Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003804.1 Kokia drynarioides strain JFW-HI SEQ_116796, 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: 18090
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1261 original size:29 final size:29
Alignment explanation
Indices: 1192--1253 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1182 TTGTAGGTTT
1192 AGTCCATATTGTCCAATTGGATCATTCTA
1 AGTCCATATTGTCCAATTGGATCATTCTA
1221 AGTCCATATTGTCCAATTGGATCATTCTA
1 AGTCCATATTGTCCAATTGGATCATTCTA
1250 AGTC
1 AGTC
1254 ACTTTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (29 bp):
AGTCCATATTGTCCAATTGGATCATTCTA
Found at i:3142 original size:5 final size:5
Alignment explanation
Indices: 3132--3165 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
3122 AGCTTTCACG
3132 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTC
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTC
3166 TCTGCTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
CTTCC
Found at i:7435 original size:22 final size:22
Alignment explanation
Indices: 7410--7470 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
7400 CGTTTACTAA
7410 TCAGCACTGTGTGTGCTTCTGT
1 TCAGCACTGTGTGTGCTTCTGT
*
7432 TCAGCACTATGTGTGCTTCTGT
1 TCAGCACTGTGTGTGCTTCTGT
*
7454 TTAGCACTGTGTGTGCT
1 TCAGCACTGTGTGTGCT
7471 CTCTATTTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.11, C:0.21, G:0.26, T:0.41
Consensus pattern (22 bp):
TCAGCACTGTGTGTGCTTCTGT
Found at i:7492 original size:23 final size:22
Alignment explanation
Indices: 7412--7483 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
7402 TTTACTAATC
* *
7412 AGCACTGTGTGTGCTTCTGTTC
1 AGCACTGTGTGTGCTTCTATTT
* *
7434 AGCACTATGTGTGCTTCTGTTT
1 AGCACTGTGTGTGCTTCTATTT
7456 AGCACTGTGTGTGCTCTCTATTT
1 AGCACTGTGTGTGCT-TCTATTT
7479 AGCAC
1 AGCAC
7484 GTTTCGTGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 34 0.76
23 11 0.24
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (22 bp):
AGCACTGTGTGTGCTTCTATTT
Found at i:7521 original size:23 final size:24
Alignment explanation
Indices: 7489--7545 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
7479 AGCACGTTTC
* *
7489 GTGCCATCTG-ATCAACACTTTGT
1 GTGCCCTCTGTATCAACACTTCGT
* *
7512 GTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTG-TATCAACACTTCGT
7537 GTGCCCTCT
1 GTGCCCTCT
7546 ATTACCCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 9 0.32
25 19 0.68
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (24 bp):
GTGCCCTCTGTATCAACACTTCGT
Found at i:11601 original size:21 final size:22
Alignment explanation
Indices: 11508--11651 Score: 107
Period size: 23 Copynumber: 6.4 Consensus size: 22
11498 CTAGCACGCG
*
11508 CTCTGTTTAGCACGTT-TCGTGCC
1 CTCTGTTTAGCAC-TTAT-GTGCT
* *
11531 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGTTTAGCAC-TTATGTGCT
* *
11554 CTCTGTTTAGCAGTTAGTGTACT
1 CTCTGTTTAGCACTTA-TGTGCT
11577 CTCTGTTTAGCAC-TATGTGCT
1 CTCTGTTTAGCACTTATGTGCT
* *
11598 CTCTATTGCCCAGCACTTATGTGCT
1 CTCTGTT---TAGCACTTATGTGCT
* *
11623 CTCTG-TTAGTACTT-TGGTACT
1 CTCTGTTTAGCACTTAT-GTGCT
11644 CTCTGTTT
1 CTCTGTTT
11652 GTTTCGTATA
Statistics
Matches: 98, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
20 1 0.01
21 26 0.27
22 6 0.06
23 46 0.47
24 7 0.07
25 12 0.12
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (22 bp):
CTCTGTTTAGCACTTATGTGCT
Found at i:11915 original size:5 final size:5
Alignment explanation
Indices: 11905--11935 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
11895 AGAGACCTCT
11905 CATCA CATCA CATCA CATCA CATCA CATCA C
1 CATCA CATCA CATCA CATCA CATCA CATCA C
11936 TATTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CATCA
Found at i:14409 original size:35 final size:35
Alignment explanation
Indices: 14370--14458 Score: 92
Period size: 37 Copynumber: 2.5 Consensus size: 35
14360 TAAAAACTAT
*
14370 TTCAT-TACAAGTTTATATATACTTTTT-AATTTTTA
1 TTCATATA-AAGTTTAAATATA-TTTTTAAATTTTTA
*
14405 TTCATGATAAATTTTAAATATATTTTTCAAATTTTTA
1 TTCAT-ATAAAGTTTAAATATATTTTT-AAATTTTTA
*
14442 TTCATAATAAATTTTAA
1 TTCAT-ATAAAGTTTAA
14459 GGATAAAGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
35 10 0.21
36 11 0.23
37 26 0.55
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (35 bp):
TTCATATAAAGTTTAAATATATTTTTAAATTTTTA
Found at i:14443 original size:37 final size:36
Alignment explanation
Indices: 14381--14458 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
14371 TCATTACAAG
* *
14381 TTTATATATACTTTTTAATTTTTATTCATGATAAAT
1 TTTAAATATACTTTTTAATTTTTATTCATAATAAAT
14417 TTTAAATATA-TTTTTCAAATTTTTATTCATAATAAAT
1 TTTAAATATACTTTTT--AATTTTTATTCATAATAAAT
14454 TTTAA
1 TTTAA
14459 GGATAAAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 5 0.13
36 9 0.24
37 24 0.63
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (36 bp):
TTTAAATATACTTTTTAATTTTTATTCATAATAAAT
Found at i:17832 original size:16 final size:15
Alignment explanation
Indices: 17781--17834 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
17771 TTTGGTTCGT
17781 TGTAATGGAATAGAAC
1 TGTAATGGAATAG-AC
* *
17797 TATAATGGAATAGAGT
1 TGTAATGGAATAGA-C
17813 TGTAATGGAATATGAC
1 TGTAATGGAATA-GAC
17829 TGTAAT
1 TGTAAT
17835 AAGTAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.91
17 2 0.06
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (15 bp):
TGTAATGGAATAGAC
Found at i:17869 original size:47 final size:44
Alignment explanation
Indices: 17816--17909 Score: 120
Period size: 47 Copynumber: 2.1 Consensus size: 44
17806 ATAGAGTTGT
17816 AATGGAATATGA-CTGTAATAAGTAATTCAGT-TGTTTGGTTTGAATGG
1 AATGGAATA-GAGCTGTAAT-AGT-ATT-AGTGTGTTTGG-TTGAATGG
*
17863 AATGGAATAGAGCTGTAATAGTATTATTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAGTATTAGTGTGTTTGGTTGAATGG
17907 AAT
1 AAT
17910 AGTGCTGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 13 0.30
45 10 0.23
46 5 0.11
47 16 0.36
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAGTATTAGTGTGTTTGGTTGAATGG
Done.