Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014809.1 Kokia drynarioides strain JFW-HI SEQ_129851, 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: 52753
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:557 original size:51 final size:50
Alignment explanation
Indices: 481--582 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 50
471 ACATATCTTG
481 TCTATATGCTTGCCCTTCAACATCCTATCATAAAAGACCCATTCTCAGCAT
1 TCTATATGCTTGCCCTTCAACATCCTATCAT-AAAGACCCATTCTCAGCAT
* *
532 TCTATATGCTTGCCCTTCAACATCCTATGATAAAGTCCCATTCTCAGCAT
1 TCTATATGCTTGCCCTTCAACATCCTATCATAAAGACCCATTCTCAGCAT
582 T
1 T
583 GCTCGATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 19 0.39
51 30 0.61
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.33
Consensus pattern (50 bp):
TCTATATGCTTGCCCTTCAACATCCTATCATAAAGACCCATTCTCAGCAT
Found at i:6971 original size:13 final size:13
Alignment explanation
Indices: 6953--6978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6943 TAGTGTTTGA
6953 ATCTAAATTTTTT
1 ATCTAAATTTTTT
6966 ATCTAAATTTTTT
1 ATCTAAATTTTTT
6979 CTGTGAGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
ATCTAAATTTTTT
Found at i:20170 original size:53 final size:54
Alignment explanation
Indices: 20064--20171 Score: 121
Period size: 53 Copynumber: 2.0 Consensus size: 54
20054 GTTCTCATTG
* * * *
20064 TTAATATATAAAATATAACTATAACTTCATAAATTTAGAATTATAATTAAATTA
1 TTAATATATAAAATACAACTATAACTTCATAAATATACAATTAAAATTAAATTA
* * **
20118 TTAAT-TATCAAATACAATTATAACTTTGTAAATATACAATTTAAAATT-AATTA
1 TTAATATATAAAATACAACTATAACTTCATAAATATACAA-TTAAAATTAAATTA
20171 T
1 T
20172 GGTAACTAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
53 33 0.73
54 12 0.27
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (54 bp):
TTAATATATAAAATACAACTATAACTTCATAAATATACAATTAAAATTAAATTA
Found at i:20842 original size:23 final size:24
Alignment explanation
Indices: 20794--20843 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
20784 ATGCTATCAT
20794 GGTGAAATGAATGGTAATTTTGGG
1 GGTGAAATGAATGGTAATTTTGGG
*
20818 GGTGAAATGAATGGTAATTTGGGG
1 GGTGAAATGAATGGTAATTTTGGG
20842 GG
1 GG
20844 GTTTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.42, T:0.30
Consensus pattern (24 bp):
GGTGAAATGAATGGTAATTTTGGG
Found at i:22253 original size:248 final size:246
Alignment explanation
Indices: 21817--22313 Score: 859
Period size: 248 Copynumber: 2.0 Consensus size: 246
21807 ACTCAGTTGT
* * * *
21817 TCTTGCTTTTCAGGTCTTAAGTCATTTTGTCTTTCCTATTACCTTAGGATATAGATTATCAGCAC
1 TCTTGCTTTTCAGGTCTTAAGTCATTTTGTCTTCCCTATTACCTTAGAACATAGATTATAAGCAC
* * *
21882 TTATTGATGATTTACTTTGTTTTAATAGCATGTAAAAGAAAAATGGCCCTGGGAATTGTCATTGC
66 TAATTGATGATTTACTTTATTTTAATAGCATGTAAAAGAAAAATGGCCCTGGGAATTGCCATTGC
*
21947 CTCTGCCCTCTAGTGTCAAGACTTTGTCATTAATTCTATGGGACCTATGAAAATGTTAACACACA
131 CTCTGCCCTCTAGTATCAAGACTTTGTCATTAATTCTATGGGACCTATGAAAATGTTAACACACA
22012 ATTATAGTTATGTTTCTGTTATAGATATATCAAGGTTTTGCTGACCCATCC
196 ATTATAGTTATGTTTCTGTTATAGATATATCAAGGTTTTGCTGACCCATCC
22063 TCTTGCTTTTCAGGTCTTAAGTCATTTTGTCTTCCCTATTACCTTAGAACATAGATTATAAGCAC
1 TCTTGCTTTTCAGGTCTTAAGTCATTTTGTCTTCCCTATTACCTTAGAACATAGATTATAAGCAC
*
22128 TAATTGATGATTTACATTTTATTTTAGTAGCATGTAAAAGAAAAATGGCCCTGGGAATTGCCATT
66 TAATTGATGATTTAC--TTTATTTTAATAGCATGTAAAAGAAAAATGGCCCTGGGAATTGCCATT
*
22193 GCCTCTGCCCTCTAGTATCAAGACTTTGTCATTAATTCTATGGGACCTATGAAAATGTTAACGCA
129 GCCTCTGCCCTCTAGTATCAAGACTTTGTCATTAATTCTATGGGACCTATGAAAATGTTAACACA
* * *
22258 CAATTATAGTTTTGTTTCTGTTATAGATGTATCAATGTTTTGCTGACCCATCC
194 CAATTATAGTTATGTTTCTGTTATAGATATATCAAGGTTTTGCTGACCCATCC
22311 TCT
1 TCT
22314 GTAAAGGCAA
Statistics
Matches: 236, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
246 75 0.32
248 161 0.68
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (246 bp):
TCTTGCTTTTCAGGTCTTAAGTCATTTTGTCTTCCCTATTACCTTAGAACATAGATTATAAGCAC
TAATTGATGATTTACTTTATTTTAATAGCATGTAAAAGAAAAATGGCCCTGGGAATTGCCATTGC
CTCTGCCCTCTAGTATCAAGACTTTGTCATTAATTCTATGGGACCTATGAAAATGTTAACACACA
ATTATAGTTATGTTTCTGTTATAGATATATCAAGGTTTTGCTGACCCATCC
Found at i:29647 original size:2 final size:2
Alignment explanation
Indices: 29640--29664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29630 ATCATCCCTT
29640 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
29665 TTCTACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30297 original size:3 final size:3
Alignment explanation
Indices: 30291--30318 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30281 GGTTTCACTT
30291 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
30319 GTGTTCTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:33935 original size:2 final size:2
Alignment explanation
Indices: 33928--33958 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33918 TTTCACCTAA
33928 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
33959 AAATGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:36982 original size:16 final size:18
Alignment explanation
Indices: 36963--36995 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36953 TTAATATTCT
36963 CACA-ATAT-TATATATG
1 CACATATATATATATATG
36979 CACATATATATATATAT
1 CACATATATATATATAT
36996 ATATATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (18 bp):
CACATATATATATATATG
Found at i:37140 original size:2 final size:2
Alignment explanation
Indices: 37128--37159 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
37118 GCCATGCAAG
*
37128 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37160 AACAGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:42957 original size:166 final size:166
Alignment explanation
Indices: 42683--43020 Score: 640
Period size: 166 Copynumber: 2.0 Consensus size: 166
42673 AAGTATCCGA
*
42683 CCTAAAATAAATTGGTGATAGTGGCAGGCCCCAACTTTAACACAAGACCACAGGATACCTAATAC
1 CCTAAAATAAATTGGTGATAGTGGCAGGCCCCAACTTTAACACAAAACCACAGGATACCTAATAC
*
42748 TTAATAAATGTGGGATAACACCACTTGGCAAAGCACTTTATAAGGATGCACTTTCCATCCTGCCA
66 TTAACAAATGTGGGATAACACCACTTGGCAAAGCACTTTATAAGGATGCACTTTCCATCCTGCCA
*
42813 ATAACTTGACACTGAAAGGTAGGTATAATAGATGCC
131 ATAACTTGACACTGAAAGGTAGGTATAACAGATGCC
42849 CCTAAAATAAATTGGTGATAGTGGCAGGCCCCAACTTTAACACAAAACCACAGGATACCTAATAC
1 CCTAAAATAAATTGGTGATAGTGGCAGGCCCCAACTTTAACACAAAACCACAGGATACCTAATAC
42914 TTAACAAATGTGGGATAACACCACTTGGCAAAGCACTTTATAAGGATGCACTTTCCATCCTGCCA
66 TTAACAAATGTGGGATAACACCACTTGGCAAAGCACTTTATAAGGATGCACTTTCCATCCTGCCA
42979 ATAACTTGACACTGAAAGGTAGGTATAACAGATGCC
131 ATAACTTGACACTGAAAGGTAGGTATAACAGATGCC
*
43015 ACTAAA
1 CCTAAA
43021 TTTGACTCAA
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 168 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (166 bp):
CCTAAAATAAATTGGTGATAGTGGCAGGCCCCAACTTTAACACAAAACCACAGGATACCTAATAC
TTAACAAATGTGGGATAACACCACTTGGCAAAGCACTTTATAAGGATGCACTTTCCATCCTGCCA
ATAACTTGACACTGAAAGGTAGGTATAACAGATGCC
Found at i:47322 original size:18 final size:19
Alignment explanation
Indices: 47284--47324 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
47274 ATTACAAAAT
*
47284 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTCAA
47303 AATTCAAAAT-ATTTTCAA
1 AATTCAAAATAATTTTCAA
47321 AATT
1 AATT
47325 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTTCAA
Found at i:47355 original size:19 final size:19
Alignment explanation
Indices: 47333--47375 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47323 TTTAAATTTA
47333 AAAAAAAAT-TAAAAATTCT
1 AAAAAAAATAT-AAAATTCT
* *
47352 AAAAAATATATAAAATTTT
1 AAAAAAAATATAAAATTCT
47371 AAAAA
1 AAAAA
47376 TTTTCGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAAAAATATAAAATTCT
Found at i:50025 original size:23 final size:23
Alignment explanation
Indices: 49999--50109 Score: 116
Period size: 23 Copynumber: 4.8 Consensus size: 23
49989 TTAATGTTCA
**
49999 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
*
50022 CGAATATGTTCACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
*
50045 CGAACATGTTCACGAACATTAAA
1 CGAACATGTTCACGAACATTAAT
* *
50068 CAAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
* **
50092 TGAACACATTCACGAACA
1 CGAACATGTTCACGAACA
50110 ATGTTAATGA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
22 3 0.04
23 54 0.74
24 16 0.22
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:50261 original size:12 final size:12
Alignment explanation
Indices: 50204--50262 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
50194 TCATTAATAA
*
50204 ATAAAAGAGC-T
1 ATAAACGAGCTT
50215 ATAAACGAG-TT
1 ATAAACGAGCTT
*
50226 AATAAACGAACTT
1 -ATAAACGAGCTT
*
50239 ATAAACAAGCTT
1 ATAAACGAGCTT
*
50251 TTAAACGAGCTT
1 ATAAACGAGCTT
50263 GTTCGTGAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 9 0.23
12 28 0.72
13 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:51023 original size:96 final size:95
Alignment explanation
Indices: 50838--51024 Score: 218
Period size: 96 Copynumber: 1.9 Consensus size: 95
50828 TCTTTGCGAA
* **
50838 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
* * * *
50903 AAATCGGAGATAAGGAAACGTTGCCTCGATT
66 AAACCCGAAATAAAGAAAC-TTGCCTCGATT
* * *
50934 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTCAA-GCGCAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTT-AAGGCGCAATA-TTT
50997 CGAAACCCGAAATGAAAGAATA-TTGCCT
64 CGAAACCCGAAAT-AAAGAA-ACTTGCCT
51025 TGATATTAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 68 0.88
97 7 0.09
98 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (95 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCCGAAATAAAGAAACTTGCCTCGATT
Found at i:51400 original size:30 final size:30
Alignment explanation
Indices: 51364--51460 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
51354 AATTCGGAGG
51364 TAAAAATGGACCTTTTGAAAGTTTTGGGGT
1 TAAAAATGGACCTTTTGAAAGTTTTGGGGT
*
51394 TAAAAATGGACCTTTTGAAAGTTTCGGGG-
1 TAAAAATGGACCTTTTGAAAGTTTTGGGGT
* * * *
51423 TCAAAATGGGA-TTTTTTAAAGTTTTGAGGT
1 TAAAAAT-GGACCTTTTGAAAGTTTTGGGGT
51453 TAAAAATG
1 TAAAAATG
51461 AGATTTTTAG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.36
30 37 0.64
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (30 bp):
TAAAAATGGACCTTTTGAAAGTTTTGGGGT
Found at i:51511 original size:58 final size:58
Alignment explanation
Indices: 51336--51584 Score: 263
Period size: 59 Copynumber: 4.2 Consensus size: 58
51326 ATTCAACGTC
* * * * * * *
51336 AAAAATAGGATTTTTAGAAATTCGGAGGTAAAAAT-GGACCTTTTGAAAGTTTTGGGGTT
1 AAAAAT-GGATTTTTAGAAGTTTGGGGGTAAAAATGGGA-TTTTTGGAAGTTTCGAGGTT
* * * ** *
51395 AAAAATGGACCTTTT-GAAAGTTTCGGGGTCAAAATGGGATTTTTTAAAGTTTTGAGGTT
1 AAAAATGGA-TTTTTAG-AAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTT
*
51454 AAAAATGAGATTTTTAGAAGTTTGGGGGT-AAAATGGGATTTTTGGAAGTTTCAAGGTT
1 AAAAATG-GATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTT
* *
51512 AAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAG-TTCGAGGGT
1 AAAAAT-GGATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTT
51570 AAAAATGGAATTTTT
1 AAAAATGG-ATTTTT
51585 GAACAATTTA
Statistics
Matches: 164, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 74 0.45
59 82 0.50
60 6 0.04
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (58 bp):
AAAAATGGATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTT
Found at i:51585 original size:29 final size:29
Alignment explanation
Indices: 51356--51585 Score: 180
Period size: 29 Copynumber: 7.8 Consensus size: 29
51346 TTTTTAGAAA
** *
51356 TTCGGAGGTAAAAATGGACCTTTTGAAAGT
1 TTCGG-GGTAAAAATGGAATTTTTGGAAGT
* ** *
51386 TTTGGGGTTAAAAATGGACCTTTTGAAAGT
1 TTCGGGG-TAAAAATGGAATTTTTGGAAGT
* * **
51416 TTCGGGGTCAAAATGGGATTTTTTAAAGT
1 TTCGGGGTAAAAATGGAATTTTTGGAAGT
* * *
51445 TTTGAGGTTAAAAAT-GAGATTTTTAGAAGT
1 TTCG-GGGTAAAAATGGA-ATTTTTGGAAGT
* *
51475 TTGGGGGT-AAAATGGGATTTTTGGAAGT
1 TTCGGGGTAAAAATGGAATTTTTGGAAGT
* * * *
51503 TTCAAGGTTAAAAATGGGATTTTTAGAAG-
1 TTC-GGGGTAAAAATGGAATTTTTGGAAGT
*
51532 TTCGGGGGTAAAAATGGGATTTTTGGAAG-
1 TTC-GGGGTAAAAATGGAATTTTTGGAAGT
51561 TTCGAGGGTAAAAATGGAATTTTTG
1 TTCG-GGGTAAAAATGGAATTTTTG
51586 AACAATTTAG
Statistics
Matches: 167, Mismatches: 26, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
28 19 0.11
29 77 0.46
30 71 0.43
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
TTCGGGGTAAAAATGGAATTTTTGGAAGT
Done.