Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010308.1 Kokia drynarioides strain JFW-HI SEQ_125168, 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: 2846
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:449 original size:24 final size:25
Alignment explanation
Indices: 417--468 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
407 CTCCTTTTTC
417 TTTTTC-TTTTCT-TCTTTTTCCTTT
1 TTTTTCTTTTTCTCT-TTTTTCCTTT
441 TTTTTCTTTTTCTCTTTTTTCCTTT
1 TTTTTCTTTTTCTCTTTTTTCCTTT
466 TTT
1 TTT
469 CAATTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 6 0.23
25 19 0.73
26 1 0.04
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTCTTTTTCTCTTTTTTCCTTT
Found at i:465 original size:16 final size:15
Alignment explanation
Indices: 406--467 Score: 72
Period size: 16 Copynumber: 4.1 Consensus size: 15
396 CACCTCGACC
*
406 TCTCCTTTTTCTTTT
1 TCTCTTTTTTCTTTT
*
421 TCT-TTTCTTCTTTT
1 TCTCTTTTTTCTTTT
*
435 TCCTTTTTTTTCTTTT
1 T-CTCTTTTTTCTTTT
451 TCTCTTTTTTCCTTTT
1 TCTCTTTTTT-CTTTT
467 T
1 T
468 TCAATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.25
15 13 0.32
16 17 0.43
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTCTTTTTTCTTTT
Found at i:475 original size:25 final size:26
Alignment explanation
Indices: 423--486 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
413 TTTCTTTTTC
*
423 TTTTCT-TCTTTTTCCTTTTTT--TTCT
1 TTTTCTCT-TTTTTCCTTTTTTCAAT-T
448 TTTTCTCTTTTTTCCTTTTTTCAATT
1 TTTTCTCTTTTTTCCTTTTTTCAATT
*
474 TTTTGTCTTTTTT
1 TTTTCTCTTTTTT
487 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 19 0.56
26 14 0.41
27 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTCTCTTTTTTCCTTTTTTCAATT
Found at i:484 original size:9 final size:9
Alignment explanation
Indices: 431--486 Score: 55
Period size: 8 Copynumber: 6.6 Consensus size: 9
421 TCTTTTCTTC
431 TTTTTC-CT
1 TTTTTCTCT
*
439 TTTTTTTC-
1 TTTTTCTCT
447 TTTTTCTCT
1 TTTTTCTCT
456 TTTTTC-CT
1 TTTTTCTCT
**
464 TTTTTCAAT
1 TTTTTCTCT
*
473 TTTTTGTCT
1 TTTTTCTCT
482 TTTTT
1 TTTTT
487 TTTTTAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 20 0.51
9 19 0.49
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:1229 original size:6 final size:6
Alignment explanation
Indices: 1220--1269 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
1210 TCGACCTCTC
*
1220 CTTTTT CTTTTT CGTTTCTT CTTTTT CCTTTT -TTTTT CTTTTT CTCTTTT
1 CTTTTT CTTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT
1270 TTCCTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 4 0.11
6 21 0.55
7 10 0.26
8 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:1243 original size:20 final size:17
Alignment explanation
Indices: 1220--1301 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 17
1210 TCGACCTCTC
1220 CTTTTTCTTTTTCGTTTCTT
1 CTTTTTCTTTTT--TTT-TT
*
1240 CTTTTTCCTTTTTTTTT
1 CTTTTTCTTTTTTTTTT
* *
1257 CTTTTTC-TCTTTTTTC
1 CTTTTTCTTTTTTTTTT
** *
1273 CTTTTTTCAATTTTTTGT
1 C-TTTTTCTTTTTTTTTT
1291 CTTTTT-TTTTT
1 CTTTTTCTTTTT
1302 AAATTTCTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
16 11 0.22
17 20 0.39
18 9 0.18
20 11 0.22
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (17 bp):
CTTTTTCTTTTTTTTTT
Found at i:1251 original size:26 final size:26
Alignment explanation
Indices: 1222--1279 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
1212 GACCTCTCCT
1222 TTTTCTTTTTCGTTTCT-TC-TTTTTCC
1 TTTT-TTTTTC-TTTCTCTCTTTTTTCC
*
1248 TTTTTTTTTCTTTTTCTCTTTTTTCC
1 TTTTTTTTTCTTTCTCTCTTTTTTCC
1274 TTTTTT
1 TTTTTT
1280 CAATTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 8 0.28
26 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTTTTTTCTTTCTCTCTTTTTTCC
Found at i:1255 original size:11 final size:10
Alignment explanation
Indices: 1221--1300 Score: 54
Period size: 10 Copynumber: 7.5 Consensus size: 10
1211 CGACCTCTCC
1221 TTTTTCTTTT
1 TTTTTCTTTT
* *
1231 TCGTTTCTTCT
1 T-TTTTCTTTT
*
1242 TTTTCCTTTT
1 TTTTTCTTTT
1252 TTTTTCTTTT
1 TTTTTCTTTT
1262 TCTCTTT-TTTCCT
1 T-T-TTTCTTT--T
*
1275 TTTTTCAATTT
1 TTTTTC-TTTT
*
1286 TTTGTCTTTT
1 TTTTTCTTTT
1296 TTTTT
1 TTTTT
1301 TAAATTTCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
10 24 0.45
11 21 0.40
12 4 0.08
13 4 0.08
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1260 original size:17 final size:18
Alignment explanation
Indices: 1220--1271 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
1210 TCGACCTCTC
1220 CTTTTTCT-TTTTCGTTTCTT
1 CTTTTTCTCTTTT--TTT-TT
1240 CTTTTTC-CTTTTTTTTT
1 CTTTTTCTCTTTTTTTTT
1257 CTTTTTCTCTTTTTT
1 CTTTTTCTCTTTTTT
1272 CCTTTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.30
18 10 0.33
20 11 0.37
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (18 bp):
CTTTTTCTCTTTTTTTTT
Found at i:1261 original size:8 final size:8
Alignment explanation
Indices: 1234--1298 Score: 51
Period size: 9 Copynumber: 7.4 Consensus size: 8
1224 TTCTTTTTCG
1234 TTTCTTCTT
1 TTTCTT-TT
1243 TTTCCTTTT
1 TTT-CTTTT
1252 TTT-TTCTT
1 TTTCTT-TT
1260 TTTCTCTTT
1 TTTCT-TTT
*
1269 TTTCCTTT
1 TTTCTTTT
1277 TTTCAATTTT
1 TTTC--TTTT
1287 TTGTCTTTT
1 TT-TCTTTT
1296 TTT
1 TTT
1299 TTTAAATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
7 2 0.04
8 13 0.28
9 21 0.45
10 9 0.19
11 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1287 original size:26 final size:26
Alignment explanation
Indices: 1241--1297 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1231 TCGTTTCTTC
**
1241 TTTTTCCTTTTTTTTTCTTTTTCTCT
1 TTTTTCCTTTTTTAATCTTTTTCTCT
*
1267 TTTTTCCTTTTTTCAAT-TTTTTGTCT
1 TTTTTCCTTTTTT-AATCTTTTTCTCT
1293 TTTTT
1 TTTTT
1298 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTTCCTTTTTTAATCTTTTTCTCT
Done.