Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009713.1 Kokia drynarioides strain JFW-HI SEQ_124432, 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: 7079
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Found at i:3698 original size:200 final size:200
Alignment explanation
Indices: 3340--3824 Score: 528
Period size: 200 Copynumber: 2.4 Consensus size: 200
3330 CAAGCTTACA
* * * *
3340 AAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGCCGAAGCAATAAAAGGGTAGC
1 AAATCTTCAAAACCCAGCTTCCTGATGAAACACTGAGAAGCAGGCCGAAGCAATAAAAGGGTAGC
* * * *
3405 TTCCTGATGAGATACTGAGAAGTGAACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATT
66 TTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATT
* *
3470 GAAACGATAATGGGACCACCTTCCTGATGAGACACTGAGGAGAAGACCCGAACGAGGCTCAAAGT
131 GAAACGACAACGGGACCACCTTCCTGATGAGACACTGAGGAGAAGACCCGAACGAGGCTCAAAGT
3535 GAGCG
196 GAGCG
* ** *
3540 AAATCTTCAAAACCCAGCTTCCTGATGAAACACTGAGAAGTAGGTGGAAGCAAT-AAAGGTTAGC
1 AAATCTTCAAAACCCAGCTTCCTGATGAAACACTGAGAAGCAGGCCGAAGCAATAAAAGGGTAGC
* * *
3604 TTTCTGATGAGATCCTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACACAGGGAAGCGAATT
66 TTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATT
* * * * * * * *
3669 GAAACAGACGACGTGG-TCATCTTCCTGATGAGATACTGAGAAGGAA-ACCAAACCAAACCCACG
131 GAAAC-GACAACG-GGACCACCTTCCTGATGAGACACTGAGGA-GAAGA-C---CCGAA-CGAGG
* * *
3732 CTCGATGTGAG-T
188 CTCAAAGTGAGCG
* * * * * * * *
3744 AAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAGTAAAACAGTTAG
1 AAATCTTCAAAACCCAGCTTCCTGATGAAACACTGAGAAGCAGGCCGAAGCAATAAAA-GGGTAG
*
3809 CTTCCTGATAAGATAC
65 CTTCCTGATGAGATAC
3825 AGAGAAGCGA
Statistics
Matches: 236, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
199 72 0.31
200 74 0.31
201 6 0.03
204 51 0.22
205 15 0.06
206 18 0.08
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (200 bp):
AAATCTTCAAAACCCAGCTTCCTGATGAAACACTGAGAAGCAGGCCGAAGCAATAAAAGGGTAGC
TTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATT
GAAACGACAACGGGACCACCTTCCTGATGAGACACTGAGGAGAAGACCCGAACGAGGCTCAAAGT
GAGCG
Found at i:3962 original size:170 final size:169
Alignment explanation
Indices: 3640--4001 Score: 609
Period size: 170 Copynumber: 2.1 Consensus size: 169
3630 CCAAATTCGT
* *
3640 CTTCCTGATGAGACACAGGGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATAC
*
3705 TGAGAAGGAAACCAAACCAAACCCACGCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCTTGAT
66 TGAGAAGGAAACCAAACCAAACCCACGCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTGAT
* *
3770 GAGACACTGAGAAGCAGGTCGAAGCAGTAAAACAGTTAG
131 GAGACACTGAGAAGCAGGTCGAAGCAATAAAACAGATAG
*
3809 CTTCCTGATAAGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATAC
3874 TGAGAA-GAAGACCAAACCCAAACCCACGCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTG
66 TGAGAAGGAA-ACCAAA-CCAAACCCACGCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTG
* *
3938 ATGAGACACTGGGAAGCAGGTCGAAGCAATAAAACGGATAG
129 ATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACAGATAG
* *
3979 CTCCCTGAGGAGATACAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
4002 TGAACCAAAT
Statistics
Matches: 180, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
168 3 0.02
169 74 0.41
170 103 0.57
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (169 bp):
CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATAC
TGAGAAGGAAACCAAACCAAACCCACGCTCGATGTGAGTAAATCTTCGAACCCCAGCTTCCTGAT
GAGACACTGAGAAGCAGGTCGAAGCAATAAAACAGATAG
Found at i:4330 original size:17 final size:17
Alignment explanation
Indices: 4307--4435 Score: 159
Period size: 17 Copynumber: 7.4 Consensus size: 17
4297 CCAAATTCCC
4307 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
4324 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
4342 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
4360 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
4377 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
4394 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
4412 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
4429 TTTAAAT
1 TTTAAAT
4436 GAATCTGAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
17 53 0.56
18 38 0.40
19 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4346 original size:35 final size:34
Alignment explanation
Indices: 4307--4435 Score: 150
Period size: 35 Copynumber: 3.7 Consensus size: 34
4297 CCAAATTCCC
* *
4307 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTT-AAAA
**
4342 TTTAAATTTATTTTTAAATTTAAATTTATTTTGAA
1 TTTAAATTTA-TTTTAAATTTAAATTTATTTAAAA
* * *
4377 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTTA-TTTAAAA
* *
4412 TTTAAAATTATTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
4436 GAATCTGAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
34 15 0.19
35 47 0.59
36 18 0.22
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAA
Found at i:4348 original size:6 final size:6
Alignment explanation
Indices: 4339--4435 Score: 78
Period size: 6 Copynumber: 16.7 Consensus size: 6
4329 ATTTGTTTAA
** * *
4339 AAATTT AAATTT ATTTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
4386 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAAATT --ATTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATT-T AAATTT
4432 AAAT
1 AAAT
4436 GAATCTGAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
4 2 0.03
5 14 0.20
6 48 0.68
7 7 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:5232 original size:15 final size:15
Alignment explanation
Indices: 5188--5237 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5178 GTATTAATAA
* *
5188 TAATATTAATGACAT
1 TAATAATAATGGCAT
* *
5203 TAATAATGGATGGCAG
1 TAATAAT-AATGGCAT
5219 TAATAATAATGGCAT
1 TAATAATAATGGCAT
5234 TAAT
1 TAAT
5238 GACGGTGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (15 bp):
TAATAATAATGGCAT
Found at i:5271 original size:3 final size:3
Alignment explanation
Indices: 5263--5294 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5253 TGAACGTTTT
5263 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5295 TCTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6469 original size:59 final size:59
Alignment explanation
Indices: 6357--6857 Score: 668
Period size: 59 Copynumber: 8.5 Consensus size: 59
6347 GGAGGTCCCT
* * *
6357 AAACCTTCTAAAAATTATCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* * * * *
6416 AAACTTTCTAAAAATTACCATTTTACCCCCCGAACTTCCATAAATCTCA-TTTTGACCCT
1 AAACCTTCTAAAAATTACCATTTTA-CCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* * *
6475 AAACTTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATACCATTTTTGACCTC
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* *
6534 GAACCTTCTAAAAATTACCATTTTACCCCCTGAACTTCCAAAAATCCCA-TTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCC-AAACTTCCAAAAATCCCATTTTTGACCCC
* *** *
6593 GAACCTTCTAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCTC
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
6652 GAACCTTCTAAAAATTAACATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* * *
6711 GAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCAATTTTTGACCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* *
6770 AAACCTT-TCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACTCC
1 AAACCTTCT-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
6829 AAACCTAC-CAAAACTACCATTTTGCCCCC
1 AAACCTTCTAAAAATTACCATTTTACCCCC
6858 GTGCATTTGA
Statistics
Matches: 396, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
58 54 0.14
59 306 0.77
60 36 0.09
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:6849 original size:30 final size:30
Alignment explanation
Indices: 6357--6851 Score: 331
Period size: 30 Copynumber: 16.8 Consensus size: 30
6347 GGAGGTCCCT
* *
6357 AAACCTTCTAAAAATTATCA-TTTT-ACCCTC
1 AAACCTTCCAAAAA-TACCATTTTTGACCC-C
* *
6387 GAA-CTTCCAAAAATCCCATTTTTGACCCC
1 AAACCTTCCAAAAATACCATTTTTGACCCC
* * ***
6416 AAACTTTCTAAAAATTACCATTTTACCCCCC
1 AAACCTTCCAAAAA-TACCATTTTTGACCCC
* * *
6447 GAA-CTTCCATAAAT-CTCA-TTTTGACCCT
1 AAACCTTCCAAAAATAC-CATTTTTGACCCC
* *
6475 AAACTTTCTAAAAATTACCA-TTTT-ACCCCC
1 AAACCTTCCAAAAA-TACCATTTTTGA-CCCC
*
6505 AAA-CTTCCAAAAATACCATTTTTGACCTC
1 AAACCTTCCAAAAATACCATTTTTGACCCC
* *
6534 GAACCTTCTAAAAATTACCA-TTTT-ACCCCC
1 AAACCTTCCAAAAA-TACCATTTTTGA-CCCC
* *
6564 TGAA-CTTCCAAAAATCCCA-TTTTGACCCC
1 -AAACCTTCCAAAAATACCATTTTTGACCCC
* * *
6593 GAACCTTCTAAAAATTACCA-TTTT-ACCCTT
1 AAACCTTCCAAAAA-TACCATTTTTGACCC-C
* * *
6623 GAA-CTTCCAAAAATCCCATTTTTGACCTC
1 AAACCTTCCAAAAATACCATTTTTGACCCC
* * *
6652 GAACCTTCTAAAAATTAACA-TTTT-ACCCC
1 AAACCTTCCAAAAA-TACCATTTTTGACCCC
*
6681 TAAA-CTTCCAAAAATTCCATTTTTGACCCC
1 -AAACCTTCCAAAAATACCATTTTTGACCCC
*
6711 GAACCTTCCAAAAATTACCA-TTTT-ACCCCC
1 AAACCTTCCAAAAA-TACCATTTTTGA-CCCC
6741 AAA-CTTCCAAAAAT-CCAATTTTTGACCCC
1 AAACCTTCCAAAAATACC-ATTTTTGACCCC
*
6770 AAACCTTTCAAAAATTACCA-TTTT-ACCCTC
1 AAACCTTCCAAAAA-TACCATTTTTGACCC-C
* *
6800 AAA-CTTCCAAAAATCCCATTTTTGACTCC
1 AAACCTTCCAAAAATACCATTTTTGACCCC
* *
6829 AAACCTACCAAAACTACCATTTT
1 AAACCTTCCAAAAATACCATTTT
6852 GCCCCCGTGC
Statistics
Matches: 369, Mismatches: 57, Indels: 78
0.73 0.11 0.15
Matches are distributed among these distances:
27 2 0.01
28 33 0.09
29 148 0.40
30 152 0.41
31 32 0.09
32 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (30 bp):
AAACCTTCCAAAAATACCATTTTTGACCCC
Found at i:6852 original size:29 final size:29
Alignment explanation
Indices: 6357--6857 Score: 345
Period size: 29 Copynumber: 17.0 Consensus size: 29
6347 GGAGGTCCCT
* *
6357 AAACCTTCTAAAAATTATCATTTT-ACCCTC
1 AAACCTTCCAAAAA-TACCATTTTGACCC-C
* *
6387 GAA-CTTCCAAAAATCCCATTTTTGACCCC
1 AAACCTTCCAAAAATACCA-TTTTGACCCC
* *
6416 AAACTTTCTAAAAATTACCATTTT-ACCCCCC
1 AAACCTTCCAAAAA-TACCATTTTGA--CCCC
* * *
6447 GAA-CTTCCATAAAT-CTCATTTTGACCCT
1 AAACCTTCCAAAAATAC-CATTTTGACCCC
* *
6475 AAACTTTCTAAAAATTACCATTTT-ACCCCC
1 AAACCTTCCAAAAA-TACCATTTTGA-CCCC
*
6505 AAA-CTTCCAAAAATACCATTTTTGACCTC
1 AAACCTTCCAAAAATACCA-TTTTGACCCC
* *
6534 GAACCTTCTAAAAATTACCATTTT-ACCCCC
1 AAACCTTCCAAAAA-TACCATTTTGA-CCCC
* *
6564 TGAA-CTTCCAAAAATCCCATTTTGACCCC
1 -AAACCTTCCAAAAATACCATTTTGACCCC
* * *
6593 GAACCTTCTAAAAATTACCATTTT-ACCCTT
1 AAACCTTCCAAAAA-TACCATTTTGACCC-C
* * *
6623 GAA-CTTCCAAAAATCCCATTTTTGACCTC
1 AAACCTTCCAAAAATACCA-TTTTGACCCC
* * *
6652 GAACCTTCTAAAAATTAACATTTT-ACCCC
1 AAACCTTCCAAAAA-TACCATTTTGACCCC
*
6681 TAAA-CTTCCAAAAATTCCATTTTTGACCCC
1 -AAACCTTCCAAAAATACCA-TTTTGACCCC
*
6711 GAACCTTCCAAAAATTACCATTTT-ACCCCC
1 AAACCTTCCAAAAA-TACCATTTTGA-CCCC
6741 AAA-CTTCCAAAAAT-CCAATTTTTGACCCC
1 AAACCTTCCAAAAATACC-A-TTTTGACCCC
*
6770 AAACCTTTCAAAAATTACCATTTT-ACCCTC
1 AAACCTTCCAAAAA-TACCATTTTGACCC-C
* *
6800 AAA-CTTCCAAAAATCCCATTTTTGACTCC
1 AAACCTTCCAAAAATACCA-TTTTGACCCC
* * *
6829 AAACCTACCAAAACTACCATTTTGCCCCC
1 AAACCTTCCAAAAATACCATTTTGACCCC
6858 GTGCATTTGA
Statistics
Matches: 376, Mismatches: 53, Indels: 85
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.01
28 30 0.08
29 161 0.43
30 153 0.41
31 28 0.07
32 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACCTTCCAAAAATACCATTTTGACCCC
Done.