Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014805.1 Kokia drynarioides strain JFW-HI SEQ_129847, 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: 29170
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Warning! 62 characters in sequence are not A, C, G, or T
Found at i:89 original size:21 final size:21
Alignment explanation
Indices: 64--105 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54 ATCAGGGGAT
64 GGAAGTTTATCAGCATCCATC
1 GGAAGTTTATCAGCATCCATC
85 GGAAGTTTATCAGCATCCATC
1 GGAAGTTTATCAGCATCCATC
106 CCATAGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (21 bp):
GGAAGTTTATCAGCATCCATC
Found at i:1541 original size:94 final size:94
Alignment explanation
Indices: 1364--1562 Score: 246
Period size: 94 Copynumber: 2.1 Consensus size: 94
1354 CCCTCAAATT
* *
1364 AAAAAAAAAAAAATTAAACCTCTGTTTTTTTTTTTTTTACACTCAATTGGGTACTTGAATTTCAA
1 AAAAAAAAAAAAATTAAACCTCTGTTTTTTTTTTTCTTACACTCAATTGGATACTTGAATTTCAA
1429 AATACATAAAAAGGACCCTTAAAC-GTTTC
66 AATACATAAAAAGGACCCTT-AACTGTTTC
*
1458 AAAAAAAAAACAATTAAA-CTCT-TATCTTTTTTTTTCTT-CACTCAATTGGATACTTGAACTTT
1 AAAAAAAAAAAAATTAAACCTCTGT-T-TTTTTTTTTCTTACACTCAATTGGATACTTGAA-TTT
* * * *
1520 CAAAATGCACTAAAGA-TACCCTTAACTTTTTC
63 CAAAATACA-TAAAAAGGACCCTTAACTGTTTC
*
1552 AAAAACAAAAA
1 AAAAAAAAAAA
1563 TTAAGCCCCT
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
92 1 0.01
93 27 0.30
94 58 0.64
95 5 0.05
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (94 bp):
AAAAAAAAAAAAATTAAACCTCTGTTTTTTTTTTTCTTACACTCAATTGGATACTTGAATTTCAA
AATACATAAAAAGGACCCTTAACTGTTTC
Found at i:1582 original size:94 final size:92
Alignment explanation
Indices: 1365--1583 Score: 239
Period size: 93 Copynumber: 2.3 Consensus size: 92
1355 CCTCAAATTA
* *
1365 AAAAAAAAAAAATTAAACCTCTGTTTTTTTTTTTTTTACACTCAATTGGGTACTTGAATTTCAAA
1 AAAAAAAAAAAATT-AACCTCTATTTTTTTTTTTTTTACACTCAATTGGATACTTGAATTTCAAA
1430 ATACATAAAAAGGACCCTTAAACGTTTC
65 ATACATAAAAAGGACCCTTAAACGTTTC
* * *
1458 AAAAAAAAAACAATTAAACTCTTATCTTTTTTTTTCTT-CACTCAATTGGATACTTGAACTTTCA
1 AAAAAAAAAA-AATTAACCTC-TATTTTTTTTTTTTTTACACTCAATTGGATACTTGAA-TTTCA
* * * *
1522 AAATGCACTAAAGA-TACCCTT-AACTTTTTC
63 AAATACA-TAAAAAGGACCCTTAAAC-GTTTC
* * *
1552 -AAAAACAAAAATTAAGCCCCTAATTTTTTTTT
1 AAAAAAAAAAAATTAA-CCTCTATTTTTTTTTT
1584 ACTCAATTGG
Statistics
Matches: 106, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
92 16 0.15
93 47 0.44
94 38 0.36
95 5 0.05
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.37
Consensus pattern (92 bp):
AAAAAAAAAAAATTAACCTCTATTTTTTTTTTTTTTACACTCAATTGGATACTTGAATTTCAAAA
TACATAAAAAGGACCCTTAAACGTTTC
Found at i:1784 original size:29 final size:30
Alignment explanation
Indices: 1738--1840 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 30
1728 AAGCTATAAA
*
1738 AATAAAAA-TAAATAAAATTTATTAAATTTT
1 AATAAAAATTATA-AAAATTTATTAAATTTT
* *
1768 AATAAAAA-TATAAAAATTAATT--TTTTT
1 AATAAAAATTATAAAAATTTATTAAATTTT
* *
1795 TATAAAAATTATAAAAAATTA-TAAACTTTT
1 AATAAAAATTATAAAAATTTATTAAA-TTTT
1825 -ATAAAAATTATAAAAA
1 AATAAAAATTATAAAAA
1841 AATCATAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 12 0.19
28 10 0.16
29 25 0.40
30 15 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
AATAAAAATTATAAAAATTTATTAAATTTT
Found at i:1813 original size:10 final size:10
Alignment explanation
Indices: 1794--1852 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
1784 TTAATTTTTT
1794 TTAT-AAAAA
1 TTATAAAAAA
1803 TTATAAAAAA
1 TTATAAAAAA
***
1813 TTATAAACTT
1 TTATAAAAAA
1823 TTAT-AAAAA
1 TTATAAAAAA
1832 TTATAAAAAAA
1 TTAT-AAAAAA
*
1843 TCATAAAAAA
1 TTATAAAAAA
1853 CCTTTTAACC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
9 10 0.25
10 22 0.55
11 8 0.20
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:1816 original size:19 final size:20
Alignment explanation
Indices: 1794--1840 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1784 TTAATTTTTT
1794 TTATAAAAATTATA-AAAAA
1 TTATAAAAATTATATAAAAA
* *
1813 TTAT-AAACTTTTATAAAAA
1 TTATAAAAATTATATAAAAA
1832 TTATAAAAA
1 TTATAAAAA
1841 AATCATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 13 0.57
20 3 0.13
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TTATAAAAATTATATAAAAA
Found at i:2070 original size:19 final size:19
Alignment explanation
Indices: 2024--2075 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2014 TAGTACGATA
2024 ATTTTTATATTTTTTTACG
1 ATTTTTATATTTTTTTACG
*
2043 AATTTTATATTTTTTTAC-
1 ATTTTTATATTTTTTTACG
2061 ATTTTCTATAATTTT
1 ATTTT-TAT-ATTTT
2076 CTTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 20 0.69
20 5 0.17
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTATATTTTTTTACG
Found at i:2074 original size:10 final size:10
Alignment explanation
Indices: 2061--2115 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
2051 ATTTTTTTAC
2061 ATTTTCTATA
1 ATTTTCTATA
*
2071 ATTTTCTTAAA
1 ATTTTC-TATA
* *
2082 ATTTTATAAA
1 ATTTTCTATA
2092 ATTTTCTAT-
1 ATTTTCTATA
2101 A-TTTCTATA
1 ATTTTCTATA
2110 TATTTT
1 -ATTTT
2116 ATAATCTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 18 0.49
11 11 0.30
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTCTATA
Found at i:2089 original size:19 final size:19
Alignment explanation
Indices: 2043--2090 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2033 TTTTTTTACG
* *
2043 AATTTTAT-ATTTTTTTAC
1 AATTTTATAATTTTCTTAA
*
2061 ATTTTCTATAATTTTCTTAA
1 AATTT-TATAATTTTCTTAA
2081 AATTTTATAA
1 AATTTTATAA
2091 AATTTTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 8 0.33
20 12 0.50
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTATAATTTTCTTAA
Found at i:2106 original size:29 final size:31
Alignment explanation
Indices: 2061--2188 Score: 85
Period size: 29 Copynumber: 4.3 Consensus size: 31
2051 ATTTTTTTAC
2061 ATTTTCTATAATTTTCT-TAAAATTTTATAAA
1 ATTTTCTATAATTTTCTAT-AAATTTTATAAA
* *
2092 ATTTTCTAT-A-TTTCTATATATTTTATAAT
1 ATTTTCTATAATTTTCTATAAATTTTATAAA
* * * *
2121 CTATT-T-TAATTTT-TAATAAA-ATT-TAAT
1 ATTTTCTATAATTTTCT-ATAAATTTTATAAA
* * *
2148 ATTTTTTATAGTTTT-TATAATTTTTAATAAA
1 ATTTTCTATAATTTTCTATAAATTTT-ATAAA
2179 ATTTTCTATA
1 ATTTTCTATA
2189 TATATATATA
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
27 8 0.11
28 10 0.13
29 34 0.45
30 2 0.03
31 21 0.28
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTTCTATAATTTTCTATAAATTTTATAAA
Found at i:2151 original size:19 final size:20
Alignment explanation
Indices: 2127--2182 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
2117 TAATCTATTT
2127 TAATTTTTAATAAAATTTAA
1 TAATTTTTAATAAAATTTAA
* ** *
2147 T-ATTTTTTAT-AGTTTTTA
1 TAATTTTTAATAAAATTTAA
2165 TAATTTTTAATAAAATTT
1 TAATTTTTAATAAAATTT
2183 TCTATATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
18 6 0.22
19 16 0.59
20 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TAATTTTTAATAAAATTTAA
Found at i:2164 original size:9 final size:9
Alignment explanation
Indices: 2021--2173 Score: 64
Period size: 9 Copynumber: 16.1 Consensus size: 9
2011 TTTTAGTACG
2021 ATAATTTTT
1 ATAATTTTT
2030 AT-ATTTTT
1 ATAATTTTT
* *
2038 TTACGAATTTT
1 ATA--ATTTTT
2049 AT-ATTTTT
1 ATAATTTTT
*
2057 TTACATTTTCT
1 ATA-ATTTT-T
2068 ATAATTTTCTT
1 ATAA-TTT-TT
*
2079 AAAATTTTAT
1 ATAATTTT-T
*
2089 AAAATTTTCT
1 ATAATTTT-T
*
2099 AT-ATTTCT
1 ATAATTTTT
2107 AT-ATATTTT
1 ATAAT-TTTT
2116 ATAATCTATTT
1 ATAAT-T-TTT
2127 -TAATTTTT
1 ATAATTTTT
* *
2135 AATAAAATTTA
1 -AT-AATTTTT
*
2146 ATATTTTTT
1 ATAATTTTT
*
2155 ATAGTTTTT
1 ATAATTTTT
2164 ATAATTTTT
1 ATAATTTTT
2173 A
1 A
2174 ATAAAATTTT
Statistics
Matches: 110, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
8 21 0.19
9 34 0.31
10 30 0.27
11 24 0.22
12 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:2177 original size:10 final size:10
Alignment explanation
Indices: 2127--2177 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
2117 TAATCTATTT
2127 TAATTTTTAA
1 TAATTTTTAA
**
2137 TAAAATTTAA
1 TAATTTTTAA
*
2147 T-ATTTTTTA
1 TAATTTTTAA
*
2156 TAGTTTTT-A
1 TAATTTTTAA
2165 TAATTTTTAA
1 TAATTTTTAA
2175 TAA
1 TAA
2178 AATTTTCTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 14 0.44
10 18 0.56
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:8529 original size:16 final size:15
Alignment explanation
Indices: 8496--8530 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
8486 AAGCCTTACC
*
8496 ATCAAGATGAGTCAG
1 ATCAAGATGAGGCAG
8511 ATCAAGATCGAGGCAG
1 ATCAAGAT-GAGGCAG
8527 ATCA
1 ATCA
8531 CACCGAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (15 bp):
ATCAAGATGAGGCAG
Found at i:16299 original size:25 final size:24
Alignment explanation
Indices: 16266--16317 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
16256 AAAAAAAAAT
16266 ATTTATGTTC-TTTTATAGTAATTA
1 ATTTATGTTCATTTTATA-TAATTA
16290 ATTTAATGTTCAATTTTATATAATTA
1 ATTT-ATGTTC-ATTTTATATAATTA
16316 AT
1 AT
16318 AATATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.16
25 6 0.24
26 8 0.32
27 7 0.28
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (24 bp):
ATTTATGTTCATTTTATATAATTA
Found at i:26355 original size:121 final size:121
Alignment explanation
Indices: 26173--26407 Score: 416
Period size: 121 Copynumber: 1.9 Consensus size: 121
26163 TTGGAGAATA
* *
26173 AAAATTCAGGATATTAAGCAAATTAGGAAAATTAATGATTCGATTTGAGGCTTAGAGTTAGGAAA
1 AAAATTCAGGACATTAAGCAAATTAGGAAAATTAAGGATTCGATTTGAGGCTTAGAGTTAGGAAA
*
26238 TAATTGGGGATTTTAGATTTAGTAATTTACATAAATTAGAAATTAAGGAAATTATG
66 TAATTGGGGATTTTAAATTTAGTAATTTACATAAATTAGAAATTAAGGAAATTATG
* *
26294 AAAATTCGGGACATTAAGCAAATTAGGAAAATTAAGGATTCGATTTGAGGCTTAGATTTAGGAAA
1 AAAATTCAGGACATTAAGCAAATTAGGAAAATTAAGGATTCGATTTGAGGCTTAGAGTTAGGAAA
*
26359 TAATTGGGGATTTTAAATTTAGTAATTTACATAAATTAGGAATTAAGGA
66 TAATTGGGGATTTTAAATTTAGTAATTTACATAAATTAGAAATTAAGGA
26408 TTTCAAAAAT
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 108 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (121 bp):
AAAATTCAGGACATTAAGCAAATTAGGAAAATTAAGGATTCGATTTGAGGCTTAGAGTTAGGAAA
TAATTGGGGATTTTAAATTTAGTAATTTACATAAATTAGAAATTAAGGAAATTATG
Found at i:27840 original size:9 final size:9
Alignment explanation
Indices: 27826--27864 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
27816 TAAGAATTAA
27826 AAATTAAAT
1 AAATTAAAT
27835 AAATTAAAT
1 AAATTAAAT
*
27844 -ATTTAAAT
1 AAATTAAAT
*
27852 AAATTAAAA
1 AAATTAAAT
27861 AAAT
1 AAAT
27865 CAAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:27851 original size:17 final size:16
Alignment explanation
Indices: 27820--27861 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
27810 TTGAATTAAG
27820 AATTAAAAATTAAATA
1 AATTAAAAATTAAATA
*
27836 AATTAAATATTTAAATA
1 AATTAAA-AATTAAATA
27853 AATTAAAAA
1 AATTAAAAA
27862 AATCAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAAAATTAAATA
Done.