Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013589.1 Kokia drynarioides strain JFW-HI SEQ_128616, 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: 4960
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.32
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30 AATTTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1948 original size:161 final size:160
Alignment explanation
Indices: 1674--2160 Score: 694
Period size: 161 Copynumber: 3.0 Consensus size: 160
1664 AAATATTTGA
*
1674 CTATACCAGTCTTGTTTGGTCGATGGGAAAATGTAGGAAAATTTGGAAAGTTT-TTGTTGCTGAA
1 CTATACCAGTCTTGTTTGGTTGATGGGAAAATGTAGGAAAATTT-GAAA-TTTCTTGTTGCTGAA
* * *
1738 GATTTTGCACTTAGTTTTGAACTGTGATTGGATCTTGGGAA-AA-GAAAGATTGATGGGTTTGTA
64 GAATTTGCACTTGGTTTTGAACTGTGATTGGATCTT--GAAGAAGGAAAGATTGATGGGTTTGTG
* *
1801 TTTGAAATTTGAATTATGATAACCCATTTGTTAC
127 TTTGAAATTTGAAATATGATAACCCATTTGTTAT
* * *
1835 CTATACCAGTCTTATTTGGTTGATGGGAAAATGTAGAAAAATTTCGAAATTTCTTATTGCTGAAG
1 CTATACCAGTCTTGTTTGGTTGATGGGAAAATGTAGGAAAATTT-GAAATTTCTTGTTGCTGAAG
*
1900 AATTTGCACTTGGTTTTGAACTGTGATTGGATCTTAAAGAAGGAAAGATTGATGGGTTTGTGTTT
65 AATTTGCACTTGGTTTTGAACTGTGATTGGATCTTGAAGAAGGAAAGATTGATGGGTTTGTGTTT
*
1965 GAAATTTGAACTATGATAACCCATTTGTTAT
130 GAAATTTGAAATATGATAACCCATTTGTTAT
* * * *
1996 CTATACC-GATCTTGTTTGGTTGATAGGAAAATGTAGGAAAATCTGAAAATTTCTTGTTACCGAA
1 CTATACCAG-TCTTGTTTGGTTGATGGGAAAATGTAGGAAAATTTG-AAATTTCTTGTTGCTGAA
* ** **
2060 GAATTTACACTTGGTTTTGAACTGTGATTGGATCTTGGGGAAGGAAAGATTGATGAATTTGTGTT
64 GAATTTGCACTTGGTTTTGAACTGTGATTGGATCTTGAAGAAGGAAAGATTGATGGGTTTGTGTT
*
2125 TGAAATTTGAAATATGATAATCCATTTGTTAT
129 TGAAATTTGAAATATGATAACCCATTTGTTAT
2157 CTAT
1 CTAT
2161 GCAAAAATCT
Statistics
Matches: 295, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
159 2 0.01
160 7 0.02
161 286 0.97
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (160 bp):
CTATACCAGTCTTGTTTGGTTGATGGGAAAATGTAGGAAAATTTGAAATTTCTTGTTGCTGAAGA
ATTTGCACTTGGTTTTGAACTGTGATTGGATCTTGAAGAAGGAAAGATTGATGGGTTTGTGTTTG
AAATTTGAAATATGATAACCCATTTGTTAT
Found at i:2325 original size:30 final size:29
Alignment explanation
Indices: 2289--2360 Score: 126
Period size: 29 Copynumber: 2.4 Consensus size: 29
2279 ATTAAAATTA
2289 TTTAATAATTTTATTATTTAAAAAAATAAT
1 TTTAATAATTTTA-TATTTAAAAAAATAAT
*
2319 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAAATAAT
2348 TTTAATAATTTTA
1 TTTAATAATTTTA
2361 AAATCATTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:2347 original size:20 final size:22
Alignment explanation
Indices: 2322--2363 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
2312 AAATAATTTT
2322 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
2342 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
2364 TCATTGCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:3534 original size:96 final size:96
Alignment explanation
Indices: 3350--3541 Score: 264
Period size: 96 Copynumber: 2.0 Consensus size: 96
3340 TTTTTGGGAA
**
3350 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
3415 AAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
3446 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* *
3510 GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 -AAAATCGAAGATAAAGA-AACATTGCCTCGATT
3542 TTAAAGTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 2 0.02
96 75 0.88
97 8 0.09
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:3996 original size:29 final size:30
Alignment explanation
Indices: 3928--4186 Score: 201
Period size: 30 Copynumber: 8.8 Consensus size: 30
3918 TTTAAGGTTG
* *
3928 AAAATGGGA-TTTTTAGAAGTTTTGGGGTTA
1 AAAATGGGATTTTTTGGAAG-TTTGGGGGTA
*
3958 AAAATGGGATTTTTTGGAGGTTTGGGGGTA
1 AAAATGGGATTTTTTGGAAGTTTGGGGGTA
*
3988 AAAAT-GGATTTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGATTTTTTGGAAGTTTGGGGGT-A
* *
4018 AAAGTGGGA-TTTTTGGAAGTTTAGGGGTA
1 AAAATGGGATTTTTTGGAAGTTTGGGGGTA
* * * * *
4047 AAAAT-GGAATTTTAGGAAGGTTCGAGGTTA
1 AAAATGGGATTTTTTGGAA-GTTTGGGGGTA
* * * *
4077 AAAATGAGA-TTTTTAGAAGTTCGAGGGT-
1 AAAATGGGATTTTTTGGAAGTTTGGGGGTA
* * *
4105 AAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGATTTTTTGGAAGTTTGGGGGT-A
* ** * *
4136 AAAATAGGA-TTTTTAAAAGTTCGAGGGT-
1 AAAATGGGATTTTTTGGAAGTTTGGGGGTA
* *
4164 AAAATGGTAATTTTTGGAAGTTT
1 AAAATGGGATTTTTTGGAAGTTT
4187 CGGGACCTCC
Statistics
Matches: 184, Mismatches: 35, Indels: 21
0.77 0.15 0.09
Matches are distributed among these distances:
28 17 0.09
29 68 0.37
30 79 0.43
31 20 0.11
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (30 bp):
AAAATGGGATTTTTTGGAAGTTTGGGGGTA
Found at i:3997 original size:59 final size:58
Alignment explanation
Indices: 3928--4186 Score: 243
Period size: 59 Copynumber: 4.4 Consensus size: 58
3918 TTTAAGGTTG
* *
3928 AAAATGGGATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTTGGAGGTTTGGGGGTA
1 AAAAT-GGATTTTTAGAAGTTTTGGGGTCAAAAATGGGA-TTTTTGGAAGTTTGGGGGTA
* * *
3988 AAAATGGATTTTTTGGAAGTTTTGGGGTCAAAAGTGGGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGA-TTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTA
* * * * * * * * *
4047 AAAATGGAATTTTAGGAAGGTTCGAGGTTAAAAATGAGATTTTTAGAAGTTCGAGGGT-
1 AAAATGGATTTTTA-GAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTA
* * ** * *
4105 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATAGGATTTTTAAAAGTTCGAGGGT-
1 AAAATGG--ATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTA
*
4164 AAAATGGTAATTTTTGGAAGTTT
1 AAAATGG--ATTTTTAGAAGTTT
4187 CGGGACCTCC
Statistics
Matches: 169, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
58 11 0.07
59 121 0.72
60 37 0.22
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (58 bp):
AAAATGGATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTA
Found at i:4896 original size:7 final size:7
Alignment explanation
Indices: 4884--4913 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4874 CCGTCGCCTT
*
4884 CCACGCA
1 CCACGCG
4891 CCACGCG
1 CCACGCG
4898 CCACGCG
1 CCACGCG
4905 CCACGCG
1 CCACGCG
4912 CC
1 CC
4914 TCCGTCGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.60, G:0.23, T:0.00
Consensus pattern (7 bp):
CCACGCG
Done.