Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010472.1 Kokia drynarioides strain JFW-HI SEQ_125372, 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: 39109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1242 original size:29 final size:29
Alignment explanation
Indices: 1209--1543 Score: 222
Period size: 29 Copynumber: 11.3 Consensus size: 29
1199 GTCCCTGAAC
*
1209 CTTCCAAAAATTACTATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCCGAA
**
1238 CTTCCAAAAA-T-CCTATTTTTGTCCCCGAA
1 CTTCCAAAAATTACC-A-TTTTACCCCCGAA
* * *
1267 CCATCTAAAAATTACCATTTTACCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
*
1297 CTTCCAAAAA-T-CCATTTTTCACCCCGAA
1 CTTCCAAAAATTACCATTTTAC-CCCCGAA
*
1325 CCTTCTAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* * *
1355 CTTTCAAAAA-TCCCATTTTTTTA-CCCCTAA
1 CTTCCAAAAATTACCA---TTTTACCCCCGAA
*
1385 CCTTCCAAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* *
1415 CTTCCAAAAA-TCCCATTTTTGA-CCCCAAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
** * *
1444 CCTTTTAAAAATTACCATTTTACCCTCAAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* * *
1474 TTTCCAAAAA-TCCCATTTTTTGA-CTCCGAA
1 CTTCCAAAAATTACCA--TTTT-ACCCCCGAA
** * *
1504 CCTTTTTAAAAATCACCATTTTACCCTCGAA
1 -C-TTCCAAAAATTACCATTTTACCCCCGAA
1535 CTTCCAAAA
1 CTTCCAAAA
1544 TCCCATTTTT
Statistics
Matches: 237, Mismatches: 42, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
27 9 0.04
28 21 0.09
29 86 0.36
30 67 0.28
31 38 0.16
32 13 0.05
33 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:1291 original size:59 final size:59
Alignment explanation
Indices: 1205--1588 Score: 486
Period size: 59 Copynumber: 6.5 Consensus size: 59
1195 GAAGGTCCCT
* * * *
1205 GAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGTCCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
1264 GAACCATCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTTCACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* *
1322 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTTTACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCC
* * *
1382 TAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * * * *
1441 AAACCTTTTAAAAATTACCATTTTACCCTCAAATTTCCAAAAATCCCATTTTTTGACTCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCC
* * * *
1501 GAACCTTTTTAAAAATCACCATTTTACCCTCGAACTTCC-AAAATCCCATTTTTGACTCC
1 GAACC-TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1560 AAACCTTC-CAAAACTACCATTTTTCCCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCC
1589 CTCCGTGCAT
Statistics
Matches: 288, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
57 16 0.06
58 54 0.19
59 111 0.39
60 77 0.27
61 30 0.10
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (59 bp):
GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:1463 original size:119 final size:119
Alignment explanation
Indices: 1214--1588 Score: 490
Period size: 119 Copynumber: 3.2 Consensus size: 119
1204 TGAACCTTCC
* * * * *
1214 AAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGT-CCCCGAACCATCTAAAAA
1 AAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTTTACCCCGAACCTTCTAAAAA
* * *
1278 TTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTTCACCCCGAACCTTCT
66 TTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTT
* *
1331 AAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTTTACCCCTAACCTTCCAAAAA
1 AAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTTTACCCCGAACCTTCTAAAAA
* *
1396 TTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTT
66 TTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTT
* * * * *
1450 AAAAATTACCATTTTACCCTC-AAATTTCCAAAAATCCCATTTTTTGACTCCGAACCTTTTTAAA
1 AAAAATTACCATTTTACCCCCGAACTTT-CAAAAATCCCATTTTTTTACCCCGAACC-TTCTAAA
* * *
1514 AATCACCATTTTACCCTCGAACTTCC-AAAATCCCATTTTTGACTCCAAACC-TTC
64 AATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTT
* * *
1568 CAAAACTACCATTTTTCCCCC
1 AAAAATTACCATTTTACCCCC
1589 CTCCGTGCAT
Statistics
Matches: 226, Mismatches: 28, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
117 42 0.19
118 67 0.30
119 89 0.39
120 28 0.12
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (119 bp):
AAAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTTTACCCCGAACCTTCTAAAAA
TTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTT
Found at i:1582 original size:30 final size:29
Alignment explanation
Indices: 1206--1588 Score: 220
Period size: 29 Copynumber: 13.0 Consensus size: 29
1196 AAGGTCCCTG
* *
1206 AACCTTCCAAAAATTACTA-TTTTACCCCCG
1 AACCTTCCAAAAA-TACCATTTTTA-CCCCA
* *
1236 AA-CTTCCAAAAAT-CCTATTTTTGTCCCCG
1 AACCTTCCAAAAATACC-ATTTTT-ACCCCA
* * *
1265 AACCATCTAAAAATTACCA-TTTTACCCTCG
1 AACCTTCCAAAAA-TACCATTTTTACCC-CA
*
1295 AA-CTTCCAAAAAT-CCATTTTTCACCCCG
1 AACCTTCCAAAAATACCATTTTT-ACCCCA
* *
1323 AACCTTCTAAAAATTACCA-TTTTACCCCCG
1 AACCTTCCAAAAA-TACCATTTTTA-CCCCA
* * *
1353 AA-CTTTCAAAAATCCCATTTTTTTACCCCT
1 AACCTTCCAAAAATACCA--TTTTTACCCCA
1383 AACCTTCCAAAAATTACCA-TTTTACCCCCA
1 AACCTTCCAAAAA-TACCATTTTTA-CCCCA
*
1413 AA-CTTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCCAAAAATACCATTTTT-ACCCCA
**
1442 AACCTTTTAAAAATTACCA-TTTTACCCTCA
1 AACCTTCCAAAAA-TACCATTTTTACCC-CA
* * * *
1472 AA-TTTCCAAAAATCCCATTTTTTGACTCCG
1 AACCTTCCAAAAATACCA-TTTTT-ACCCCA
** *
1502 AACCTTTTTAAAAATCACCA-TTTTACCCTCG
1 AACC-TTCCAAAAAT-ACCATTTTTACCC-CA
* *
1533 AA-CTTCC-AAAATCCCATTTTTGACTCCA
1 AACCTTCCAAAAATACCATTTTT-ACCCCA
* *
1561 AACCTTCCAAAACTACCATTTTTCCCCC
1 AACCTTCCAAAAATACCATTTTTACCCC
1589 CTCCGTGCAT
Statistics
Matches: 279, Mismatches: 39, Indels: 71
0.72 0.10 0.18
Matches are distributed among these distances:
27 7 0.03
28 35 0.13
29 104 0.37
30 82 0.29
31 34 0.12
32 14 0.05
33 3 0.01
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (29 bp):
AACCTTCCAAAAATACCATTTTTACCCCA
Found at i:15424 original size:18 final size:17
Alignment explanation
Indices: 15401--15438 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
15391 CTTTACTTTT
*
15401 ATTTTATTTTACCAATGA
1 ATTTTATTTTAACAA-GA
15419 ATTTTATTTTAACAAGA
1 ATTTTATTTTAACAAGA
15436 ATT
1 ATT
15439 CTAGTCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTTATTTTAACAAGA
Found at i:15473 original size:41 final size:41
Alignment explanation
Indices: 15427--15522 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
15417 GAATTTTATT
* *
15427 TTAACAAGAATTCTAGTCAGCCAATTTTAACAATATCCATC
1 TTAACAAGAATTCTAGTCAGCCAATTCTAACAATATCCACC
* * *
15468 TTAACAAGAATTCTAGTTATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCAGCCAATTCTAACAATATCCACC
*
15509 TTGACAAGAATTCT
1 TTAACAAGAATTCT
15523 TTACGAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCAGCCAATTCTAACAATATCCACC
Found at i:15534 original size:17 final size:17
Alignment explanation
Indices: 15512--15550 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
15502 CTCCACCTTG
* *
15512 ACAAGAATTCTTTACGA
1 ACAAGAACTCTCTACGA
*
15529 ACAAGAACTCTCTGCGA
1 ACAAGAACTCTCTACGA
15546 ACAAG
1 ACAAG
15551 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (17 bp):
ACAAGAACTCTCTACGA
Found at i:25121 original size:19 final size:17
Alignment explanation
Indices: 25088--25123 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
25078 TAATTTTTCA
25088 TTTTTATTAATTTAATT
1 TTTTTATTAATTTAATT
25105 TTTTTAATTATATTTAATT
1 TTTTT-ATTA-ATTTAATT
25124 ATTAATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATTAATTTAATT
Found at i:25421 original size:2 final size:2
Alignment explanation
Indices: 25416--25448 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
25406 CTTTTTTTTC
25416 CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
25449 TAGATGAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:25622 original size:5 final size:5
Alignment explanation
Indices: 25612--25644 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
25602 TTTTCTTCTT
*
25612 AAAA- AAAAA AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
25645 CTCACTACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:25752 original size:5 final size:5
Alignment explanation
Indices: 25724--25767 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
25714 ATACAGTGAG
* *
25724 AAAGA AAGAGA CAGAGA AAGGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AA-AGA -AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
25768 GGAGTGAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 26 0.79
6 6 0.18
7 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (5 bp):
AAAGA
Done.