Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014214.1 Kokia drynarioides strain JFW-HI SEQ_129247, 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: 5913
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2821 original size:47 final size:46
Alignment explanation
Indices: 2720--2821 Score: 177
Period size: 46 Copynumber: 2.2 Consensus size: 46
2710 ACAACAACAA
*
2720 GAAATAAAACAACCTTGATTTTGAAAATTAGCTAATTCAATTACTT
1 GAAATAAAACAACCTTGATTTTGAAAAATAGCTAATTCAATTACTT
*
2766 GAAATAAAACAACCTTGATTTTGAAAAATATCTAATTCAATTACTT
1 GAAATAAAACAACCTTGATTTTGAAAAATAGCTAATTCAATTACTT
2812 GAAAATAAAA
1 G-AAATAAAA
2822 AAATATTAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
46 45 0.85
47 8 0.15
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (46 bp):
GAAATAAAACAACCTTGATTTTGAAAAATAGCTAATTCAATTACTT
Found at i:4143 original size:18 final size:18
Alignment explanation
Indices: 4119--4171 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
4109 TCAGAACGTT
4119 TTAAT-AATAACAATAA-A
1 TTAATAAAT-ACAATAATA
4136 TATAATAAATACAATAATA
1 T-TAATAAATACAATAATA
*
4155 TTAATAAA-ATAATAATA
1 TTAATAAATACAATAATA
4172 AAAGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.28
18 18 0.56
19 5 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAATAAATACAATAATA
Found at i:5210 original size:30 final size:29
Alignment explanation
Indices: 5176--5730 Score: 296
Period size: 29 Copynumber: 18.6 Consensus size: 29
5166 CCGAACATTT
*
5176 AAAAATCCAATTTTTAACCCCAAAACTCCC
1 AAAAATCC-ATTTTTAACCCCAAAACTTCC
*
5206 AAAAATTCCA-TTTT-ACCCTC-GAACTTCC
1 AAAAA-TCCATTTTTAACCC-CAAAACTTCC
* * *
5234 AAAAATTTCATTTTTGACCCCAAAACTCCC
1 AAAAA-TCCATTTTTAACCCCAAAACTTCC
5264 AAAAATTCCATTTTT-ACCCCAAACTTTCGAAACTTCC
1 AAAAA-TCCATTTTTAACCCC--A------AAACTTCC
* *
5301 AAAAATCCCA-TTTTAACCCTAAAACTACC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
*
5330 AAAAAATCCATTTTTAACCTC-AAACTTCC
1 -AAAAATCCATTTTTAACCCCAAAACTTCC
5359 AAAAATCCCA-TTTTAACCCCAAAACTTCC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
** *
5388 AAAAATTCCATTTTT-ACCCCCGAACTTCT
1 AAAAA-TCCATTTTTAACCCCAAAACTTCC
* ** *
5417 AAAAATCCCATTTTTGATGCCAAAACTCCC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
* ** *
5447 AAAAATTTCATTTTT-ACCCCTCGAACTTTC
1 AAAAA-TCCATTTTTAACCCC-AAAACTTCC
* * ***
5477 GAAAATCCCATTTTTTACCTTGAAACTTCC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
** ** *
5507 AAAAAATTAATTTTT-ACCCCCGAACTTTC
1 -AAAAATCCATTTTTAACCCCAAAACTTCC
* *
5536 GAAAATCCCATTTTTAACCCCAAAACTTTC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
* * **
5566 AAGAATTCCATTTTT-A-CCCACGAACTTTT
1 AA-AAATCCATTTTTAACCCCA-AAACTTCC
* * * *
5595 GAAAATACCA-TTTTGACCTCGAAACTTCC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
** **
5624 AAAAATTCCGCTTTT-ACCCCCGAACTTCC
1 AAAAA-TCCATTTTTAACCCCAAAACTTCC
* * *
5653 AAAAATCCCATTTTTTACGCTAAAACTTCC
1 AAAAAT-CCATTTTTAACCCCAAAACTTCC
*
5683 AAAAATTCCATTTTT-ACCCTC-GAACTTCC
1 AAAAA-TCCATTTTTAACCC-CAAAACTTCC
5712 AAAAATCCCATTTTTAACC
1 AAAAAT-CCATTTTTAACC
5731 TCGATTTCCC
Statistics
Matches: 408, Mismatches: 74, Indels: 86
0.72 0.13 0.15
Matches are distributed among these distances:
28 53 0.13
29 162 0.40
30 151 0.37
31 17 0.04
35 1 0.00
36 5 0.01
37 19 0.05
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATCCATTTTTAACCCCAAAACTTCC
Found at i:5238 original size:58 final size:59
Alignment explanation
Indices: 5157--5730 Score: 575
Period size: 58 Copynumber: 9.6 Consensus size: 59
5147 AAAAATTTTG
* * *
5157 TTTTTACCCCCGAACATT-TAAAAATCCAATTTTTAACCCCAAAACTCCCAAAAATTCCA
1 TTTTTACCCTCGAAC-TTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
** *
5216 -TTTTACCCTCGAACTTCCAAAAATTTCATTTTTGACCCCAAAACTCCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
* * *
5274 TTTTTACCCCAAACTTTCGAAACTTCCAAAAATCCCA-TTTTAACCCTAAAACTACCAAAAAATC
1 TTTTTA--CC---C--TCG-AACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTC
5338 CA
58 CA
* * *
5340 TTTTTAACCTCAAACTTCCAAAAATCCCA-TTTTAACCCCAAAACTTCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
* * * ** *
5398 TTTTTACCCCCGAACTTCTAAAAATCCCATTTTTGATGCCAAAACTCCCAAAAATTTCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
* * * *** * *
5457 TTTTTACCCCTCGAACTTTCGAAAATCCCATTTTTTACCTTGAAACTTCCAAAAAATT-AA
1 TTTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAAC-TCCCAAAAATTCCA
* * * ** *
5517 TTTTTACCCCCGAACTTTCGAAAATCCCATTTTTAACCCCAAAACTTTCAAGAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
* *** * * * * * *
5576 TTTTTACCCACGAACTTTTGAAAATACCA-TTTTGACCTCGAAACTTCCAAAAATTCCG
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
* * * * * *
5634 CTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACGCTAAAACTTCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
5693 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACC
1 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACC
5731 TCGATTTCCC
Statistics
Matches: 427, Mismatches: 73, Indels: 30
0.81 0.14 0.06
Matches are distributed among these distances:
57 2 0.00
58 170 0.40
59 155 0.36
60 36 0.08
61 13 0.03
64 2 0.00
66 34 0.08
67 15 0.04
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTCCCAAAAATTCCA
Found at i:5355 original size:95 final size:95
Alignment explanation
Indices: 5198--5381 Score: 244
Period size: 95 Copynumber: 1.9 Consensus size: 95
5188 TTTAACCCCA
* ** * * * *
5198 AAACTCCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATTTCATTTTTGACCCCAAAACTCC
1 AAACTCCCAAAAATCCCATTTTACCCTAAAACTACCAAAAAATCCATTTTTAACCCCAAAACTCC
* *
5263 CAAAAATTCCATTTTTACCCCAAACTTTCG
66 CAAAAATCCCATTTTAACCCCAAACTTTCG
* * *
5293 AAACTTCCAAAAATCCCATTTTAACCCTAAAACTACCAAAAAATCCATTTTTAACCTC-AAACTT
1 AAACTCCCAAAAATCCCATTTT-ACCCTAAAACTACCAAAAAATCCATTTTTAACCCCAAAACTC
5357 CCAAAAATCCCATTTTAACCCCAAA
65 CCAAAAATCCCATTTTAACCCCAAA
5382 ACTTCCAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
95 48 0.63
96 28 0.37
ACGTcount: A:0.39, C:0.31, G:0.02, T:0.28
Consensus pattern (95 bp):
AAACTCCCAAAAATCCCATTTTACCCTAAAACTACCAAAAAATCCATTTTTAACCCCAAAACTCC
CAAAAATCCCATTTTAACCCCAAACTTTCG
Found at i:5461 original size:59 final size:59
Alignment explanation
Indices: 5294--5730 Score: 495
Period size: 59 Copynumber: 7.4 Consensus size: 59
5284 AAACTTTCGA
* * * * * *
5294 AACTTCCAAAAATCCCA-TTTTAACCCTAAAACTACCAAAAAATCCATTTTTAACCTCA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
5352 AACTTCCAAAAATCCCA-TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
* * ** * *
5410 AACTTCTAAAAATCCCATTTTTGATGCCAAAACTCCCAAAAATTTCATTTTTACCCCTCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCC-CG
* * * *** *
5470 AACTTTCGAAAATCCCATTTTTTACCTTGAAACTTCCAAAAAATT-AATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCC-AAAAATTCCATTTTTACCCCCG
* * * * *
5529 AACTTTCGAAAATCCCATTTTTAACCCCAAAACTTTCAAGAATTCCATTTTTACCCACG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
*** * * * * **
5588 AACTTTTGAAAATACCA-TTTTGACCTCGAAACTTCCAAAAATTCCGCTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
* * * *
5646 AACTTCCAAAAATCCCATTTTTTACGCTAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
5705 AACTTCCAAAAATCCCATTTTTAACC
1 AACTTCCAAAAATCCCATTTTTAACC
5731 TCGATTTCCC
Statistics
Matches: 319, Mismatches: 55, Indels: 9
0.83 0.14 0.02
Matches are distributed among these distances:
58 120 0.38
59 152 0.48
60 40 0.13
61 7 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:5732 original size:29 final size:29
Alignment explanation
Indices: 5294--5734 Score: 300
Period size: 29 Copynumber: 15.0 Consensus size: 29
5284 AAACTTTCGA
**
5294 AACTTCCAAAAATCCCA-TTTTAACCCTAA
1 AACTTCCAAAAATCCCATTTTTAA-CCTCG
* *
5323 AACTACCAAAAAAT-CCATTTTTAACCTCA
1 AACTTCC-AAAAATCCCATTTTTAACCTCG
* *
5352 AACTTCCAAAAATCCCA-TTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCTC-G
* * *
5381 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCTCG
* * **
5410 AACTTCTAAAAATCCCATTTTTGATGCC-AA
1 AACTTCCAAAAATCCCATTTTT-A-ACCTCG
* ** *
5440 AACTCCCAAAAATTTCATTTTTACCCCTCG
1 AACTTCCAAAAATCCCATTTTTA-ACCTCG
* * * *
5470 AACTTTCGAAAATCCCATTTTTTACCTTG
1 AACTTCCAAAAATCCCATTTTTAACCTCG
** * *
5499 AAACTTCCAAAAAAT-TAATTTTTACCCCCG
1 -AACTTCC-AAAAATCCCATTTTTAACCTCG
* * * *
5529 AACTTTCGAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCTC-G
* * * * *
5559 AACTTTCAAGAATTCCATTTTTACCCACG
1 AACTTCCAAAAATCCCATTTTTAACCTCG
*** * *
5588 AACTTTTGAAAATACCA-TTTTGACCTCG
1 AACTTCCAAAAATCCCATTTTTAACCTCG
* ** * *
5616 AAACTTCCAAAAATTCCGCTTTTACCCCCG
1 -AACTTCCAAAAATCCCATTTTTAACCTCG
* **
5646 AACTTCCAAAAATCCCATTTTTTACGCTAA
1 AACTTCCAAAAATCCCATTTTTAAC-CTCG
* *
5676 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTAACCTCG
5705 AACTTCCAAAAATCCCATTTTTAACCTCG
1 AACTTCCAAAAATCCCATTTTTAACCTCG
5734 A
1 A
5735 TTTCCCAAAA
Statistics
Matches: 319, Mismatches: 78, Indels: 30
0.75 0.18 0.07
Matches are distributed among these distances:
28 28 0.09
29 158 0.50
30 126 0.39
31 7 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTAACCTCG
Done.