Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010293.1 Kokia drynarioides strain JFW-HI SEQ_125145, 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: 13703
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:564 original size:3 final size:3
Alignment explanation
Indices: 521--546 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
511 TCATTAATGC
521 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
547 AAACAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1150 original size:25 final size:25
Alignment explanation
Indices: 1072--1156 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
1062 TAGGCTTAGG
1072 GTATTTAGGCTGACTTGGGCCATTT
1 GTATTTAGGCTGACTTGGGCCATTT
** *
1097 GTAATTTAGTATGACATTTGGGTCA--T
1 GT-ATTTAGGCTGAC--TTGGGCCATTT
*
1123 GTATTTGGGCTGACTTGGGCCATTT
1 GTATTTAGGCTGACTTGGGCCATTT
1148 GTAATTTAG
1 GT-ATTTAG
1157 TATGGCATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
23 7 0.15
25 14 0.30
26 18 0.39
28 7 0.15
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (25 bp):
GTATTTAGGCTGACTTGGGCCATTT
Found at i:1223 original size:6 final size:6
Alignment explanation
Indices: 1199--1278 Score: 89
Period size: 6 Copynumber: 14.0 Consensus size: 6
1189 TGGACTTTTT
*
1199 TTTAAA TTTGAAA -TTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAGA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
1246 -TT-AA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1279 ATAAATTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
4 1 0.02
5 16 0.25
6 43 0.68
7 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:1231 original size:17 final size:17
Alignment explanation
Indices: 1199--1285 Score: 122
Period size: 17 Copynumber: 5.1 Consensus size: 17
1189 TGGACTTTTT
1199 TTTAAATTTGAAATTAAA
1 TTTAAATTT-AAATTAAA
1217 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
*
1234 TTTAAATTTAGATT-AA
1 TTTAAATTTAAATTAAA
*
1250 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
* *
1267 TCTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
1284 TT
1 TT
1286 AAAAAGGGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.22
17 40 0.63
18 9 0.14
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:1232 original size:11 final size:11
Alignment explanation
Indices: 1200--1285 Score: 79
Period size: 11 Copynumber: 7.6 Consensus size: 11
1190 GGACTTTTTT
1200 TTAAATTTGAAA
1 TTAAATTT-AAA
1212 TTAAATTTAAA
1 TTAAATTTAAA
1223 TTTAAA-TTAAA
1 -TTAAATTTAAA
*
1234 TTTAAATTTAGA
1 -TTAAATTTAAA
1246 TT-AATTTAAA
1 TTAAATTTAAA
*
1256 TTTAAA-ATAAA
1 -TTAAATTTAAA
1267 TCTAAATTTAAA
1 T-TAAATTTAAA
*
1279 ATAAATT
1 TTAAATT
1286 AAAAAGGGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
10 8 0.13
11 32 0.51
12 23 0.37
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:2042 original size:205 final size:205
Alignment explanation
Indices: 1796--2265 Score: 760
Period size: 205 Copynumber: 2.3 Consensus size: 205
1786 CGCTTGCTTT
* *
1796 GAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCTCTTGTTT
1 GAGCATGGGTTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
* * * *
1861 CAATCCGTTTCTTTATATCTCACCAGGAGAACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
66 CAATCCGCTTCTCTATATCTCACCAAGAGAACGAATTTGGTTCACTTCTCAATATCTCATCAGGA
* *
1926 AACTAACCGTTTATTGCTTCGACCTGCTTCTCAATGTCTCACCAAGAAGCTGGGATTCGAAACTT
131 AACTAACCATTTATTGCTTCGACCTACTTCTCAATGTCTCACCAAGAAGCTGGGATTCGAAACTT
1991 TGCTCATACC
196 TGCTCATACC
* * *
2001 GAGCGTGGGTTTGACTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCGTCGCTTGTTT
1 GAGCATGGGTTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
* * *
2066 CAATCTGCTTCTCTGTATCTCATCAAGAGAACGAATTTGGTTCACTTCTCAATATCTCATCAGGA
66 CAATCCGCTTCTCTATATCTCACCAAGAGAACGAATTTGGTTCACTTCTCAATATCTCATCAGGA
* ** *
2131 AGCTAACCATTTATTGCTTCGACCTACTTCTCGGTGTCTCACCAAGAAGCTGGGATTCGAAGCTT
131 AACTAACCATTTATTGCTTCGACCTACTTCTCAATGTCTCACCAAGAAGCTGGGATTCGAAACTT
*
2196 TGCTCATATC
196 TGCTCATACC
*
2206 GAGCATGGGTTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGCT
1 GAGCATGGGTTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCT
2266 ATTTGTGGAT
Statistics
Matches: 244, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 244 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (205 bp):
GAGCATGGGTTTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
CAATCCGCTTCTCTATATCTCACCAAGAGAACGAATTTGGTTCACTTCTCAATATCTCATCAGGA
AACTAACCATTTATTGCTTCGACCTACTTCTCAATGTCTCACCAAGAAGCTGGGATTCGAAACTT
TGCTCATACC
Found at i:2776 original size:23 final size:23
Alignment explanation
Indices: 2746--2791 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2736 AATTCTATTA
*
2746 AAAAGA-GGATCAAAGGAAACAAT
1 AAAAGAGGGAT-AAAGAAAACAAT
2769 AAAAGAGGGATAAAGAAAACAAT
1 AAAAGAGGGATAAAGAAAACAAT
2792 CACTAGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.09
Consensus pattern (23 bp):
AAAAGAGGGATAAAGAAAACAAT
Done.