Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005812.1 Kokia drynarioides strain JFW-HI SEQ_120094, 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: 1726
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Found at i:113 original size:13 final size:13
Alignment explanation
Indices: 88--126 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
78 TTTATTTGAA
88 ATAGAATATATAT
1 ATAGAATATATAT
101 ATATGAAATATATAT
1 ATA-G-AATATATAT
116 ATAGAATATAT
1 ATAGAATATAT
127 GGAATAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
ATAGAATATATAT
Found at i:1161 original size:39 final size:39
Alignment explanation
Indices: 1116--1398 Score: 216
Period size: 39 Copynumber: 7.2 Consensus size: 39
1106 ATCGGATGGT
* *
1116 CTTCAATTTGCTCTCTAGTTAGGGTAAAAGATTGGATTG
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
** * * * ** *
1155 CTTCAATCTGCCCAAT-GGTCGAGGTAAGAGATAAGATGG
1 CTTCAATCTGCCCTCTAGTTAG-GGTAAAAGATTGGATTG
1194 TCTAT-AATCTGCCCTCT-GTTTAGGGTAAAAGATTGGATTG
1 -CT-TCAATCTGCCCTCTAG-TTAGGGTAAAAGATTGGATTG
* * ** * *
1234 CTTCAATCTGCCCTATGGTCGGGGTAAGAGATTGGATGG
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
* * *
1273 TCTTCAATCTGCACTCTGGTTAGGGTAAAAGATTGGATTT
1 -CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
* * * * * *
1313 CTTCAATTTGTCC-C-ATGGTCGAGGTAAGAGATTGGATGG
1 CTTCAATCTGCCCTCTA-GTTAG-GGTAAAAGATTGGATTG
* *
1352 TCTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATTG
1 -CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
1392 CTTCAAT
1 CTTCAAT
1399 TGGCCCCATG
Statistics
Matches: 185, Mismatches: 47, Indels: 24
0.72 0.18 0.09
Matches are distributed among these distances:
38 8 0.04
39 86 0.46
40 85 0.46
41 6 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (39 bp):
CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
Found at i:1193 original size:79 final size:78
Alignment explanation
Indices: 1071--1418 Score: 477
Period size: 79 Copynumber: 4.4 Consensus size: 78
1061 TAAATAATTA
* * * * *
1071 GATTGCTTCAATCTGTCCCATGATCG-GGATAAGAGATCGGATGGTCTTCAATTTGCTCTCTAGT
1 GATTGCTTCAATCTG-CCCATGGTCGAGG-TAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGT
1135 TAGGGTAAAAGATTG
64 TAGGGTAAAAGATTG
** *
1150 GATTGCTTCAATCTGCCCAATGGTCGAGGTAAGAGATAAGATGGTCTAT-AATCTGCCCTCTGTT
1 GATTGCTTCAATCTGCCC-ATGGTCGAGGTAAGAGATTGGATGGTCT-TCAATCTGCCCTCTGGT
1214 TAGGGTAAAAGATTG
64 TAGGGTAAAAGATTG
* *
1229 GATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATTGGATGGTCTTCAATCTGCACTCTGGTT
1 GATTGCTTCAATCTGCCC-ATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTT
1294 AGGGTAAAAGATTG
65 AGGGTAAAAGATTG
* * *
1308 GATTTCTTCAATTTGTCCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGGTT
1 GATTGCTTCAATCTG-CCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTT
1373 AGGGTAAAAGATTG
65 AGGGTAAAAGATTG
*
1387 GATTGCTTCAAT-TGGCCCCATGGTCGGGGTAA
1 GATTGCTTCAATCT-G-CCCATGGTCGAGGTAA
1419 AATACTCGGG
Statistics
Matches: 242, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
78 5 0.02
79 231 0.95
80 6 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (78 bp):
GATTGCTTCAATCTGCCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
GGGTAAAAGATTG
Found at i:1221 original size:40 final size:40
Alignment explanation
Indices: 1104--1398 Score: 273
Period size: 40 Copynumber: 7.5 Consensus size: 40
1094 TCGGGATAAG
* * * *
1104 AGATCGGATGGTCTTCAATTTGCTCTCTAGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
* ** * *
1144 AGATTGGATTG-CTTCAATCTGCCCAATGG-TCGAGGTAAG
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAG-GGTAAA
** *
1183 AGATAAGATGGTCTAT-AATCTGCCCTCTGTTTAGGGTAAA
1 AGATTGGATGGTCT-TCAATCTGCCCTCTGGTTAGGGTAAA
* * ** *
1223 AGATTGGATTG-CTTCAATCTGCCCTATGGTCGGGGTAAG
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
*
1262 AGATTGGATGGTCTTCAATCTGCACTCTGGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
* * * * *
1302 AGATTGGAT-TTCTTCAATTTGTCCC-ATGG-TCGAGGTAAG
1 AGATTGGATGGTCTTCAATCTG-CCCTCTGGTTAG-GGTAAA
*
1341 AGATTGGATGGTCTTCAATCTGCCCTTTGGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
*
1381 AGATTGGATTG-CTTCAAT
1 AGATTGGATGGTCTTCAAT
1399 TGGCCCCATG
Statistics
Matches: 201, Mismatches: 43, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
38 5 0.02
39 94 0.47
40 97 0.48
41 5 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
Found at i:1417 original size:39 final size:39
Alignment explanation
Indices: 1071--1420 Score: 260
Period size: 40 Copynumber: 8.9 Consensus size: 39
1061 TAAATAATTA
* * * * *
1071 GATTGCTTCAATCTGTCCCATGATCGGGATAAGAGATCG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * * * **
1110 GATGGTCTTCAATTTGCTCTC-TAGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGC-CCCATGGTCGGGGTAAAAGATTG
* * * **
1150 GATTGCTTCAATCTGCCCAATGGTCGAGGTAAGAGATAA
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * **
1189 GATGGTCTAT-AATCTGCCCTC-TGTTTAGGGTAAAAGATTG
1 GATTG-CT-TCAATCTGCCC-CATGGTCGGGGTAAAAGATTG
* *
1229 GATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATTG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * **
1268 GATGGTCTTCAATCTGCACTC-TGGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGC-CCCATGGTCGGGGTAAAAGATTG
* * * * *
1308 GATTTCTTCAATTTGTCCCATGGTCGAGGTAAGAGATTG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* ** **
1347 GATGGTCTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
1387 GATTGCTTCAAT-TGGCCCCATGGTCGGGGTAAAA
1 GATTGCTTCAATCT-GCCCCATGGTCGGGGTAAAA
1421 TACTCGGGGT
Statistics
Matches: 231, Mismatches: 67, Indels: 26
0.71 0.21 0.08
Matches are distributed among these distances:
38 5 0.02
39 110 0.48
40 112 0.48
41 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (39 bp):
GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
Found at i:1620 original size:50 final size:50
Alignment explanation
Indices: 1493--1623 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
1483 TTAATATGCT
* * *
1493 CCTCTACAGCTTTAGGTGAATGAGATTCGTCATTGCGGCTTCAATCTGCC
1 CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
* * **
1543 CCTTTACAGCTTTAGGTGTATGAGATTTTTCATTGCAGCTTCAATCTGTT
1 CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
* *
1593 TCTCTACAGCTTTAGGGGTAT-AGGATTTGTC
1 CCTCTACAGCTTTAGGTGTATGA-GATTTGTC
1624 GTTCTATTGC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (50 bp):
CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
Done.