Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013018.1 Kokia drynarioides strain JFW-HI SEQ_128036, 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: 3064
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Found at i:366 original size:15 final size:16
Alignment explanation
Indices: 346--382 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
336 CAGTGTAAAG
346 TTTGGGCC-TTTCG-AA
1 TTTGGGCCATTT-GTAA
361 TTTGGGCCATTTGTAA
1 TTTGGGCCATTTGTAA
377 TTTGGG
1 TTTGGG
383 TTATGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.43
Consensus pattern (16 bp):
TTTGGGCCATTTGTAA
Found at i:435 original size:6 final size:6
Alignment explanation
Indices: 408--476 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
398 TTTGGACTTT
* *
408 TTTAAC TTTGAA TTTAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
*
454 TTCAAA TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
477 AAAAGGCCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 1 0.02
5 13 0.25
6 38 0.72
7 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:438 original size:17 final size:17
Alignment explanation
Indices: 418--476 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
408 TTTAACTTTG
418 AATTTAAATTAAATTTA
1 AATTTAAATTAAATTTA
435 AATTTAAGATT-AATTTA
1 AATTTAA-ATTAAATTTA
*
452 AATTCAAATTTAAA-TTA
1 AATTTAAA-TTAAATTTA
469 AATTTAAA
1 AATTTAAA
477 AAAAGGCCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 1 0.03
17 31 0.84
18 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:473 original size:23 final size:24
Alignment explanation
Indices: 421--476 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
411 AACTTTGAAT
*
421 TTAAA-TTAAATTTAAATTTAAGA
1 TTAAATTTAAATTCAAATTTAAGA
444 TT-AATTTAAATTCAAATTTAA-A
1 TTAAATTTAAATTCAAATTTAAGA
466 TTAAATTTAAA
1 TTAAATTTAAA
477 AAAAGGCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAATTTAAATTCAAATTTAAGA
Found at i:1291 original size:206 final size:205
Alignment explanation
Indices: 822--1781 Score: 1197
Period size: 206 Copynumber: 4.7 Consensus size: 205
812 CATTCATCGC
* * * * * * * * *
822 GCGTGGGTTTAATTTGGACTTCTCCTCAGTGTCTCATCAGGG-AGATGACCACGTCGTTTGTTTT
1 GCGTGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATC-GGGAAGATGACCGCATCGCTTGTTTC
* * * * * *
886 AATCTGTTTCTCTGCATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAGGGA
65 AATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGAA
* * * * * *
951 GCTATCCGTTTTATTACTTCGACTTGCTTCTC-AGTATCTTATCAGGAAGCTGGGGTTCGAAG-G
130 GCTAACCG-TTTATTACTTCGACCTACTTCTCGA-TGTCTCATCAGGAAGCTGGGGTTCGAAGAT
* * *
1014 TTTAT-TCATTGT
193 TTTATCGCTTTGA
* * * * * *
1026 GTGTGGGTTTGGTTTGGTCTTCTCCTCAGTATCTCATCAGAAAGATGACCGCATCGCTTGTTTCA
1 GCGTGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTCA
* * *
1091 ATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATTTGGAAG
66 ATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGAAG
* * **
1156 CTAACCGTTTATTACTTCGACCTACTTCTCGATGTCTCATCAAGAAGCTAGGGTTAAAAGATTTT
131 CTAACCGTTTATTACTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTT
1221 ACTCGCTTTGA
196 A-TCGCTTTGA
1232 GCGTGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTCA
1 GCGTGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTCA
* *
1297 ATCCGCTTCTTTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTAGAAG
66 ATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGAAG
* * * * *
1362 CTAATCGTTTACTGCTTCGACCTACTTCTCGGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTT
131 CTAACCGTTTATTACTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTT
*
1427 ACTCGCTTTAA
196 A-TCGCTTTGA
* * *
1438 GCGTGGGCTTGATTTGGTCTTTTTCTCAGTATCTCATCGGAAAGATGATCGCATCGCTTGTTTCA
1 GCGTGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTCA
* * *
1503 ATCCGCTTCACTATATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGAAA
66 ATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGAAG
* * *
1568 CTAACCGTTTTATTACTTTGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTT
131 CTAACCG-TTTATTACTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTGGGGTTCGAAGATTT
*
1633 GT-TCGTTTTGA
195 -TATCGCTTTGA
* * * *
1644 GC-----CTTG-TTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTC
1 GCGTGGGCTTGATTT-GGTCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTC
* * *
1703 AA-CTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTTAGTATCTCATCAGGA
65 AATC-CGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGA
1767 AGCTAACCGTTTATT
129 AGCTAACCGTTTATT
1782 GCTCCAATCT
Statistics
Matches: 666, Mismatches: 81, Indels: 22
0.87 0.11 0.03
Matches are distributed among these distances:
200 10 0.02
201 111 0.17
203 44 0.07
204 121 0.18
205 1 0.00
206 326 0.49
207 52 0.08
208 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (205 bp):
GCGTGGGCTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACCGCATCGCTTGTTTCA
ATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTCCTCAGTATCTCATCTGGAAG
CTAACCGTTTATTACTTCGACCTACTTCTCGATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTT
ATCGCTTTGA
Found at i:2406 original size:27 final size:27
Alignment explanation
Indices: 2374--2433 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
2364 TCAAAAATTT
*
2374 TATTAAGAAGAGGATCAAAAGAAACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
*
2401 TATTAAAAAGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
2428 TCATTA
1 T-ATTA
2434 GTTAAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAAGAAACAA
Done.