Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013605.1 Kokia drynarioides strain JFW-HI SEQ_128632, 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: 58600
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:158 original size:13 final size:13
Alignment explanation
Indices: 142--175 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
132 TTCTCCATGA
142 TCGTTCTGTTCAT
1 TCGTTCTGTTCAT
155 TCGTTCTGTTCAT
1 TCGTTCTGTTCAT
168 TCGTTCTG
1 TCGTTCTG
176 CAATGCCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.53
Consensus pattern (13 bp):
TCGTTCTGTTCAT
Found at i:2364 original size:17 final size:18
Alignment explanation
Indices: 2326--2366 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2316 CTTTACTTTT
* *
2326 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
2344 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
2361 ATTTTA
1 ATTTTA
2367 GTCACTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:2487 original size:30 final size:31
Alignment explanation
Indices: 2452--2514 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
2442 GTCCTGAATT
* *
2452 TTGACAACTGTTCCACGTT-AGGGCTTGAAC
1 TTGACAACTATTCCACATTGAGGGCTTGAAC
* *
2482 TTGACAATTATTCCACATTGGGGGCTTGAAC
1 TTGACAACTATTCCACATTGAGGGCTTGAAC
2513 TT
1 TT
2515 TAGGGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (31 bp):
TTGACAACTATTCCACATTGAGGGCTTGAAC
Found at i:3955 original size:14 final size:15
Alignment explanation
Indices: 3936--3964 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3926 TTAATTTGAT
3936 TTTGAAT-AATTTTA
1 TTTGAATGAATTTTA
3950 TTTGAATGAATTTTA
1 TTTGAATGAATTTTA
3965 AATAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
TTTGAATGAATTTTA
Found at i:7440 original size:25 final size:25
Alignment explanation
Indices: 7399--7446 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
7389 TTGTAAATCA
*
7399 GAAAAATATCTTTAGAG-ATTTTCT
1 GAAAAATATCTTCAGAGAATTTTCT
*
7423 GAAATAATCTCTTCAGAGAATTTT
1 GAAA-AATATCTTCAGAGAATTTT
7447 TTTTGTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 11 0.55
26 5 0.25
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (25 bp):
GAAAAATATCTTCAGAGAATTTTCT
Found at i:9688 original size:39 final size:39
Alignment explanation
Indices: 9617--9691 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
9607 CAGAATTGCG
* **
9617 CCCAGAATTGTCACTGCATAACGATGTTCAAAATTGCAA
1 CCCAAAATTGTCACTGCATAACGATGCCCAAAATTGCAA
*
9656 CCCAAAATTGTCACTGCATGA-GCATGCCCAAAATTG
1 CCCAAAATTGTCACTGCATAACG-ATGCCCAAAATTG
9692 TCGTTGTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (39 bp):
CCCAAAATTGTCACTGCATAACGATGCCCAAAATTGCAA
Found at i:41128 original size:21 final size:21
Alignment explanation
Indices: 41104--41179 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
41094 TTGGGGTAAA
41104 ACTTGTATCGGTAGAAAAATC
1 ACTTGTATCGGTAGAAAAATC
41125 ACTTGTATCGGTAGAAAAATC
1 ACTTGTATCGGTAGAAAAATC
**
41146 ACTTGTATCGGTAGAACTATC
1 ACTTGTATCGGTAGAAAAATC
*
41167 ACTTATATCGGTA
1 ACTTGTATCGGTA
41180 CAAATCTGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAAAATC
Found at i:41626 original size:34 final size:34
Alignment explanation
Indices: 41580--41656 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
41570 TGGGAAAGGA
* *
41580 AGAACATTAAACAAACACTAGGCCTGACAACCTT
1 AGAACATCAAACAAACACTAGGCCTGACAACCCT
41614 AGAACATCAAACAAACACTAGGCCTGACAACCCT
1 AGAACATCAAACAAACACTAGGCCTGACAACCCT
41648 AGAACATCA
1 AGAACATCA
41657 TTTAGGTGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.45, C:0.29, G:0.12, T:0.14
Consensus pattern (34 bp):
AGAACATCAAACAAACACTAGGCCTGACAACCCT
Found at i:50096 original size:31 final size:32
Alignment explanation
Indices: 50029--50096 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
50019 GATTAGTTAC
* *
50029 CAAATTAGGAAAAAAATGTCAAATTTAGATAT
1 CAAATTAGGAAAAAAATGTCAAATATAGATAA
* * *
50061 CAAATTAGG-AAAAAATGTTAAGTATAGGTAA
1 CAAATTAGGAAAAAAATGTCAAATATAGATAA
50092 CAAAT
1 CAAAT
50097 GTTGTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (32 bp):
CAAATTAGGAAAAAAATGTCAAATATAGATAA
Found at i:53266 original size:22 final size:21
Alignment explanation
Indices: 53241--53291 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 21
53231 TTAGGTCCCA
53241 AAATTAATATTTTAATTTTTTT
1 AAATTAAT-TTTTAATTTTTTT
*
53263 AAATGTTAATTTTTTATTTTTTT
1 AAA--TTAATTTTTAATTTTTTT
53286 AGAATT
1 A-AATT
53292 TTTATACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.20
23 13 0.52
24 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
AAATTAATTTTTAATTTTTTT
Found at i:53346 original size:20 final size:19
Alignment explanation
Indices: 53313--53376 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
53303 TAAAATATAA
53313 ATTTTGAAAATTTTATAAAT
1 ATTTTGAAAATTTTA-AAAT
**
53333 ATTTTGAATTTTTTAAAATT
1 ATTTTGAAAATTTTAAAA-T
* * *
53353 ATGTTGGAACATTTTCAAAT
1 AT-TTTGAAAATTTTAAAAT
53373 ATTT
1 ATTT
53377 ATAGTGTTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 5 0.14
20 19 0.53
21 12 0.33
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.52
Consensus pattern (19 bp):
ATTTTGAAAATTTTAAAAT
Found at i:56607 original size:29 final size:27
Alignment explanation
Indices: 56565--56624 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
56555 ATCGAGTTTG
* *
56565 AAAATGAGACTTTTCGGATACACGAGGGC
1 AAAATGAAAATTTT-GGATACACGA-GGC
* *
56594 AAAATGAAAATTTTGGATTCTCGAGGC
1 AAAATGAAAATTTTGGATACACGAGGC
56621 AAAA
1 AAAA
56625 ATGGTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 7 0.26
28 8 0.30
29 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (27 bp):
AAAATGAAAATTTTGGATACACGAGGC
Found at i:56681 original size:31 final size:32
Alignment explanation
Indices: 56621--56681 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
56611 TTCTCGAGGC
*
56621 AAAAATGGTAATTTTTGGAAAATTTAGGGTTT
1 AAAAATGGTAATTTTTAGAAAATTTAGGGTTT
56653 AAAAATGG-AATTTTTAG-AAATTTGAGGGT
1 AAAAATGGTAATTTTTAGAAAATTT-AGGGT
56682 AAAAGGGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.22
31 13 0.48
32 8 0.30
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.38
Consensus pattern (32 bp):
AAAAATGGTAATTTTTAGAAAATTTAGGGTTT
Found at i:56793 original size:29 final size:30
Alignment explanation
Indices: 56620--56998 Score: 236
Period size: 29 Copynumber: 12.8 Consensus size: 30
56610 ATTCTCGAGG
*
56620 CAAAAATGGTAATTTTTGGAAAATTT-AGGGTT
1 CAAAAATGG-AATTTTTGG-AAGTTTCAGGG-T
* * * *
56652 TAAAAATGGAATTTTTAGAAATTTGAGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCAGGGT
* * * *
56682 --AAAAGGGTAGTTTT-GAGAGTTTCGGGGGT
1 CAAAAATGGAATTTTTGGA-AGTTTC-AGGGT
* *
56711 AAAAAAAT-GAA--TTTGGAAGTTTTATGGG-
1 -CAAAAATGGAATTTTTGGAAGTTTCA-GGGT
* **
56739 CAAAAATGGAATTTTTAGAAGTTTCAAAGT
1 CAAAAATGGAATTTTTGGAAGTTTCAGGGT
*
56769 CAAAAATGGTATTTTTGGAAG-TTCAGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCAGGGT
* *
56798 CAAAAATGGAATCTTTGGAAGTTTCGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCAGGGT
* *
56828 C-AAAATGGGATTTTTGGAAGCTTT-GGGGT
1 CAAAAATGGAATTTTTGGAAG-TTTCAGGGT
* *
56857 CAAAAA-AGATATTTTTGGAAGTTTCGGGGT
1 CAAAAATGGA-ATTTTTGGAAGTTTCAGGGT
* **
56887 TAAAAAT-GAGATTTTTGGAAGTTTTGGGGT
1 CAAAAATGGA-ATTTTTGGAAGTTTCAGGGT
* **
56917 -AAAAATGGGATTTTTGGAAGTTTTGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCAGGGT
* * * *
56946 -GAAAATGGGATTTTTGGACG-TTCGGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTC-AGGGT
56975 -AAAAAT-GAGATTTTTGGACAGTTT
1 CAAAAATGGA-ATTTTTGGA-AGTTT
56999 AAGGACCTTT
Statistics
Matches: 286, Mismatches: 38, Indels: 47
0.77 0.10 0.13
Matches are distributed among these distances:
27 8 0.03
28 21 0.07
29 131 0.46
30 98 0.34
31 16 0.06
32 12 0.04
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
CAAAAATGGAATTTTTGGAAGTTTCAGGGT
Found at i:56802 original size:59 final size:59
Alignment explanation
Indices: 56620--56998 Score: 271
Period size: 59 Copynumber: 6.4 Consensus size: 59
56610 ATTCTCGAGG
* * * * * * *
56620 CAAAAATGGTAATTTTTGGAAAATTTAGGGTTTAAAAATGGAATTTTTAGAAATTTGAGGGT
1 CAAAAATGG-AATTTTTGG-AAGTTTCGGGGTCAAAAATGG-ATTTTTGGAAGTTTTAGGGT
* * * * *
56682 --AAAAGGGTAGTTTT-GAGAGTTTCGGGGGTAAAAAAAT-GA-ATTTGGAAGTTTTATGGG-
1 CAAAAATGGAATTTTTGGA-AGTTTC-GGGGT-CAAAAATGGATTTTTGGAAGTTTTA-GGGT
* *** *
56739 CAAAAATGGAATTTTTAGAAGTTTCAAAGTCAAAAATGGTATTTTTGGAAG-TTCAGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGG-ATTTTTGGAAGTTTTAGGGT
* * *
56798 CAAAAATGGAATCTTTGGAAGTTTCGGGGTC-AAAATGGGATTTTTGGAAGCTTTGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT-GGATTTTTGGAAGTTTTAGGGT
* * *
56857 CAAAAA-AGATATTTTTGGAAGTTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTTGGGGT
1 CAAAAATGGA-ATTTTTGGAAGTTTCGGGGTCAAAAATG-GATTTTTGGAAGTTTTAGGGT
* * * * ***
56917 -AAAAATGGGATTTTTGGAAGTTTTGGGGT-GAAAATGGGATTTTTGGACGTTCGGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT-GGATTTTTGGAAGTTTTAGGGT
56975 -AAAAAT-GAGATTTTTGGACAGTTT
1 CAAAAATGGA-ATTTTTGGA-AGTTT
56999 AAGGACCTTT
Statistics
Matches: 258, Mismatches: 39, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
57 18 0.07
58 71 0.28
59 121 0.47
60 48 0.19
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
CAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGATTTTTGGAAGTTTTAGGGT
Found at i:57847 original size:25 final size:22
Alignment explanation
Indices: 57797--57852 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
57787 TTTTCCTTTT
**
57797 TTATTATTAATGATTAATATTA
1 TTATTATTAATGAGCAATATTA
57819 TTATTATTAATGAGGCAATTATTA
1 TTATTATTAATGA-GCAA-TATTA
57843 CTTATTATTA
1 -TTATTATTA
57853 TTATTATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.45
23 2 0.07
24 5 0.17
25 9 0.31
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (22 bp):
TTATTATTAATGAGCAATATTA
Done.