Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004878.1 Kokia drynarioides strain JFW-HI SEQ_118556, 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: 3029
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:51 original size:24 final size:23
Alignment explanation
Indices: 14--63 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
4 TTTTAAGTAT
* *
14 TAAATGTCTGTTAATATTAATAA
1 TAAATGTCTATTAATAATAATAA
*
37 TAAATGTGCTATTAATAATGATAA
1 TAAATGT-CTATTAATAATAATAA
61 TAA
1 TAA
64 TAATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (23 bp):
TAAATGTCTATTAATAATAATAA
Found at i:1195 original size:30 final size:29
Alignment explanation
Indices: 1124--1577 Score: 291
Period size: 30 Copynumber: 15.7 Consensus size: 29
1114 GAGGTCCTTG
1124 AACTGTCCAAAAATTCCATTTTTACCCTCG-
1 AACT-TCCAAAAATTCCATTTTTACCC-CGA
*
1154 AACTTCTAAAAATTCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTT-ACCCCGA
* * *
1184 AACTTCAAAAAAATCCA-TTTTACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCCGA
* * * *
1212 AAATACCAAAAATTCCAATTTTGACCCCAA
1 AACTTCCAAAAATTCC-ATTTTTACCCCGA
* * *
1242 AAATACCAAAAATTCCAATTTT-----G-
1 AACTTCCAAAAATTCCATTTTTACCCCGA
* *
1265 -AC-CCCAAAAATTCCATTTTTAACCTCGA
1 AACTTCCAAAAATTCCATTTTT-ACCCCGA
* *
1293 AACTTTCAAAAATTCCATTTTTACACTCG-
1 AACTTCCAAAAATTCCATTTTTAC-CCCGA
** **
1322 AACTTCCAAAAACCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCGA
*
1352 AACTTCTAAAAATTCCATTTTTACCCTC-A
1 AACTTCCAAAAATTCCATTTTTACCC-CGA
* * * *
1381 GACTTCTAAAAA-TCTCATTTTTGACCTCAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCCGA
* *
1411 AACTTCCAAAAAATTCTATTTTTGACCTCGA
1 AACTTCC-AAAAATTCCATTTTT-ACCCCGA
*
1442 AACTTCCAAAAATTCTATTTTTACCCTCG-
1 AACTTCCAAAAATTCCATTTTTACCC-CGA
* *
1471 AA---CCAAAAATGCCATTTTTTACCCCAA
1 AACTTCCAAAAATTCCA-TTTTTACCCCGA
* * *
1498 AACTTCCCAAAATTTCATTTTTACCCTC-T
1 AACTTCCAAAAATTCCATTTTTACCC-CGA
* * *
1527 AACCTCCAAAATTTCCATTTTTTACCTCGA
1 AACTTCCAAAAATTCCA-TTTTTACCCCGA
1557 AAC-TCTC-AAAATTACCATTTT
1 AACTTC-CAAAAATT-CCATTTT
1578 GTGCCCGGGT
Statistics
Matches: 343, Mismatches: 48, Indels: 67
0.75 0.10 0.15
Matches are distributed among these distances:
21 16 0.05
22 1 0.00
26 11 0.03
27 12 0.03
28 20 0.06
29 115 0.34
30 141 0.41
31 25 0.07
32 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCGA
Found at i:1223 original size:58 final size:60
Alignment explanation
Indices: 1161--1275 Score: 162
Period size: 58 Copynumber: 1.9 Consensus size: 60
1151 TCGAACTTCT
* * * *
1161 AAAAATTCCATTTTTGACCCCGAAACTTCAAAAAAATCC-ATTTT-ACCCCAAAAATACC
1 AAAAATTCCAATTTTGACCCCAAAAATACAAAAAAATCCAATTTTGACCCCAAAAATACC
* *
1219 AAAAATTCCAATTTTGACCCCAAAAATACCAAAAATTCCAATTTTGACCCCAAAAAT
1 AAAAATTCCAATTTTGACCCCAAAAATACAAAAAAATCCAATTTTGACCCCAAAAAT
1276 TCCATTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 33 0.67
59 5 0.10
60 11 0.22
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.25
Consensus pattern (60 bp):
AAAAATTCCAATTTTGACCCCAAAAATACAAAAAAATCCAATTTTGACCCCAAAAATACC
Found at i:1560 original size:59 final size:59
Alignment explanation
Indices: 1271--1569 Score: 240
Period size: 59 Copynumber: 5.1 Consensus size: 59
1261 TTTGACCCCA
* * * *
1271 AAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTCCA-TTTTTACACTCG-AACTTCCA
1 AAAATTTCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTTAC-CTCGAAACTTCCC
*** * * * **
1330 AAAACCCCATTTTTGACCCTAAAACTTCTAAAAATTCCA-TTTTTACCCTC-AGACTTCTA
1 AAAATTTCATTTTT-ACCCTCAAACTTCCAAAAATTCCATTTTTTA-CCTCGAAACTTCCC
* * *
1389 AAAATCTCATTTTTGA-CCTCAAAACTTCCAAAAAATTCTATTTTTGACCTCGAAACTT-CC
1 AAAATTTCATTTTT-ACCCTC-AAACTTCC-AAAAATTCCATTTTTTACCTCGAAACTTCCC
* * * * *
1449 AAAAATTCTATTTTTACCCTCGAA---CCAAAAATGCCATTTTTTACCCCAAAACTTCCC
1 AAAATTTC-ATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACCTCGAAACTTCCC
* * * *
1506 AAAATTTCATTTTTACCCTCTAACCTCCAAAATTTCCATTTTTTACCTCGAAAC-TCTC
1 AAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACCTCGAAACTTCCC
1564 AAAATT
1 AAAATT
1570 ACCATTTTGT
Statistics
Matches: 195, Mismatches: 32, Indels: 27
0.77 0.13 0.11
Matches are distributed among these distances:
56 37 0.19
57 11 0.06
58 12 0.06
59 88 0.45
60 27 0.14
61 20 0.10
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACCTCGAAACTTCCC
Done.