Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010528.1 Kokia drynarioides strain JFW-HI SEQ_125444, 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: 65404
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:625 original size:22 final size:21
Alignment explanation
Indices: 596--637 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
586 CCTCTCCCCT
*
596 CACGCCGGCCAAGCTTCGACC
1 CACGCCGGCCAAGCTCCGACC
*
617 CACGTCCGGCCGAGCTCCGAC
1 CACG-CCGGCCAAGCTCCGAC
638 AGTGAGCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.48, G:0.26, T:0.10
Consensus pattern (21 bp):
CACGCCGGCCAAGCTCCGACC
Found at i:1920 original size:37 final size:34
Alignment explanation
Indices: 1861--1938 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 34
1851 TCTTAAATTC
1861 ATTTAAATTTGATTAAATTTAAATTTAAAAAGATAA
1 ATTTAAATTTGATTAAATTTAAA-TTAAAAA-ATAA
1897 ATTTAAATTTAAGA-TAAATTTAAATTAAAAAATAA
1 ATTTAAATTT--GATTAAATTTAAATTAAAAAATAA
1932 ATTTAAA
1 ATTTAAA
1939 CCTAATTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
35 11 0.28
36 17 0.43
37 10 0.25
38 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (34 bp):
ATTTAAATTTGATTAAATTTAAATTAAAAAATAA
Found at i:4472 original size:23 final size:22
Alignment explanation
Indices: 4442--4501 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
4432 AACAAAAATA
4442 TTAAAATATATATAGAAA-ATTAT
1 TTAAAATATATA-A-AAATATTAT
*
4465 TTAAAATATATAAAAATTTTAT
1 TTAAAATATATAAAAATATTAT
4487 TATAAAATATA-AAAA
1 T-TAAAATATATAAAA
4502 TACAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 3 0.09
22 10 0.29
23 21 0.62
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAATATATAAAAATATTAT
Found at i:4473 original size:21 final size:20
Alignment explanation
Indices: 4435--4502 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
4425 TAAAATCAAC
*
4435 AAAAA-TATTAAAATATATAT
1 AAAAATTATTTAAA-ATATAT
4455 AGAAAATTATTTAAAATATAT
1 A-AAAATTATTTAAAATATAT
*
4476 AAAAATTTTATTATAAA-ATAT
1 AAAAATTAT-TTA-AAATATAT
4497 AAAAAT
1 AAAAAT
4503 ACAAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.19
21 24 0.57
22 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAATTATTTAAAATATAT
Found at i:4803 original size:20 final size:21
Alignment explanation
Indices: 4774--4812 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4764 ATTTAAATTT
4774 TATAAATTTTTA-TATTTTTC
1 TATAAATTTTTATTATTTTTC
*
4794 TATAATTTTTTATTATTTT
1 TATAAATTTTTATTATTTT
4813 CCACCACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TATAAATTTTTATTATTTTTC
Found at i:4998 original size:18 final size:18
Alignment explanation
Indices: 4974--5031 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
4964 TTTTATAAAA
4974 TTTAATAATTTTTAT-AT
1 TTTAATAATTTTTATCAT
*
4991 TTTAAATAATTTTTATTGAT
1 TTT-AATAATTTTTA-TCAT
*
5011 TTTAATAAATTTTATCAT
1 TTTAATAATTTTTATCAT
5029 TTT
1 TTT
5032 TTGTCACATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 3 0.08
18 17 0.47
19 11 0.31
20 5 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATAATTTTTATCAT
Found at i:14218 original size:23 final size:23
Alignment explanation
Indices: 14173--14224 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
14163 AGTTTATGAA
14173 TCAATTAATAGTTCATATCATTT
1 TCAATTAATAGTTCATATCATTT
*
14196 TGAATTAAT-GTATCA-ATCGATTT
1 TCAATTAATAGT-TCATATC-ATTT
14219 TCAATT
1 TCAATT
14225 CAACCGGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (23 bp):
TCAATTAATAGTTCATATCATTT
Found at i:17031 original size:58 final size:59
Alignment explanation
Indices: 16933--17048 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 59
16923 ATATTAGTAA
* *
16933 TCACCCAACTATGAAAACTTATAAAATGGTCACCCGACTATTAGCTTTTTTT-TTTTTG
1 TCACCCAACTATGAAAACTTATAAAATGGTCACCCAACTATTAGATTTTTTTCTTTTTG
* * * * *
16991 TCACCTAACTATGAAAAGTTATAAAATGTTCACTCAACTATTCGATTTTTTTCTTTTT
1 TCACCCAACTATGAAAACTTATAAAATGGTCACCCAACTATTAGATTTTTTTCTTTTT
17049 TTGGTCATCC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 45 0.90
59 5 0.10
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (59 bp):
TCACCCAACTATGAAAACTTATAAAATGGTCACCCAACTATTAGATTTTTTTCTTTTTG
Found at i:22281 original size:15 final size:15
Alignment explanation
Indices: 22261--22307 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
22251 ATTAAAATGC
22261 ATTTTAATAATTTAT
1 ATTTTAATAATTTAT
22276 ATTTT-A-AATATTAT
1 ATTTTAATAAT-TTAT
* *
22290 AATTTAATCATTTAT
1 ATTTTAATAATTTAT
22305 ATT
1 ATT
22308 ATCGTGTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.12
14 9 0.35
15 12 0.46
16 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTAATAATTTAT
Found at i:24906 original size:24 final size:23
Alignment explanation
Indices: 24879--24926 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
24869 TTAAAAATTA
*
24879 AAAAAATATATTTTTATATTTTTT
1 AAAAAACATATTTTTAT-TTTTTT
*
24903 AAAAAACATTTTTTTATTTTTTT
1 AAAAAACATATTTTTATTTTTTT
24926 A
1 A
24927 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
AAAAAACATATTTTTATTTTTTT
Found at i:25117 original size:17 final size:18
Alignment explanation
Indices: 25075--25117 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
25065 AAAAGATCAA
*
25075 AAAATTAAATTTATTTCC
1 AAAATTAAATTTATTTAC
*
25093 AAAA-TAAATTT-TTTAT
1 AAAATTAAATTTATTTAC
25109 AAAATTAAA
1 AAAATTAAA
25118 AGATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTAAATTTATTTAC
Found at i:27454 original size:29 final size:30
Alignment explanation
Indices: 27397--27486 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
27387 GTAATGGTAC
* * * *
27397 AAAAATTGAGTGACCAGCTTATAAATTTAT
1 AAAAATTAAGTGATCAGATTGTAAATTTAT
* *
27427 -GAAATTAAGTGATCAGATTGTAAGTTTAT
1 AAAAATTAAGTGATCAGATTGTAAATTTAT
*
27456 AAATAATTAAGCGATCA-ATTTGTAAATTTAT
1 AAA-AATTAAGTGATCAGA-TTGTAAATTTAT
27487 TTTCCCATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 23 0.48
30 2 0.04
31 23 0.48
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (30 bp):
AAAAATTAAGTGATCAGATTGTAAATTTAT
Found at i:30240 original size:2 final size:2
Alignment explanation
Indices: 30233--30258 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30223 AGTTTTTAGA
30233 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30259 GTTCGTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44335 original size:30 final size:30
Alignment explanation
Indices: 44299--44386 Score: 158
Period size: 30 Copynumber: 2.9 Consensus size: 30
44289 CAATGCAGTC
44299 CCTCCACCACCTCCTCCAAAAGCTGGTGCT
1 CCTCCACCACCTCCTCCAAAAGCTGGTGCT
* *
44329 CCTCCACCACCTCCTTCAAAAGCTGGCGCT
1 CCTCCACCACCTCCTCCAAAAGCTGGTGCT
44359 CCTCCACCACCTCCTCCAAAAGCTGGTG
1 CCTCCACCACCTCCTCCAAAAGCTGGTG
44387 GTGGTCCTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.20, C:0.47, G:0.14, T:0.19
Consensus pattern (30 bp):
CCTCCACCACCTCCTCCAAAAGCTGGTGCT
Found at i:47871 original size:18 final size:19
Alignment explanation
Indices: 47848--47883 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
47838 AGGTGTAATG
*
47848 TTTTCTTTTTG-TTGACTT
1 TTTTCTTTCTGTTTGACTT
47866 TTTTCTTTCTGTTTGACT
1 TTTTCTTTCTGTTTGACT
47884 CAGTTCTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.06, C:0.14, G:0.11, T:0.69
Consensus pattern (19 bp):
TTTTCTTTCTGTTTGACTT
Found at i:59056 original size:38 final size:38
Alignment explanation
Indices: 59013--59094 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
59003 ATCGAACTTT
* * *
59013 TTAAAAATATATATATAT-AATAGTCCAATGACTTTAAA
1 TTAAAAAAATAAATATATGAATAGTCAAATGA-TTTAAA
* *
59051 TTAAAAAAATAAATATTTGAATAGTTAAATGATTTAAA
1 TTAAAAAAATAAATATATGAATAGTCAAATGATTTAAA
*
59089 TGAAAA
1 TTAAAA
59095 CTTTCAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (38 bp):
TTAAAAAAATAAATATATGAATAGTCAAATGATTTAAA
Found at i:60656 original size:23 final size:22
Alignment explanation
Indices: 60616--60660 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
60606 TTTTGAGCAA
60616 TTTAATTTTTTCCCTTATGTTTT
1 TTTAATTTTTTCCCTTAT-TTTT
* * *
60639 TTTATTTTTTTTCTTTATTTTT
1 TTTAATTTTTTCCCTTATTTTT
60661 CATTCTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTAATTTTTTCCCTTATTTTT
Found at i:61849 original size:18 final size:19
Alignment explanation
Indices: 61826--61863 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
61816 TAGTGATAAT
*
61826 AATTAAACAAAA-AATTTA
1 AATTAAAAAAAATAATTTA
61844 AATTAAAAAAAATAATTTA
1 AATTAAAAAAAATAATTTA
61863 A
1 A
61864 CTCTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAAAAAAATAATTTA
Done.