Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011582.1 Kokia drynarioides strain JFW-HI SEQ_126571, 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: 189587
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:127 original size:76 final size:76
Alignment explanation
Indices: 1--229 Score: 302
Period size: 76 Copynumber: 3.0 Consensus size: 76
1 TAAAAAACATTTTGAATTTCGTAGAAAATAATAAATAAACAATTAATAAATATATTAATATATAA
1 TAAAAAACATTTTGAATTTCGTAGAAAATAATAAATAAACAATTAATAAATATATTAATATATAA
66 TAAATAATAAG
66 TAAATAATAAG
77 TAAAAAACATTTTGAATTTCGTAGAAAATAATAAATAAACAATTAATAAATATATTAATATATAT
1 TAAAAAACATTTTGAATTTCGTAGAAAATAATAAATAAACAATTAATAAATATATTAATATATA-
142 ATTTAAA-AATAAG
65 A--TAAATAATAAG
* * * * * * * *
155 -AAAAAAAAGGCTTTGAAATTCGAAGGGAAATAATAAATAAGCAATAAATAAGTATATTAATATA
1 TAAAAAACA--TTTTGAATTTCGTA-GAAAATAATAAATAAACAATTAATAAATATATTAATATA
*
219 T-TTAAATAATA
63 TAATAAATAATA
230 TACCTTAAGA
Statistics
Matches: 137, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
76 68 0.50
77 12 0.09
78 6 0.04
79 15 0.11
80 36 0.26
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (76 bp):
TAAAAAACATTTTGAATTTCGTAGAAAATAATAAATAAACAATTAATAAATATATTAATATATAA
TAAATAATAAG
Found at i:328 original size:23 final size:22
Alignment explanation
Indices: 299--343 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
289 CTATTGCTTC
*
299 GTGTATTTTTCTATTGATTTCGA
1 GTGTA-TTGTCTATTGATTTCGA
*
322 GTGTATTGTGTATTGATTTCGA
1 GTGTATTGTCTATTGATTTCGA
344 AAATGTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.18, C:0.07, G:0.22, T:0.53
Consensus pattern (22 bp):
GTGTATTGTCTATTGATTTCGA
Found at i:1642 original size:208 final size:208
Alignment explanation
Indices: 1039--1735 Score: 932
Period size: 208 Copynumber: 3.3 Consensus size: 208
1029 CATCTTTTGG
* * * * * *
1039 TCCACTTCTCTGTATCTCATCAGTAAGACGGATTTGGTTCACTTCTTTGTATCTTATCAGGAAGA
1 TCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
* * * *
1104 TGACTGCTTTATTGCTTTATTACTTTAACCCACTTCTCTATATCTCATCAAGAAGATGGGGGTTT
66 TGA-T-C------GCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGAT-GGGGTTT
* * * *
1169 GAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTTTTTGTATCTCATCAGGAA
122 GAACTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAA
*
1234 GATGACCACTTCCTTGATTTAA
187 GATGACCACTTCATTGATTTAA
* * * * *
1256 TCCACTTCTTTATATCTCATCAAGAACGTGGATTTGGTCCACTTCTC--TATCTCATCAGGAAGG
1 TCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
* *
1319 TGATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATTAGGCAGATGGGGTTTGAACTTTCA
66 TGATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAACTTTCA
*
1384 CTCACATTGAGCTTTGTTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCAC
131 CTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCAC
*
1449 TTTATTGATTTAA
196 TTCATTGATTTAA
* * * * *
1462 TCCACTTTTATGTATCTCATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGA
1 TCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
1527 TGATCGC-TTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAACTTTC
66 TGATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGAT-GGGGTTTGAACTTTC
* * * * *
1591 ACTCACATTGAGCTTTGCTTCATTAATTTAGTCTACTTCTCTATTTCTCATCAGAAAGATGACCG
130 ACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCA
*
1656 CTTCATTAATTTAA
195 CTTCATTGATTTAA
* * * *
1670 TTCACTTCTCTATATCTCATCAGGAAGGCGAATTTAGTTCACTTCTCTGTATCTCATCAGGAAGA
1 TCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
1735 T
66 T
1736 AGGGTTTGAA
Statistics
Matches: 425, Mismatches: 52, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
206 127 0.30
207 77 0.18
208 164 0.39
213 1 0.00
214 1 0.00
215 17 0.04
217 38 0.09
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (208 bp):
TCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGA
TGATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAACTTTCA
CTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCAC
TTCATTGATTTAA
Found at i:1704 original size:37 final size:37
Alignment explanation
Indices: 1663--1733 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1653 CCGCTTCATT
1663 AATTTAATTCACTTCTCTATATCTCATCAGGAAGGCG
1 AATTTAATTCACTTCTCTATATCTCATCAGGAAGGCG
* *
1700 AATTTAGTTCACTTCTCTGTATCTCATCAGGAAG
1 AATTTAATTCACTTCTCTATATCTCATCAGGAAG
1734 ATAGGGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (37 bp):
AATTTAATTCACTTCTCTATATCTCATCAGGAAGGCG
Found at i:1756 original size:368 final size:368
Alignment explanation
Indices: 1340--2103 Score: 1156
Period size: 368 Copynumber: 2.1 Consensus size: 368
1330 TTGCTTTGAC
* * * *
1340 CCACTTCTCTGTATCTCATTAGGCAGATGGGGTTTGAACTTTCACTCACATTGAGCTTTGTTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
* *
1405 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTTATTGATTTAATCCACTTT
66 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTC
* *
1470 TATGTATCTCATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCT-CATTAGGAAGATGATCGC
131 TATGTATCTCATCAGGAA-GCAGATTTGGTCCACTTCTCTGTAT-TACATCAAGAAGATGATCGC
*
1534 -TTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGG-GGTTTGAACTTTCACTCAC
194 TTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGAT-GGTGGTTTGAACTTTCACTCAC
* * * *
1597 ATTGAGCTTTGCTTCATTAATTTAGTCTACTTCTCTATTTCTCATCAGAAAGATGACCGCTTCAT
258 ATTGAACTTTCCTTCATTAATTTAGTCTACTTCTCTATATCTCATCAGAAAGATGACCACTTCAT
* * *
1662 TAATTTAATTCACTTCTCTATATCTCATCAGGAAGGCGAATTTAGT
323 TAATTTAATCCACTTCTCTACATCTCATCAGGAAGACGAATTTAGT
* *
1708 TCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
* *
1773 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTC
* * * * *
1838 TCTGTATCTCATCAGGAAGCGGATTTGGTTCACTTCTCTGTATTACGTCAAGAAGATGATTGCTT
131 TATGTATCTCATCAGGAAGCAGATTTGGTCCACTTCTCTGTATTACATCAAGAAGATGATCGCTT
* * *
1903 TATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGGTGGTGGTTTGAAGTTTTACTCACATT
196 TATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGATGGTGGTTTGAACTTTCACTCACATT
* * * *
1968 GAACTTTCCTTCATTGATTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGA
261 GAACTTTCCTTCATTAATTTAGTCTACTTCTCTATATCTCATCAGAAAGATGACCACTTCATTAA
* * *
2033 TTTAATCCACTTCTCTGCATCTCATTAGGAAGACGAATTTGGT
326 TTTAATCCACTTCTCTACATCTCATCAGGAAGACGAATTTAGT
*
2076 CCACTTCTTTGTATCTCATCAGGAAGAT
1 CCACTTCTCTGTATCTCATCAGGAAGAT
2104 GACCGCTTTA
Statistics
Matches: 356, Mismatches: 37, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
366 1 0.00
367 39 0.11
368 316 0.89
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (368 bp):
CCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTC
TATGTATCTCATCAGGAAGCAGATTTGGTCCACTTCTCTGTATTACATCAAGAAGATGATCGCTT
TATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGATGGTGGTTTGAACTTTCACTCACATT
GAACTTTCCTTCATTAATTTAGTCTACTTCTCTATATCTCATCAGAAAGATGACCACTTCATTAA
TTTAATCCACTTCTCTACATCTCATCAGGAAGACGAATTTAGT
Found at i:1759 original size:160 final size:160
Alignment explanation
Indices: 1548--1880 Score: 551
Period size: 160 Copynumber: 2.1 Consensus size: 160
1538 TGCTTTGACC
1548 CACTTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
1 CACTTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
* *
1613 TTAATTTAGTCTACTTCTCTATTTCTCATCAGAAAGATGACCGCTTCATTAATTTAATTCACTTC
66 TTAATTTAGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTAATTTAATCCACTTC
1678 TCTATATCTCATCAGGAAGGCGAATTTAGTT
131 TCTATATCTCATCAGGAA-GCGAATTTAGTT
*
1709 CACTTCTCTGTATCTCATCAGGAAGATA-GGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 CACTTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
* * * * *
1773 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
66 TTAATTTAGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTAATTTAATCCACTTC
* * *
1838 TCTGTATCTCATCAGGAAGCGGATTTGGTT
131 TCTATATCTCATCAGGAAGCGAATTTAGTT
1868 CACTTCTCTGTAT
1 CACTTCTCTGTAT
1881 TACGTCAAGA
Statistics
Matches: 161, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
159 23 0.14
160 110 0.68
161 28 0.17
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (160 bp):
CACTTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAACTTTCACTCACATTGAGCTTTGCTTCA
TTAATTTAGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTAATTTAATCCACTTC
TCTATATCTCATCAGGAAGCGAATTTAGTT
Found at i:1919 original size:84 final size:84
Alignment explanation
Indices: 1775--1940 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 84
1765 TTGCTTCATT
* *
1775 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
*
1840 TGTATCTCATCAGGAAGCG
66 TATATCTCATCAGGAAGCG
* ** * * *
1859 GATTTGGT-TCACTTCTCTGTAT-TACGTCAAGAAGATGATTGCTTTATTGCTTTGACCCACTTC
1 GATTTGGTCT-ACTTCTCTGTATCT-CATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTC
1922 TCTATATCTCATCAGGAAG
64 TCTATATCTCATCAGGAAG
1941 GTGGTGGTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
83 2 0.03
84 69 0.97
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (84 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
TATATCTCATCAGGAAGCG
Found at i:2140 original size:85 final size:85
Alignment explanation
Indices: 1984--2148 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
1974 TCCTTCATTG
* *
1984 ATTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTCTCT
1 ATTTAGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAACCCACTTCTCT
* *
2049 GCATCTCATTAGGAAGACGA
66 ACATCTCATCAGGAAGACGA
* * * * * * * *
2069 ATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTTTGT
1 ATTTAGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAACCCACTTCTCT
*
2134 ATATCTCATCAGGAA
66 ACATCTCATCAGGAA
2149 AGTAGGGGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
ATTTAGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAACCCACTTCTCT
ACATCTCATCAGGAAGACGA
Found at i:2177 original size:209 final size:209
Alignment explanation
Indices: 1709--2649 Score: 1247
Period size: 209 Copynumber: 4.5 Consensus size: 209
1699 GAATTTAGTT
* * *
1709 CACTTCTCTGTATCTCATCAGG-AAGATA-GGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
1 CACTTCTCTATATCTCATCAGGAAAG-TAGGGGTTTGAAGTTTTACTCACATTGAGCTTTCCTTC
*
1772 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTT
65 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTT
* * * * * **
1837 CTCTGTATCTCATCAGGAAG-CGGATTTGGTTCACTTCTCTGTAT-TACGTCAAGAAGATGATTG
130 CTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCT-CATCAGGAAGATGACCG
1900 CTTTATTGCTTTGACC
194 CTTTATTGCTTTGACC
* *
1916 CACTTCTCTATATCTCATCAGGAAGGT-GGTGGTTTGAAGTTTTACTCACATTGAACTTTCCTTC
1 CACTTCTCTATATCTCATCAGGAAAGTAGG-GGTTTGAAGTTTTACTCACATTGAGCTTTCCTTC
*
1980 ATTGATTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTT
65 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTT
* *
2045 CTCTGCATCTCATTAGGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCGC
130 CTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
2110 TTTATTGCTTTGACC
195 TTTATTGCTTTGACC
* * * *
2125 CACTTTTGTATATCTCATCAGGAAAGTAGGGGTTTGAAGTTTCAATCACATTGAGCTTTCCTTCA
1 CACTTCTCTATATCTCATCAGGAAAGTAGGGGTTTGAAGTTTTACTCACATTGAGCTTTCCTTCA
* * * * *
2190 TTGATTTAGTTTACTTTTCTGTATCTCATCAAGAAGATGACCACTTCATTGATTTAACCCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTC
*
2255 TCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATTTCATCAGGAAGATGACCGCT
131 TCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
*
2320 TTATTACTTTGACC
196 TTATTGCTTTGACC
* * * * * *
2334 CACTTTTCTGTATCTCATCA--ATA-TGATGAGGGTTTGAAGTTTTGCTCACATTAAGCTTTGCT
1 CACTTCTCTATATCTCATCAGGAAAGT-A-G-GGGTTTGAAGTTTTACTCACATTGAGCTTTCCT
* ** *
2396 TCATTAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGATTTAATCCAC
63 TCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCAC
* * * * * *
2461 TTCTCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTT-TGTTGTATCTCGTGAGGAAGATAAC
128 TTCTCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCT-CTGTATCTCATCAGGAAGATGAC
* *
2525 TGCTTTATTGCTTTGATC
192 CGCTTTATTGCTTTGACC
* * * * *
2543 CACTTCTCTGTATCTCATCAGGAAGGTGGGGGTTTGAAGTTTTGCTCACATTGGGC-TTCACTTC
1 CACTTCTCTATATCTCATCAGGAAAGTAGGGGTTTGAAGTTTTACTCACATTGAGCTTTC-CTTC
* * *
2607 ATT-ATTCTGGTTTACTTCTCTGTATCTCATCAAGAACATGACC
65 ATTGATT-TGGTCTACTTCTCTGTATCTCATCAGGAAGATGACC
2650 GTTTGAAGTT
Statistics
Matches: 651, Mismatches: 68, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
206 1 0.00
207 26 0.04
208 121 0.19
209 497 0.76
210 4 0.01
211 1 0.00
212 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (209 bp):
CACTTCTCTATATCTCATCAGGAAAGTAGGGGTTTGAAGTTTTACTCACATTGAGCTTTCCTTCA
TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTC
TCTGCATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
TTATTGCTTTGACC
Found at i:2463 original size:48 final size:48
Alignment explanation
Indices: 2392--2567 Score: 160
Period size: 48 Copynumber: 3.9 Consensus size: 48
2382 CATTAAGCTT
* * * *
2392 TGCTTCATTAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAC
1 TGCTTTATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
*
2440 TGCTTTATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAG--G-C
1 TGCTTTATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
* * * * *
2485 -G----A---ATTTGGTCCACTT-TGTTGTATCTCGTGAGGAAGATAAC
1 TGCTTTATTGATTTGATCCACTTCT-CTGTATCTCATCAGGAAGATGAC
*
2525 TGCTTTATTGCTTTGATCCACTTCTCTGTATCTCATCAGGAAG
1 TGCTTTATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAG
2568 GTGGGGGTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
36 1 0.01
37 26 0.26
40 2 0.02
41 1 0.01
44 1 0.01
45 2 0.02
46 1 0.01
48 64 0.65
49 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (48 bp):
TGCTTTATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAC
Found at i:2544 original size:85 final size:85
Alignment explanation
Indices: 2401--2568 Score: 257
Period size: 85 Copynumber: 2.0 Consensus size: 85
2391 TTGCTTCATT
* *
2401 AATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGATTTAATCCACTTCTC
1 AATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATAACTGCTTTATTGATTTAATCCACTTCTC
2466 TGTATCTCATCAGGAAGGCG
66 TGTATCTCATCAGGAAGGCG
* * * * *
2486 AATTTGGTCCACTT-TGTTGTATCTCGTGAGGAAGATAACTGCTTTATTGCTTTGATCCACTTCT
1 AATTTGGTCCACTTCT-CTGTATCTCATCAGGAAGATAACTGCTTTATTGATTTAATCCACTTCT
2550 CTGTATCTCATCAGGAAGG
65 CTGTATCTCATCAGGAAGG
2569 TGGGGGTTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
84 1 0.01
85 74 0.99
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (85 bp):
AATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATAACTGCTTTATTGATTTAATCCACTTCTC
TGTATCTCATCAGGAAGGCG
Found at i:7808 original size:14 final size:15
Alignment explanation
Indices: 7772--7808 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7762 TTTTATTTTT
7772 ATGTATG-TAATGAA
1 ATGTATGCTAATGAA
7786 ATGTAATGCTAAT-AA
1 ATGT-ATGCTAATGAA
7801 ATGTATGC
1 ATGTATGC
7809 ATGTAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 9 0.43
16 4 0.19
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (15 bp):
ATGTATGCTAATGAA
Found at i:11356 original size:20 final size:20
Alignment explanation
Indices: 11319--11363 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11309 CAATTACATT
*
11319 AATAATAAATATACAAAACA
1 AATAATAAAAATACAAAACA
*
11339 AATATATAAAAATA-AAAATA
1 AATA-ATAAAAATACAAAACA
11359 AATAA
1 AATAA
11364 AATACACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.59
21 8 0.36
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (20 bp):
AATAATAAAAATACAAAACA
Found at i:11585 original size:30 final size:30
Alignment explanation
Indices: 11536--11648 Score: 95
Period size: 30 Copynumber: 3.8 Consensus size: 30
11526 AAAAATGAAA
** *
11536 TTTTGTGGAAGTTCGAGGGTCAAATCCAAAT
1 TTTTG-GGAAGTTTAAGGGTCAAAACCAAAT
* **
11567 TTTTGGGAAGTTTAAGGGTTAAAACTTAAT
1 TTTTGGGAAGTTTAAGGGTCAAAACCAAAT
* * **
11597 TTTTGGAAAGTTTAGGGGTCAAAACTTAA-
1 TTTTGGGAAGTTTAAGGGTCAAAACCAAAT
* *
11626 TTTTGGAAAGTTT-AGGGTTAAAA
1 TTTTGGGAAGTTTAAGGGTCAAAA
11649 TATAATTTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
28 8 0.11
29 13 0.18
30 45 0.63
31 5 0.07
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (30 bp):
TTTTGGGAAGTTTAAGGGTCAAAACCAAAT
Found at i:11678 original size:30 final size:29
Alignment explanation
Indices: 11567--11687 Score: 149
Period size: 30 Copynumber: 4.1 Consensus size: 29
11557 AAATCCAAAT
*
11567 TTTTGGGAAGTTTAAGGGTTAAAACTTAA
1 TTTTGGAAAGTTTAAGGGTTAAAACTTAA
* *
11596 TTTTTGGAAAGTTTAGGGGTCAAAACTTAA
1 -TTTTGGAAAGTTTAAGGGTTAAAACTTAA
11626 TTTTGGAAAGTTT-AGGGTTAAAA-TATAA
1 TTTTGGAAAGTTTAAGGGTTAAAACT-TAA
*
11654 TTTTGGAAAAGTTTAAGAGTTAAAA-TGTAA
1 TTTTGG-AAAGTTTAAGGGTTAAAACT-TAA
11684 TTTT
1 TTTT
11688 TGAATAAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
27 1 0.01
28 17 0.21
29 20 0.25
30 43 0.53
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (29 bp):
TTTTGGAAAGTTTAAGGGTTAAAACTTAA
Found at i:11685 original size:58 final size:59
Alignment explanation
Indices: 11567--11687 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 59
11557 AAATCCAAAT
* * *
11567 TTTTGGGAAGTTTAAGGGTTAAAACTTAATTTTTGGAAAGTTTAGGGGTCAAAACTTAA
1 TTTTGGAAAGTTTAAGGGTTAAAACTTAATTTTTGGAAAGTTTAAGAGTCAAAACTTAA
*
11626 TTTTGGAAAGTTT-AGGGTTAAAA-TATAA-TTTTGGAAAAGTTTAAGAGTTAAAA-TGTAA
1 TTTTGGAAAGTTTAAGGGTTAAAACT-TAATTTTTGG-AAAGTTTAAGAGTCAAAACT-TAA
11684 TTTT
1 TTTT
11688 TGAATAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
57 8 0.15
58 35 0.64
59 12 0.22
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (59 bp):
TTTTGGAAAGTTTAAGGGTTAAAACTTAATTTTTGGAAAGTTTAAGAGTCAAAACTTAA
Found at i:12662 original size:30 final size:30
Alignment explanation
Indices: 12615--12687 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
12605 AAAAATAATA
*
12615 AATAAACAATTAA-TAAATATATTAATATAT
1 AATAAA-AAATAAGTAAATATATTAATATAT
12645 AATAAAAAATAAGTAAATATATTAATATAT
1 AATAAAAAATAAGTAAATATATTAATATAT
* *
12675 ATTTAAAAATAAG
1 AATAAAAAATAAG
12688 AAAAAAAGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
AATAAAAAATAAGTAAATATATTAATATAT
Found at i:12761 original size:13 final size:13
Alignment explanation
Indices: 12743--12775 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12733 ATAAGTATAT
12743 TAATATATTTAAA
1 TAATATATTTAAA
12756 TAATATATTTAAA
1 TAATATATTTAAA
12769 TAATATA
1 TAATATA
12776 CCTTAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATATATTTAAA
Found at i:18041 original size:11 final size:11
Alignment explanation
Indices: 18022--18051 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18012 TTAGGATATT
18022 ATTTATATTTA
1 ATTTATATTTA
*
18033 ATTTGTATTTA
1 ATTTATATTTA
18044 ATTTATAT
1 ATTTATAT
18052 ATATCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:19632 original size:20 final size:20
Alignment explanation
Indices: 19607--19644 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19597 ACAGTTTACT
*
19607 GTTGACCGTTGACTTTTTGG
1 GTTGACCATTGACTTTTTGG
19627 GTTGACCATTGACTTTTT
1 GTTGACCATTGACTTTTT
19645 TCGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (20 bp):
GTTGACCATTGACTTTTTGG
Found at i:22650 original size:24 final size:22
Alignment explanation
Indices: 22606--22652 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
22596 GACAAATAAG
*
22606 AAAATAAATAAATAAATAGAAA
1 AAAATAAATAAATAAAAAGAAA
*
22628 AAAATATATAAAATTAAAAAGAAA
1 AAAATAAAT-AAA-TAAAAAGAAA
22652 A
1 A
22653 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAATAAATAAATAAAAAGAAA
Found at i:22659 original size:19 final size:21
Alignment explanation
Indices: 22603--22659 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
22593 CTGGACAAAT
22603 AAGAAAATAAATAAATAAATAG
1 AAGAAAATAAA-AAATAAATAG
* *
22625 AAAAAAATATATAAAATTAA-A-
1 AAGAAAATA-A-AAAATAAATAG
22646 AAGAAAATAAAAAA
1 AAGAAAATAAAAAA
22660 AATTGGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 8 0.27
22 9 0.30
23 7 0.23
24 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (21 bp):
AAGAAAATAAAAAATAAATAG
Found at i:28309 original size:75 final size:75
Alignment explanation
Indices: 28224--28372 Score: 298
Period size: 75 Copynumber: 2.0 Consensus size: 75
28214 GCATACAAAG
28224 CCCGTTATCCATTTAGGATTTAGGTATGCTACACTATAAATGTCACAAGTGAATAAAACCATAAA
1 CCCGTTATCCATTTAGGATTTAGGTATGCTACACTATAAATGTCACAAGTGAATAAAACCATAAA
28289 AAGATTTAGC
66 AAGATTTAGC
28299 CCCGTTATCCATTTAGGATTTAGGTATGCTACACTATAAATGTCACAAGTGAATAAAACCATAAA
1 CCCGTTATCCATTTAGGATTTAGGTATGCTACACTATAAATGTCACAAGTGAATAAAACCATAAA
28364 AAGATTTAG
66 AAGATTTAG
28373 GATCTATTCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (75 bp):
CCCGTTATCCATTTAGGATTTAGGTATGCTACACTATAAATGTCACAAGTGAATAAAACCATAAA
AAGATTTAGC
Found at i:30778 original size:19 final size:19
Alignment explanation
Indices: 30613--30779 Score: 156
Period size: 19 Copynumber: 8.8 Consensus size: 19
30603 TCATTAAATT
* *
30613 GCTCTTACGAGTCAATATC
1 GCTCTTACGAGCCAGTATC
*
30632 GCTCTTACGAGCCAATATC
1 GCTCTTACGAGCCAGTATC
* *
30651 GCTCTCACGAGCCAATATC
1 GCTCTTACGAGCCAGTATC
* *
30670 GCTCTTACAAGCCACTATC
1 GCTCTTACGAGCCAGTATC
**
30689 GCTCCAAC-AGCCAGTATC
1 GCTCTTACGAGCCAGTATC
* * * *
30707 ACACCTACAAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
* * *
30726 GATCCTACAAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
* **
30745 ACTCCAACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
30764 GCTCTTACGAGCCAGT
1 GCTCTTACGAGCCAGT
30780 TTTGCTTTAG
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
18 14 0.11
19 112 0.89
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (19 bp):
GCTCTTACGAGCCAGTATC
Found at i:46142 original size:9 final size:8
Alignment explanation
Indices: 46125--46162 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
46115 CAGTCACTTG
46125 AAAAAGAA
1 AAAAAGAA
46133 AAATAAGAA
1 AAA-AAGAA
46142 AAAGAA-AA
1 AAA-AAGAA
46150 AAAAAGAA
1 AAAAAGAA
46158 AAAAA
1 AAAAA
46163 ATTATGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 2 0.07
8 15 0.56
9 10 0.37
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:46144 original size:15 final size:16
Alignment explanation
Indices: 46124--46160 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
46114 TCAGTCACTT
*
46124 GAAAAAG-AAAAATAA
1 GAAAAAGAAAAAAAAA
46139 GAAAAAGAAAAAAAAA
1 GAAAAAGAAAAAAAAA
46155 GAAAAA
1 GAAAAA
46161 AAATTATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
GAAAAAGAAAAAAAAA
Found at i:50778 original size:29 final size:28
Alignment explanation
Indices: 50740--50823 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
50730 AAAATCCAAA
*
50740 AAAATAAAAATTCTAAACCAAAATCTCC
1 AAAATAAAAATTCTAAACCAAAATCCCC
* * **
50768 AAAATAAAAAATCCTAGATTAAAATCCCC
1 AAAAT-AAAAATTCTAAACCAAAATCCCC
* * *
50797 AAATTCAAAAACTCGAAACCAAAATCC
1 AAAAT-AAAAATTCTAAACCAAAATCC
50824 AACTCCAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (28 bp):
AAAATAAAAATTCTAAACCAAAATCCCC
Found at i:63068 original size:38 final size:38
Alignment explanation
Indices: 62952--63068 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 38
62942 ATTGGGTTCG
* *
62952 TTTTAAGCAAACAAAAGA-GCAATGTGAAC-CGAGTTTG
1 TTTTAAGCAAACAAAAGAGGTAATGTGAACTCGA-TTTT
* * * * * *
62989 TTTTAAGCAAACAAAAGTGGTAATTTCAACTGGGTTCT
1 TTTTAAGCAAACAAAAGAGGTAATGTGAACTCGATTTT
* * *
63027 TTTTAAGAAAACAAAAAAGGTAATGTGAACTTGATTTT
1 TTTTAAGCAAACAAAAGAGGTAATGTGAACTCGATTTT
63065 TTTT
1 TTTT
63069 TCTAGAGAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
37 17 0.27
38 44 0.71
39 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (38 bp):
TTTTAAGCAAACAAAAGAGGTAATGTGAACTCGATTTT
Found at i:70569 original size:24 final size:24
Alignment explanation
Indices: 70531--70585 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
70521 CTTAATATAT
*
70531 TATTAATATTATAATCATAAAAA-A
1 TATT-ATAATATAATCATAAAAATA
*
70555 GTATTATAATATAATTATAAAAATA
1 -TATTATAATATAATCATAAAAATA
70580 TATTAT
1 TATTAT
70586 TTATCTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TATTATAATATAATCATAAAAATA
Found at i:77286 original size:37 final size:37
Alignment explanation
Indices: 77231--77331 Score: 148
Period size: 37 Copynumber: 2.7 Consensus size: 37
77221 TTGCAATTTA
* *
77231 TTCAAGCTATGTGCCTAGTAAGCTTCGTGTCGGTGTT
1 TTCAAGCTATGTGCCTAGTAGGCTTCGTGTCGCTGTT
* *
77268 TTCAGGCTATGTGCCTAGTAGGCTTCATGTCGCTGTT
1 TTCAAGCTATGTGCCTAGTAGGCTTCGTGTCGCTGTT
**
77305 TTCAAGCTATGTGTTTAGTAGGCTTCG
1 TTCAAGCTATGTGCCTAGTAGGCTTCG
77332 AGCCGGTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.39
Consensus pattern (37 bp):
TTCAAGCTATGTGCCTAGTAGGCTTCGTGTCGCTGTT
Found at i:80825 original size:15 final size:17
Alignment explanation
Indices: 80807--80850 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
80797 ATAAATAAAT
80807 TTTTCTTTTTTT-TC-A
1 TTTTCTTTTTTTCTCAA
80822 TTTTCTTCCTTTTTCTCAA
1 TTTTCTT--TTTTTCTCAA
80841 TTTTCTTTTT
1 TTTTCTTTTT
80851 AAGTGACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
17 8 0.32
18 2 0.08
19 8 0.32
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTTTTTTTCTCAA
Found at i:96928 original size:20 final size:21
Alignment explanation
Indices: 96900--96939 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
96890 AGTTAGAATA
*
96900 AAATTTGTTGTGT-TTTAATG
1 AAATATGTTGTGTATTTAATG
96920 AAATATGTTGTGTATTTAAT
1 AAATATGTTGTGTATTTAAT
96940 TCCGTAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (21 bp):
AAATATGTTGTGTATTTAATG
Found at i:109831 original size:39 final size:39
Alignment explanation
Indices: 109788--109933 Score: 179
Period size: 39 Copynumber: 3.8 Consensus size: 39
109778 AGCATTACGA
*
109788 TGTTTACAGTGTCACTGCCAGTTCAGTATATCATTGTAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATATCATTGTAG
* *
109827 TGTTTACAGTGTCACTGTCAATTAAGTATATCATTGTAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATATCATTGTAG
* * * *
109866 TGCTT--AGTGTCACTGCCAATTCGGTAAATCATTGCAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATATCATTGTAG
* * * *
109903 TATTTACAGTGTCACTGTCGATTCAATATAT
1 TGTTTACAGTGTCACTGCCAATTCAGTATAT
109934 TTCCAACGTG
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
37 30 0.34
39 59 0.66
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (39 bp):
TGTTTACAGTGTCACTGCCAATTCAGTATATCATTGTAG
Found at i:117305 original size:29 final size:28
Alignment explanation
Indices: 117272--117337 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 28
117262 ATCATTATAA
*
117272 TTTTTAAATAATTGAATT-AAATTTTTATT
1 TTTTTAAA-AATTAAATTGAAA-TTTTATT
*
117301 TTTTTAGAAAATTAAATTGTAATTTTATT
1 TTTTTA-AAAATTAAATTGAAATTTTATT
117330 TTTATTAA
1 TTT-TTAA
117338 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTTAAAAATTAAATTGAAATTTTATT
Found at i:120965 original size:24 final size:24
Alignment explanation
Indices: 120910--120966 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
120900 TAAACTAATA
*
120910 AGAGTTTGATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
120934 ATAATTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
120958 AGAGTTTAA
1 AGAGTTTAA
120967 CTGGAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:123674 original size:21 final size:21
Alignment explanation
Indices: 123648--123699 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
123638 CCTACTAGGT
*
123648 ACAAAGCCTAAAAATATCGGC
1 ACAAAGCCTAAAAACATCGGC
*
123669 ACAAAGCCTGAAAACATCGGC
1 ACAAAGCCTAAAAACATCGGC
*
123690 ACGAAGCCTA
1 ACAAAGCCTA
123700 CTAGGCACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.12
Consensus pattern (21 bp):
ACAAAGCCTAAAAACATCGGC
Found at i:123677 original size:37 final size:37
Alignment explanation
Indices: 123551--123677 Score: 128
Period size: 37 Copynumber: 3.4 Consensus size: 37
123541 GTTATTGGAT
* * * *
123551 CACCGGCACAAAGCCTACTAGGCATATAGCCCGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
* * *
123588 CACCGGCACGAAGCCTACTAGGCACAAAACTTGAAAA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
* ** * *
123625 CACCAGCACGCAGCCTACTAGGTACAAAGCCTAAAAA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
* *
123662 TATCGGCACAAAGCCT
1 CACCGGCACAAAGCCT
123678 GAAAACATCG
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
Found at i:123683 original size:58 final size:59
Alignment explanation
Indices: 123608--123721 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 59
123598 AAGCCTACTA
* * *
123608 GGCACAAAACTTGAAAACACCAGCACGCAGCCTACTAGGTACAAAGCCT-AAAAATATC
1 GGCACAAAACCTGAAAACACCAGCACGAAGCCTACTAGGCACAAAGCCTGAAAAATATC
* * *
123666 GGCACAAAGCCTGAAAACATCGGCACGAAGCCTACTAGGCACAAAGCCTGAAAAAT
1 GGCACAAAACCTGAAAACACCAGCACGAAGCCTACTAGGCACAAAGCCTGAAAAAT
123722 TTGTAAGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 43 0.88
59 6 0.12
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.12
Consensus pattern (59 bp):
GGCACAAAACCTGAAAACACCAGCACGAAGCCTACTAGGCACAAAGCCTGAAAAATATC
Found at i:125312 original size:24 final size:24
Alignment explanation
Indices: 125259--125318 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
125249 TAAACTAATA
* *
125259 AGAGTTTGACTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
125283 ATAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
125307 AGAGTTTTACTG
1 AGAGTTTAACTG
125319 GAATATTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:135847 original size:18 final size:19
Alignment explanation
Indices: 135821--135887 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
135811 GGTTGGGGGG
*
135821 AAGTAAAAATTTTGAGGGA
1 AAGTAAAAGTTTTGAGGGA
* *
135840 AAGTAAAATTTTTGAGGGG
1 AAGTAAAAGTTTTGAGGGA
* *
135859 ATGTAAAAGTTTTGAAAGGA
1 AAGTAAAAGTTTTG-AGGGA
*
135879 AAATAAAAG
1 AAGTAAAAG
135888 AAAAAAAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (19 bp):
AAGTAAAAGTTTTGAGGGA
Found at i:145553 original size:39 final size:39
Alignment explanation
Indices: 145499--145604 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 39
145489 TGATTCTGGC
* * *
145499 TTAGCATTGATAACCAATGAAGTAGAAGTAGAGTCCGGA
1 TTAGCATTGTTAACCAGTGAAGTTGAAGTAGAGTCCGGA
* * *
145538 TTAGCATTGTTAACCAGTAAATTTGAAGTAGAGTCCGGT
1 TTAGCATTGTTAACCAGTGAAGTTGAAGTAGAGTCCGGA
** *
145577 TTAGCGCTGTTAAGCAGTGAAGTTGAAG
1 TTAGCATTGTTAACCAGTGAAGTTGAAG
145605 CAGGTGATTC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (39 bp):
TTAGCATTGTTAACCAGTGAAGTTGAAGTAGAGTCCGGA
Found at i:146789 original size:20 final size:21
Alignment explanation
Indices: 146756--146796 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
146746 TTCTACTTTA
*
146756 TTTTGAAAACTTTAAATAATT
1 TTTTGAAAACTTTAAAAAATT
*
146777 TTTTTAAAA-TTTAAAAAATT
1 TTTTGAAAACTTTAAAAAATT
146797 AGATCCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTGAAAACTTTAAAAAATT
Found at i:147625 original size:15 final size:14
Alignment explanation
Indices: 147584--147625 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
147574 AATTATGATA
*
147584 AAAATTAAAATACAT
1 AAAATT-AAATATAT
*
147599 AAAATTAAATAT-C
1 AAAATTAAATATAT
147612 AAAATTAAATATAT
1 AAAATTAAATATAT
147626 TAGAGTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 12 0.52
14 5 0.22
15 6 0.26
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTAAATATAT
Found at i:147830 original size:24 final size:25
Alignment explanation
Indices: 147798--147852 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
147788 CGATAAAAAA
*
147798 TATAATTTTACT-A-TTTTAATAGAT
1 TATAATTTTA-TAATTTTTAAAAGAT
*
147822 TATATTTTTATAATTTTTAAAAGAT
1 TATAATTTTATAATTTTTAAAAGAT
147847 TA-AATT
1 TATAATT
147853 AAATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 13 0.50
25 12 0.46
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
TATAATTTTATAATTTTTAAAAGAT
Found at i:147893 original size:31 final size:29
Alignment explanation
Indices: 147827--147902 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
147817 TAGATTATAT
* *
147827 TTTTATAATTTTT-AAAAGATTAAATTAAA
1 TTTTAT-ATTTTTAAAAAAATTAAAGTAAA
147856 TATTTATATTTTTAAGAAAAATTAAAGTACAA
1 T-TTTATATTTTTAA-AAAAATTAAAGTA-AA
*
147888 TTTTATCTTTATTAA
1 TTTTATATTT-TTAA
147903 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.18
30 6 0.15
31 19 0.49
32 7 0.18
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTTATATTTTTAAAAAAATTAAAGTAAA
Found at i:154613 original size:17 final size:17
Alignment explanation
Indices: 154591--154624 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
154581 TTTGGAAGAT
154591 TCAATTTCTAACCCAAA
1 TCAATTTCTAACCCAAA
*
154608 TCAATTTCTAACTCAAA
1 TCAATTTCTAACCCAAA
154625 CCAACCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (17 bp):
TCAATTTCTAACCCAAA
Found at i:156158 original size:16 final size:16
Alignment explanation
Indices: 156127--156160 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
156117 AAAACTTTTG
**
156127 TATATTTTAAGTATAT
1 TATATTTTAAAAATAT
156143 TATATTTTAAAAATAT
1 TATATTTTAAAAATAT
156159 TA
1 TA
156161 CGATTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATATTTTAAAAATAT
Found at i:166241 original size:28 final size:28
Alignment explanation
Indices: 166201--166310 Score: 193
Period size: 28 Copynumber: 3.9 Consensus size: 28
166191 TTAGTCCAGG
*
166201 ATTATGTAGATTCAATGATTTCCTTATA
1 ATTATGAAGATTCAATGATTTCCTTATA
166229 ATTATGAAGATTCAATGATTTCCTTATA
1 ATTATGAAGATTCAATGATTTCCTTATA
*
166257 ATTATGAAGATTCAGTGATTTCCTTATA
1 ATTATGAAGATTCAATGATTTCCTTATA
*
166285 ATTATGAAGATTCAGTGATTTCCTTA
1 ATTATGAAGATTCAATGATTTCCTTA
166311 ATCCTTACAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 80 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (28 bp):
ATTATGAAGATTCAATGATTTCCTTATA
Found at i:167147 original size:36 final size:37
Alignment explanation
Indices: 167079--167148 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
167069 GTTTGTAAAA
* *
167079 TATCATTCTTAAATAACATTAGTCTGCTCTGCATAAG
1 TATCATTCTTAAACAACATTAGTCTGCCCTGCATAAG
*
167116 TATCATTCTT-AACAACGTTAGTCTGCCCTGCAT
1 TATCATTCTTAAACAACATTAGTCTGCCCTGCAT
167149 CTATGATGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (37 bp):
TATCATTCTTAAACAACATTAGTCTGCCCTGCATAAG
Found at i:168410 original size:32 final size:32
Alignment explanation
Indices: 168374--168436 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
168364 GTCTATGGAG
*
168374 ATTAATTTTTTCGATGTTTATGACTGCCTAAT
1 ATTAATTTTTTCGATGTTCATGACTGCCTAAT
168406 ATTAATTTTTTCGATGTTCATGACTGCCTAA
1 ATTAATTTTTTCGATGTTCATGACTGCCTAA
168437 CAAACATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (32 bp):
ATTAATTTTTTCGATGTTCATGACTGCCTAAT
Found at i:168577 original size:56 final size:56
Alignment explanation
Indices: 168510--168662 Score: 209
Period size: 56 Copynumber: 2.7 Consensus size: 56
168500 AATAGTTACA
*
168510 TAGAAATCAAATTGTTAAAAGATAATATCTCATAATAATATCCAACAATATCCCAT
1 TAGAAATCAAATTGTTAAAAGATAATATCACATAATAATATCCAACAATATCCCAT
* * * * * *
168566 TAGAAATCAAATTGCTAAGAGATAATATCACATAATAATATTCTATAATATCCTAT
1 TAGAAATCAAATTGTTAAAAGATAATATCACATAATAATATCCAACAATATCCCAT
* *
168622 TA-AGAATCAAATTGTTGAAAGATAATATCCCATAATAATAT
1 TAGA-AATCAAATTGTTAAAAGATAATATCACATAATAATAT
168663 TAACACCCCT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
55 1 0.01
56 84 0.99
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (56 bp):
TAGAAATCAAATTGTTAAAAGATAATATCACATAATAATATCCAACAATATCCCAT
Found at i:172524 original size:17 final size:16
Alignment explanation
Indices: 172475--172525 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
172465 CCACTTCACT
172475 TATAATTCTTTCAATAAA
1 TATAATT-TTTC-ATAAA
*
172493 T-TAATTTTTTTATAAA
1 TATAA-TTTTTCATAAA
172509 TATAATTTTTACATAAA
1 TATAATTTTT-CATAAA
172526 AATTTTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 11 0.39
17 14 0.50
18 3 0.11
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAATTTTTCATAAA
Found at i:175420 original size:19 final size:19
Alignment explanation
Indices: 175380--175422 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
175370 AAAAATAATT
*
175380 TTAATCAAATAAAATTAGA
1 TTAATCAAATAAAATTAAA
*
175399 TTAATCAAAT-TAATTAAAA
1 TTAATCAAATAAAATT-AAA
175418 TTAAT
1 TTAAT
175423 ATGATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
TTAATCAAATAAAATTAAA
Found at i:175863 original size:29 final size:29
Alignment explanation
Indices: 175829--175884 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
175819 AATAGTATTT
175829 TATT-AATTTAATATTAAAGATTATCTTAG
1 TATTAAATTTAAT-TTAAAGATTATCTTAG
* *
175858 TATTAAATTTAATTTAATGTTTATCTT
1 TATTAAATTTAATTTAAAGATTATCTT
175885 GTAGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (29 bp):
TATTAAATTTAATTTAAAGATTATCTTAG
Found at i:175893 original size:29 final size:30
Alignment explanation
Indices: 175833--175894 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
175823 GTATTTTATT
*
175833 AATTTAATATTAAAGATTATCTTAGTATTA
1 AATTTAATATTAAAGATTATCTTAGTAATA
* *
175863 AATTTAAT-TTAATGTTTATCTT-GTAGATA
1 AATTTAATATTAAAGATTATCTTAGTA-ATA
175892 AAT
1 AAT
175895 ATTCTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 17 0.61
30 8 0.29
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (30 bp):
AATTTAATATTAAAGATTATCTTAGTAATA
Found at i:177003 original size:13 final size:13
Alignment explanation
Indices: 176966--176996 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
176956 TCAATTAGAA
176966 AATTTGATTAAAG
1 AATTTGATTAAAG
176979 AATTTGATTAAAG
1 AATTTGATTAAAG
176992 AATTT
1 AATTT
176997 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (13 bp):
AATTTGATTAAAG
Found at i:177628 original size:61 final size:61
Alignment explanation
Indices: 177559--177675 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 61
177549 AATGAATTTA
* * *
177559 ATATTAAATTTAATTTAATATTTATCTAGATAGTATTTTATTAATGTGATATTAATATGAG
1 ATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAG
177620 ATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAAT
1 ATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAAT
177676 GTGATTAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (61 bp):
ATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATATAATATTAATATGAG
Found at i:186661 original size:17 final size:17
Alignment explanation
Indices: 186639--186680 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
186629 AGTGTGATTG
186639 TCTTCAAGATGATCTGA
1 TCTTCAAGATGATCTGA
186656 TCTTCAAGATGATCTGA
1 TCTTCAAGATGATCTGA
186673 TCTTCAAG
1 TCTTCAAG
186681 TCACAAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (17 bp):
TCTTCAAGATGATCTGA
Done.