Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011526.1 Kokia drynarioides strain JFW-HI SEQ_126512, 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: 5858
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1270 original size:29 final size:27
Alignment explanation
Indices: 1236--1623 Score: 250
Period size: 29 Copynumber: 13.4 Consensus size: 27
1226 GAGGTCCCTA
*
1236 AACTTCTAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAA-TACCATTTTACCC-CG
1265 AACTTCCAAAAAT-CTCATTTTTTACCCCG
1 AACTTCCAAAAATAC-CA--TTTTACCCCG
*
1294 AACCTTCTAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAA-TACCATTTTACCC-CG
*
1324 AACTTCCAAAAATCCCATTTTTTACCCCG
1 AACTTCCAAAAATACCA--TTTTACCCCG
*
1353 AACCTTCTAAAAAATACCATTTTACCCCCG
1 AA-CTTC-CAAAAATACCATTTTA-CCCCG
*
1383 AACTTCCAAAAATCCCAATTTTGACCCCG
1 AACTTCCAAAAATACC-ATTTT-ACCCCG
*
1412 AACCTTCTAAAAAGTATCACCATTTTACCCCG
1 AA-CTTC-CAAAA--AT-ACCATTTTACCCCG
* **
1444 AGACTTCCAAAAATCCCATTTT----TT
1 A-ACTTCCAAAAATACCATTTTACCCCG
* * *
1468 TAC-CCCAAAAATTATCATTTTACCCTCG
1 AACTTCCAAAAA-TACCATTTTACCC-CG
* *
1496 GACTTCCAAAAATCCCATTTTTGACCCCG
1 AACTTCCAAAAATACCA-TTTT-ACCCCG
*
1525 AGCCTTCCAAAAATTACCATTTTACCCTCG
1 A-ACTTCCAAAAA-TACCATTTTACCC-CG
*
1555 AACTTCCAAAAATCCCATTTTTTACCCCG
1 AACTTCCAAAAATACCA--TTTTACCCCG
* * *
1584 AAACATCCAAAAATTACTATTTTGCTCCCG
1 -AACTTCCAAAAA-TACCATTTTAC-CCCG
1614 AA-TGTCCAAA
1 AACT-TCCAAA
1624 GACTCCGTTT
Statistics
Matches: 287, Mismatches: 34, Indels: 76
0.72 0.09 0.19
Matches are distributed among these distances:
22 7 0.02
23 9 0.03
27 1 0.00
28 31 0.11
29 101 0.35
30 89 0.31
31 27 0.09
32 12 0.04
33 8 0.03
34 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.30
Consensus pattern (27 bp):
AACTTCCAAAAATACCATTTTACCCCG
Found at i:1290 original size:30 final size:29
Alignment explanation
Indices: 1254--1597 Score: 256
Period size: 30 Copynumber: 11.8 Consensus size: 29
1244 AAAATTACCA
*
1254 TTTTACCCTCGAACTTCCAAAAATCTCATT
1 TTTTACCC-CGAACTTCCAAAAATCCCATT
* *
1284 TTTTACCCCGAACCTTCTAAAAATTACCA--
1 TTTTACCCCGAA-CTTCCAAAAA-TCCCATT
1313 TTTTACCCTCGAACTTCCAAAAATCCCATT
1 TTTTACCC-CGAACTTCCAAAAATCCCATT
* *
1343 TTTTACCCCGAACCTTCTAAAAAATACCA--
1 TTTTACCCCGAA-CTTC-CAAAAATCCCATT
*
1372 TTTTACCCCCGAACTTCCAAAAATCCCAAT
1 TTTTA-CCCCGAACTTCCAAAAATCCCATT
* *
1402 TTTGACCCCGAACCTTCTAAAAAGTATCACCA--
1 TTTTACCCCGAA-CTTC-CAAAA--ATC-CCATT
1434 TTTTACCCCGAGACTTCCAAAAATCCCATTT
1 TTTTACCCCGA-ACTTCCAAAAATCCCA-TT
*
1465 TTTTACCCC-AA-----AAATTAT--CA--
1 TTTTACCCCGAACTTCCAAA-AATCCCATT
*
1485 TTTTACCCTCGGACTTCCAAAAATCCCATT
1 TTTTACCC-CGAACTTCCAAAAATCCCATT
* * *
1515 TTTGACCCCGAGCCTTCCAAAAATTACCA--
1 TTTTACCCCGA-ACTTCCAAAAA-TCCCATT
1544 TTTTACCCTCGAACTTCCAAAAATCCCATT
1 TTTTACCC-CGAACTTCCAAAAATCCCATT
*
1574 TTTTACCCCGAAACATCCAAAAAT
1 TTTTACCCCG-AACTTCCAAAAAT
1598 TACTATTTTG
Statistics
Matches: 253, Mismatches: 24, Indels: 74
0.72 0.07 0.21
Matches are distributed among these distances:
20 8 0.03
21 1 0.00
22 1 0.00
23 2 0.01
24 3 0.01
25 2 0.01
26 2 0.01
27 3 0.01
28 22 0.09
29 66 0.26
30 89 0.35
31 33 0.13
32 14 0.06
33 4 0.02
34 3 0.01
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (29 bp):
TTTTACCCCGAACTTCCAAAAATCCCATT
Found at i:1330 original size:59 final size:59
Alignment explanation
Indices: 1238--1606 Score: 497
Period size: 59 Copynumber: 6.3 Consensus size: 59
1228 GGTCCCTAAA
*
1238 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTTACCCCGAAC
1 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
1297 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
1 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
* * * *
1356 CTTCTAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCGAAC
1 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
1415 CTTCTAAAAAGTATCACCATTTTACCC-CGAGACTTCCAAAAATCCCATTTTTTTA---C---C
1 CTTCTAAAAA-T-T-ACCATTTTACCCTCGA-ACTTCCAAAAATCCCA-TTTTTTACCCCGAAC
* * * *
1472 C--C-AAAAATTATCATTTTACCCTCGGACTTCCAAAAATCCCATTTTTGACCCCGAGC
1 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
* *
1528 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAA
1 CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
* * *
1587 CATCCAAAAATTACTATTTT
1 CTTCTAAAAATTACCATTTT
1607 GCTCCCGAAT
Statistics
Matches: 277, Mismatches: 18, Indels: 30
0.85 0.06 0.09
Matches are distributed among these distances:
50 6 0.02
51 27 0.10
52 3 0.01
53 2 0.01
54 5 0.02
55 1 0.00
56 2 0.01
57 2 0.01
58 1 0.00
59 190 0.69
60 1 0.00
61 4 0.01
62 28 0.10
63 5 0.02
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
CTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAC
Found at i:2267 original size:29 final size:28
Alignment explanation
Indices: 2233--2613 Score: 264
Period size: 29 Copynumber: 13.1 Consensus size: 28
2223 GAGGTCCCTA
*
2233 AACTTCTAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTACCATTTTA-CCCCG
2262 AACTTCCAAAAA-T-CTCATTTTTTACCCCG
1 AACTTCCAAAAATTAC-CA--TTTTACCCCG
*
2291 AACCTTCAAAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAATTACCATTTTACCC-CG
* *
2321 AACTTCCAAAAA-TCCCATTTTTTACCTCG
1 AACTTCCAAAAATTACCA--TTTTACCCCG
*
2350 AACCTTCTAAAAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
*
2380 AACTTCCAAAAA-TCCCAATTTTGACCCCG
1 AACTTCCAAAAATTACC-ATTTT-ACCCCG
*
2409 AACCTTCAAAAAATTACCACCATTTTACCCCG
1 AA-CTTCCAAAAATT---ACCATTTTACCCCG
* ***
2441 AGACTTCCAAAAA-TCCCATTTT---TTT
1 A-ACTTCCAAAAATTACCATTTTACCCCG
* * *
2466 TAC-CCCAAAAATTATCATTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTACCC-CG
2494 AACTTCCAAAAA-T-CTCATTTTTGACCCCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCCG
*
2523 AGCATTCCAAAAATTACCATTTTACCCTCG
1 AAC-TTCCAAAAATTACCATTTTACCC-CG
*
2553 AACTTCCAAAAA-TCCCATTTTTGACCCCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCCG
* * *
2582 AAACATCCAAAAATTACTATTTTGCTCCCG
1 -AACTTCCAAAAATTACCATTTTAC-CCCG
2612 AA
1 AA
2614 TGTCCAATGA
Statistics
Matches: 280, Mismatches: 34, Indels: 76
0.72 0.09 0.19
Matches are distributed among these distances:
23 7 0.03
24 9 0.03
27 1 0.00
28 26 0.09
29 102 0.36
30 94 0.34
31 15 0.05
32 18 0.06
33 6 0.02
34 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCCCG
Found at i:2287 original size:30 final size:29
Alignment explanation
Indices: 2251--2595 Score: 197
Period size: 30 Copynumber: 11.8 Consensus size: 29
2241 AAAATTACCA
2251 TTTTACCCCCGAACTTCCAAAAATCTCATT
1 TTTTA-CCCCGAACTTCCAAAAATCTCATT
*
2281 TTTTACCCCGAACCTTCAAAAAAT-TACCA--
1 TTTTACCCCGAA-CTTCCAAAAATCT--CATT
*
2310 TTTTACCCTCGAACTTCCAAAAATCCCATT
1 TTTTACCC-CGAACTTCCAAAAATCTCATT
* *
2340 TTTTACCTCGAACCTTCTAAAAAT-TACCA--
1 TTTTACCCCGAA-CTTCCAAAAATCT--CATT
* *
2369 TTTTACCCCCGAACTTCCAAAAATCCCAAT
1 TTTTA-CCCCGAACTTCCAAAAATCTCATT
* * **
2399 TTTGACCCCGAACCTTCAAAAAAT-TACCACCA
1 TTTTACCCCGAA-CTTCCAAAAATCT--CA-TT
*
2431 TTTTACCCCGAGACTTCCAAAAATCCCATTTT
1 TTTTACCCCGA-ACTTCCAAAAATCTCA--TT
* *
2463 TTTTACCCC--A-----AAAATTATCA--
1 TTTTACCCCGAACTTCCAAAAATCTCATT
2483 TTTTACCCTCGAACTTCCAAAAATCTCATT
1 TTTTACCC-CGAACTTCCAAAAATCTCATT
* *
2513 TTTGACCCCGAGCATTCCAAAAAT-TACCA--
1 TTTTACCCCGAAC-TTCCAAAAATCT--CATT
*
2542 TTTTACCCTCGAACTTCCAAAAATCCCATT
1 TTTTACCC-CGAACTTCCAAAAATCTCATT
* *
2572 TTTGACCCCGAAACATCCAAAAAT
1 TTTTACCCCG-AACTTCCAAAAAT
2596 TACTATTTTG
Statistics
Matches: 244, Mismatches: 32, Indels: 78
0.69 0.09 0.22
Matches are distributed among these distances:
20 8 0.03
21 1 0.00
23 1 0.00
24 7 0.03
28 14 0.06
29 77 0.32
30 96 0.39
31 10 0.04
32 29 0.12
33 1 0.00
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.30
Consensus pattern (29 bp):
TTTTACCCCGAACTTCCAAAAATCTCATT
Found at i:2332 original size:59 final size:59
Alignment explanation
Indices: 2235--2604 Score: 459
Period size: 59 Copynumber: 6.3 Consensus size: 59
2225 GGTCCCTAAA
* * * *
2235 CTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTACCCCGAAC
1 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * *
2294 CTTCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCTCGAAC
1 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * *
2353 CTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCGAAC
1 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* ***
2412 CTTCAAAAAATTACCACCATTTTACCC-CGAGACTTCCAAAAATCCCATTTTT-----TTTAC
1 CTTCCAAAAATT---ACCATTTTACCCTCGA-ACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * *
2469 C--CCAAAAATTATCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAGC
1 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
2526 ATTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAA
1 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
2585 CATCCAAAAATTACTATTTT
1 CTTCCAAAAATTACCATTTT
2605 GCTCCCGAAT
Statistics
Matches: 270, Mismatches: 29, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
52 31 0.11
53 3 0.01
55 8 0.03
57 4 0.01
59 189 0.70
61 3 0.01
62 32 0.12
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
Found at i:2605 original size:30 final size:29
Alignment explanation
Indices: 2470--2613 Score: 104
Period size: 30 Copynumber: 4.9 Consensus size: 29
2460 TTTTTTTACC
*
2470 CCAAAAATTA-TCATTTT-ACCCTCGAACTT
1 CCAAAAATTACT-ATTTTGACCC-CGAACAT
*
2499 CCAAAAA-T-CTCATTTTTGACCCCGAGCATT
1 CCAAAAATTACT-A-TTTTGACCCCGAACA-T
* *
2529 CCAAAAATTACCATTTT-ACCCTCGAACTT
1 CCAAAAATTACTATTTTGACCC-CGAACAT
* *
2558 CCAAAAA-TCCCATTTTTGACCCCGAAACAT
1 CCAAAAATTACTA-TTTTGACCCCG-AACAT
2588 CCAAAAATTACTATTTTG-CTCCCGAA
1 CCAAAAATTACTATTTTGAC-CCCGAA
2614 TGTCCAATGA
Statistics
Matches: 94, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
28 8 0.09
29 36 0.38
30 44 0.47
31 5 0.05
32 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.30
Consensus pattern (29 bp):
CCAAAAATTACTATTTTGACCCCGAACAT
Done.