Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008493.1 Kokia drynarioides strain JFW-HI SEQ_123168, 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: 23875
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:1243 original size:22 final size:22
Alignment explanation
Indices: 1218--1263 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1208 TTTAGTTGAT
1218 ATTTTAATT-TTTTTTAAAAATA
1 ATTTTAATTATTTTTTAAAAA-A
1240 A-TTTAATTATTTTTTAAAAAA
1 ATTTTAATTATTTTTTAAAAAA
1261 ATT
1 ATT
1264 AATAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTAATTATTTTTTAAAAAA
Found at i:1260 original size:24 final size:21
Alignment explanation
Indices: 1220--1263 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1210 TAGTTGATAT
1220 TTTAATTTTTTTTAAAAATAA
1 TTTAATTTTTTTTAAAAATAA
1241 TTTAATTATTTTTTAAAAA-AA
1 TTTAATT-TTTTTTAAAAATAA
1262 TT
1 TT
1264 AATAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATTTTTTTTAAAAATAA
Found at i:9576 original size:22 final size:22
Alignment explanation
Indices: 9537--9578 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9527 AGATGATTAT
*
9537 ATATAAAATTTTAATAAATAAA
1 ATATAAAATATTAATAAATAAA
* *
9559 ATATATAATATTATTAAATA
1 ATATAAAATATTAATAAATA
9579 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAAATATTAATAAATAAA
Found at i:15337 original size:193 final size:193
Alignment explanation
Indices: 15000--15368 Score: 485
Period size: 194 Copynumber: 1.9 Consensus size: 193
14990 GGGAGGACAT
* * * * *
15000 AATTAAATTGTATATTTTACGATTATAAAAATGCAATTTCATCATTTTAATGGTCTATATCTTTA
1 AATTAAATTGTATATTTTACGATTATAAAAATGCAAGTTCACCACTTTAATAGTCTATATATTTA
* * * * *
15065 TAATTTTTAAAGGATAAAACTAATTTTTTATTATTTTGAGGGGGACAGAGTGCAATTTTACCATT
66 TAATTTTTAAAAGATAAAACTAAATTTTTATTATTTTGAGGAGGACAAAGTGCAATCTTACCATT
** *
15130 ACTAATTCAAAATTTTATAAATTATAAAGGGTCTAAATGAAAAAAATTTCATTTTAGGGGCAG
131 ACTAATTCAAAATTTTATAAATTATAAAAAGTCTAAACGAAAAAAATTTCATTTTAGGGGCAG
*
15193 AATTAAATTGTATATTTTTATGA-TAGTAAAAATGCAAGTTCACCACTTTAATAGTCTATATATT
1 AATTAAATTGTATA-TTTTACGATTA-TAAAAATGCAAGTTCACCACTTTAATAGTCTATATATT
* * * * *
15257 TATATTTTTTAAAAGATTAAA-TCAAATTTTTATTATTTTTA-GAGGATTAAAGTGTAA-CTTAC
64 TATAATTTTTAAAAGATAAAACT-AAATTTTTATTATTTTGAGGAGGA-CAAAGTGCAATCTTAC
* *
15319 CATTACTAATTTAAAATTTTATAAATTATAAAAAGTTTAAACGAAAAAAA
127 CATTACTAATTCAAAATTTTATAAATTATAAAAAGTCTAAACGAAAAAAA
15369 AAATCATTTT
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
193 70 0.46
194 81 0.54
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (193 bp):
AATTAAATTGTATATTTTACGATTATAAAAATGCAAGTTCACCACTTTAATAGTCTATATATTTA
TAATTTTTAAAAGATAAAACTAAATTTTTATTATTTTGAGGAGGACAAAGTGCAATCTTACCATT
ACTAATTCAAAATTTTATAAATTATAAAAAGTCTAAACGAAAAAAATTTCATTTTAGGGGCAG
Found at i:16544 original size:32 final size:31
Alignment explanation
Indices: 16508--16577 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
16498 AACTTTTATG
** *
16508 TTTAAAAAATACAATGGACTAAAGTTGATCAA
1 TTTAAAAAATACAA-AAACTAAAATTGATCAA
*
16540 TTTAAAAAATATAAAAACTAAAATTGATCAA
1 TTTAAAAAATACAAAAACTAAAATTGATCAA
*
16571 ATTAAAA
1 TTTAAAA
16578 TATATAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 20 0.61
32 13 0.39
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (31 bp):
TTTAAAAAATACAAAAACTAAAATTGATCAA
Found at i:16560 original size:31 final size:31
Alignment explanation
Indices: 16525--16585 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
16515 AATACAATGG
* *
16525 ACTAAAGTTGATCAATTTAAAAAATATAAAA
1 ACTAAAATTGATCAAATTAAAAAATATAAAA
*
16556 ACTAAAATTGATCAAATTAAAATATATAAA
1 ACTAAAATTGATCAAATTAAAAAATATAAA
16586 CTAAATTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (31 bp):
ACTAAAATTGATCAAATTAAAAAATATAAAA
Found at i:17218 original size:21 final size:21
Alignment explanation
Indices: 17179--17217 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17169 TTTACAGTTG
17179 GATTCAAATTCATTTAAAATC
1 GATTCAAATTCATTTAAAATC
*
17200 GATTTAAATTC-TTTAAAA
1 GATTCAAATTCATTTAAAA
17218 AATGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (21 bp):
GATTCAAATTCATTTAAAATC
Found at i:18807 original size:29 final size:28
Alignment explanation
Indices: 18760--18818 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
18750 TTTTATTTTT
*
18760 TTCAATAGTACAGGAACTAAATTGATTCA
1 TTCAATAGTACAGGAACTAAATCGA-TCA
*
18789 TTCAATAGTTA-AGGGACTAAATCGATCA
1 TTCAATAG-TACAGGAACTAAATCGATCA
18817 TT
1 TT
18819 TCTCTCATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 20 0.74
30 2 0.07
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (28 bp):
TTCAATAGTACAGGAACTAAATCGATCA
Found at i:23219 original size:18 final size:18
Alignment explanation
Indices: 23196--23230 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23186 TCACTCACTT
23196 TCAAACT-AAAACAAACAC
1 TCAAACTCAAAA-AAACAC
23214 TCAAACTCAAAAAAACA
1 TCAAACTCAAAAAAACA
23231 AAATCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.63, C:0.26, G:0.00, T:0.11
Consensus pattern (18 bp):
TCAAACTCAAAAAAACAC
Done.