Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011287.1 Kokia drynarioides strain JFW-HI SEQ_126266, 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: 2278
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Found at i:571 original size:18 final size:17
Alignment explanation
Indices: 544--606 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
534 GGACTTTTCT
* *
544 AAATTTAATTTTATAATA
1 AAATTAAATTTCA-AATA
562 AAATTAAATTTCAAATA
1 AAATTAAATTTCAAATA
* *
579 AACTTAAATTTAAAAT-
1 AAATTAAATTTCAAATA
*
595 AAATTCAATTTC
1 AAATTAAATTTC
607 CAACGGGCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.24
17 18 0.47
18 11 0.29
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAAATTTCAAATA
Found at i:596 original size:34 final size:33
Alignment explanation
Indices: 543--606 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
533 TGGACTTTTC
* * *
543 TAAATTTAATTTTATAATAAAATTAAATTTCAAA
1 TAAACTTAAATTTAAAAT-AAATTAAATTTCAAA
*
577 TAAACTTAAATTTAAAATAAATTCAATTTC
1 TAAACTTAAATTTAAAATAAATTAAATTTC
607 CAACGGGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.42
34 15 0.58
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAACTTAAATTTAAAATAAATTAAATTTCAAA
Found at i:1424 original size:198 final size:198
Alignment explanation
Indices: 838--1475 Score: 654
Period size: 198 Copynumber: 3.2 Consensus size: 198
828 GTTTTATTGA
* * *
838 TTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTTCTCT
* * * * *
903 ATACCTCATTAGGAATAC-GAGTTTGGT-TCACTTCTCAGTATCTCATCAGGAAGCTAACCTTGT
66 ATATCTCATCAAGAAGACGGA-TTTGGTCT-ACTTCTCCGTATCTCATCAGGAAGCTAA---T-T
* * * * *
966 ATTGTTTCGAC-CTGCTTTTCAGTATCTTCTTTAGGAAGCTGGGGGTTCGAAGATTTTGTT--TG
125 A---CTTCGACAC-GCTTCTCAGTATC-TCATTAGGGAGCT-GTGGTTCGAAGA-TTTGTTCATG
* * * ***
1028 CTTTGACCGTGGGTTCAA
183 --TCGAGCATGGGTTTGG
* * * *
1046 TTTAGTCTTC--CTCAATATCTCATTAGGAAGATGA-TCGCGTCGTTTGTTT-TATCCGCTTCTC
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACT-GCGTCGTTTGTTTCAATCCGCTTCTC
*
1107 TATATCTCATC-AGAAAGACGAATTTGGTCTACTTCTCCGTA--TC-TC----A---AATTACTT
65 TATATCTCATCAAG-AAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTT
* *
1161 CAACACGCTTCTCAGTATCTCATTAGAGAGCTGTGGTTCGAAGATTT-TCTCATGTCGAGCATGG
129 CGACACGCTTCTCAGTATCTCATTAGGGAGCTGTGGTTCGAAGATTTGT-TCATGTCGAGCATGG
1225 GTTTGG
193 GTTTGG
* * * *
1231 TTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGA-TCGCGTTGCTCGTTTCAATCCGCTTCTC
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACT-GCGTCGTTTGTTTCAATCCGCTTCTC
*
1295 TGTATCTCATCAAGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTC
65 TATATCTCATCAAGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTC
*
1360 GACACGCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCGAAGATTTGTTCATGTCGAGCATGGGT
130 GACACGCTTCTCAGTATCTCATTAGGGAGCTGTGGTTCGAAGATTTGTTCATGTCGAGCATGGGT
1425 TTGG
195 TTGG
*
1429 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTTGTTT
1 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTT
1476 TGTGGGTGTC
Statistics
Matches: 366, Mismatches: 40, Indels: 58
0.79 0.09 0.12
Matches are distributed among these distances:
184 1 0.00
185 23 0.06
186 11 0.03
187 47 0.13
188 64 0.17
189 3 0.01
190 2 0.01
191 4 0.01
192 1 0.00
195 3 0.01
198 116 0.32
199 2 0.01
202 2 0.01
203 2 0.01
204 1 0.00
205 40 0.11
206 35 0.10
208 9 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (198 bp):
TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTTCTCT
ATATCTCATCAAGAAGACGGATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCG
ACACGCTTCTCAGTATCTCATTAGGGAGCTGTGGTTCGAAGATTTGTTCATGTCGAGCATGGGTT
TGG
Done.