Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013212.1 Kokia drynarioides strain JFW-HI SEQ_128231, 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: 6453
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Warning! 152 characters in sequence are not A, C, G, or T
Found at i:407 original size:30 final size:30
Alignment explanation
Indices: 367--480 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
357 CAAAAGGCCT
* * * *
367 TTAAATTTTTCTAAAATCACGTTTTGACC-
1 TTAAACTTTTCAAAAATCACATTTTAACCA
*
396 TCTAAACTTTTCAAAAATTACATTTTAACCA
1 T-TAAACTTTTCAAAAATCACATTTTAACCA
* * * *
427 TTAAACTTTCCAAAAATTACA-TTTCACCC
1 TTAAACTTTTCAAAAATCACATTTTAACCA
* * *
456 TCAAACTTCTCAAAAATTACATTTT
1 TTAAACTTTTCAAAAATCACATTTT
481 GTCTCAAACT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
29 25 0.35
30 45 0.63
31 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
TTAAACTTTTCAAAAATCACATTTTAACCA
Found at i:461 original size:29 final size:29
Alignment explanation
Indices: 407--720 Score: 263
Period size: 29 Copynumber: 10.9 Consensus size: 29
397 CTAAACTTTT
* * *
407 CAAAAATTACATTTTAACCATTAAACTTTC
1 CAAAAATTACATTTTTACCCTCAAAC-TTC
*
437 CAAAAATTACA-TTTCACCCTCAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
465 TCAAAAATTACATTTTGT---CTCAAACTTC
1 -CAAAAATTACATTTT-TACCCTCAAACTTC
* **
493 TCAAAAATTACA-TTTTCCCCTTTAACTTC
1 -CAAAAATTACATTTTTACCCTCAAACTTC
* * *
522 CAAAAATTACATTTTTGCCCCCAAACATC
1 CAAAAATTACATTTTTACCCTCAAACTTC
*
551 TCAAAAATTACATTTTTACCCCCAAACTTC
1 -CAAAAATTACATTTTTACCCTCAAACTTC
* * *
581 CAAAAAATACATTTTTATCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* *
610 C---AATCACATTTTTACCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* **
636 CAAAAATCACATTTTTACCC-CGAATTTTC
1 CAAAAATTACATTTTTACCCTC-AAACTTC
* * *
665 CTAAAATGACATTTTTACCCCTAAAACTTTC
1 CAAAAATTACATTTTTA-CCCTCAAAC-TTC
* *
696 C-AAAATTACGTTTTAACCCT-AAACT
1 CAAAAATTACATTTTTACCCTCAAACT
721 CTTCGAAACT
Statistics
Matches: 238, Mismatches: 31, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
26 24 0.10
27 4 0.02
28 41 0.17
29 107 0.45
30 58 0.24
31 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCAAACTTC
Found at i:1110 original size:92 final size:94
Alignment explanation
Indices: 996--1184 Score: 256
Period size: 92 Copynumber: 2.0 Consensus size: 94
986 AAAATATTTA
* * ** *
996 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
1 AAATCGAGACAATATTCCTTTATCTCGGACTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1061 TTTTCTTC-A-GGATAATCGAATACCCTT
66 TTTTCTTCAACGGATAATCGAATACCCTT
* * * *
1088 AAATCGAGACAATGTTTCTTTATCTCTGACTTTGAAATTTTGTGCCTTAACTTACTAGGCACGAC
1 AAATCGAGACAATATTCCTTTATCTCGGACTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1153 TTTTCTTCAAACCGGGATAATCGAATACCCTT
66 TTTTCTTC-AA-C-GGATAATCGAATACCCTT
1185 TTTCAAGGTT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
92 64 0.77
94 1 0.01
97 18 0.22
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (94 bp):
AAATCGAGACAATATTCCTTTATCTCGGACTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
TTTTCTTCAACGGATAATCGAATACCCTT
Found at i:2426 original size:51 final size:51
Alignment explanation
Indices: 2350--2459 Score: 220
Period size: 51 Copynumber: 2.2 Consensus size: 51
2340 CAACCCCACC
2350 CCCTTTCTGCCCCACTAGCTTTTCTCTATTTCTCTTCAACTCTTTTTCTTT
1 CCCTTTCTGCCCCACTAGCTTTTCTCTATTTCTCTTCAACTCTTTTTCTTT
2401 CCCTTTCTGCCCCACTAGCTTTTCTCTATTTCTCTTCAACTCTTTTTCTTT
1 CCCTTTCTGCCCCACTAGCTTTTCTCTATTTCTCTTCAACTCTTTTTCTTT
2452 CCCTTTCT
1 CCCTTTCT
2460 CTTTAATTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.09, C:0.36, G:0.04, T:0.51
Consensus pattern (51 bp):
CCCTTTCTGCCCCACTAGCTTTTCTCTATTTCTCTTCAACTCTTTTTCTTT
Found at i:3772 original size:21 final size:22
Alignment explanation
Indices: 3748--3789 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3738 AAATTTTTTT
3748 ATAAAAATA-TATAAAATATTA
1 ATAAAAATATTATAAAATATTA
*
3769 ATAAAAATATTTTAAAATATT
1 ATAAAAATATTATAAAATATT
3790 TTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAATATTATAAAATATTA
Found at i:4009 original size:29 final size:29
Alignment explanation
Indices: 3971--4043 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
3961 AAATTTTATA
*
3971 TTTAATAATGA-AAAAAATTACATTTTCACT
1 TTTAA-AATGATAAAAAATTA-ATTTTAACT
** *
4001 TTTAAAATGATAAAATTTTAATTTTAATT
1 TTTAAAATGATAAAAAATTAATTTTAACT
*
4030 TTTAAAATTATAAA
1 TTTAAAATGATAAA
4044 TATATAAGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTAAAATGATAAAAAATTAATTTTAACT
Done.