Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011316.1 Kokia drynarioides strain JFW-HI SEQ_126296, 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: 41383
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Warning! 193 characters in sequence are not A, C, G, or T
Found at i:1718 original size:30 final size:30
Alignment explanation
Indices: 1677--1743 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1667 CACGACGGTC
* *
1677 GATATTTGGGTGGTGGTGG-AACAGACGACG
1 GATAATTGGGTGGTGG-GGAAACAGAAGACG
*
1707 GATAATTGGGTGGTGGGGAAATAGAAGACG
1 GATAATTGGGTGGTGGGGAAACAGAAGACG
1737 GATAATT
1 GATAATT
1744 TTGAACTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.30, C:0.06, G:0.40, T:0.24
Consensus pattern (30 bp):
GATAATTGGGTGGTGGGGAAACAGAAGACG
Found at i:1873 original size:107 final size:107
Alignment explanation
Indices: 1707--1927 Score: 300
Period size: 107 Copynumber: 2.1 Consensus size: 107
1697 ACAGACGACG
* ** * *
1707 GATAATTGGGTGGTGGGGAAATAGAAGACGGATAATTTTGAACTCCATAACCAGGTGCATAAGAC
1 GATAA-TGGGTGGTGGGGAAACAGAAGACGGATAACCTTGAACTACATAACCAGATGCATAAGAC
*
1772 TGTTGGTACTGTGGTGGATATCCATCCATAGGATGATTTTGAT
65 TGTTGGTACTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
* * * * **
1815 GATAATGGAGTGGTGGGG-AACAGACGGCGGATAACCTTGAGCTACATAACTAGATGCATAAGGT
1 GATAATGG-GTGGTGGGGAAACAGAAGACGGATAACCTTGAACTACATAACCAGATGCATAAGAC
*
1879 TGTTGGTATTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
65 TGTTGGTACTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
1922 GATAAT
1 GATAAT
1928 TGGTCCGCAA
Statistics
Matches: 99, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 85 0.86
108 14 0.14
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (107 bp):
GATAATGGGTGGTGGGGAAACAGAAGACGGATAACCTTGAACTACATAACCAGATGCATAAGACT
GTTGGTACTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
Found at i:2521 original size:31 final size:32
Alignment explanation
Indices: 2486--2563 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
2476 CCTCTTAAAA
* * *
2486 TTTTTAAAAATTCTCATTCAGCCCCTCAATTT
1 TTTTTAAAAATTCTAATTAAGCCCCACAATTT
* * *
2518 TTTTCAGAAATTTTAATTAAGCCCCACAATTT
1 TTTTTAAAAATTCTAATTAAGCCCCACAATTT
*
2550 TTTTTGAAAATTCT
1 TTTTTAAAAATTCT
2564 TACTAATCCC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (32 bp):
TTTTTAAAAATTCTAATTAAGCCCCACAATTT
Found at i:3741 original size:29 final size:29
Alignment explanation
Indices: 3682--3741 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3672 TATTATAAAG
* *
3682 AATGGATCAAATTAGTCCCTCTATTACTA
1 AATGGATCAAATTAGTCCCTATACTACTA
* *
3711 AATGGATCAATTTAGTCCCTATACTATTA
1 AATGGATCAAATTAGTCCCTATACTACTA
3740 AA
1 AA
3742 AAGAATCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (29 bp):
AATGGATCAAATTAGTCCCTATACTACTA
Found at i:6151 original size:22 final size:21
Alignment explanation
Indices: 6118--6159 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
6108 TTTATTAATT
6118 TAAATTTGTTATGATGTAAAAA
1 TAAATTTGTTAT-ATGTAAAAA
*
6140 TAAATATT-TTATATTTAAAA
1 TAAAT-TTGTTATATGTAAAA
6160 CAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAATTTGTTATATGTAAAAA
Found at i:11843 original size:10 final size:10
Alignment explanation
Indices: 11828--11856 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
11818 CCCAAAGAAT
11828 CAATAAATTC
1 CAATAAATTC
11838 CAATAAATTC
1 CAATAAATTC
11848 CAATAAATT
1 CAATAAATT
11857 ATAAAGGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (10 bp):
CAATAAATTC
Found at i:21273 original size:23 final size:21
Alignment explanation
Indices: 21247--21308 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
21237 GCTCAATAAT
21247 TAAAAT-ATTACAACACGATAACA
1 TAAAATAATTA-AA-AC-ATAACA
21270 T-AAATAATTAAAACATAACA
1 TAAAATAATTAAAACATAACA
*
21290 T-AAATAATTAAAATATAAC
1 TAAAATAATTAAAACATAAC
21309 TTTATATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 24 0.65
21 2 0.05
22 6 0.16
23 5 0.14
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAATAATTAAAACATAACA
Found at i:21289 original size:20 final size:20
Alignment explanation
Indices: 21264--21308 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
21254 TTACAACACG
21264 ATAACATAAATAATTAAAAC
1 ATAACATAAATAATTAAAAC
*
21284 ATAACATAAATAATTAAAAT
1 ATAACATAAATAATTAAAAC
21304 ATAAC
1 ATAAC
21309 TTTATATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (20 bp):
ATAACATAAATAATTAAAAC
Found at i:26092 original size:24 final size:26
Alignment explanation
Indices: 26061--26113 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
26051 AGCAATGTCC
* *
26061 AATTACAAA-G-CCCAATTGAGCCCA
1 AATTACAAATGACCCAAGTCAGCCCA
26085 AATTACAAATGACCCAAGTCAGCCCA
1 AATTACAAATGACCCAAGTCAGCCCA
26111 AAT
1 AAT
26114 ACTATAAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 15 0.60
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (26 bp):
AATTACAAATGACCCAAGTCAGCCCA
Found at i:27180 original size:21 final size:21
Alignment explanation
Indices: 27154--27194 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27144 TAGCCGACCG
27154 AGAGGGGTGAGAGGTTTTTTA
1 AGAGGGGTGAGAGGTTTTTTA
* **
27175 AGAGGGTTTTGAGGTTTTTT
1 AGAGGGGTGAGAGGTTTTTT
27195 TTTAAAGCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (21 bp):
AGAGGGGTGAGAGGTTTTTTA
Found at i:39909 original size:204 final size:204
Alignment explanation
Indices: 39556--40160 Score: 933
Period size: 204 Copynumber: 2.9 Consensus size: 204
39546 CGACGCAGTC
* * * * * *
39556 ATCTTCCTGATGAAATACTGAGAAGAAGACCAAATCAAATTCACGCTTAAAGCGAGCAAAATCTT
1 ATCTTCCTGATGAGACACTGAGAAGAAGACC---T-AAA-TAAGGCTCAAAACGAGCAAAATCTT
* *
39621 CGAACCCCAGCTTCCTGATGAGACACTGAGACGCAGGTCGAAGCAATAAAAGGTTAGCTTCCAT-
61 CGAACCCCAGCTTCCTGATGAAACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCC-TG
* *
39685 ATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAAAA
125 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACA
*
39750 AACAGCGATATGATC
190 AACAGCGATATGATA
* *
39765 ATCTTCTTGATGAGACACTGAGAAGAAGACCTAAATAAGGCTCGAAACGAGCAAAATCTTCGAAC
1 ATCTTCCTGATGAGACACTGAGAAGAAGACCTAAATAAGGCTCAAAACGAGCAAAATCTTCGAAC
* *
39830 CTCAGCTTCCTAATGAAACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGA
66 CCCAGCTTCCTGATGAAACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGA
*
39895 TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAGAGCGAATTGAAACAAACAGC
131 TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGC
*
39960 GATGTGATA
196 GATATGATA
* *
39969 ATCTTCCTGATGAGACACTGAGAAGAAGACCTAAATGAGGCTCAAAACGAGCAAAATCTTCAAAC
1 ATCTTCCTGATGAGACACTGAGAAGAAGACCTAAATAAGGCTCAAAACGAGCAAAATCTTCGAAC
*
40034 CCCAGCTTCCTGATGAAACATTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGA
66 CCCAGCTTCCTGATGAAACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGA
* * * *
40099 TATTGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATGCAGAGAAGCGAATTGAAACAAAC
131 TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAAC
40161 GATGCAGTCA
Statistics
Matches: 366, Mismatches: 29, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
203 1 0.00
204 333 0.91
205 3 0.01
206 1 0.00
209 28 0.08
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (204 bp):
ATCTTCCTGATGAGACACTGAGAAGAAGACCTAAATAAGGCTCAAAACGAGCAAAATCTTCGAAC
CCCAGCTTCCTGATGAAACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGA
TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGC
GATATGATA
Done.