Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011795.1 Kokia drynarioides strain JFW-HI SEQ_126790, 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, 877
Length: 1462
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:872 original size:7 final size:7
Alignment explanation
Indices: 860--944 Score: 55
Period size: 7 Copynumber: 11.7 Consensus size: 7
850 CCTTTTGTTA
860 ATTTTTT
1 ATTTTTT
867 ATTTTTT
1 ATTTTTT
874 ATTTTATT
1 ATTTT-TT
882 -TTATTTT
1 ATT-TTTT
* *
889 ATTTATC
1 ATTTTTT
*
896 ATTTATT
1 ATTTTTT
903 ATTTATTT
1 ATTT-TTT
**
911 CCTTTTT
1 ATTTTTT
*
918 ATCTGTTT
1 AT-TTTTT
*
926 ATTATTT
1 ATTTTTT
*
933 AATTTTT
1 ATTTTTT
940 ATTTT
1 ATTTT
945 ATTTTTCTCT
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
7 44 0.73
8 16 0.27
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (7 bp):
ATTTTTT
Found at i:883 original size:11 final size:11
Alignment explanation
Indices: 863--950 Score: 65
Period size: 11 Copynumber: 7.9 Consensus size: 11
853 TTTGTTAATT
863 TTTTATTTTTTA
1 TTTTA-TTTTTA
875 TTTTA-TTTTA
1 TTTTATTTTTA
*
885 TTTTATTTATCA
1 TTTTATTT-TTA
897 -TTTATTATTTA
1 TTTTATT-TTTA
**
908 TTTCCTTTTTA
1 TTTTATTTTTA
* *
919 TCTGT-TTATTA
1 T-TTTATTTTTA
*
930 TTTAATTTTTA
1 TTTTATTTTTA
941 TTTTATTTTT
1 TTTTATTTTT
951 CTCTCTATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 11 0.19
11 35 0.59
12 13 0.22
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:908 original size:33 final size:31
Alignment explanation
Indices: 864--978 Score: 85
Period size: 33 Copynumber: 3.6 Consensus size: 31
854 TTGTTAATTT
*
864 TTTATTTTTTATTTTATTTTATTTTATTTATCA
1 TTTA-TTTTTATTTTATTTTA-TCTATTTATCA
* *
897 TTTATTATTTATTTCCT-TTTTATCTGTTTATTA
1 TTTATT-TTTATTT--TATTTTATCTATTTATCA
* *
930 TTTAATTTTTATTTTATTTT-TCTCTCTAT-A
1 TTT-ATTTTTATTTTATTTTATCTATTTATCA
960 TATT-TTTTTATATTTATTT
1 T-TTATTTTTAT-TTTATTT
979 CTTTATTATT
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
29 7 0.10
30 9 0.13
31 10 0.14
32 6 0.09
33 29 0.41
34 8 0.11
35 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTATTTTTATTTTATTTTATCTATTTATCA
Found at i:1366 original size:7 final size:7
Alignment explanation
Indices: 1354--1438 Score: 55
Period size: 7 Copynumber: 11.7 Consensus size: 7
1344 CCTTTTGTTA
1354 ATTTTTT
1 ATTTTTT
1361 ATTTTTT
1 ATTTTTT
1368 ATTTTATT
1 ATTTT-TT
1376 -TTATTTT
1 ATT-TTTT
* *
1383 ATTTATC
1 ATTTTTT
*
1390 ATTTATT
1 ATTTTTT
1397 ATTTATTT
1 ATTT-TTT
**
1405 CCTTTTT
1 ATTTTTT
*
1412 ATCTGTTT
1 AT-TTTTT
*
1420 ATTATTT
1 ATTTTTT
*
1427 AATTTTT
1 ATTTTTT
1434 ATTTT
1 ATTTT
1439 ATTTTTCTCT
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
7 44 0.73
8 16 0.27
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (7 bp):
ATTTTTT
Found at i:1377 original size:11 final size:11
Alignment explanation
Indices: 1357--1444 Score: 65
Period size: 11 Copynumber: 7.9 Consensus size: 11
1347 TTTGTTAATT
1357 TTTTATTTTTTA
1 TTTTA-TTTTTA
1369 TTTTA-TTTTA
1 TTTTATTTTTA
*
1379 TTTTATTTATCA
1 TTTTATTT-TTA
1391 -TTTATTATTTA
1 TTTTATT-TTTA
**
1402 TTTCCTTTTTA
1 TTTTATTTTTA
* *
1413 TCTGT-TTATTA
1 T-TTTATTTTTA
*
1424 TTTAATTTTTA
1 TTTTATTTTTA
1435 TTTTATTTTT
1 TTTTATTTTT
1445 CTCTCTATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 11 0.19
11 35 0.59
12 13 0.22
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1444 original size:33 final size:34
Alignment explanation
Indices: 1349--1444 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 34
1339 TCTTTCCTTT
* * * *
1349 TGTTAATTTTTTATTTTTTATTTTA-TTTTATTT
1 TGTTTATTATTTAATTTTTATTTTATTTTTATTC
* * **
1382 TATTTATCATTTA-TTATTTATTTCCTTTTTA-TC
1 TGTTTATTATTTAATT-TTTATTTTATTTTTATTC
1415 TGTTTATTATTTAATTTTTATTTTATTTTT
1 TGTTTATTATTTAATTTTTATTTTATTTTT
1445 CTCTCTATAT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
32 2 0.04
33 40 0.82
34 7 0.14
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (34 bp):
TGTTTATTATTTAATTTTTATTTTATTTTTATTC
Found at i:1447 original size:494 final size:484
Alignment explanation
Indices: 520--1462 Score: 1715
Period size: 494 Copynumber: 1.9 Consensus size: 484
510 ATCTAAAACC
*
520 CTACTTACCGACCACATCAGTCGTTCGACCAACTACCTCCAGCGAGCACCAACCAATTCAACATC
1 CTACTTACCGACCACATCAGTCGATCGACCAACTACCTCCAGCGAGCACCAACCAATTCAACATC
* *
585 GCGAGCCCATCTCCCCCTTCGCACCCCGCACCGATTTGTTCCGCCTTCGCACCTCCGCGTGCTTG
66 GCGAGCCCATCTCCCCCTTCGCACCCCGCACCGATTTGTTCCGCCTTCACACCTCCGCATGCTTG
650 GGCGCATCTAGCTAACACCATTCGAACCTTGATCCACAAGTTTATTCCCTCATTCGCATGATCAC
131 GGCGCATCTAGCTAACACCATTCGAACCTTGATCCACAAGTTTATTCCCTCATTCGCATGATCAC
*
715 TAGCTACTATCGCTCATCTCCCCTCCGTTCTAATAGTCACACGACGTCACCCTTCCCTTGATCTC
196 TAGCTACTATCGCTCATCCCCCCTCCGTTCTAATAGTCACACGACGTCACCCTTCCCTTGATCTC
780 GCTGTTCGCGAACCACCACCGTCCACCTTCCAACCACCGTAACCCACTGTTTGCCCTTTCATTAT
261 GCTGTTCGCGAACCACCACCGTCCACCTTCCAACCACCGTAACCCACTGTTTGCCCTTTCATTAT
845 TCTTTCCTTTTGTTAATTTTTTATTTTTTATTTTATTTTATTTTATTTATCATTTATTATTTATT
326 TCTTTCCTTTTGTTAATTTTTTATTTTTTATTTTATTTTATTTTATTTATCATTTATTATTTATT
910 TCCTTTTTATCTGTTTATTATTTAATTTTTATTTTATTTTTCTCTCTATATATTTTTTTATATTT
391 TCCTTTTTATCTGTTTATTATTTAATTTTTATTTTATTTTTCTCTCTATATATTTTTTTATATTT
975 ATTTCTTTATTATTATTATTGTTCTTATT
456 ATTTCTTTATTATTATTATTGTTCTTATT
*
1004 NNNNNNNNNNCTACTTACCGACCACATCAGTCGATCGACCGACTACCTCCAGCGAGCACCAACCA
1 ----------CTACTTACCGACCACATCAGTCGATCGACCAACTACCTCCAGCGAGCACCAACCA
* *
1069 ATTCAACGTCGCGAGCCCATCTCCCCCTTTGCACCCCGCACCGATTTGTTCCGCCTTCACACCTC
56 ATTCAACATCGCGAGCCCATCTCCCCCTTCGCACCCCGCACCGATTTGTTCCGCCTTCACACCTC
1134 CGCATGCTTGGGCGCATCTAGCTAACACCATTCGAACCTTGATCCACAAGTTTATTCCCTCATTC
121 CGCATGCTTGGGCGCATCTAGCTAACACCATTCGAACCTTGATCCACAAGTTTATTCCCTCATTC
*
1199 GCATGATCACTGGCTACTATCGCTCATCCCCCCTCCGTTCTAATAGTCACACGACGTCACCCTTC
186 GCATGATCACTAGCTACTATCGCTCATCCCCCCTCCGTTCTAATAGTCACACGACGTCACCCTTC
*
1264 CCTTGATCTTGCTGTTCGCGAACCACCACCGTCCACCTTCCAACCACCGTAACCCACTGTTTGCC
251 CCTTGATCTCGCTGTTCGCGAACCACCACCGTCCACCTTCCAACCACCGTAACCCACTGTTTGCC
1329 CTTTCATTATTCTTTCCTTTTGTTAATTTTTTATTTTTTATTTTATTTTATTTTATTTATCATTT
316 CTTTCATTATTCTTTCCTTTTGTTAATTTTTTATTTTTTATTTTATTTTATTTTATTTATCATTT
1394 ATTATTTATTTCCTTTTTATCTGTTTATTATTTAATTTTTATTTTATTTTTCTCTCTATATATTT
381 ATTATTTATTTCCTTTTTATCTGTTTATTATTTAATTTTTATTTTATTTTTCTCTCTATATATTT
1459 TTTT
446 TTTT
Statistics
Matches: 440, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
494 440 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.39
Consensus pattern (484 bp):
CTACTTACCGACCACATCAGTCGATCGACCAACTACCTCCAGCGAGCACCAACCAATTCAACATC
GCGAGCCCATCTCCCCCTTCGCACCCCGCACCGATTTGTTCCGCCTTCACACCTCCGCATGCTTG
GGCGCATCTAGCTAACACCATTCGAACCTTGATCCACAAGTTTATTCCCTCATTCGCATGATCAC
TAGCTACTATCGCTCATCCCCCCTCCGTTCTAATAGTCACACGACGTCACCCTTCCCTTGATCTC
GCTGTTCGCGAACCACCACCGTCCACCTTCCAACCACCGTAACCCACTGTTTGCCCTTTCATTAT
TCTTTCCTTTTGTTAATTTTTTATTTTTTATTTTATTTTATTTTATTTATCATTTATTATTTATT
TCCTTTTTATCTGTTTATTATTTAATTTTTATTTTATTTTTCTCTCTATATATTTTTTTATATTT
ATTTCTTTATTATTATTATTGTTCTTATT
Done.