Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000910.1 Kokia drynarioides strain JFW-HI SEQ_112047, 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: 2171
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Found at i:1268 original size:30 final size:28
Alignment explanation
Indices: 1232--1398 Score: 90
Period size: 29 Copynumber: 5.8 Consensus size: 28
1222 AAAATCAAAC
* *
1232 TTTTGGAAAGTTTGAGGGTAAAATGGTGA
1 TTTTTGAAAGTTCGAGGGTAAAAT-GTGA
* * *
1261 TTTTTGGATA-CTCGA-GGCAAAATGGTGA
1 TTTTT-GAAAGTTCGAGGGTAAAAT-GTGA
* * * * *
1289 TTTTTGAGAGTTCGGGGGAAAAAAAGTAA
1 TTTTTGAAAGTTCGAGGG-TAAAATGTGA
* *
1318 TTTTTGAGAAGTTCGAGGGTAAAAATATAA
1 TTTTTGA-AAGTTCGAGGGT-AAAATGTGA
* *
1348 TTTTTGAAAATT-TAGGGGTAAAAATGTGA
1 TTTTTGAAAGTTCGA-GGGT-AAAATGTGA
* *
1377 TTTTTGGAAGTTC-AGGGGAAAA
1 TTTTTGAAAGTTCGAGGGTAAAA
1399 ATGTAAATTT
Statistics
Matches: 107, Mismatches: 23, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
27 7 0.07
28 24 0.22
29 46 0.43
30 30 0.28
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTTGAAAGTTCGAGGGTAAAATGTGA
Found at i:1320 original size:29 final size:30
Alignment explanation
Indices: 1288--1423 Score: 120
Period size: 29 Copynumber: 4.7 Consensus size: 30
1278 CAAAATGGTG
*
1288 ATTTTTGAG-AGTTCGGGGGAAAAAAAGTA
1 ATTTTTGAGAAGTTCAGGGGAAAAAAAGTA
* *
1317 ATTTTTGAGAAGTTCGAGGGTAAAAATA-TA
1 ATTTTTGAGAAGTTC-AGGGGAAAAAAAGTA
* * * * *
1347 ATTTTTGA-AAATTTAGGGGTAAAAATGTG
1 ATTTTTGAGAAGTTCAGGGGAAAAAAAGTA
*
1376 ATTTTTG-GAAGTTCAGGGG-AAAAATGTA
1 ATTTTTGAGAAGTTCAGGGGAAAAAAAGTA
* * *
1404 AATTTTAAGAAGTTTAGGGG
1 ATTTTTGAGAAGTTCAGGGG
1424 TTAAAATGTA
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
28 21 0.24
29 41 0.48
30 15 0.17
31 9 0.10
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (30 bp):
ATTTTTGAGAAGTTCAGGGGAAAAAAAGTA
Found at i:1518 original size:29 final size:29
Alignment explanation
Indices: 1309--1566 Score: 169
Period size: 30 Copynumber: 8.8 Consensus size: 29
1299 TTCGGGGGAA
* * ** *
1309 AAAAAGTAATTTTTGAGAAGTTCGAGGGTA
1 AAAATGTAAATTTTG-GAAGTTTAAGGGTT
* * * * * *
1339 AAAATATAATTTTTGAAAATTTAGGGGTA
1 AAAATGTAAATTTTGGAAGTTTAAGGGTT
* * * **
1368 AAAATGTGATTTTTGGAAG-TTCAGGGGA
1 AAAATGTAAATTTTGGAAGTTTAAGGGTT
* *
1396 AAAATGTAAATTTTAAGAAGTTTAGGGGTT
1 AAAATGTAAATTTT-GGAAGTTTAAGGGTT
* ** *
1426 AAAATGTATATTTTATAAATTTTAAGGGTT
1 AAAATGTAAATTTT-GGAAGTTTAAGGGTT
* * *
1456 AAAATATAATTTTTGAGAAGTTTAAGGGTC
1 AAAATGTAAATTTTG-GAAGTTTAAGGGTT
*
1486 AAAATGTAAAATTTGGAAGTTTAAGGGTT
1 AAAATGTAAATTTTGGAAGTTTAAGGGTT
** * * *
1515 AAAATGTATTTTTTGAAAAGTTTAGGGGTC
1 AAAATGTAAATTTTG-GAAGTTTAAGGGTT
1545 AAAATGT-AATTTTGGGAAGTTT
1 AAAATGTAAATTTT-GGAAGTTT
1567 GGGGCCAAAT
Statistics
Matches: 177, Mismatches: 46, Indels: 11
0.76 0.20 0.05
Matches are distributed among these distances:
28 18 0.10
29 63 0.36
30 96 0.54
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATGTAAATTTTGGAAGTTTAAGGGTT
Found at i:1585 original size:59 final size:58
Alignment explanation
Indices: 1309--1594 Score: 247
Period size: 59 Copynumber: 4.9 Consensus size: 58
1299 TTCGGGGGAA
* ** * * *
1309 AAAAAGTAATTTTTGAGAAGTTCGAGGGTAAAAATATAATTTTTGAAAA-TTTAGGGGTA
1 AAAATGTAA-TTTTG-GAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTTTAGGGGTC
* * ** * *
1368 AAAATGTGATTTTTGGAAG-TTCAGGGGAAAAATGTAAATTTT-AAGAAGTTTAGGGGTT
1 AAAATGT-AATTTTGGAAGTTTAAGGGTTAAAATGTAATTTTTGAA-AAGTTTAGGGGTC
** * * * *
1426 AAAATGTATATTTTATAAATTTTAAGGGTTAAAATATAATTTTTGAGAAGTTTAAGGGTC
1 AAAATGTA-ATTTT-GGAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTTTAGGGGTC
* *
1486 AAAATGTAAAATTTGGAAGTTTAAGGGTTAAAATGTATTTTTTGAAAAGTTTAGGGGTC
1 AAAATGT-AATTTTGGAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTTTAGGGGTC
* ** * *
1545 AAAATGTAATTTTGGGAAGTTT-GGGGCCAAATTGTAATTTTTGATAAGTT
1 AAAATGTAATTTT-GGAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTT
1595 CAAGGACCTT
Statistics
Matches: 183, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
56 2 0.01
57 21 0.11
58 51 0.28
59 66 0.36
60 41 0.22
61 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTTTAGGGGTC
Found at i:1593 original size:29 final size:30
Alignment explanation
Indices: 1339--1594 Score: 152
Period size: 29 Copynumber: 8.7 Consensus size: 30
1329 TTCGAGGGTA
* **
1339 AAAATATAATTTTTGAAAA-TTTAGGGGTA
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
* * * *
1368 AAAATGTGATTTTTG-GAAGTTCAGGGG-A
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
* **
1396 AAAATGTAAATTTT-AAGAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAA-AAGTTTAGGGGCC
* * **
1426 AAAATGT-ATATTTT-ATAAATTTTAAGGGTT
1 AAAATGTAAT-TTTTGA-AAAGTTTAGGGGCC
* * * *
1456 AAAATATAATTTTTGAGAAGTTTAAGGGTC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
** * * **
1486 AAAATGTAAAATTTG-GAAGTTTAAGGGTT
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
* *
1515 AAAATGTATTTTTTGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
**
1545 AAAATGTAA-TTTTGGGAAGTTT-GGGGCC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
* *
1573 AAATTGTAATTTTTGATAAGTT
1 AAAATGTAATTTTTGAAAAGTT
1595 CAAGGACCTT
Statistics
Matches: 184, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
28 28 0.15
29 77 0.42
30 75 0.41
31 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGAAAAGTTTAGGGGCC
Done.