Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011173.1 Kokia drynarioides strain JFW-HI SEQ_126149, 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: 15271
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1113 original size:27 final size:27
Alignment explanation
Indices: 1030--1124 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 27
1020 TCTGAGTTCA
* * * * *
1030 CCACAAAGACTGTTTATTTAGAATTTA
1 CCACAAAGGCTATTCATTCAGAATTTG
* *
1057 CCATAAAGGCTATTCATTCAGAGA-TCG
1 CCACAAAGGCTATTCATTCAGA-ATTTG
* *
1084 CCACAGAGGTTATTCATTCAGAATTTG
1 CCACAAAGGCTATTCATTCAGAATTTG
1111 CCACAAAGGCTATT
1 CCACAAAGGCTATT
1125 TATTGATGTC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
26 1 0.02
27 51 0.96
28 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (27 bp):
CCACAAAGGCTATTCATTCAGAATTTG
Found at i:3355 original size:58 final size:58
Alignment explanation
Indices: 3258--3540 Score: 189
Period size: 59 Copynumber: 4.8 Consensus size: 58
3248 GGATTCTTGA
* * ** *
3258 GGGTGAAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATGGAATTTTTAAACATTTGG
1 GGGT-AAAGGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAAACATTCGG
* * * **
3317 GGGTAAAAGGGTAA-TTTT-GAGAGTTTCGAGGTTGAAAATGGAGTCTTCGAACATTCGG
1 GGGT-AAAGGGTAATTTTTGGA-AGTTTCGAGGTTAAAAATGGAATTTTTAAACATTCGG
* * * * * *
3375 GGGTAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAA-GTTCGG
1 GGGTAAAGGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTT-AAACATTCGG
* ** * * * * * *
3433 GAGTAAAAATGCAATTTTTGGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAA-GTTCAG
1 GGGT-AAAGGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTT-AAACATTCGG
*** * *
3492 GGGTAAGAACATAATTTTTGGAAGTTTC-AGGGTCAAAAATGGGATTTTT
1 GGGTAA-AGGGTAATTTTTGGAAGTTTCGA-GGTTAAAAATGGAATTTTT
3541 GGAAGTTTTG
Statistics
Matches: 185, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
57 10 0.05
58 71 0.38
59 104 0.56
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGTAAAGGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTAAACATTCGG
Found at i:3423 original size:30 final size:29
Alignment explanation
Indices: 3387--3667 Score: 304
Period size: 30 Copynumber: 9.5 Consensus size: 29
3377 GTAAATGGTA
3387 ATTTTTGGAAGTTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGT-AAAAATGGG
**
3417 ATTTTTGGAAG-TTCGGGAGTAAAAATGCA
1 ATTTTTGGAAGTTTCGGG-GTAAAAATGGG
*
3446 ATTTTTGGAAGTTTCGAGGTAAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGT-AAAAATGGG
*
3476 ATTTTTGGAAG-TTCAGGGGTAAGAACAT--A
1 ATTTTTGGAAGTTTC-GGGGTAA-AA-ATGGG
*
3505 ATTTTTGGAAGTTTCAGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGT-AAAAATGGG
*
3535 ATTTTTGGAAGTTTTGGGGTCAAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGT--AAAAATGGG
* *
3566 ATTTTTAGAAG-TTCGGGGGTAAAAATGGA
1 ATTTTTGGAAGTTTC-GGGGTAAAAATGGG
* * *
3595 ATTTTAGGAAGTTTTGGGGTCAAAAATTGG
1 ATTTTTGGAAGTTTCGGGGT-AAAAATGGG
*
3625 ATTTTTGGAAG-TTCGGGGTAAAAATGGA
1 ATTTTTGGAAGTTTCGGGGTAAAAATGGG
3653 ATTTTTGGACAGTTT
1 ATTTTTGGA-AGTTT
3668 AGGGACCTTC
Statistics
Matches: 211, Mismatches: 24, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
28 18 0.09
29 79 0.37
30 88 0.42
31 26 0.12
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAGTTTCGGGGTAAAAATGGG
Found at i:3667 original size:59 final size:58
Alignment explanation
Indices: 3386--3667 Score: 315
Period size: 59 Copynumber: 4.8 Consensus size: 58
3376 GGTAAATGGT
*
3386 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGAGTAAAAATG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTTGGG-GTAAAAATG
* * **
3444 CAATTTTTGGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCAGGGGTAAGAACAT-
1 -AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGTAA-AA-ATG
*
3504 AATTTTTGGAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGT--AAAAAT-G
* * * *
3565 GATTTTTAGAAG-TTCGGGGGT-AAAAATGGAATTTTAGGAAGTTTTGGGGTCAAAAATTG
1 AATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGT-AAAAA-TG
* *
3624 GATTTTTGGAAG-TTCGGGGT-AAAAATGGAATTTTTGGACAGTTT
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGA-AGTTT
3668 AGGGACCTTC
Statistics
Matches: 196, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
58 22 0.11
59 117 0.60
60 39 0.20
61 18 0.09
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (58 bp):
AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGTAAAAATG
Found at i:5382 original size:18 final size:17
Alignment explanation
Indices: 5323--5380 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 17
5313 AATTAGACAT
5323 TTTAAA-TTTATAATAAA
1 TTTAAATTTTA-AATAAA
5340 TTTAAATTTTAAATAAAA
1 TTTAAATTTTAAAT-AAA
5358 TTTAAATTTTAAATAAA
1 TTTAAATTTTAAATAAA
*
5375 CTTAAA
1 TTTAAA
5381 ATAAATTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
17 17 0.45
18 21 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATTTTAAATAAA
Found at i:9336 original size:12 final size:12
Alignment explanation
Indices: 9319--9360 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
9309 TACGAATAGG
9319 TGGTTGCGAAGA
1 TGGTTGCGAAGA
* * *
9331 TGGTTGTGGAGC
1 TGGTTGCGAAGA
9343 TGGTTGCGAAGA
1 TGGTTGCGAAGA
9355 TGGTTG
1 TGGTTG
9361 TAGAGCTGGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.07, G:0.45, T:0.31
Consensus pattern (12 bp):
TGGTTGCGAAGA
Found at i:9351 original size:24 final size:24
Alignment explanation
Indices: 9319--9382 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
9309 TACGAATAGG
*
9319 TGGTTGCGAAGATGGTTGTGGAGC
1 TGGTTGCGAAGATGGTTGTAGAGC
9343 TGGTTGCGAAGATGGTTGTAGAGC
1 TGGTTGCGAAGATGGTTGTAGAGC
* *
9367 TGGTTACGAATATGGT
1 TGGTTGCGAAGATGGT
9383 CCACCTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.20, C:0.08, G:0.41, T:0.31
Consensus pattern (24 bp):
TGGTTGCGAAGATGGTTGTAGAGC
Found at i:10492 original size:43 final size:42
Alignment explanation
Indices: 10443--10532 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 42
10433 TCAAATAAGC
*
10443 TTATTCAAAGTTGTAATTTTCTTATTTTTATTTTGACTAAAT
1 TTATTCAAAGTTGTAATTTTCTTAATTTTATTTTGACTAAAT
* *
10485 TATATTCAAATTTGTTATTTTCTTAATTTTATTTTGACTAAAT
1 T-TATTCAAAGTTGTAATTTTCTTAATTTTATTTTGACTAAAT
10528 TTATT
1 TTATT
10533 TATTTTAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 5 0.11
43 39 0.89
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (42 bp):
TTATTCAAAGTTGTAATTTTCTTAATTTTATTTTGACTAAAT
Found at i:13539 original size:27 final size:27
Alignment explanation
Indices: 13508--13563 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
13498 ACTATTTATG
*
13508 TAATTTACCGTTATTTATGTAATCTTT
1 TAATTTACCCTTATTTATGTAATCTTT
*
13535 TAATTTACCCTTATTTATGTGATCTTT
1 TAATTTACCCTTATTTATGTAATCTTT
13562 TA
1 TA
13564 TATATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (27 bp):
TAATTTACCCTTATTTATGTAATCTTT
Done.