Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011003.1 Kokia drynarioides strain JFW-HI SEQ_125973, 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: 30874
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:18 original size:13 final size:13
Alignment explanation
Indices: 1--26 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1 TTTCTTTCTTTCC
1 TTTCTTTCTTTCC
14 TTTCTTTCTTTCC
1 TTTCTTTCTTTCC
27 CGTTTATTTG
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTTTCTTTCC
Found at i:1570 original size:96 final size:96
Alignment explanation
Indices: 1381--1572 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
1371 TTTTTGCGAA
* * *
1381 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCA
* *
1446 AAATCGAAGATAAGGAAACATTGTCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
1477 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAATGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATA-TTTC
* *
1541 GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 -AAAATCGAAGATAAAGA-AACATTGCCTCGATT
1573 TTAAAGCTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 2 0.02
96 73 0.88
97 8 0.10
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:1884 original size:29 final size:29
Alignment explanation
Indices: 1842--2138 Score: 323
Period size: 29 Copynumber: 10.1 Consensus size: 29
1832 TGTTTAGACA
*
1842 TTCGAGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGA-GGTCAAAATGGGATTTTTGGAAGT
*
1872 TTAGAGGTCAAAAATGGGATTTTTGGAAG-
1 TTCGAGGTC-AAAATGGGATTTTTGGAAGT
*
1901 TTCGGGGGTCAAAATGGGATTTTTGGAAG-
1 TTC-GAGGTCAAAATGGGATTTTTGGAAGT
*
1930 TTCGGGGGTCAAAATGGGATTTTTGGAAGT
1 TTC-GAGGTCAAAATGGGATTTTTGGAAGT
*
1960 TTCGAGGTCAAAAATGGAATTTTTGGAAG-
1 TTCGAGGTC-AAAATGGGATTTTTGGAAGT
* *
1989 CTCGAGGGTCAAAATGGGATTTTTTGAAGTT
1 TTCGA-GGTCAAAATGGGATTTTTGGAAG-T
* * *
2020 TTTG-GGTAAAAATTGGATTTTTGGAAGT
1 TTCGAGGTCAAAATGGGATTTTTGGAAGT
* * *
2048 TTGGGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGAGGTCAAAATGGGATTTTTGGAAGT
* *
2077 TTTGAGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGA-GGTCAAAATGGGATTTTTGGAAGT
* * *
2107 TTCGGGGTAAAAATGAGATTTTTGGATAGT
1 TTCGAGGTCAAAATGGGATTTTTGGA-AGT
2137 TT
1 TT
2139 AGGAACTTCC
Statistics
Matches: 236, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
28 4 0.02
29 145 0.61
30 85 0.36
31 2 0.01
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (29 bp):
TTCGAGGTCAAAATGGGATTTTTGGAAGT
Found at i:1915 original size:59 final size:59
Alignment explanation
Indices: 1842--2137 Score: 363
Period size: 59 Copynumber: 5.0 Consensus size: 59
1832 TGTTTAGACA
* *
1842 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTAGAGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* *
1901 TTCGGGGGTCAAAATGGGATTTTTGGAAG-TTCGGGGGTC-AAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGAAG
* * *
1959 TTTCGA-GGTCAAAAATGGAATTTTTGGAAG-CTCGAGGGTC-AAAATGGGATTTTTTGAAG
1 -TTCGAGGGT-AAAAATGGGATTTTTGGAAGTTTCG-GGGTCAAAAATGGGATTTTTGGAAG
*** * *
2018 TTTTTGGGTAAAAATTGGATTTTTGGAAGTTTGGGGGT-AAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* *
2076 TTTTGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGT-AAAAATGAGATTTTTGGATAG
1 -TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGA-AG
2136 TT
1 TT
2138 TAGGAACTTC
Statistics
Matches: 206, Mismatches: 22, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
58 67 0.33
59 137 0.67
60 2 0.01
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:1972 original size:88 final size:88
Alignment explanation
Indices: 1842--2140 Score: 413
Period size: 88 Copynumber: 3.4 Consensus size: 88
1832 TGTTTAGACA
* *
1842 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTAGAGGTCAAAAATGGGATTTTTGGAAGTTCGGG
1 TTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGAGGTCAAAAATGGGATTTTTGGAAGTTCGAG
1907 GGTCAAAATGGGATTTTTGGAAG
66 GGTCAAAATGGGATTTTTGGAAG
* * * *
1930 TTCGGGGGTCAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGCTCGAG
1 TTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGAGGTCAAAAATGGGATTTTTGGAAGTTCGAG
*
1995 GGTCAAAATGGGATTTTTTGAAG
66 GGTCAAAATGGGATTTTTGGAAG
*** * * * *
2018 TTTTTGGGTAAAAATTGGATTTTTGGAAGTTTGGGGGT-AAAAATGGGATTTTTGGAAGTTTTGA
1 TTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGAGGTCAAAAATGGGATTTTTGGAAG-TTCGA
*
2082 GGGTAAAAATGGGATTTTTGGAAG
65 GGGTCAAAATGGGATTTTTGGAAG
*
2106 TTTC-GGGGTAAAAATGAGATTTTTGGATAGTTTAG
1 -TTCGGGGGTAAAAATGGGATTTTTGGA-AGTTTAG
2141 GAACTTCCAG
Statistics
Matches: 184, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
87 19 0.10
88 157 0.85
89 8 0.04
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (88 bp):
TTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGAGGTCAAAAATGGGATTTTTGGAAGTTCGAG
GGTCAAAATGGGATTTTTGGAAG
Found at i:3196 original size:3 final size:3
Alignment explanation
Indices: 3190--3259 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
3180 TAGACTTTTT
* * * * * *
3190 TTA TTA TTA ATA TTA ATA TTAA TTA ATA TTA TCA TTA TTA -CA ATA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
*
3235 TTTA TTA TTA TTA ATA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA
3260 ATAACCATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
2 1 0.02
3 45 0.88
4 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:3246 original size:27 final size:27
Alignment explanation
Indices: 3204--3256 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3194 TATTAATATT
3204 AATATTAATTAATATT-ATCATTATTAC
1 AATATTAATTAATATTAAT-ATTATTAC
* *
3231 AATATTTATTATTATTAATATTATTA
1 AATATTAATTAATATTAATATTATTA
3257 TTAATAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (27 bp):
AATATTAATTAATATTAATATTATTAC
Found at i:4116 original size:2 final size:2
Alignment explanation
Indices: 4109--4135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4099 ACACAATTGA
4109 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 A
4136 AACCAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9891 original size:19 final size:22
Alignment explanation
Indices: 9846--9892 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 22
9836 TTTGCTTTTC
9846 TATAAAATAATTCTCAATTAAA
1 TATAAAATAATTCTCAATTAAA
* *
9868 AATAAAA-AA-TCT-AATTAAT
1 TATAAAATAATTCTCAATTAAA
9887 TATAAA
1 TATAAA
9893 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 11 0.50
20 3 0.14
21 2 0.09
22 6 0.27
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (22 bp):
TATAAAATAATTCTCAATTAAA
Found at i:12254 original size:2 final size:2
Alignment explanation
Indices: 12247--12279 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12237 TCGTATTTCA
12247 AT AT 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 AT AT A
12280 AAGTAGATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13446 original size:62 final size:62
Alignment explanation
Indices: 13374--13500 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
13364 ATTCAGACGA
*
13374 TATCCTTCAATCTATTTCTTCATCAAAACATTCTCCTTTTCTTTCTTTACTTCCGTTAATAC
1 TATCCCTCAATCTATTTCTTCATCAAAACATTCTCCTTTTCTTTCTTTACTTCCGTTAATAC
13436 TATCCCTCAATCTATTTCTTCATCAAAACATTCTCCTTTTCTTTCTTTACTTCCGTTAATAC
1 TATCCCTCAATCTATTTCTTCATCAAAACATTCTCCTTTTCTTTCTTTACTTCCGTTAATAC
13498 TAT
1 TAT
13501 GTATCAATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.48
Consensus pattern (62 bp):
TATCCCTCAATCTATTTCTTCATCAAAACATTCTCCTTTTCTTTCTTTACTTCCGTTAATAC
Done.