Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009400.1 Kokia drynarioides strain JFW-HI SEQ_124107, 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: 33176
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:359 original size:6 final size:6
Alignment explanation
Indices: 350--417 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
340 ATTTAATATT
* **
350 AATTTA AATTTT AA-TTA AATTTA AATTTAAA AAGATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTT--A AATTTA AATTTA AATTTA
399 AGA--TA AATTTA AATTTA AA
1 A-ATTTA AATTTA AATTTA AA
418 ATAATTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 7 0.14
6 37 0.74
7 1 0.02
8 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:364 original size:23 final size:23
Alignment explanation
Indices: 335--380 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
325 TATTTTGGGT
*
335 TTTTAATTTAATATT-AATTTAAA
1 TTTTAATTAAAT-TTAAATTTAAA
358 TTTTAATTAAATTTAAATTTAAA
1 TTTTAATTAAATTTAAATTTAAA
381 AAGATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAATTAAATTTAAATTTAAA
Found at i:370 original size:17 final size:18
Alignment explanation
Indices: 350--429 Score: 94
Period size: 17 Copynumber: 4.5 Consensus size: 18
340 ATTTAATATT
* *
350 AATTTAAATTTTAA-TTA
1 AATTTAAATTTAAAGATA
367 AATTTAAATTTAAAAAGATA
1 AATTTAAATTT--AAAGATA
387 AATTTAAATTT-AAGATA
1 AATTTAAATTTAAAGATA
404 AATTTAAATTTAAA-ATA
1 AATTTAAATTTAAAGATA
*
421 ATTTTAAAT
1 AATTTAAAT
430 CAATTTAAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
17 39 0.70
18 2 0.04
19 2 0.04
20 13 0.23
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AATTTAAATTTAAAGATA
Found at i:3272 original size:137 final size:138
Alignment explanation
Indices: 3116--3394 Score: 524
Period size: 137 Copynumber: 2.0 Consensus size: 138
3106 AAGATAAAAA
3116 CAAAACCCCGAAACCCGAAAACAAAGAACCCTAAAAACATAAACATAAATTTCTCCAAAAGTGTT
1 CAAAACCCCGAAACCCGAAAACAAAGAACCCTAAAAACATAAACATAAATTTCTCCAAAAGTGTT
3181 AAGAGTTATAATATCTAAT-GGCGTATTTTCTAAGGTTGTAAAAGAGTCTATTTATAGGTTAAAT
66 AAGAGTTATAATATCTAATGGGCGTATTTTCTAAGGTTGTAAAAGAGTCTATTTATAGGTTAAAT
3245 TCCTAGGT
131 TCCTAGGT
* * *
3253 CAAAACCTCGAAACTCGAAAACAAAGAACCCTAAAAACGTAAACATAAATTTCTCCAAAAGTGTT
1 CAAAACCCCGAAACCCGAAAACAAAGAACCCTAAAAACATAAACATAAATTTCTCCAAAAGTGTT
3318 AAGAGTTATAATATCTAATGGGCGTATTTTCTAAGGTTGTAAAAGAGTCTATTTATAGGTTAAAT
66 AAGAGTTATAATATCTAATGGGCGTATTTTCTAAGGTTGTAAAAGAGTCTATTTATAGGTTAAAT
3383 TCCTAGGT
131 TCCTAGGT
3391 CAAA
1 CAAA
3395 TAATAATAAA
Statistics
Matches: 138, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
137 81 0.59
138 57 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (138 bp):
CAAAACCCCGAAACCCGAAAACAAAGAACCCTAAAAACATAAACATAAATTTCTCCAAAAGTGTT
AAGAGTTATAATATCTAATGGGCGTATTTTCTAAGGTTGTAAAAGAGTCTATTTATAGGTTAAAT
TCCTAGGT
Found at i:14994 original size:17 final size:18
Alignment explanation
Indices: 14972--15005 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
14962 ATAACAACTA
14972 TGAAGATTTTGG-ATATG
1 TGAAGATTTTGGCATATG
14989 TGAAGATTTTGGCATAT
1 TGAAGATTTTGGCATAT
15006 TCTCCCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (18 bp):
TGAAGATTTTGGCATATG
Found at i:15502 original size:17 final size:17
Alignment explanation
Indices: 15480--15515 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15470 TTGACATTAT
15480 ATGATTTTGATAGATGC
1 ATGATTTTGATAGATGC
15497 ATGATTTTGATAGATGC
1 ATGATTTTGATAGATGC
15514 AT
1 AT
15516 CTACAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (17 bp):
ATGATTTTGATAGATGC
Found at i:18782 original size:6 final size:6
Alignment explanation
Indices: 18773--18803 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
18763 CCATCATACT
18773 ACTCCA ACTCCA ACTCCA ACTCCA ACTCCA A
1 ACTCCA ACTCCA ACTCCA ACTCCA ACTCCA A
18804 ACCCATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTCCA
Found at i:23566 original size:26 final size:26
Alignment explanation
Indices: 23537--23589 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
23527 CCTTAGTCGG
*
23537 TGAAACGATAGAAGCCAAATGAACAA
1 TGAAACGATAGAAGCCAAATAAACAA
* *
23563 TGAAATGATAGAAGCCACATAAACAA
1 TGAAACGATAGAAGCCAAATAAACAA
23589 T
1 T
23590 TATCGCTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (26 bp):
TGAAACGATAGAAGCCAAATAAACAA
Found at i:27267 original size:20 final size:20
Alignment explanation
Indices: 27239--27281 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
27229 TAAAATTATG
27239 AAAAATATTTTTTA-TATTTT
1 AAAAATA-TTTTTACTATTTT
*
27259 AAAATTATTTTTACTATTTT
1 AAAAATATTTTTACTATTTT
27279 AAA
1 AAA
27282 TATGAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AAAAATATTTTTACTATTTT
Found at i:28238 original size:2 final size:2
Alignment explanation
Indices: 28233--28269 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28223 TTCATTTCTA
28233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28270 TTTTAATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28332 original size:22 final size:20
Alignment explanation
Indices: 28301--28357 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
28291 TTTTTTTGTA
*
28301 ATTTTCTAAAATTTTGCTATAT
1 ATTTTCT-AAATTTT-CTAAAT
* *
28323 ATTTTTTAAATCTTCTAAAT
1 ATTTTCTAAATTTTCTAAAT
*
28343 ATTTTGTGAAATTTT
1 ATTTTCT-AAATTTT
28358 TAGGTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 11 0.38
21 12 0.41
22 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTCTAAATTTTCTAAAT
Found at i:28333 original size:21 final size:21
Alignment explanation
Indices: 28309--28357 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28299 TAATTTTCTA
* *
28309 AAATTTTGCTATATATTTT-TT
1 AAATTTT-CTAAATATTTTGTG
*
28330 AAATCTTCTAAATATTTTGTG
1 AAATTTTCTAAATATTTTGTG
28351 AAATTTT
1 AAATTTT
28358 TAGGTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (21 bp):
AAATTTTCTAAATATTTTGTG
Found at i:28418 original size:32 final size:30
Alignment explanation
Indices: 28362--28420 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
28352 AATTTTTAGG
*
28362 TTTTTTTTTTTTAATTTAACTATTTAACTA
1 TTTTTTTTTTTCAATTTAACTATTTAACTA
*
28392 TTTTTTATTTTTCAATTATAATTATTTAA
1 TTTTTT-TTTTTCAATT-TAACTATTTAA
28421 TTTTTTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 9 0.36
32 10 0.40
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTTTTTTTTCAATTTAACTATTTAACTA
Done.