Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012850.1 Kokia drynarioides strain JFW-HI SEQ_127864, 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: 20532
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1174 original size:30 final size:30
Alignment explanation
Indices: 1099--1557 Score: 403
Period size: 30 Copynumber: 15.4 Consensus size: 30
1089 AACTATTCAG
* * * *
1099 AAATTACATTTTTACCCCCG-AACATCCAA
1 AAATTCCATTTTTACCCTCGAAACTTCTAA
*
1128 AAATTCCATTTTTTTACCCCCGAAACTTCTAA
1 AAATTCCA--TTTTTACCCTCGAAACTTCTAA
* * * *
1160 AAATTACATTTTTACCCTTG-AACATCCAAA
1 AAATTCCATTTTTACCCTCGAAAC-TTCTAA
* *
1190 AAATTCCATTTTTAACCTCGAAACTTTTAA
1 AAATTCCATTTTTACCCTCGAAACTTCTAA
1220 AAATTCCATTTTTATCCC-CGAAACTTCTAA
1 AAATTCCATTTTTA-CCCTCGAAACTTCTAA
* **
1250 AAATTCCATTTTTA-CTTCCGAATTTTC-AA
1 AAATTCCATTTTTACCCT-CGAAACTTCTAA
* * * *
1279 AAATTCCTTTTTTGA-CCTTGAGACTTCCAA
1 AAATTCCATTTTT-ACCCTCGAAACTTCTAA
*
1309 AAATTCCATTTTTACCCTTG-AACTT-TCAA
1 AAATTCCATTTTTACCCTCGAAACTTCT-AA
* *
1338 AAATTCCATTTTTGA-CCTCGAGACTTCCAA
1 AAATTCCATTTTT-ACCCTCGAAACTTCTAA
* *
1368 AAATTCCATTTTTACCCCCG-AACTTCCAA
1 AAATTCCATTTTTACCCTCGAAACTTCTAA
*
1397 AAATTCCATTTTTGACCCT-AAAACTTCTAA
1 AAATTCCATTTTT-ACCCTCGAAACTTCTAA
1427 AAATTCCATTTTTACCCTC-AAACTT-TCAA
1 AAATTCCATTTTTACCCTCGAAACTTCT-AA
*
1456 AAATTCCATTTTTGA-CCTCGAAACTTCCAA
1 AAATTCCATTTTT-ACCCTCGAAACTTCTAA
* ** *
1486 AAACTATATTTTTACCCTC-AAACCTCTAA
1 AAATTCCATTTTTACCCTCGAAACTTCTAA
*
1515 AATTTCCATTTTTAACCC-CGAAACTT-TCAA
1 AAATTCCATTTTT-ACCCTCGAAACTTCT-AA
1545 AAATTACCATTTT
1 AAATT-CCATTTT
1558 GCATTTGTTA
Statistics
Matches: 354, Mismatches: 48, Indels: 54
0.78 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 125 0.35
30 189 0.53
31 24 0.07
32 14 0.04
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATTCCATTTTTACCCTCGAAACTTCTAA
Found at i:1305 original size:59 final size:58
Alignment explanation
Indices: 1089--1557 Score: 423
Period size: 59 Copynumber: 7.9 Consensus size: 58
1079 GAGGTCTCTA
* * * *
1089 AACTATTCAGAAATTACATTTTT-ACCCCCG-AACATCCAAAAATTCCATTTTTTTACCCCCG
1 AACT-TTCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCA--TTTTTA-CCCCG
* * * *
1150 AAAC-TTCTAAAAATTACATTTTT-ACCCTTG-AACATCCAAAAAATTCCATTTTTAACCTCG
1 -AACTTTC-AAAAATTCCATTTTTGA-CCTCGAAACTTCC-AAAAATTCCATTTTT-ACCCCG
* * * *
1210 AAACTTTTAAAAATTCCATTTTT-ATCCCCGAAACTTCTAAAAATTCCATTTTTACTTCCG
1 -AACTTTCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTAC-CCCG
* * * * *
1270 AATTTTCAAAAATTCCTTTTTTGACCTTGAGACTTCCAAAAATTCCATTTTTACCCTTG
1 AACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCC-CG
*
1329 AACTTTCAAAAATTCCATTTTTGACCTCGAGACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTA-CCCCG
* * * *
1388 AACTTCCAAAAATTCCATTTTTGACC-CTAAAACTTCTAAAAATTCCATTTTTACCCTCA
1 AACTTTCAAAAATTCCATTTTTGACCTC-GAAACTTCCAAAAATTCCATTTTTACCC-CG
* ** *
1447 AACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAACTATATTTTTACCCTCA
1 AACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCC-CG
* * * * *
1506 AAC-CTCTAAAATTTCCATTTTTAACCCCGAAACTTTCAAAAATTACCATTTT
1 AACTTTC-AAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATT-CCATTTT
1558 GCATTTGTTA
Statistics
Matches: 348, Mismatches: 45, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
58 7 0.02
59 233 0.67
60 61 0.18
61 34 0.10
62 13 0.04
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (58 bp):
AACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:1497 original size:118 final size:118
Alignment explanation
Indices: 1088--1557 Score: 493
Period size: 118 Copynumber: 3.9 Consensus size: 118
1078 AGAGGTCTCT
* * * *
1088 AAACTATTCAGAAATTACATTTTT-ACCCCCG-AACATCCAAAAATTCCATTTTTTTACCCCCGA
1 AAACT-TTCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCA--TTTTTACCCCCG-
* * * * *
1151 AACTTCTAAAAATTACATTTTT-ACCCTTG-AACATCCAAAAAATTCCATTTTTAACCTC
61 AACTTCCAAAAATTCCATTTTTGACCC-TGAAAC-TTCTAAAAATTCCATTTTTACCCTC
* * * ** *
1209 GAAACTTTTAAAAATTCCATTTTT-ATCCCCGAAACTTCTAAAAATTCCATTTTTACTTCCGAAT
1 -AAACTTTCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAAC
* * * * * *
1273 TTTCAAAAATTCCTTTTTTGACCTTGAGACTTCCAAAAATTCCATTTTTACCCTT
64 TTCCAAAAATTCCATTTTTGACCCTGAAACTTCTAAAAATTCCATTTTTACCCTC
* *
1328 GAACTTTCAAAAATTCCATTTTTGACCTCGAGACTTCCAAAAATTCCATTTTTACCCCCGAACTT
1 AAACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
*
1393 CCAAAAATTCCATTTTTGACCCTAAAACTTCTAAAAATTCCATTTTTACCCTC
66 CCAAAAATTCCATTTTTGACCCTGAAACTTCTAAAAATTCCATTTTTACCCTC
* ** * * *
1446 AAACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAACTATATTTTTACCCTCAAACCT
1 AAACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
* * * *
1511 CTAAAATTTCCATTTTTAACCCCGAAACTT-TCAAAAATTACCATTTT
66 CCAAAAATTCCATTTTTGACCCTGAAACTTCT-AAAAATT-CCATTTT
1558 GCATTTGTTA
Statistics
Matches: 295, Mismatches: 47, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
117 1 0.00
118 190 0.64
119 48 0.16
120 15 0.05
121 21 0.07
122 20 0.07
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (118 bp):
AAACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
CCAAAAATTCCATTTTTGACCCTGAAACTTCTAAAAATTCCATTTTTACCCTC
Found at i:4007 original size:95 final size:94
Alignment explanation
Indices: 3875--4144 Score: 346
Period size: 95 Copynumber: 2.9 Consensus size: 94
3865 CAGTGGAGTG
** * * *
3875 GAGTGAAACTTCAAATCTCATCTTCCTAATAAAGTACAGAGAAGTAAGTCGATACAATATGTTAA
1 GAGTGAAACTTCAAATCTCATCTTCCTGGTGAGGTACAGAGAAGTAAGTCGATACAGTATGTTAA
*
3940 ATCAAAACAACGAAGTTAAACTCAAATGT
66 ATCAAAACAACGAAGTCAAACTCAAATGT
3969 GAGTGAAACTTCAAATTCTCATCTTCCTGGTGAGGTACAGAGAAGCATAA--CGATACAGTATGT
1 GAGTGAAACTTCAAA-TCTCATCTTCCTGGTGAGGTACAGAGAAG--TAAGTCGATACAGTATGT
* * **
4032 TAAATCAAAACAACAAAGTCGAGTTCAAATGT
63 TAAATCAAAACAACGAAGTCAAACTCAAATGT
* * * ** *
4064 GAGTGAAACTTTAAAATCCCATCTTTCTGGTGAGGTACAGAGAAGTGGGTCGATACAGTCTGTTA
1 GAGTGAAAC-TTCAAATCTCATCTTCCTGGTGAGGTACAGAGAAGTAAGTCGATACAGTATGTTA
4129 AATCAAAACAACGAAG
65 AATCAAAACAACGAAG
4145 CCGAGATCAA
Statistics
Matches: 153, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
93 1 0.01
94 15 0.10
95 129 0.84
96 5 0.03
97 3 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (94 bp):
GAGTGAAACTTCAAATCTCATCTTCCTGGTGAGGTACAGAGAAGTAAGTCGATACAGTATGTTAA
ATCAAAACAACGAAGTCAAACTCAAATGT
Found at i:4416 original size:123 final size:122
Alignment explanation
Indices: 4197--4516 Score: 337
Period size: 123 Copynumber: 2.6 Consensus size: 122
4187 CTTTAAATCC
* * *
4197 CATCTTCCTGGTGAGTTACAAAAAAGTGGGTCAAACAACAAAGCGATCATCTTCCTGATGAA-AT
1 CATCTTCCTAGTAAGATACAAAAAAGTGGGTCAAACAACAAAGCGATCATCTTCCTGAT-AAGAT
* * * * *
4261 ACAAAGAAATGGCACAAAATAATGAGGTGAAGCTCAAATGTGAGTGAAACTGCAAA-CT
65 ACAGAGAAGTGGCACAAAACAATGAGGCGAAGCTC-AATGTGAGTAAAACTGCAAACCT
* * * * *
4319 CCATCTT-CTTGATAATATACATAAAAGTGGGTCAGACAACGAAGC-AGTCATCTTCCTGATAAG
1 -CATCTTCCTAG-TAAGATACAAAAAAGTGGGTCAAACAACAAAGCGA-TCATCTTCCTGATAAG
* *
4382 ATACAGAGAAGTGG-ACCAAAACAATGTA-GCGAAGCTCCATGTGAGTAAAACTTCAAACCT
63 ATACAGAGAAGTGGCA-CAAAACAATG-AGGCGAAGCTCAATGTGAGTAAAACTGCAAACCT
* * * * * *
4442 CATCTTCCTAGTGAGATACAGAGAAGTAGGTCAAAGTAACAAAGCGATCATCTTCCTGATGAGAT
1 CATCTTCCTAGTAAGATACAAAAAAGTGGGTCAAA-CAACAAAGCGATCATCTTCCTGATAAGAT
4507 ACAGAGAAGT
65 ACAGAGAAGT
4517 AGATCGAAAT
Statistics
Matches: 164, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
122 48 0.29
123 114 0.70
124 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (122 bp):
CATCTTCCTAGTAAGATACAAAAAAGTGGGTCAAACAACAAAGCGATCATCTTCCTGATAAGATA
CAGAGAAGTGGCACAAAACAATGAGGCGAAGCTCAATGTGAGTAAAACTGCAAACCT
Found at i:9946 original size:31 final size:30
Alignment explanation
Indices: 9860--9947 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
9850 TGTATATATG
* *
9860 AACTTTAA-TTTGATGTAATTATACACGTGA
1 AACTTTAATTTTGATTTAA-TATATACGTGA
** * * *
9890 AACTTTAATCGTGGTTAAAATATATACTTGA
1 AACTTTAATTTTGATT-TAATATATACGTGA
9921 AACTTTAATTTTGATTTAATCATATAC
1 AACTTTAATTTTGATTTAAT-ATATAC
9948 ATTTAAAGAA
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
30 11 0.25
31 31 0.70
32 2 0.05
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTTGATTTAATATATACGTGA
Found at i:11593 original size:13 final size:13
Alignment explanation
Indices: 11577--11601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11567 GGTCTATTTG
11577 TTTTACAAACAAA
1 TTTTACAAACAAA
11590 TTTTACAAACAA
1 TTTTACAAACAA
11602 TATATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTTACAAACAAA
Found at i:13649 original size:29 final size:27
Alignment explanation
Indices: 13616--13677 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 27
13606 TAAATCTTAA
*
13616 AATTATACATTAATTATGATTTTATGTGT
1 AATTATACATAAATTATGA-TTT-TGTGT
*
13645 AATTATATACATAAATTTTGATTTTGTGT
1 AA-T-TATACATAAATTATGATTTTGTGT
13674 AATT
1 AATT
13678 TTATACGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 9 0.31
30 4 0.14
31 14 0.48
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (27 bp):
AATTATACATAAATTATGATTTTGTGT
Found at i:13682 original size:29 final size:31
Alignment explanation
Indices: 13618--13683 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
13608 AATCTTAAAA
*
13618 TTATACATTAATTATGATTTTATGTGTAATT
1 TTATACATAAATTATGATTTTATGTGTAATT
* *
13649 ATATACATAAATTTTGA-TTT-TGTGTAATT
1 TTATACATAAATTATGATTTTATGTGTAATT
13678 TTATAC
1 TTATAC
13684 GTGAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.45
30 3 0.10
31 14 0.45
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (31 bp):
TTATACATAAATTATGATTTTATGTGTAATT
Found at i:13690 original size:29 final size:28
Alignment explanation
Indices: 13619--13695 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
13609 ATCTTAAAAT
*
13619 TATACATTAATTATGATTTTATGTGTAATTA
1 TATACATAAATT-TGA-TTT-TGTGTAATTA
*
13650 TATACATAAATTTTGATTTTGTGTAATTT
1 TATACATAAA-TTTGATTTTGTGTAATTA
* *
13679 TATACGTGAATTTGATT
1 TATACATAAATTTGATT
13696 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.17
29 17 0.41
30 3 0.07
31 12 0.29
32 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (28 bp):
TATACATAAATTTGATTTTGTGTAATTA
Found at i:20505 original size:16 final size:18
Alignment explanation
Indices: 20466--20499 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20456 TAAGTTTATA
20466 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
20483 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
20500 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Done.