Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009567.1 Kokia drynarioides strain JFW-HI SEQ_124280, 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: 2285
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:166 original size:20 final size:20
Alignment explanation
Indices: 141--182 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
131 GGTGTCACTG
*
141 TTTTATTCAATCCTTTTCCA
1 TTTTATTCAATCATTTTCCA
161 TTTTATTCAATCATTTTCCA
1 TTTTATTCAATCATTTTCCA
181 TT
1 TT
183 GAAGAAGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATTCAATCATTTTCCA
Found at i:548 original size:221 final size:221
Alignment explanation
Indices: 160--2285 Score: 2835
Period size: 221 Copynumber: 9.4 Consensus size: 221
150 ATCCTTTTCC
* * *
160 ATTTTATTCAATCATTTTCCATTGAAGAAGAGCAAGGATTGTATGAAATAGGGATATTA-CCCTT
1 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* * *
224 TCCAATGGTTTTATTCCACACCAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTG-T
66 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
* * *
288 TTTTCTCAGGATGAAAATGTTGACATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAA
131 TTTT-TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAA
*
353 AAGGGACACAAACGACGTGGTGTCACT
195 AAGGGACACAAATGACGTGGTGTCACT
*
380 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAATAGGGATATTATCCCTT
1 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* *
445 TCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAGTTTGAT
66 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
* *
510 TTTTTCAGGATGAAAATGATGAAATTAAGAAAGAAAATACTGATGTGGCGTAAAACTATTAGAAA
131 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAA
* * *
575 AGGGACATAGATGACGTCGTGTCACT
196 AGGGACACAAATGACGTGGTGTCACT
* * * *
601 GTTTCATTCAATCCTTTTCCATTGAAGAAGAGGAAGGATTGTATAAAACAGGGATATTATCCCTT
1 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* *
666 TCCAATAGTTTTATGCCATACCAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGAT
66 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
* * *
731 TTTTTCAGGATGAAAATGTTGAAATTAAGAATAAAAATACTGATATGGTGTAAAACTATTAGAAA
131 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAA
*
796 ATGGACACAAATGACGTGGTGTCACTGTTTCATT
196 AGGGACACAAATGACGTGGTGTCA------C--T
* * * * **
830 CAATCCTTTTCCATTTCATTCATTCCTTTTCCATTAAAGAAGAGAAAGGCTGGTATGAAGTAGGG
1 --A----TTT-CA-TTCA---A-TCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGG
* * *
895 ATATTATCCCTTTCCGATAGTTTTTTGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAA
54 ATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAA
* * * *
960 TTTTAATTTGTTTCTTTTCAGGATGTAAATGTTGAAATTAAGAATGAAAATACTTATGTAGCGTA
119 TTTTAATTTGATT-TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTA
* *
1025 AAATTATTA-ACAAAGGGACACAAATGACGTGGTTTCACTTTTTTATT
183 AAACTATTAGA-AAAGGGACACAAATGACGTGGTGTCAC--------T
* * *
1072 CAATCCTTTTCCATTTTATTAAATCATTTTCCATTGAAGATGAGAAAGGATTGTATGAAACAAGG
1 --A----TTT-C-----ATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGG
* * *
1137 ATATTATCCCTTTCCAATAGCTTTATGCCACACCAACAATTTCATCCTAAATTTTAGGATTTTAA
54 ATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAA
* * * * *
1202 TTTTAATTTGATTTTCTCAGGATGAAAATGTTGACATTAAGAATGAATATATTGATGTGGCATAA
119 TTTTAATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGT-A
*
1267 AAAC-AATAGAAAAGGGACACAAATGACGTGGTGTCACT
183 AAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACT
*
1305 GTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
1 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* *
1370 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCTGGATTTTAATTTTAATTTGAT
66 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
*
1435 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAAA
131 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAA
1500 AGGGACACAAATGACGTGGTGTCACT
196 AGGGACACAAATGACGTGGTGTCACT
* * * * *
1526 TTTTCATTCAATCCTTTCCCATTGAAGAAGAGAAAGGATTGTATAAAACAGTGATATTATCCCTT
1 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* * *
1591 TCCAATAGTTTTATGCCACATCAATAATTTCATCCTTAATTTCAGGATTTTAATTTTAATTTGAT
66 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
* * * *
1656 TTTTACAGGATGAAAATGTT-AAATTTAAGAATGAAAATACTGATGTGGCGTAAAATTTTTGGAA
131 TTTTTCAGGATGAAAATGTTGAAA-TTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAA
* * *
1720 AAGGGACTCAAATGACGTTGTGTCGCT
195 AAGGGACACAAATGACGTGGTGTCACT
* * * *
1747 GTTTCGTTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTCTGAAACAGGTATATTATCCCTT
1 ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* * * ** * *
1812 TCCAATTGTTTTATGCCACATCAGCAATTTCATTTTGAATTTTAGGATTTTAATTTTAATTTAAT
66 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
* * * *
1877 TTTTACAGGACGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAA
131 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAA
1942 AGGGACACAAATGACGTGGTGTCACT
196 AGGGACACAAATGACGTGGTGTCACT
* * * *
1968 ATTTCATTCAATTC-TTTTCCATTGAAGAGGAGAAAGGATTGCATAAAATAGGGATATTATCCCT
1 ATTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCT
*
2032 TTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGA
65 TTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGA
* * *
2097 TTTTTTCAGGATGAAAATGTTAAAATTAAGAATCAAAATACTGATGTGGCGTAAAACTATTGGAA
130 TTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAA
** *
2162 AAGAAACACAAATGACGTGGTGCCACT
195 AAGGGACACAAATGACGTGGTGTCACT
* * **
2189 GTTTCATTCAATTC-TTTTCCATTGAAGAAGAGAAAGGATTGTATGACACAAAGATATTATCCCT
1 ATTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCT
*
2253 TTCCAATAGTTTTATGCCACATCAACAATTTCA
65 TTCCAATAGTTTTATGCCACACCAACAATTTCA
Statistics
Matches: 1691, Mismatches: 174, Indels: 81
0.87 0.09 0.04
Matches are distributed among these distances:
220 65 0.04
221 1212 0.72
222 10 0.01
226 1 0.00
227 4 0.00
229 1 0.00
233 1 0.00
235 3 0.00
236 3 0.00
237 4 0.00
240 1 0.00
241 179 0.11
242 202 0.12
243 1 0.00
246 3 0.00
247 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (221 bp):
ATTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAA
AGGGACACAAATGACGTGGTGTCACT
Found at i:848 original size:20 final size:20
Alignment explanation
Indices: 823--864 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
813 GGTGTCACTG
823 TTTCATTCAATCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
*
843 TTTCATTCATTCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
863 TT
1 TT
865 AAAGAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTCATTCAATCCTTTTCCA
Found at i:1090 original size:20 final size:20
Alignment explanation
Indices: 1065--1106 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1055 GGTTTCACTT
* *
1065 TTTTATTCAATCCTTTTCCA
1 TTTTATTAAATCATTTTCCA
1085 TTTTATTAAATCATTTTCCA
1 TTTTATTAAATCATTTTCCA
1105 TT
1 TT
1107 GAAGATGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATTAAATCATTTTCCA
Done.