Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010128.1 Kokia drynarioides strain JFW-HI SEQ_124922, 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: 3369
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:423 original size:7 final size:7
Alignment explanation
Indices: 413--451 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
403 TTCCCTTTTT
413 TTATTAA
1 TTATTAA
420 TTATTAA
1 TTATTAA
*
427 TTAATAA
1 TTATTAA
434 TTATTAA
1 TTATTAA
441 -TATT-A
1 TTATTAA
446 TTATTA
1 TTATTA
452 TTAATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 8 0.29
7 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:453 original size:15 final size:15
Alignment explanation
Indices: 413--458 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
403 TTCCCTTTTT
413 TTATTAATTATTAAT-
1 TTATT-ATTATTAATA
* *
428 TAATAATTATTAATA
1 TTATTATTATTAATA
443 TTATTATTATTAATA
1 TTATTATTATTAATA
458 T
1 T
459 CAAAACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:824 original size:15 final size:16
Alignment explanation
Indices: 784--829 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
774 CCCCTTTTTT
784 TTATTAATTAATAATTAA
1 TTATT-ATTAAT-ATTAA
*
802 TAATTATTAATATT-A
1 TTATTATTAATATTAA
817 TTATTATTAATAT
1 TTATTATTAATAT
830 CAAAACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
16 3 0.12
17 6 0.23
18 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTATTAATATTAA
Found at i:1459 original size:15 final size:15
Alignment explanation
Indices: 1439--1507 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
1429 TTTTAGGTAG
1439 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
1454 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
* *
1469 TCTGTAACTGGGCCA
1 TTTGTAATTGGGCCA
* *
1484 TTTGTTATTGGGTCA
1 TTTGTAATTGGGCCA
1499 TTTGTAATT
1 TTTGTAATT
1508 AGACTTTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:1625 original size:16 final size:17
Alignment explanation
Indices: 1541--1626 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
1531 TTGGACTTTC
*
1541 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
1558 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
1575 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
1592 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
1608 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
1624 TAA
1 TAA
1627 GTCTAGACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
15 7 0.11
16 12 0.19
17 38 0.60
18 6 0.10
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:2330 original size:140 final size:139
Alignment explanation
Indices: 2131--2461 Score: 520
Period size: 140 Copynumber: 2.4 Consensus size: 139
2121 TCAATTCGCT
2131 TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTA-CCTCATCTGGAAGATCTGCTCGTTT
1 TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCC-CATCTGGAAGATCTGCTCGTTT
* * *
2195 CGAGCCTCGTTTGGGTCTTCTTCTCAGCGTCTCATCAGGAAGGTGATCCCATCACTGTTTCAATC
65 CGAGCCTCATTTGGGTCTTCTTCTCAACGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
*
2260 TGCTTCTCTG
130 CGCTTCTCTG
* * * *
2270 TATTTCATCAGGAAGACGAATTTTGGTTCACTTCTGAGTATCCCATCTGGAAGATTTGCTCGTTT
1 TATCTCATCAGGAAGATGAA-TTTGGTTCACTTCTCAGTATCCCATCTGGAAGATCTGCTCGTTT
* *
2335 CGAGCCTCATTTGGGTTTTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
65 CGAGCCTCATTTGGGTCTTCTTCTCAACGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATC
*
2400 CGTTTCTCTG
130 CGCTTCTCTG
* *
2410 TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAG
1 TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAG
2462 CTAACCGTTT
Statistics
Matches: 174, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
139 47 0.27
140 125 0.72
141 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (139 bp):
TATCTCATCAGGAAGATGAATTTGGTTCACTTCTCAGTATCCCATCTGGAAGATCTGCTCGTTTC
GAGCCTCATTTGGGTCTTCTTCTCAACGTCTCATCAGGAAGATGATCCCATCACTGTTTCAATCC
GCTTCTCTG
Done.