Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010895.1 Kokia drynarioides strain JFW-HI SEQ_125863, 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: 10567
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:2030 original size:204 final size:204
Alignment explanation
Indices: 1681--2544 Score: 1286
Period size: 204 Copynumber: 4.3 Consensus size: 204
1671 TTCGATTATC
* * * * *
1681 CAAACAACGATGTGATCATCTTCCTGATGAGACACTGACAAGAAAATCCAAATGAGGCTCAAAAT
1 CAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
* * * * **
1746 GAGCAAAATCTTCAAACCCCGCCTTCCTAAAGAGACATTGAGAAGTGGGTCGAAGCAATAAAAGG
66 GAACGAAATCTTCGAACCCCGCCTTCCTGAAGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGG
* *
1811 TTAGCTTCTTGATGAGATACTGAAAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGC
131 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGC
**
1876 GAATTGATC
196 GAATTGAAA
* * *
1885 CAAACAGCAATGTGATCATCTTCCTGATAAGACACTGAGAAGAAGATCTAAACGAGGCTCAAAAC
1 CAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
* * * *
1950 GAGCGAAATCTTCGAACCCCACCTTCCTGAACAGACATTGAGAAGCGGGTCGAAGCAATAAAAGG
66 GAACGAAATCTTCGAACCCCGCCTTCCTGAAGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGG
* *
2015 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTTTTCTGATGAGGTACAGAGGAGC
131 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGC
2080 GAATTGAAA
196 GAATTGAAA
* *
2089 CAAACAGCGGTATGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
1 CAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
*
2154 GAACGAAATCTTCGAACCCCGCCTTCCTGAAGAGACATTGAGAAGCAGGTTGAAGCAATAAAAGG
66 GAACGAAATCTTCGAACCCCGCCTTCCTGAAGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGG
* * *
2219 TTAGCTTCCTAATGAGATACTGATAAGTGAACCAAATTCGTCTTCCTAATGAGGTACAGAGGAGC
131 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGC
*
2284 AAATTGAAA
196 GAATTGAAA
* *
2293 TAAACAGCGATATGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
1 CAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
* * * *
2358 GAACGAAATCTTCGAACCCCGCCTTCCCGATGAGATATTGAGAAGTAGGTCGAAGCAATAAAAGG
66 GAACGAAATCTTCGAACCCCGCCTTCCTGAAGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGG
* * * * *
2423 TTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATGAGATATAGAGAAGC
131 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGC
*
2488 GAATCGAAA
196 GAATTGAAA
* **
2497 C-AA-A-TGATGCAATCATCTTCCTGATGAGACACTGAGAAGAAGA-CCAAA
1 CAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAA
2545 TTAGTGAAAC
Statistics
Matches: 602, Mismatches: 58, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
200 5 0.01
201 35 0.06
202 1 0.00
203 2 0.00
204 559 0.93
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (204 bp):
CAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAAAAC
GAACGAAATCTTCGAACCCCGCCTTCCTGAAGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGG
TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGC
GAATTGAAA
Found at i:2791 original size:11 final size:12
Alignment explanation
Indices: 2784--2825 Score: 61
Period size: 11 Copynumber: 3.7 Consensus size: 12
2774 TTTAATTTAT
*
2784 TTTAAATTT-GA
1 TTTAAATTTAAA
2795 TTTAAATTTAAA
1 TTTAAATTTAAA
2807 TTTAAATTT-AA
1 TTTAAATTTAAA
2818 TTTAAATT
1 TTTAAATT
2826 AAAAAGTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:2806 original size:17 final size:17
Alignment explanation
Indices: 2777--2825 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2767 GGCCCTTTTT
*
2777 AATTTATTTTAAATTT-
1 AATTTAATTTAAATTTA
*
2793 GATTTAAATTTAAATTTA
1 AATTT-AATTTAAATTTA
2811 AATTTAATTTAAATT
1 AATTTAATTTAAATT
2826 AAAAAGTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:2828 original size:5 final size:6
Alignment explanation
Indices: 2784--2825 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
2774 TTTAATTTAT
*
2784 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA TTT-AA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
2826 AAAAAGTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:4780 original size:29 final size:29
Alignment explanation
Indices: 4747--5124 Score: 355
Period size: 29 Copynumber: 12.8 Consensus size: 29
4737 GTCCCTAAAC
4747 CTTCCAAAAATTACCATTTTACCCCAAAA
1 CTTCCAAAAATTACCATTTTACCCCAAAA
4776 CTTCCAAAAA-T-CTCATTTTTAACCCCAAAA
1 CTTCCAAAAATTAC-CA-TTTT-ACCCCAAAA
* *
4806 CCTCCAAAAATTACCATTTTACCCCCAAA
1 CTTCCAAAAATTACCATTTTACCCCAAAA
* *
4835 CTTCCAAAAA-TCCCATTTTAACCCAAAAA
1 CTTCCAAAAATTACCATTTT-ACCCCAAAA
* **
4864 CCTCC-AAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCAAAA
4892 CTTCCAAAAA-T-CCATTTTTGACCCCCAAAA
1 CTTCCAAAAATTACCA-TTTT-A-CCCCAAAA
* **
4922 CTTCCGAAAATTACCATTTTACCCCCCGAA
1 CTTCCAAAAATTACCATTTTA-CCCCAAAA
* *
4952 CTTCTAAAAATT-CCATTTTAACCCCGAAA
1 CTTCCAAAAATTACCATTTT-ACCCCAAAA
* *
4981 CTCCCAAAAATTACCATTTTACCCCCAAA
1 CTTCCAAAAATTACCATTTTACCCCAAAA
* *
5010 CTTCCAAAAA-TCCCATTTTTGATCCCAAAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCAAAA
* *
5040 CTTCAAAAAATTACCATTTTA-CCCACGAA
1 CTTCCAAAAATTACCATTTTACCCCA-AAA
*
5069 C-TCCTAAAAA-TCCCATTTTTAACCCCAAAA
1 CTTCC-AAAAATTACCA-TTTT-ACCCCAAAA
5099 CTTCCTAAAAATTACCATTTTTACCC
1 CTTCC-AAAAATTACCA-TTTTACCC
5125 TAGAATATCT
Statistics
Matches: 289, Mismatches: 35, Indels: 48
0.78 0.09 0.13
Matches are distributed among these distances:
27 4 0.01
28 44 0.15
29 112 0.39
30 87 0.30
31 29 0.10
32 13 0.04
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.28
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCAAAA
Found at i:4836 original size:59 final size:59
Alignment explanation
Indices: 4743--5124 Score: 497
Period size: 59 Copynumber: 6.5 Consensus size: 59
4733 GGAGGTCCCT
* *
4743 AAACCTTCCAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCTCATTTTTAACCCCA
1 AAACC-TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
*
4803 AAACCTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTAACCCAA
1 AAACCTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
* *
4861 AAACCTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACCCCCA
1 AAACCTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT-AACCCCA
* * * * * *
4919 AAACTTCCGAAAATTACCATTTTACCCCCCGAACTTCTAAAAATTCCA-TTTTAACCCCG
1 AAACCTCCAAAAATTACCATTTTA-CCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
* *
4978 AAA-CTCCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGATCCCA
1 AAACCT-CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
5037 AAACTTCAAAAAATTACCATTTTACCCACGAAC-TCCTAAAAATCCCATTTTTAACCCCA
1 AAACCTCCAAAAATTACCATTTTACCCCCAAACTTCC-AAAAATCCCATTTTTAACCCCA
*
5096 AAACTTCCTAAAAATTACCATTTTTACCC
1 AAACCTCC-AAAAATTACCA-TTTTACCC
5125 TAGAATATCT
Statistics
Matches: 286, Mismatches: 25, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
56 3 0.01
57 37 0.13
58 54 0.19
59 142 0.50
60 39 0.14
61 11 0.04
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.27
Consensus pattern (59 bp):
AAACCTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:7203 original size:23 final size:22
Alignment explanation
Indices: 7163--7276 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 22
7153 AGTGTTAGTA
** *
7163 ACAAAAGCATTGATGTGCTATAT
1 ACAAAAGCATCAAAGTGCTA-AT
*
7186 ACAGAAGCATCAAAGTGCTAAAT
1 ACAAAAGCATCAAAGTGCT-AAT
* * *
7209 ACAGAAGCAT-AGATGTGCTGCAT
1 ACAAAAGCATCA-AAGTGCT-AAT
*
7232 ACAAAAGCACCAAAGTGCTAATT
1 ACAAAAGCATCAAAGTGCTAA-T
*
7255 ACAAAAGCATCCAAGTGCTAAT
1 ACAAAAGCATCAAAGTGCTAAT
7277 CATCTCTCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
22 3 0.04
23 69 0.93
24 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (22 bp):
ACAAAAGCATCAAAGTGCTAAT
Found at i:7273 original size:46 final size:46
Alignment explanation
Indices: 7146--7264 Score: 148
Period size: 46 Copynumber: 2.6 Consensus size: 46
7136 TCACAGTATT
* * * * * *
7146 GCACCAAAGTGTTAGTAACAAAAGCATTGATGTGCTATATACAGAA
1 GCACCAAAGTGCTAATTACAAAAGCATAGATGTGCTACATACAAAA
* * * *
7192 GCATCAAAGTGCTAAATACAGAAGCATAGATGTGCTGCATACAAAA
1 GCACCAAAGTGCTAATTACAAAAGCATAGATGTGCTACATACAAAA
7238 GCACCAAAGTGCTAATTACAAAAGCAT
1 GCACCAAAGTGCTAATTACAAAAGCAT
7265 CCAAGTGCTA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (46 bp):
GCACCAAAGTGCTAATTACAAAAGCATAGATGTGCTACATACAAAA
Done.