Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014475.1 Kokia drynarioides strain JFW-HI SEQ_129514, 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: 8322
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:293 original size:22 final size:22
Alignment explanation
Indices: 268--309 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
258 CATTGTAATC
268 ATTGAAAAATAAAAATAAAAGT
1 ATTGAAAAATAAAAATAAAAGT
*
290 ATTGAAAAATAAAATTAAAA
1 ATTGAAAAATAAAAATAAAA
310 CTTCAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
ATTGAAAAATAAAAATAAAAGT
Found at i:962 original size:28 final size:28
Alignment explanation
Indices: 929--1167 Score: 192
Period size: 28 Copynumber: 8.5 Consensus size: 28
919 AAATTTCACT
*
929 ATTTTACAGTTTTACCATTGTTTTCCAA
1 ATTTTACAGTTTTGCCATTGTTTTCCAA
* * * *
957 ATTTTACGGTTTTGCCACTATTTTCCAG
1 ATTTTACAGTTTTGCCATTGTTTTCCAA
* * * *
985 ATTTTATAGTTTTTCCATTATTTTCTAGA
1 ATTTTACAGTTTTGCCATTGTTTTCCA-A
* * * * ** *
1014 A-TTTATAGATTTGTCACTGTTTTTTAG
1 ATTTTACAGTTTTGCCATTGTTTTCCAA
* *
1041 ATTTTACAGTTGTGCCATTATTTTCCAA
1 ATTTTACAGTTTTGCCATTGTTTTCCAA
* * ** *
1069 ATTTCACAGTTTTGCCACTGGTTCCCCAG
1 ATTTTACAGTTTTGCCA-TTGTTTTCCAA
* * *
1098 ATTTTACAGTTTTGCTACTGTTTTCCAG
1 ATTTTACAGTTTTGCCATTGTTTTCCAA
*
1126 ATTTTAAAGTTTTGCCATTGGTTTTCCAA
1 ATTTTACAGTTTTGCCATT-GTTTTCCAA
*
1155 ATTTTACAATTTT
1 ATTTTACAGTTTT
1168 ACCACTATTT
Statistics
Matches: 161, Mismatches: 46, Indels: 7
0.75 0.21 0.03
Matches are distributed among these distances:
27 1 0.01
28 119 0.74
29 41 0.25
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (28 bp):
ATTTTACAGTTTTGCCATTGTTTTCCAA
Found at i:1088 original size:56 final size:56
Alignment explanation
Indices: 929--1179 Score: 234
Period size: 56 Copynumber: 4.4 Consensus size: 56
919 AAATTTCACT
* * * *
929 ATTTTACAGTTTTACCATTGTTTTCCAAATTTTACGGTTTTGCCACTATTTTCCAG
1 ATTTTACAGTTTTGCCATTATTTTCCAAATTTTACAGTTTTGCCACTGTTTTCCAG
* * * * * * **
985 ATTTTATAGTTTTTCCATTATTTTCTAGAA-TTTATAGATTTGTCACTGTTTTTTAG
1 ATTTTACAGTTTTGCCATTATTTTCCA-AATTTTACAGTTTTGCCACTGTTTTCCAG
* * **
1041 ATTTTACAGTTGTGCCATTATTTTCCAAATTTCACAGTTTTGCCACTGGTTCCCCAG
1 ATTTTACAGTTTTGCCATTATTTTCCAAATTTTACAGTTTTGCCACT-GTTTTCCAG
* * * * * * *
1098 ATTTTACAGTTTTGCTACTGTTTTCCAGATTTTAAAGTTTTGCCATTGGTTTTCCAA
1 ATTTTACAGTTTTGCCATTATTTTCCAAATTTTACAGTTTTGCCACT-GTTTTCCAG
* * *
1155 ATTTTACAATTTTACCACTATTTTC
1 ATTTTACAGTTTTGCCATTATTTTC
1180 AAAAAGAAAA
Statistics
Matches: 154, Mismatches: 38, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
55 2 0.01
56 78 0.51
57 74 0.48
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (56 bp):
ATTTTACAGTTTTGCCATTATTTTCCAAATTTTACAGTTTTGCCACTGTTTTCCAG
Found at i:1137 original size:57 final size:57
Alignment explanation
Indices: 929--1179 Score: 175
Period size: 57 Copynumber: 4.4 Consensus size: 57
919 AAATTTCACT
* * * * ** * **
929 ATTTTACAGTTTTACCATTGTTTTCCAAATTTTACGGTTTTGCCACT-ATTTTCCAG
1 ATTTTACAGTTTTGCCACTATTTTCCAAATTTCAAAGTTTTGCCACTGGTTCCCCAG
* * * * * * * ****
985 ATTTTATAGTTTTTCCATTATTTTCTAGAATTT-ATAGATTTGTCACT-GTTTTTTAG
1 ATTTTACAGTTTTGCCACTATTTTCCA-AATTTCAAAGTTTTGCCACTGGTTCCCCAG
* * *
1041 ATTTTACAGTTGTGCCATTATTTTCCAAATTTCACAGTTTTGCCACTGGTTCCCCAG
1 ATTTTACAGTTTTGCCACTATTTTCCAAATTTCAAAGTTTTGCCACTGGTTCCCCAG
* * * * * ** *
1098 ATTTTACAGTTTTGCTACTGTTTTCCAGATTTTAAAGTTTTGCCATTGGTTTTCCAA
1 ATTTTACAGTTTTGCCACTATTTTCCAAATTTCAAAGTTTTGCCACTGGTTCCCCAG
* *
1155 ATTTTACAATTTTACCACTATTTTC
1 ATTTTACAGTTTTGCCACTATTTTC
1180 AAAAAGAAAA
Statistics
Matches: 155, Mismatches: 37, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
55 5 0.03
56 73 0.47
57 77 0.50
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (57 bp):
ATTTTACAGTTTTGCCACTATTTTCCAAATTTCAAAGTTTTGCCACTGGTTCCCCAG
Found at i:1680 original size:45 final size:45
Alignment explanation
Indices: 1625--2224 Score: 831
Period size: 45 Copynumber: 13.5 Consensus size: 45
1615 ATAAGATGAT
* * * *
1625 TATTATTTGATTGATTATGTTATACAATATGTATGATATGATAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* * *
1670 TATGATTTGATTGATTATGTTATACGATATGCATGACATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
*
1715 TATTATTTGATTGATTATGCTATACGATATGTATGATATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* *
1760 TATTATTTGATTGATTATGCTATATGATATGCATGATATCGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* *
1805 TATTATTTTATTGATTATGCTATACGATATGCATGACATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* * *
1850 TATTATTTGATTAATCATGCTATACGATATGTATGATATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* *
1895 TATTATTTGATTG---AT--TAT--G-TATGCATGACATGATAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* * *
1932 TATTATTTGATTGATTATGCTATATGATATGTATGATATTGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* * * *
1977 TATTATTTGATTGATTATGCTACACGGTATGCATGACACGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* *
2022 TATTATTTGATTGATTATGTTATACGATATGTATGATATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* * *
2067 TATAATTGGATTGATTATGCTATATGATATGCA-GATATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
*
2111 TATTATTTGATTGATTATGCTATACGATATGCATGACATGGTAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
* * * *
2156 TATTATTTGATTGATTATGTTATACGATATGAATGACATGATAAA
1 TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
2201 TATTATTTGATTGATTATGCTATA
1 TATTATTTGATTGATTATGCTATA
2225 AGAGCAAATG
Statistics
Matches: 491, Mismatches: 55, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
37 28 0.06
38 1 0.00
40 5 0.01
42 5 0.01
44 42 0.09
45 410 0.84
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
TATTATTTGATTGATTATGCTATACGATATGCATGATATGGTAAA
Found at i:1935 original size:37 final size:37
Alignment explanation
Indices: 1877--1950 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1867 TGCTATACGA
* * *
1877 TATGTATGATATGGTAAATATTATTTGATTGATTATG
1 TATGCATGACATGATAAATATTATTTGATTGATTATG
1914 TATGCATGACATGATAAATATTATTTGATTGATTATG
1 TATGCATGACATGATAAATATTATTTGATTGATTATG
1951 CTATATGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (37 bp):
TATGCATGACATGATAAATATTATTTGATTGATTATG
Found at i:2357 original size:19 final size:19
Alignment explanation
Indices: 2321--2364 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2311 CTAGTACAGT
*
2321 ATATTGCTCTTGCGAGCCA
1 ATATTGCTCTTGCAAGCCA
2340 ATATTGCTCTTTG-AAGCCA
1 ATATTGCTC-TTGCAAGCCA
*
2359 GTATTG
1 ATATTG
2365 GTCATTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (19 bp):
ATATTGCTCTTGCAAGCCA
Found at i:4515 original size:40 final size:39
Alignment explanation
Indices: 4460--4593 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 39
4450 AGTTATCTTG
*
4460 GATAGAATTCAAGCTTCAGCTTAGTAGGCTATGAGCCGAT
1 GATAGAATTCAAGCTTC-GCTTAGCAGGCTATGAGCCGAT
* * *
4500 GATAGAATTCAAGCTTTGGCTTAGCAGGCTATGAGCTGGT
1 GATAGAATTCAAGC-TTCGCTTAGCAGGCTATGAGCCGAT
* * * *
4540 GATAAAATTCAAGCTTCGACTTAGCAGACTACGAGTC-AGT
1 GATAGAATTCAAGCTTCG-CTTAGCAGGCTATGAGCCGA-T
4580 GATAGAATTCAAGC
1 GATAGAATTCAAGC
4594 CAAGCTATGG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 74 0.94
41 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (39 bp):
GATAGAATTCAAGCTTCGCTTAGCAGGCTATGAGCCGAT
Found at i:7271 original size:28 final size:28
Alignment explanation
Indices: 7212--7271 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
7202 AAACCCAGAT
**
7212 CAAAATAATTCTCTATTGAGCAAGAGTT
1 CAAAATAATTCTCTATTGAGCAAGAGAC
* *
7240 CAAAATATTTCTCT-TATGAGCCAGAGAC
1 CAAAATAATTCTCTAT-TGAGCAAGAGAC
7268 CAAA
1 CAAA
7272 TTATCGCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (28 bp):
CAAAATAATTCTCTATTGAGCAAGAGAC
Found at i:7309 original size:28 final size:28
Alignment explanation
Indices: 7276--7365 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
7266 ACCAAATTAT
*
7276 CGCTCTTTCGAGCTAGAATACAGAACAA
1 CGCTCTTTCGAGCTAGAATACAGAATAA
* * *
7304 CACTCTTTCGAGCCAGAATACAAAATAA
1 CGCTCTTTCGAGCTAGAATACAGAATAA
*
7332 CGCTCTTTCGATCTAGAATACAGAATAA
1 CGCTCTTTCGAGCTAGAATACAGAATAA
7360 CGCTCT
1 CGCTCT
7366 CTTGAGCCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (28 bp):
CGCTCTTTCGAGCTAGAATACAGAATAA
Done.