Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002541.1 Kokia drynarioides strain JFW-HI SEQ_114722, 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: 17671
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Found at i:156 original size:60 final size:60
Alignment explanation
Indices: 65--305 Score: 284
Period size: 60 Copynumber: 4.0 Consensus size: 60
55 TCACCAACTT
*
65 CACCCATTAAGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTATCACCTC
1 CACCCATTAGGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTATCACCTC
** * * * * * * *
125 CACCTGTTAGGTCTCTACCTCCACCAATACAATCGCGACATCCACCATCTTTATCACCTT
1 CACCCATTAGGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTATCACCTC
* * * * * **
185 TACCCATCAGGTCTATACCACCACCAGTACAATCCCAACTTCCACCAACTCTATCACCAA
1 CACCCATTAGGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTATCACCTC
* * * * *
245 AACCCATTAGGTCTCTATCACCACCAGTACAGTCCCGACCTTCACCAACTCTATCTCCTC
1 CACCCATTAGGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTATCACCTC
305 C
1 C
306 TCCTGTTTTG
Statistics
Matches: 145, Mismatches: 36, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 145 1.00
ACGTcount: A:0.28, C:0.42, G:0.07, T:0.23
Consensus pattern (60 bp):
CACCCATTAGGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTATCACCTC
Found at i:2080 original size:30 final size:29
Alignment explanation
Indices: 2045--2324 Score: 245
Period size: 30 Copynumber: 9.3 Consensus size: 29
2035 CATAAATAAT
2045 ATTTTAACACCTAAACTTTTCCAAAATTAC
1 ATTTTAAC-CCTAAACTTTTCCAAAATTAC
* *
2075 ATTTTAACCACCAAACTTTTCCAAAATTTC
1 ATTTTAACC-CTAAACTTTTCCAAAATTAC
* **
2105 ATTTTGAACCTTAAGTTTTTCCAAAATTAC
1 ATTTT-AACCCTAAACTTTTCCAAAATTAC
* * *
2135 ATTTTTACCCCAAACCTTTCCAAAATTAC
1 ATTTTAACCCTAAACTTTTCCAAAATTAC
* *
2164 ATTTTAACCCCTGAACTTTTCTAAAATTAC
1 ATTTTAA-CCCTAAACTTTTCCAAAATTAC
* * * * *
2194 ATTTTTACCATTAAACTTCTCCAAAATCAT
1 ATTTTAACC-CTAAACTTTTCCAAAATTAC
* * *
2224 GTTTTAATCCCTAAACCTTTCTAAAATTAC
1 ATTTTAA-CCCTAAACTTTTCCAAAATTAC
* * * *
2254 ATTTTGACCCCTCAAACCTTCTCAAAAATCAC
1 ATTTT-AACCCT-AAA-CTTTTCCAAAATTAC
* * * *
2286 ATTTTGACCCTAAGCTTCTCCAAAATCAC
1 ATTTTAACCCTAAACTTTTCCAAAATTAC
2315 ATTTTAACCC
1 ATTTTAACCC
2325 CGTATTCTTT
Statistics
Matches: 198, Mismatches: 44, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
29 50 0.25
30 118 0.60
31 14 0.07
32 16 0.08
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
ATTTTAACCCTAAACTTTTCCAAAATTAC
Found at i:2256 original size:119 final size:121
Alignment explanation
Indices: 2045--2323 Score: 316
Period size: 119 Copynumber: 2.3 Consensus size: 121
2035 CATAAATAAT
* *
2045 ATTTTAACACCTAAACTTTTCCAAAATTACATTTTAACCACCAAACTTTTCCAAAATTTCATTTT
1 ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCACCAAACTTCTCCAAAA-TTCATTTT
* *** * * *
2110 GAACCTTAAGTTTTTCCAAAATTACATTTTTA-CCC-CAAACCTT-TCCAAAATTAC
65 GAACCCTAAACCTTTCCAAAATTACATTTTGACCCCTCAAACCTTCTCAAAAATCAC
* * * **
2164 ATTTTAACCCCTGAACTTTTCTAAAATTACATTTTTACCATTAAACTTCTCCAAAA-TCATGTTT
1 ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCACCAAACTTCTCCAAAATTCAT-TTT
* *
2228 TAATCCCTAAACCTTTCTAAAATTACATTTTGACCCCTCAAACCTTCTCAAAAATCAC
65 GAA-CCCTAAACCTTTCCAAAATTACATTTTGACCCCTCAAACCTTCTCAAAAATCAC
* * * *
2286 ATTTTGA-CCCTAAGCTTCTCCAAAATCACATTTTAACC
1 ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACC
2324 CCGTATTCTT
Statistics
Matches: 132, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
117 4 0.03
118 5 0.04
119 72 0.55
120 3 0.02
121 33 0.25
122 15 0.11
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (121 bp):
ATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCACCAAACTTCTCCAAAATTCATTTTG
AACCCTAAACCTTTCCAAAATTACATTTTGACCCCTCAAACCTTCTCAAAAATCAC
Found at i:9224 original size:10 final size:10
Alignment explanation
Indices: 9207--9240 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
9197 TATTTCACCT
9207 AAAAAAGAAA
1 AAAAAAGAAA
*
9217 AGAAAAGAAAA
1 AAAAAAG-AAA
9228 AAAAAAGAAA
1 AAAAAAGAAA
9238 AAA
1 AAA
9241 GAGAGGTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:9233 original size:16 final size:17
Alignment explanation
Indices: 9207--9238 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9197 TATTTCACCT
9207 AAAAAAGAAAAGAAAAG
1 AAAAAAGAAAAGAAAAG
9224 AAAAAA-AAAAGAAAA
1 AAAAAAGAAAAGAAAA
9239 AAGAGAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAAG
Found at i:9239 original size:11 final size:11
Alignment explanation
Indices: 9207--9240 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9197 TATTTCACCT
9207 AAAAAAG-AAA
1 AAAAAAGAAAA
*
9217 AGAAAAGAAAA
1 AAAAAAGAAAA
9228 AAAAAAGAAAA
1 AAAAAAGAAAA
9239 AA
1 AA
9241 GAGAGGTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:10604 original size:39 final size:39
Alignment explanation
Indices: 10555--10881 Score: 250
Period size: 39 Copynumber: 8.4 Consensus size: 39
10545 TGAAGATTCT
* *
10555 AATCTCTTACCCCGAGCCTGGGGCAGATTGCAGTCATCC
1 AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
* * * * *
10594 GATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATTC
1 AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
* * * * *
10633 AATCTTTTACCCCGAGCCTGGGGCAAATCAACATCGAT-C
1 AATCTCTTACCCCGAGCCTGGGGCAGAT-TACAGCCATCC
** * *
10672 AATCTCTTACCCCGAGCCTGAAGTAGATTGCAGCCATCC
1 AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
* *
10711 GATCTTTTACCCCGAGCCTGGGGCAGA-T-CA-CCATAGGCC
1 AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCAT---CC
* * * *
10750 AATCTCTTACCCTGAGCCTGAGGTAGATTACAGCCATTC
1 AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
* * * * * * * *
10789 GATCTTTTACACCAAGCCTGAGGCAGATCACCA-TCAGCC
1 AATCTCTTACCCCGAGCCTGGGGCAGATTA-CAGCCATCC
* * * **
10828 AATCTCTTACCCCGAGCTTGGGGCAAATTACAACCATTT
1 AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
*
10867 GATCTCTTACCCCGA
1 AATCTCTTACCCCGA
10882 TCATAGGGTA
Statistics
Matches: 223, Mismatches: 55, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
36 4 0.02
37 2 0.01
38 8 0.04
39 196 0.88
40 7 0.03
41 2 0.01
42 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
AATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATCC
Found at i:10651 original size:78 final size:77
Alignment explanation
Indices: 10537--10881 Score: 329
Period size: 78 Copynumber: 4.4 Consensus size: 77
10527 TAATCAAGAA
* * ** *
10537 GGGCAGATTGAAG--ATTCTAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGTCATCCGATCTC
1 GGGCAGATTGCAGCCATTC-AATCTTTTACCCCGAGCCTGGGGCAGATCACA-TCATCCAATCTC
*
10600 TTACCCCGAGCTTG
64 TTACCCCGAGCCTG
* *
10614 GGGCAGATTGCAGTCATTCAATCTTTTACCCCGAGCCTGGGGCAAATCAACATCGAT-CAATCTC
1 GGGCAGATTGCAGCCATTCAATCTTTTACCCCGAGCCTGGGGCAGATC-ACATC-ATCCAATCTC
10678 TTACCCCGAGCCTG
64 TTACCCCGAGCCTG
** * * * *
10692 AAGTAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGATCACCAT-AGGCCAATCTC
1 GGGCAGATTGCAGCCATTCAATCTTTTACCCCGAGCCTGGGGCAGATCA-CATCA-TCCAATCTC
*
10756 TTACCCTGAGCCTG
64 TTACCCCGAGCCTG
* * * * * * * *
10770 AGGTAGATTACAGCCATTCGATCTTTTACACCAAGCCTGAGGCAGATCACCATCAGCCAATCTCT
1 GGGCAGATTGCAGCCATTCAATCTTTTACCCCGAGCCTGGGGCAGATCA-CATCATCCAATCTCT
*
10835 TACCCCGAGCTTG
65 TACCCCGAGCCTG
* * * ** *
10848 GGGCAAATTACAACCATTTGATCTCTTACCCCGA
1 GGGCAGATTGCAGCCATTCAATCTTTTACCCCGA
10882 TCATAGGGTA
Statistics
Matches: 228, Mismatches: 32, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
76 1 0.00
77 13 0.06
78 205 0.90
79 9 0.04
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (77 bp):
GGGCAGATTGCAGCCATTCAATCTTTTACCCCGAGCCTGGGGCAGATCACATCATCCAATCTCTT
ACCCCGAGCCTG
Found at i:10761 original size:117 final size:117
Alignment explanation
Indices: 10555--10769 Score: 292
Period size: 117 Copynumber: 1.8 Consensus size: 117
10545 TGAAGATTCT
** * *
10555 AATCTCTTACCCCGAGCCTGGGGCAGATTGCAGTCATCCGATCTCTTACCCCGAGCTTGGGGCAG
1 AATCTCTTACCCCGAGCCTGAAGCAGATTGCAGCCATCCGATCTCTTACCCCGAGCCTGGGGCAG
* * *
10620 ATTGCAGTCATTCAATCTTTTACCCCGAGCCTGGGGCAAATCAACATCGATC
66 ATTGCAGCCATCCAATCTCTTACCCCGAGCCTGGGGCAAATCAACATCGATC
* *
10672 AATCTCTTACCCCGAGCCTGAAGTAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAG
1 AATCTCTTACCCCGAGCCTGAAGCAGATTGCAGCCATCCGATCTCTTACCCCGAGCCTGGGGCAG
*
10737 A-T-CA-CCATAGGCCAATCTCTTACCCTGAGCCTG
66 ATTGCAGCCAT---CCAATCTCTTACCCCGAGCCTG
10770 AGGTAGATTA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
114 3 0.04
115 2 0.02
116 1 0.01
117 79 0.93
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.24
Consensus pattern (117 bp):
AATCTCTTACCCCGAGCCTGAAGCAGATTGCAGCCATCCGATCTCTTACCCCGAGCCTGGGGCAG
ATTGCAGCCATCCAATCTCTTACCCCGAGCCTGGGGCAAATCAACATCGATC
Found at i:11120 original size:48 final size:48
Alignment explanation
Indices: 11041--11163 Score: 174
Period size: 48 Copynumber: 2.6 Consensus size: 48
11031 TTAAACCCTA
* * * * *
11041 TCTTTCTGATGAGATATAGAGAAATGGGTCAAAGCAATAAAGAGGACG
1 TCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAAGAAAAAGGACG
* * *
11089 TCTTCCTTATGAGATACAGAGAAGTGGGTCAAGGCAAGAAAAAGGTCG
1 TCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAAGAAAAAGGACG
11137 TCTTCCTGATGAGATACAGAGAAGTGG
1 TCTTCCTGATGAGATACAGAGAAGTGG
11164 ACCAAATTCG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAAGAAAAAGGACG
Found at i:12511 original size:18 final size:17
Alignment explanation
Indices: 12485--12520 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
12475 TTACCAGAAA
12485 AAAAGGAGAGAAAAAAG
1 AAAAGGAGAGAAAAAAG
*
12502 AAAAGAGAGAGAAGAAAG
1 AAAAG-GAGAGAAAAAAG
12520 A
1 A
12521 GGTTTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAAGGAGAGAAAAAAG
Found at i:12858 original size:30 final size:27
Alignment explanation
Indices: 12824--13016 Score: 131
Period size: 30 Copynumber: 6.5 Consensus size: 27
12814 TAAGTCCCTG
12824 AACTTTTCATAAATCATATCTTAACCCTTA
1 AACTTTTCA-AAATCAT-T-TTAACCCTTA
* *
12854 AACTTCTCCAAAAATACATTTTAACCCCTA
1 AACTT-TTC-AAAAT-CATTTTAACCCTTA
*
12884 AA-TTTTACCAAAATTTCATTTTGACCC-TA
1 AACTTTT--CAAAA--TCATTTTAACCCTTA
12913 AACTTTTCTAAAATTTCATTTTAACCCTTA
1 AACTTTTC-AAAA--TCATTTTAACCCTTA
12943 AACTTTTCCAAAATTACATTTTAACCCTTA
1 AACTTTT-CAAAA-T-CATTTTAACCCTTA
*
12973 AACTTCTCCAAAATAACATTTTAATCCC-TA
1 AACTT-TTCAAAAT--CATTTTAA-CCCTTA
*
13003 AACCTTTCTAAAAT
1 AACTTTTC-AAAAT
13017 TATATTTTGA
Statistics
Matches: 139, Mismatches: 8, Indels: 32
0.78 0.04 0.18
Matches are distributed among these distances:
28 2 0.01
29 32 0.23
30 88 0.63
31 13 0.09
32 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (27 bp):
AACTTTTCAAAATCATTTTAACCCTTA
Found at i:12911 original size:29 final size:29
Alignment explanation
Indices: 12844--13119 Score: 232
Period size: 30 Copynumber: 9.2 Consensus size: 29
12834 AAATCATATC
* *
12844 TTAACCCTTAAACTTCTCCAAAAATACATT
1 TTAACCC-TAAACTTTTCCAAAATTACATT
*
12874 TTAACCCCTAAA-TTTTACCAAAATTTCATT
1 TTAA-CCCTAAACTTTT-CCAAAATTACATT
* * *
12904 TTGACCCTAAACTTTTCTAAAATTTCATT
1 TTAACCCTAAACTTTTCCAAAATTACATT
12933 TTAACCCTTAAACTTTTCCAAAATTACATT
1 TTAACCC-TAAACTTTTCCAAAATTACATT
* *
12963 TTAACCCTTAAACTTCTCCAAAATAACATT
1 TTAACCC-TAAACTTTTCCAAAATTACATT
* * *
12993 TTAATCCCTAAACCTTTCTAAAATTATATT
1 TTAA-CCCTAAACTTTTCCAAAATTACATT
* * * **
13023 TTGACCCCTCAAACTTCTCCAAAATCATGTT
1 TT-AACCCT-AAACTTTTCCAAAATTACATT
* * * *
13054 TTGACCCTCAACCCTTCTT-AAAAATCACATT
1 TTAACCCT-AA-ACTT-TTCCAAAATTACATT
* * *
13085 TTGACCCTAAACTTCTCCAAAATCACATT
1 TTAACCCTAAACTTTTCCAAAATTACATT
13114 TTAACC
1 TTAACC
13120 TCATTTTCAA
Statistics
Matches: 204, Mismatches: 32, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
28 1 0.00
29 47 0.23
30 110 0.54
31 45 0.22
32 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAACCCTAAACTTTTCCAAAATTACATT
Found at i:13005 original size:60 final size:59
Alignment explanation
Indices: 12844--13119 Score: 256
Period size: 60 Copynumber: 4.6 Consensus size: 59
12834 AAATCATATC
*
12844 TTAACCCTTAAACTTCTCCAAAA-ATACATTTTAACCCCTAAA-TTTTACCAAAATTTCATT
1 TTAACCCTTAAACTTCTCCAAAATA-ACATTTTAA-CCCTAAACTTTT-CCAAAATTACATT
* * * **
12904 TTGACCC-TAAACTTTTCTAAAATTTCATTTTAACCCTTAAACTTTTCCAAAATTACATT
1 TTAACCCTTAAACTTCTCCAAAATAACATTTTAACCC-TAAACTTTTCCAAAATTACATT
* * *
12963 TTAACCCTTAAACTTCTCCAAAATAACATTTTAATCCCTAAACCTTTCTAAAATTATATT
1 TTAACCCTTAAACTTCTCCAAAATAACATTTTAA-CCCTAAACTTTTCCAAAATTACATT
* * * ** * * * *
13023 TTGACCCCTCAAACTTCTCCAAAATCATGTTTTGACCCTCAACCCTTCTT-AAAAATCACATT
1 TT-AACCCTTAAACTTCTCCAAAATAACATTTTAACCCT-AA-ACTT-TTCCAAAATTACATT
* *
13085 TTGACCC-TAAACTTCTCCAAAATCACATTTTAACC
1 TTAACCCTTAAACTTCTCCAAAATAACATTTTAACC
13120 TCATTTTCAA
Statistics
Matches: 176, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
58 3 0.02
59 43 0.24
60 81 0.46
61 34 0.19
62 13 0.07
63 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (59 bp):
TTAACCCTTAAACTTCTCCAAAATAACATTTTAACCCTAAACTTTTCCAAAATTACATT
Found at i:13126 original size:11 final size:12
Alignment explanation
Indices: 13110--13138 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13100 TCCAAAATCA
13110 CATTTT-AACCT
1 CATTTTCAACCT
13121 CATTTTCAACCT
1 CATTTTCAACCT
13133 CATTTT
1 CATTTT
13139 TTCCTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CATTTTCAACCT
Found at i:14868 original size:57 final size:57
Alignment explanation
Indices: 14800--14913 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
14790 CTATTGTAAG
14800 ATAGAAAACACAAGTTATATTTGGTAAATTTAAAATAGTATATAAATATGAGCCTTA
1 ATAGAAAACACAAGTTATATTTGGTAAATTTAAAATAGTATATAAATATGAGCCTTA
14857 ATAGAAAACACAAGTTATATTTGGTAAATTTAAAATAGTATATAAATATGAGCCTTA
1 ATAGAAAACACAAGTTATATTTGGTAAATTTAAAATAGTATATAAATATGAGCCTTA
14914 CATTTCGCGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (57 bp):
ATAGAAAACACAAGTTATATTTGGTAAATTTAAAATAGTATATAAATATGAGCCTTA
Found at i:16975 original size:42 final size:42
Alignment explanation
Indices: 16913--17184 Score: 120
Period size: 42 Copynumber: 6.5 Consensus size: 42
16903 AGATTCACCA
* *
16913 TCACCACCA-T-C-CGTCTACTCCTCACCCTCACCAATGGAC
1 TCACCACCACTACTCGTCCACTCCTCACCCTCATCAATGGAC
*
16952 TCACCACCACTACTCGTCCACTCCCCACACC-CATCAGA-GCG-C
1 TCACCACCACTACTCGTCCACTCCTCAC-CCTCATCA-ATG-GAC
* * * * * * *
16994 TTACCAACACT-TTCCATCCA-TACCTCACCCCCA-CTAGGGCAC
1 TCACCACCACTACT-CGTCCACT-CCTCACCCTCATCAATGG-AC
* * * *
17036 TCACCATCACCA-TCCGTCCACT-CTCAACCCTCATCAGTGCAC
1 TCACCACCACTACT-CGTCCACTCCTC-ACCCTCATCAATGGAC
* * * * * * **
17078 TCACCACCACAACTCGACCACTCCCCA-CATCAATTAGTACAC
1 TCACCACCACTACTCGTCCACTCCTCACCCTC-ATCAATGGAC
* *
17120 TCTCCACCACTA-TCTGTCCACTCCTCACCCTCACCAATGGAC
1 TCACCACCACTACTC-GTCCACTCCTCACCCTCATCAATGGAC
* * *
17162 TCACCACGACCACCCGTCCACTC
1 TCACCACCACTACTCGTCCACTC
17185 ACCACCAACA
Statistics
Matches: 172, Mismatches: 39, Indels: 41
0.68 0.15 0.16
Matches are distributed among these distances:
39 9 0.05
40 3 0.02
41 15 0.09
42 131 0.76
43 14 0.08
ACGTcount: A:0.25, C:0.49, G:0.07, T:0.19
Consensus pattern (42 bp):
TCACCACCACTACTCGTCCACTCCTCACCCTCATCAATGGAC
Found at i:17146 original size:126 final size:124
Alignment explanation
Indices: 16917--17184 Score: 274
Period size: 126 Copynumber: 2.1 Consensus size: 124
16907 TCACCATCAC
* * * *
16917 CACCATCCGTCTACTCCTCACCCTCACCAATGGACTCACCACCACTACTCGTCCACTCCCCACAC
1 CACCATCCGTCCACT-CTCACCCTCACCAATGCACTCACCACCACAACTCGACCACTCCCCACAC
* * * *
16982 CCATCAGAGCGCTTACCAACACTTTCCATCCATACCTCACCCCCA-CTAGGGCACTCACCA
65 CAATCAGAGCACTTACCAACACTATCCATCCATACCTCACCCCCACCAAGGG-ACTCACCA
* *
17042 TCACCATCCGTCCACTCTCAACCCTCATCAGTGCACTCACCACCACAACTCGACCACTCCCCACA
1 -CACCATCCGTCCACTCTC-ACCCTCACCAATGCACTCACCACCACAACTCGACCACTCCCCACA
* * * ** * *
17107 TCAATTAGTA-CACTCT-CCACCACTATCTGTCCACT-CCTCACCCTCACCAATGGACTCACCA
64 CCAATCAG-AGCACT-TACCAACACTATCCATCCA-TACCTCACCCCCACCAAGGGACTCACCA
*
17168 CGACCACCCGTCCACTC
1 C-ACCATCCGTCCACTC
17185 ACCACCAACA
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
125 4 0.03
126 107 0.91
127 7 0.06
ACGTcount: A:0.25, C:0.49, G:0.07, T:0.19
Consensus pattern (124 bp):
CACCATCCGTCCACTCTCACCCTCACCAATGCACTCACCACCACAACTCGACCACTCCCCACACC
AATCAGAGCACTTACCAACACTATCCATCCATACCTCACCCCCACCAAGGGACTCACCA
Found at i:17183 original size:84 final size:84
Alignment explanation
Indices: 17033--17189 Score: 190
Period size: 84 Copynumber: 1.9 Consensus size: 84
17023 CCCACTAGGG
* * * *
17033 CACTCACCATCACCATCCGTCCACTCTCAACCCTCATCAGTGCACTCACCACCACAACTCGACCA
1 CACTCACCACCACCATCCGTCCACTCTCAACCCTCACCAATGCACTCACCACCACAACCCGACCA
*
17098 CTCCCCACATCAATTAGTA
66 CTCACCACATCAATTAGTA
* * * * * * *
17117 CACTCTCCACCACTATCTGTCCACTCCTC-ACCCTCACCAATGGACTCACCACGACCACCCGTCC
1 CACTCACCACCACCATCCGTCCACT-CTCAACCCTCACCAATGCACTCACCACCACAACCCGACC
17181 ACTCACCAC
65 ACTCACCAC
17190 CAACATTAGA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
84 57 0.95
85 3 0.05
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.18
Consensus pattern (84 bp):
CACTCACCACCACCATCCGTCCACTCTCAACCCTCACCAATGCACTCACCACCACAACCCGACCA
CTCACCACATCAATTAGTA
Found at i:17296 original size:42 final size:42
Alignment explanation
Indices: 17232--17321 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
17222 CACTCCTCAT
** * * *
17232 CCCCACTAGATTATTCACCACCACCACTCATCCATTCTTTAC
1 CCCCACTAGAGCATTCACCACCACCACCCATCCATTCTTCAA
* * *
17274 CCCCACTAGAGCATTCATCACCACTACCCGTCCATTCTTCAA
1 CCCCACTAGAGCATTCACCACCACCACCCATCCATTCTTCAA
17316 CCCCAC
1 CCCCAC
17322 AAGGGCTCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.46, G:0.04, T:0.24
Consensus pattern (42 bp):
CCCCACTAGAGCATTCACCACCACCACCCATCCATTCTTCAA
Done.