Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013204.1 Kokia drynarioides strain JFW-HI SEQ_128223, 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: 2419
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Found at i:1001 original size:29 final size:29
Alignment explanation
Indices: 963--1249 Score: 232
Period size: 30 Copynumber: 9.7 Consensus size: 29
953 TTCGGATGCA
* *
963 CGGGGGCAAAATGGTAGTTTTGGAAGGTT
1 CGGGGTCAAAATGGTATTTTTGGAAGGTT
*
992 CGGAGTCAAAAATAGG-ATTTTTGGAA-GTT
1 CGGGGTC-AAAAT-GGTATTTTTGGAAGGTT
* *
1021 CGATGGT-AAAATGGTAATTTTTGAAAGGTT
1 CG-GGGTCAAAATGGT-ATTTTTGGAAGGTT
* *
1051 CAGGGTCAAAAATGGGATTTTTGGAA-GTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGGTT
* *
1080 CGGGGGT-AAAATGGTAATTTTAGAAGGTT
1 C-GGGGTCAAAATGGTATTTTTGGAAGGTT
*
1109 CAAGGGGGTCAAAAATGGGATTTTTGGAA-GTT
1 C---GGGGTC-AAAATGGTATTTTTGGAAGGTT
*
1141 CGAGGGT-AAAATGGTAATTTTTAGAAGGTT
1 CG-GGGTCAAAATGGT-ATTTTTGGAAGGTT
* *
1171 CGAGGTCAAAAATGGGATTTTTGGAA-GTT
1 CGGGGTC-AAAATGGTATTTTTGGAAGGTT
*
1200 CAGGGGT-AAAATGGTAATTTTTAGAAGGTT
1 C-GGGGTCAAAATGGT-ATTTTTGGAAGGTT
*
1230 CGGGGTCAAAAATGGGATTT
1 CGGGGTC-AAAATGGTATTT
1250 GAGAAGTTCG
Statistics
Matches: 208, Mismatches: 26, Indels: 47
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.01
28 34 0.16
29 61 0.29
30 63 0.30
31 29 0.14
32 4 0.02
33 15 0.07
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.31
Consensus pattern (29 bp):
CGGGGTCAAAATGGTATTTTTGGAAGGTT
Found at i:1049 original size:59 final size:59
Alignment explanation
Indices: 970--1278 Score: 393
Period size: 59 Copynumber: 5.2 Consensus size: 59
960 GCACGGGGGC
* * * *
970 AAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATAGGATTTTTGGAAGTTCGATGGT
1 AAAATGGTAATTTTTGAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
1028 AAAATGGTAATTTTTGAAAGGTTCAGG-GTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGAAAGGTTC-GGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
1087 AAAATGGTAATTTTAG-AAGGTTCAAGGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGAAAGGTTC---GGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1148 AAAATGGTAATTTTT-AGAAGGTTC-GAGGTCAAAAATGGGATTTTTGGAAGTTC-AGGGGT
1 AAAATGGTAATTTTTGA-AAGGTTCGGA-GTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* *
1207 AAAATGGTAATTTTT-AGAAGGTTCGGGGTCAAAAATGGGA--TTTGAGAAGTTCGAGCGT
1 AAAATGGTAATTTTTGA-AAGGTTCGGAGTCAAAAATGGGATTTTTG-GAAGTTCGAGGGT
1265 AAAATGGTAATTTT
1 AAAATGGTAATTTT
1279 CAAAAAGTTT
Statistics
Matches: 227, Mismatches: 12, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
57 4 0.02
58 41 0.18
59 125 0.55
60 5 0.02
61 45 0.20
62 7 0.03
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:1149 original size:120 final size:117
Alignment explanation
Indices: 963--1278 Score: 469
Period size: 120 Copynumber: 2.7 Consensus size: 117
953 TTCGGATGCA
* * * * * *
963 CGGGGGCAAAATGGTAGTTTTGGAAGGTTCGGAGTCAAAAATAGGATTTTTGGAAGTTCGATGGT
1 CGGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1028 AAAATGGTAATTTTT-GAAAGGTTC-AGGGTCAAAAATGGGATTTTTGGAAGTT
66 AAAATGGTAATTTTTAG-AAGGTTCGA-GGTCAAAAATGGGATTTTTGGAAGTT
1080 CGGGGGTAAAATGGTAATTTTAGAAGGTTCAAGGGGGTCAAAAATGGGATTTTTGGAAGTTCGAG
1 CGGGGGTAAAATGGTAATTTTAGAAGGTTC---GGGGTCAAAAATGGGATTTTTGGAAGTTCGAG
1145 GGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
63 GGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* *
1200 CAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGA--TTTGAGAAGTTCGAGC
1 CGGGGGTAAAATGGTAA-TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTG-GAAGTTCGAGG
1263 GTAAAATGGTAATTTT
64 GTAAAATGGTAATTTT
1279 CAAAAAGTTT
Statistics
Matches: 184, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
116 4 0.02
117 53 0.29
118 16 0.09
120 96 0.52
121 15 0.08
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.31
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
AAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:2114 original size:22 final size:22
Alignment explanation
Indices: 2089--2132 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2079 TTTAAAAAAA
*
2089 CAGATCTAGGTCTAGAT-CAAAC
1 CAGATCTA-GCCTAGATCCAAAC
2111 CAGATCTAGCCTAGATCCAAAC
1 CAGATCTAGCCTAGATCCAAAC
2133 GATTTTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (22 bp):
CAGATCTAGCCTAGATCCAAAC
Found at i:2338 original size:3 final size:3
Alignment explanation
Indices: 2330--2363 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2320 ACCTTTCGTT
*
2330 TTA TTA TTA TTA TTA TTA TTCA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
2364 ACATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2396 original size:16 final size:16
Alignment explanation
Indices: 2340--2396 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
2330 TTATTATTAT
* *
2340 TATTATTATTCATTAA
1 TATTATTATTAATAAA
2356 TATTATTAACATTAA-AAA
1 TATTATT---ATTAATAAA
2374 TATTTATTATTAATAAA
1 TA-TTATTATTAATAAA
2391 TATTAT
1 TATTAT
2397 GAAAACCGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 16 0.47
17 5 0.15
18 4 0.12
19 9 0.26
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTATTATTAATAAA
Done.