Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007683.1 Kokia drynarioides strain JFW-HI SEQ_122314, 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: 3773
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.31
Warning! 163 characters in sequence are not A, C, G, or T
Found at i:2079 original size:30 final size:29
Alignment explanation
Indices: 2012--2079 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
2002 TGAATGCTAG
* *
2012 AGGGT-AAAATGGTAATTTTGGACACTTC
1 AGGGTCAAAACGGTAATTTTGGAAACTTC
* * *
2040 AGGGGCAAAACGGTAAATTTTGGAAAGTTT
1 AGGGTCAAAACGGT-AATTTTGGAAACTTC
2070 AGGGTCAAAA
1 AGGGTCAAAA
2080 ATGCAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 4 0.12
29 7 0.22
30 21 0.66
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (29 bp):
AGGGTCAAAACGGTAATTTTGGAAACTTC
Found at i:2104 original size:30 final size:29
Alignment explanation
Indices: 2070--2167 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 29
2060 TGGAAAGTTT
2070 AGGGTCAAAAATGCAATTTTAGGAAATTCG
1 AGGGT-AAAAATGCAATTTTAGGAAATTCG
* * * *
2100 AGGGTAACATTGTAATTTTTGGAAAATTCG
1 AGGGTAAAAATGCAATTTTAGG-AAATTCG
* * * * *
2130 -GGATAAAAAATGGAATTTTCGGACATCCG
1 AGGGT-AAAAATGCAATTTTAGGAAATTCG
2159 AGGGTAAAA
1 AGGGTAAAA
2168 TGGTAATTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
29 25 0.47
30 28 0.53
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (29 bp):
AGGGTAAAAATGCAATTTTAGGAAATTCG
Found at i:2120 original size:59 final size:59
Alignment explanation
Indices: 2046--2471 Score: 279
Period size: 59 Copynumber: 7.3 Consensus size: 59
2036 CTTCAGGGGC
* *
2046 AAAACGGTAAATTTTGGAAAGTTTAGGGTCAAAAATGCAATTTTAGGAAATTCGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGCAATTTTAGGAAATTCGAGGGT
* * * * * * * * *
2105 AACATTGTAATTTTTGGAAA-ATTCGGGATAAAAAATGGAATTTTCGGACATCCGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGG-TCAAAAATGCAATTTTAGGAAATTCGAGGGT
* * **
2164 AAAATGGTAATTATTGG-ATGTTCGGGGGGGT-AAAAA--CATAGTTTT-GGAAAGTTTCG-GGG
1 AAAATGGTAATTTTTGGAAAGTT---TAGGGTCAAAAATGCA-A-TTTTAGGAAA--TTCGAGGG
2223 T
59 T
* * * * *
2224 ATAATGGTAATTTTTGGAAAATTT-GGGATCAAAAATGGAATTTTTA-GACATTTGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGG-TCAAAAATGCAA-TTTTAGGAAATTCGAGGGT
** * * * * **
2283 AAAATGGTAATTTTTCAAAAATTTGGGGT-TAAAATGAAATTTTA-GAAATTTAAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGCAATTTTAGGAAATTCGAGGGT
* * * ** * * * *
2340 AAAATGGTAATTTTTAGAAAGTTCAGGGTCGAAAATGGTATTTTTGGGAGTT-TAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGCAATTTTAGGAAATTCGAGGGT
* * *
2398 AAAATGGTAA-TTTTAGAAAGTTTAGGGTCAAAATTGCAATTTTAGGAAGTTC-AGGGT
1 AAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGCAATTTTAGGAAATTCGAGGGT
*
2455 CAAAAT-GTGATTTTTGG
1 -AAAATGGTAATTTTTGG
2472 TCTGTTCAGG
Statistics
Matches: 287, Mismatches: 58, Indels: 45
0.74 0.15 0.12
Matches are distributed among these distances:
57 85 0.30
58 55 0.19
59 97 0.34
60 39 0.14
61 8 0.03
62 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAGTTTAGGGTCAAAAATGCAATTTTAGGAAATTCGAGGGT
Found at i:2368 original size:86 final size:85
Alignment explanation
Indices: 2220--2469 Score: 217
Period size: 86 Copynumber: 2.9 Consensus size: 85
2210 GAAAGTTTCG
* * * * * * *
2220 GGGTATAATGGTAATTTTTGGAAAATTT-GGGATCAAAAATGGAATTTTTAGACATTTGAGGGT-
1 GGGTAAAATGG-AAATTTTAGAAAGTTTAGGG-TC-AAAATGGAATTTTTAGAAAGTTCAGGGTC
*
2283 AAAATGGTAATTTTTCAAAAATTTG
63 AAAATGGT-ATTTTT-AAAAATTTA
2308 GGGTTAAAAT-GAAATTTTAGAAA-TTTAAGGGT-AAAATGGTAATTTTTAGAAAGTTCAGGGTC
1 GGG-TAAAATGGAAATTTTAGAAAGTTT-AGGGTCAAAATGG-AATTTTTAGAAAGTTCAGGGTC
*** *
2370 GAAAATGGTATTTTTGGGAGTTTA
63 -AAAATGGTATTTTTAAAAATTTA
* * *
2394 GGGTAAAATGGTAATTTTAGAAAGTTTAGGGTCAAAATTGCAA-TTTTAGGAAGTTCAGGGTCAA
1 GGGTAAAATGGAAATTTTAGAAAGTTTAGGGTCAAAA-TGGAATTTTTAGAAAGTTCAGGGTCAA
2458 AAT-GTGATTTTT
65 AATGGT-ATTTTT
2470 GGTCTGTTCA
Statistics
Matches: 137, Mismatches: 14, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
84 2 0.01
85 24 0.18
86 63 0.46
87 26 0.19
88 17 0.12
89 5 0.04
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (85 bp):
GGGTAAAATGGAAATTTTAGAAAGTTTAGGGTCAAAATGGAATTTTTAGAAAGTTCAGGGTCAAA
ATGGTATTTTTAAAAATTTA
Found at i:2441 original size:29 final size:29
Alignment explanation
Indices: 2226--2461 Score: 177
Period size: 29 Copynumber: 8.1 Consensus size: 29
2216 TTCGGGGTAT
* *
2226 AATGGTAATTTTTGGAAAATTT-GGGATCAAA
1 AATGGTAA-TTTTAGAAAGTTTAGGG-TC-AA
*
2257 AATGG-AATTTTTAGACA-TTTGAGGGT-AA
1 AATGGTAA-TTTTAGAAAGTTT-AGGGTCAA
* * *
2285 AATGGTAATTTTTCA-AAAATTTGGGGTTAA
1 AATGGTAA-TTTT-AGAAAGTTTAGGGTCAA
*
2315 AAT-GAAATTTTAGAAA-TTTAAGGGT-AA
1 AATGGTAATTTTAGAAAGTTT-AGGGTCAA
*
2342 AATGGTAATTTTTAGAAAGTTCAGGGTCGAA
1 AATGGTAA-TTTTAGAAAGTTTAGGGTC-AA
* **
2373 AATGGT-ATTTTTGGGAGTTTAGGGT-AA
1 AATGGTAATTTTAGAAAGTTTAGGGTCAA
2400 AATGGTAATTTTAGAAAGTTTAGGGTCAA
1 AATGGTAATTTTAGAAAGTTTAGGGTCAA
* * * *
2429 AATTGCAATTTTAGGAAGTTCAGGGTCAA
1 AATGGTAATTTTAGAAAGTTTAGGGTCAA
2458 AATG
1 AATG
2462 TGATTTTTGG
Statistics
Matches: 170, Mismatches: 20, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
27 17 0.10
28 37 0.22
29 77 0.45
30 23 0.14
31 16 0.09
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
AATGGTAATTTTAGAAAGTTTAGGGTCAA
Found at i:2454 original size:57 final size:57
Alignment explanation
Indices: 2220--2469 Score: 222
Period size: 57 Copynumber: 4.3 Consensus size: 57
2210 GAAAGTTTCG
* * * *
2220 GGGTATAATGGTAATTTTTGGAAAATTT-GGGATCAAAAATGGAATTTTTA-GACATTTGA
1 GGGTAAAATGGTAATTTTTAGAAAATTTAGGG-TC-AAAATGGAA-TTTTAGGA-AGTTAA
* * * * *
2279 GGGTAAAATGGTAATTTTTCA-AAAATTTGGGGTTAAAATGAAATTTTAGAAATTTAA
1 GGGTAAAATGGTAATTTTT-AGAAAATTTAGGGTCAAAATGGAATTTTAGGAAGTTAA
* * * * * *
2336 GGGTAAAATGGTAATTTTTAGAAAGTTCAGGGTCGAAAATGGTATTTTTGGGAGTTTA
1 GGGTAAAATGGTAATTTTTAGAAAATTTAGGGTC-AAAATGGAATTTTAGGAAGTTAA
* * *
2394 GGGTAAAATGGTAA-TTTTAGAAAGTTTAGGGTCAAAATTGCAATTTTAGGAAGTTCA
1 GGGTAAAATGGTAATTTTTAGAAAATTTAGGGTCAAAA-TGGAATTTTAGGAAGTTAA
*
2451 GGGTCAAAAT-GTGATTTTT
1 GGGT-AAAATGGTAATTTTT
2470 GGTCTGTTCA
Statistics
Matches: 159, Mismatches: 24, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
56 5 0.03
57 77 0.48
58 48 0.30
59 26 0.16
60 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTAGAAAATTTAGGGTCAAAATGGAATTTTAGGAAGTTAA
Done.