size:6
Alignment explanation
Indices: 2233--2332 Score: 82
Period size: 6 Copynumber: 17.2 Consensus size: 6
2223 TATTGTAAGA
* ** *
2233 TTAAAT TTAAAT TT-AAT TTAAGT TTAAAT TTATCT TTGAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* ** * *
2280 TT-AAT TTAAGT TTAAAT TTATCT TTGAAT TTAAAA TT--AT TATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT
2326 TTAAAT T
1 TTAAAT T
2333 GAAAGTCCAA
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
4 2 0.03
5 11 0.15
6 55 0.77
7 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:2275 original size:35 final size:35
Alignment explanation
Indices: 2236--2332 Score: 160
Period size: 35 Copynumber: 2.8 Consensus size: 35
2226 TGTAAGATTA
2236 AATTTAAATTTAATTTAAGTTTAAATTTATCTTTG
1 AATTTAAATTTAATTTAAGTTTAAATTTATCTTTG
2271 AATTTAAATTTAATTTAAGTTTAAATTTATCTTTG
1 AATTTAAATTTAATTTAAGTTTAAATTTATCTTTG
* *
2306 AATTTAAAATT-ATTATAAATTTAAATT
1 AATTTAAATTTAATT-TAAGTTTAAATT
2333 GAAAGTCCAA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 3 0.05
35 56 0.95
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (35 bp):
AATTTAAATTTAATTTAAGTTTAAATTTATCTTTG
Found at i:4192 original size:30 final size:28
Alignment explanation
Indices: 4158--4631 Score: 124
Period size: 29 Copynumber: 16.3 Consensus size: 28
4148 TAAAAATCAT
4158 ATTTTGACCCCTGAACTTTTCCAAAATTCC
1 ATTTT-ACCCCTGAAC-TTTCCAAAATTCC
** * *
4188 ATTTTTA-CAGTCGAACTTTCAAAAAATTAC
1 A-TTTTACCCCT-GAACTTTC-CAAAATTCC
* * *
4218 ATTTTTACCCTCT-AACTTTCAAAAAAATAC
1 A-TTTTACCC-CTGAACTTTC-CAAAATTCC
** *
4248 ATTTTTGACTTC-AAACTTTCCAAAATTCC
1 A-TTTT-ACCCCTGAACTTTCCAAAATTCC
*
4277 ATTTTTGA-CCCTGAATTTTCCAAAATTTACC
1 A-TTTT-ACCCCTGAACTTTCCAAAA-TT-CC
*
4308 GTTTTA-CCCTCGAAC-TTCCAATAATTCC
1 ATTTTACCCCT-GAACTTTCCAA-AATTCC
* * *
4336 ATTTTTAACCCT-AATTTTTCAAAAATTTACC
1 A-TTTTACCCCTGAA-CTTTCCAAAA-TT-CC
*
4367 ATTTCA-CCCTCGAAC-TTCCAAAAATTCC
1 ATTTTACCCCT-GAACTTTCC-AAAATTCC
* *
4395 ATTTTTGA-CCCTG-ATTTTTCAAAATTTACC
1 A-TTTT-ACCCCTGAACTTTCCAAAA-TT-CC
* ** *
4425 ATTTCACCCCCCAAC-TTCTAAAAATTCC
1 ATTTTACCCCTGAACTTTC-CAAAATTCC
* * * *
4453 ATTTTTA-ACCTCAATTTTCTAAAATTACC
1 A-TTTTACCCCTGAACTTTCCAAAATT-CC
* * * * * *
4482 ATTTTACCTC-AAACTGTCTAAATTTTC
1 ATTTTACCCCTGAACTTTCCAAAATTCC
*
4509 ATTTTAACCCC-AAACTTTCCAAAATTACC
1 ATTTT-ACCCCTGAACTTTCCAAAATT-CC
* * *
4538 ATTTTA-CCCTCGAAC-ATCTAAAATTTC
1 ATTTTACCCCT-GAACTTTCCAAAATTCC
*
4565 ATTTTTGACTCC-GAA-TATTCCAAAATTACC
1 A-TTTT-ACCCCTGAACT-TTCCAAAATT-CC
* *
4595 ATTTTACCCCT-AAGTGTCCAAAATTACC
1 ATTTTACCCCTGAACTTTCCAAAATT-CC
4623 ATTTTACCC
1 ATTTTACCC
4632 TCGGGCATCA
Statistics
Matches: 339, Mismatches: 60, Indels: 92
0.69 0.12 0.19
Matches are distributed among these distances:
27 11 0.03
28 103 0.30
29 113 0.33
30 97 0.29
31 14 0.04
32 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (28 bp):
ATTTTACCCCTGAACTTTCCAAAATTCC
Found at i:4296 original size:29 final size:30
Alignment explanation
Indices: 4159--4599 Score: 148
Period size: 30 Copynumber: 15.1 Consensus size: 30
4149 AAAAATCATA
4159 TTTTGACCC-CTGAACTTTTCCAAAATTCCAT
1 TTTTGACCCTC-GAA-TTTTCCAAAATTCCAT
** * * *
4190 TTTT-ACAGTCGAACTTTCAAAAAATTACAT
1 TTTTGACCCTCGAATTTTC-CAAAATTCCAT
* * * * *
4220 TTTT-ACCCTCTAACTTTCAAAAAAATACAT
1 TTTTGACCCTCGAATTTTC-CAAAATTCCAT
* * *
4250 TTTTGA-CTTCAAACTTTCCAAAATTCCAT
1 TTTTGACCCTCGAATTTTCCAAAATTCCAT
*
4279 TTTTGACCCT-GAATTTTCCAAAATTTACC-G
1 TTTTGACCCTCGAATTTTCCAAAA-TT-CCAT
*
4309 TTTT-ACCCTCGAA-CTTCCAATAATTCCAT
1 TTTTGACCCTCGAATTTTCCAA-AATTCCAT
* *
4338 TTTTAACCCT--AATTTTTCAAAAATTTACCA-
1 TTTTGACCCTCGAA-TTTTCCAAAA-TT-CCAT
* *
4368 -TTTCACCCTCGAA-CTTCCAAAAATTCCAT
1 TTTTGACCCTCGAATTTTCC-AAAATTCCAT
*
4397 TTTTGACCCT-G-ATTTTTCAAAATTTACCA-
1 TTTTGACCCTCGAATTTTCCAAAA-TT-CCAT
* * * * *
4426 -TTTCACCCCCCAA-CTTCTAAAAATTCCAT
1 TTTTGACCCTCGAATTTTC-CAAAATTCCAT
* *
4455 TTTT-AACCTC-AATTTTCTAAAATTACCA-
1 TTTTGACCCTCGAATTTTCCAAAATT-CCAT
* * * * * *
4483 TTTT-A-CCTCAAACTGTCTAAATTTTCA-
1 TTTTGACCCTCGAATTTTCCAAAATTCCAT
* * *
4510 TTTTAACCC-CAAACTTTCCAAAATTACCA-
1 TTTTGACCCTCGAATTTTCCAAAATT-CCAT
** * *
4539 TTTT-ACCCTCGAA-CATCTAAAATTTCAT
1 TTTTGACCCTCGAATTTTCCAAAATTCCAT
* *
4567 TTTTGACTC-CGAATATTCCAAAATTACCAT
1 TTTTGACCCTCGAATTTTCCAAAATT-CCAT
4597 TTT
1 TTT
4600 ACCCCTAAGT
Statistics
Matches: 316, Mismatches: 56, Indels: 77
0.70 0.12 0.17
Matches are distributed among these distances:
27 12 0.04
28 80 0.25
29 103 0.33
30 108 0.34
31 13 0.04
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTTGACCCTCGAATTTTCCAAAATTCCAT
Found at i:4476 original size:28 final size:29
Alignment explanation
Indices: 4440--4562 Score: 112
Period size: 28 Copynumber: 4.3 Consensus size: 29
4430 ACCCCCCAAC
*
4440 TTCTAAAAATT-CCATTTTTAACCTC-AATT
1 TTCT-AAAATTACCA-TTTTAACCTCAAACT
4469 TTCTAAAATTACCATTTT-ACCTCAAACT
1 TTCTAAAATTACCATTTTAACCTCAAACT
* ** *
4497 GTCT-AAATTTTCATTTTAACCCCAAACT
1 TTCTAAAATTACCATTTTAACCTCAAACT
* * *
4525 TTCCAAAATTACCATTTTACCCTCGAAC-
1 TTCTAAAATTACCATTTTAACCTCAAACT
*
4553 ATCTAAAATT
1 TTCTAAAATT
4563 TCATTTTTGA
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
27 16 0.21
28 35 0.46
29 25 0.33
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
TTCTAAAATTACCATTTTAACCTCAAACT
Found at i:4502 original size:57 final size:59
Alignment explanation
Indices: 4269--4603 Score: 307
Period size: 59 Copynumber: 5.8 Consensus size: 59
4259 CAAACTTTCC
* * * *
4269 AAAATTCCATTTTTGACC-CTGAATTTTCCAAAATTTACCGTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCTC-AAATTTTCCAAAATTTACCATTTTACCCTCGAACTTCTA
* * * * *
4328 ATAATTCCATTTTTAACC-CTAATTTTTCAAAAATTTACCATTTCACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCTC-AAATTTTCCAAAATTTACCATTTTACCCTCGAACTTCTA
* ** * * * *
4387 AAAATTCCATTTTTGACC-CTGATTTTTCAAAATTTACCATTTCACCCCCCAACTTCTA
1 AAAATTCCATTTTTAACCTCAAATTTTCCAAAATTTACCATTTTACCCTCGAACTTCTA
* *
4445 AAAATTCCATTTTTAACCTC-AATTTTCTAAAA-TTACCATTTTA-CCTCAAACTGTCT-
1 AAAATTCCATTTTTAACCTCAAATTTTCCAAAATTTACCATTTTACCCTCGAACT-TCTA
* * * * *
4501 AAATTTTCA-TTTTAACCCCAAACTTTCCAAAA-TTACCATTTTACCCTCGAACATCT-
1 AAAATTCCATTTTTAACCTCAAATTTTCCAAAATTTACCATTTTACCCTCGAACTTCTA
* * * *
4557 AAAATTTCATTTTTGA-CTCCGAATATTCCAAAA-TTACCATTTTACCC
1 AAAATTCCATTTTTAACCT-CAAATTTTCCAAAATTTACCATTTTACCC
4604 CTAAGTGTCC
Statistics
Matches: 233, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
55 9 0.04
56 47 0.20
57 50 0.21
58 57 0.24
59 70 0.30
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCTCAAATTTTCCAAAATTTACCATTTTACCCTCGAACTTCTA
Found at i:4504 original size:27 final size:28
Alignment explanation
Indices: 4473--4631 Score: 121
Period size: 28 Copynumber: 5.6 Consensus size: 28
4463 TCAATTTTCT
*
4473 AAAATTACCATTTTACCTCAAACTGT-C
1 AAAATTACCATTTTACCCCAAACTGTCC
* ** *
4500 TAAATTTTCATTTTAACCCCAAACTTTCC
1 AAAATTACCATTTT-ACCCCAAACTGTCC
* * *
4529 AAAATTACCATTTTACCCTCGAAC-ATCT
1 AAAATTACCATTTTACCC-CAAACTGTCC
* *
4557 AAAATT-TCATTTTTGACTCCGAATA-T-TCC
1 AAAATTACCA-TTTT-AC-CCCAA-ACTGTCC
* *
4586 AAAATTACCATTTTACCCCTAAGTGTCC
1 AAAATTACCATTTTACCCCAAACTGTCC
4614 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
4632 TCGGGCATCA
Statistics
Matches: 103, Mismatches: 18, Indels: 21
0.73 0.13 0.15
Matches are distributed among these distances:
26 1 0.01
27 17 0.17
28 49 0.48
29 31 0.30
30 5 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCAAACTGTCC
Found at i:7627 original size:19 final size:19
Alignment explanation
Indices: 7605--7641 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7595 AAGAGCTTGG
7605 AGTTTAGGAAAAGGATAAA
1 AGTTTAGGAAAAGGATAAA
* *
7624 AGTTTTGGAAGAGGATAA
1 AGTTTAGGAAAAGGATAA
7642 GATGAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (19 bp):
AGTTTAGGAAAAGGATAAA
Done.