Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001709.1 Hibiscus syriacus cultivar Beakdansim tig00003435_pilon, 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: 1326839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:677159 original size:24 final size:24
Alignment explanation
Indices: 677125--677174 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
677115 CTGAAAAATC
*
677125 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* *
677149 ATCAAAGTCCGGGTATTCACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
677173 AT
1 AT
677175 TAAATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:678039 original size:20 final size:20
Alignment explanation
Indices: 678014--678080 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
678004 AAATTCAGTA
678014 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
678034 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
678054 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
678074 TTGCGAT
1 TTGCGAT
678081 TTACGTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:678219 original size:20 final size:20
Alignment explanation
Indices: 678067--678216 Score: 246
Period size: 20 Copynumber: 7.5 Consensus size: 20
678057 CGATAGTCAG
*
678067 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
678087 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
678107 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
678127 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
678147 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
678167 TTTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
678187 ATTCGCATTGTGATTTACAT
1 ATTCGCATTGCGATTTACGT
678207 ATTCGCATTG
1 ATTCGCATTG
678217 TGAATTAGGA
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 121 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:681587 original size:10 final size:10
Alignment explanation
Indices: 681549--681617 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
681539 GTGTTTGTGT
681549 TGTTCGTTTA
1 TGTTCGTTTA
*
681559 TGTTTGTTTA
1 TGTTCGTTTA
681569 TGTTCG-TT-
1 TGTTCGTTTA
* *
681577 CGTTCATGTTCA
1 TGTTC--GTTTA
*
681589 T-TT-GTTTG
1 TGTTCGTTTA
681597 TGTTCGTTTA
1 TGTTCGTTTA
681607 TGTTCGTTTA
1 TGTTCGTTTA
681617 T
1 T
681618 TTATTTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
8 8 0.18
9 4 0.09
10 30 0.67
11 3 0.07
ACGTcount: A:0.09, C:0.10, G:0.20, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:681708 original size:16 final size:16
Alignment explanation
Indices: 681683--681715 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
681673 AAAAAAATTA
681683 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
681699 TGTTCTTTTATGTTCG
1 TGTTCGTTTATGTTCG
681715 T
1 T
681716 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:687233 original size:42 final size:42
Alignment explanation
Indices: 687186--687265 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
687176 AATAAGTAAG
687186 TCCTTCGTGC-CATCAGTAAGTCTTTCGAGC-ATGATGATTAAA
1 TCCTTCG-GCTCATCAGTAAGTCTTTCGAGCGA-GATGATTAAA
* *
687228 TCCTTCGGCTCATCTGTAAGTCTTTTGAGCGAGATGAT
1 TCCTTCGGCTCATCAGTAAGTCTTTCGAGCGAGATGAT
687266 AAGTCATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 2 0.06
42 31 0.91
43 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
TCCTTCGGCTCATCAGTAAGTCTTTCGAGCGAGATGATTAAA
Found at i:687263 original size:256 final size:254
Alignment explanation
Indices: 686805--687757 Score: 1213
Period size: 256 Copynumber: 3.7 Consensus size: 254
686795 ATTAAGATTG
* *
686805 TTTGAAAATGAGAAAGCGATTTCCAAAGTTTTTCATTTATTGTTTTCAGAAAATGAAATTTTTGA
1 TTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
* * * * ** *
686870 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCCAAATTGGTAAGTCCTT
66 AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATAAGTAAGTCATT
* * *
686935 CAGGCCATCTA-TAAGTCTTTTAAGCATGATGATTAAATCTTTCAGGTCATCTATAAGT-TTTTC
131 C-GGCCATC-AGTAAGTCTTTCAAGCATGATGATTAAATCCTTC-GGTCATCTGTAAGTCTTTT-
* *
686998 GACCGAGATGACAAGTTCTTCGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCCCATGAA
192 GAGCGAGATGATAAGTTCTTCGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCCCATGAA
* * * *
687061 TTTGAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATGTTTTCAGGAAATAAAATTTTTTA
1 TTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
* * * * *
687126 AAAGTCAGAAAGTGATTTCCAACGTTTATTATCCAGTAAATTATTTCCAAAATAAGTAAGTCCTT
66 AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATAAGTAAGTCATT
*
687191 CGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTAAGTCTTTTGA
131 CG-GCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGG-TCATCTGTAAGTCTTTTGA
* *
687256 GCGAGATGATAAG-TCATTCAGGCCATCCGTAAGACCTTC-AGGTAGGATGTTTTCACATGAA
194 GCGAGATGATAAGTTC-TTCGGGCCATCCGTAAGACCTTCGA-GTAGGATGTTTTCCCATGAA
* * * *
687317 TTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCTTTTAATATTTTTATAAAATGAAATTTTTGA
1 TTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
* *
687382 AAAGTAAGAAAGTGATTTTCAAAGTTTCTTACCCAGTAAATTATTTTCAAAATTAA-TAAGTCAT
66 AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAA-TAAGTAAGTCAT
* * * * * * *
687446 TCGGGCCATCAGTAAGTCTTTCGATCATGATGATTAAATCATTTTGGTTATCTTTCAGTCTTTTG
130 TC-GGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATC-CTTCGGTCATCTGTAAGTCTTTTG
* * * * * * *
687511 AGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTT-GGGCAGGAT-ATTTCCACATGAT
193 AGCGAGATGATAAGTTCTTCGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCC-CATGAA
* *
687572 TTTCGAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAATTTTT
1 TTT-G-AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTT
* * *
687637 GAAAAGTAAGAAAACT-ATTTTCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTC
64 GAAAAGTAAG-AAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATAAGTAAGTC
* *
687701 ATTCGAG-CATCAGTAAGTCTTTCAAACATGATGATTAAATCCTTCGGGTAATCTGTA
128 ATTCG-GCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTC-GGTCATCTGTA
687758 TGCCTCACTT
Statistics
Matches: 610, Mismatches: 69, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
254 4 0.01
255 23 0.04
256 454 0.74
257 125 0.20
258 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (254 bp):
TTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATAAGTAAGTCATT
CGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGTCATCTGTAAGTCTTTTGAGC
GAGATGATAAGTTCTTCGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCCCATGAA
Found at i:687891 original size:3 final size:3
Alignment explanation
Indices: 687883--687920 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
687873 TTTGTCCAGG
*
687883 TTA TTA TTA ATA TTTA TTA TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
687921 TTAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:687913 original size:11 final size:11
Alignment explanation
Indices: 687887--687919 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
687877 TCCAGGTTAT
*
687887 TATTAATATT-
1 TATTATTATTA
687897 TATTATTATTA
1 TATTATTATTA
687908 TATTATTATTA
1 TATTATTATTA
687919 T
1 T
687920 TTTAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTATTA
Found at i:687940 original size:11 final size:12
Alignment explanation
Indices: 687883--687941 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
687873 TTTGTCCAGG
687883 TTATTATTAATAT
1 TTATTATT-ATAT
687896 TTATTATTATTAT
1 TTATTATTA-TAT
687909 ATTATTATTAT-T
1 -TTATTATTATAT
*
687921 TTA-AATTTATAT
1 TTATTA-TTATAT
687933 TTATT-TTAT
1 TTATTATTAT
687942 TACAGGCCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
10 1 0.03
11 11 0.28
12 6 0.15
13 12 0.31
14 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:689508 original size:258 final size:256
Alignment explanation
Indices: 689020--690297 Score: 1299
Period size: 258 Copynumber: 5.0 Consensus size: 256
689010 AAGCAAGATG
* * *
689020 ATAAGTCCTTCGGGCAAGATGTTTTCACATGATTTTACAAAAAATGAGAAAGCGATTTCCAAAGT
1 ATAAGACCTTCGGGCAGGATGTTTTCACATGATTTT-C-AAAAATGAGAAAGCGATTTTCAAAGT
* * * *
689085 TTCTAATTTAGTGTTTTCAGAAAATGAATTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTTT
64 TTCTCATTTAGTCTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCT
* * * * * *
689150 TATCTAGTAAACTATTTTCAAAATCAGTAAGTCATTTGGGCCATCAGTAAGTCTTTTGAGCATGC
129 TACCCAGTAAACTATTTCCAAAAT-AGTAAGTCATTCGAGCCATCAGTAAGTCTTTTGAGCATGA
* * * * * * *
689215 TGATTAAATCCTTCAGGTTATCTGTTAGGCTTTCGAGCAATATTATAAGTCTTTCGGGCCATCT
193 TGATTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCT
* * * *
689279 ATAAGACCTTCGGGCGGGATGTTTTCACATGATTTTCAAAAACTAAGAAAGCGATTTTTAAAATT
1 ATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCAAAAA-TGAGAAAGCGATTTTCAAAGTT
* * * *
689344 TCTCATTTAGTATTTTCAGGAAGTGAAATTTTTGAAAAGTATGAAAGTGATTTCCAAAGTTTCTT
65 TCTCATTTAGTCTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTT
* * *
689409 ACCCAGTAAACTATTTCCAAAATTGTTAAGTCATTCGAGCCATCAATAAGTCTTTCGAGCATGAT
130 ACCCAGTAAACTATTTCCAAAATAG-TAAGTCATTCGAGCCATCAGTAAGTCTTTTGAGCATGAT
* * *
689474 GATTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCC
194 GATTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCT
* * * * * *
689537 GTAAGAGCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAATGGGAAAGCGATTTTCAAAGTTT
1 ATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCAAAAATGAGAAAGCGATTTTCAAAGTTT
* * * * ** * *
689602 CCCATATAATCTTTTCTGAAAATGAAATTTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTC-T-
66 CTCATTTAGTCTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTA
* * *
689665 -----T--AC----T------TAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTTGAGCATGATGA
131 CCCAGTAAACTATTTCCAAAATAGTAAGTCATTCGAGCCATCAGTAAGTCTTTTGAGCATGATGA
* * * *
689713 TTAAATCATTCGCGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTTTTTTGGGCCATTT
196 TTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCT
* * * * * * * * * ** *
689774 GTAAGACATTCGGGTAGGATATTTTCATATGAATTTGAAAAAAGGGAAATTGATTTTCAATGTTT
1 ATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCAAAAATGAGAAAGCGATTTTCAAAGTTT
* * ** * *
689839 CCCATTTAATCTTTTTTGAAAATGAAATTTTCGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTA
66 CTCATTTAGTCTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTA
* * *** *
689904 CTCAGT-AAGTCA-TTCGCTCTATCAGTAAGTCATTCG-GTCCATCAGTAAGTCTTTCGAGCATG
131 CCCAGTAAACT-ATTTC-CAAAAT-AGTAAGTCATTCGAG-CCATCAGTAAGTCTTTTGAGCATG
* * * * * *
689966 ATTATTAAATCCTTCGGGTCATTTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATCT
192 ATGATTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCT
** ** * *
690031 ATAAGACCTTTAGGCATAATGTTTTCACATGATATTTAAAAAAAATGAGAAAGCGATTTCCAAAG
1 ATAAGACCTTCGGGCAGGATGTTTTCACATGAT-TTT--CAAAAATGAGAAAGCGATTTTCAAAG
* * * * * *
690096 TTTCTCATATAGTGTTTTAATAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGATTC
63 TTTCTCATTTAGTCTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTC
* * * *
690161 TTACCTATTAAACTATTTCCAAAACTGGTAAGTCCTTC-AGGCCATCAGTAAGTCTTTTGAGCAT
128 TTACCCAGTAAACTATTTCCAAAA-TAGTAAGTCATTCGA-GCCATCAGTAAGTCTTTTGAGCAT
* * * * *
690225 GATGATTAAATCATTTGGATCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCATTT-GGGTCAT
191 GATGATTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTC-TTTCGGGCCAT
690289 CT
255 CT
690291 ATAAGAC
1 ATAAGAC
690298 TTTTGGGTAA
Statistics
Matches: 848, Mismatches: 139, Indels: 63
0.81 0.13 0.06
Matches are distributed among these distances:
237 205 0.24
238 3 0.00
244 2 0.00
245 1 0.00
248 2 0.00
249 1 0.00
250 1 0.00
256 3 0.00
257 187 0.22
258 223 0.26
259 33 0.04
260 177 0.21
261 10 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (256 bp):
ATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTCAAAAATGAGAAAGCGATTTTCAAAGTTT
CTCATTTAGTCTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTA
CCCAGTAAACTATTTCCAAAATAGTAAGTCATTCGAGCCATCAGTAAGTCTTTTGAGCATGATGA
TTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCT
Found at i:689541 original size:41 final size:42
Alignment explanation
Indices: 689455--689541 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
689445 GAGCCATCAA
* ** *
689455 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTG
1 TAAGTCTTTCGAGCAAGATGATTAAATCATTCGGACCATCCG
* *
689497 TAAGTCTTTCGAGCAAGATGA-TAAGTCCTTCGGACCATCCG
1 TAAGTCTTTCGAGCAAGATGATTAAATCATTCGGACCATCCG
689538 TAAG
1 TAAG
689542 AGCTTCGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 19 0.49
42 20 0.51
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGATTAAATCATTCGGACCATCCG
Found at i:689930 original size:20 final size:20
Alignment explanation
Indices: 689905--689959 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
689895 AGTTTCTTAC
*
689905 TCAGTAAGTCATTCGCTCTA
1 TCAGTAAGTCATTCGCTCCA
*
689925 TCAGTAAGTCATTCGGTCCA
1 TCAGTAAGTCATTCGCTCCA
*
689945 TCAGTAAGTCTTTCG
1 TCAGTAAGTCATTCG
689960 AGCATGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (20 bp):
TCAGTAAGTCATTCGCTCCA
Found at i:689933 original size:237 final size:237
Alignment explanation
Indices: 689435--690164 Score: 753
Period size: 237 Copynumber: 3.0 Consensus size: 237
689425 CCAAAATTGT
* *
689435 TAAGTCATTCGAGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTAA
1 TAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGCGTCATCTGTAA
*
689500 GTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCGTAAGAGCTTCGGGTAGGATGTTTTCAC
66 GTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCGTAAGAGCTTCGGGTAGGATATTTTCAC
*
689565 ATGAATTTGAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTTCTGAAAATGAAAT
131 ATGAATTTGAAAAAAGGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTTCTGAAAATGAAAT
*
689630 TTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTCTTACTTAG
196 TTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTCTTACTCAG
* * * *
689672 TAAGTCCTTCGGGCCATTAGTAAGTCTTTTGAGCATGATGATTAAATCATTCGCGTCATCTGTAA
1 TAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGCGTCATCTGTAA
** * * **
689737 GTCTTTCGAGCAAGATGATAAGTTTTTTGGGCCATTTGTAAGA-CATTCGGGTAGGATATTTTCA
66 GTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCGTAAGAGC-TTCGGGTAGGATATTTTCA
* ** * * *
689801 TATGAATTTGAAAAAAGGGAAATTGATTTTCAATGTTTCCCATTTAATCTTTTTTGAAAATGAAA
130 CATGAATTTGAAAAAAGGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTTCTGAAAATGAAA
* *
689866 TTTTCGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTCAG
195 TTTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTCTTACTCAG
*
689909 TAAGTCATTCGCTCTATCAGTAAGTCATTCGGTCCATCAGTAAGTCTTTCGAGCATGATTATTAA
1 TAAGTCA-------T-TC-----G--A----G-CCATCAGTAAGTCTTTCGAGCATGATGATTAA
* * * * ** ** *
689974 ATCCTTCGGGTCATTTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATCTATAAGACC
46 ATCATTCGCGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCGTAAGAGC
** * ** * * * * *
690039 TTTAGGCATAATGTTTTCACATGATATTTAAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCAT
111 TTCGGGTAGGATATTTTCACATGA-ATTT-GAAAAAA-GGGAAAGCGATTTTCAAAGTTTCCCAT
* * * ** *** *
690104 ATAGTGTTTTAAT-AAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGATTCTTAC
173 ATAATCTTTT-CTGAAAATGAAATTTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTCTTAC
690165 CTATTAAACT
Statistics
Matches: 407, Mismatches: 60, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
236 1 0.00
237 218 0.54
244 1 0.00
245 2 0.00
250 1 0.00
256 1 0.00
257 99 0.24
258 5 0.01
259 6 0.01
260 72 0.18
261 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (237 bp):
TAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGCGTCATCTGTAA
GTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCGTAAGAGCTTCGGGTAGGATATTTTCAC
ATGAATTTGAAAAAAGGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTTCTGAAAATGAAAT
TTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTCTTACTCAG
Found at i:689975 original size:494 final size:496
Alignment explanation
Indices: 689175--690164 Score: 1197
Period size: 494 Copynumber: 2.0 Consensus size: 496
689165 TTTCAAAATC
* * * *
689175 AGTAAGTCATTTGGGCCATCAGTAAGTCTTTTGAGCATGCTGATTAAATCCTTCAGGTTATCTGT
1 AGTAAGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCAGGTCATCTGT
* * * * * *
689240 TAGGCTTTCGAGCAATATTATAAGTCTTTCGGGCCATCTATAAGACCTTCGGGCGGGATGTTTTC
66 AAGGCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCTATAAGACATTCGGGCAGGATATTTTC
* * * * * *
689305 ACATGATTTTCAAAAACTAAGAAAGCGATTTTTAAAATTTCTCATTTAGTATTTTCAGGAAGTGA
131 ACATGAATTTCAAAAAC-AAGAAAGCGATTTTCAAAATTTCCCATTTAATATTTTCAGAAAATGA
* * * *
689370 AATTTTTGAAAAGTATGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGT
195 AATTTTCGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATAGT
689435 TAAGTCATTCGAGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTAA
260 TAAGTCATTCGAGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTAA
* * * * *
689500 GTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCGTAAGAGCTTCGGGTAGGATGTTTTCAC
325 GTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGCAGAATGTTTTCAC
* * * *
689565 ATGA-ATTT-GAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATATAATCTTTT-CTGAAAATGA
390 ATGATATTTAAAAAAATGAGAAAGCGATTTCCAAAGTTTCCCATATAATCTTTTAAT-AAAATGA
* *
689627 AATTTTCAAAAAGTAAGAAAATAATTTCCAAAGTTTCTTACTT
454 AATTTTCAAAAAGTAAGAAAACAATTTCCAAAGATTCTTACTT
* *
689670 AGTAAGTCCTTCGGGCCATTAGTAAGTCTTTTGAGCATGATGATTAAATCATTC-GCGTCATCTG
1 AGTAAGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCAG-GTCATCTG
* * * * * *
689734 TAAGTCTTTCGAGCAAGATGATAAGTTTTTTGGGCCATTTGTAAGACATTCGGGTAGGATATTTT
65 TAAGGCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCTATAAGACATTCGGGCAGGATATTTT
* * * ** ** * **
689799 CATATGAATTTGAAAAA-AGGGAAATTGATTTTCAATGTTTCCCATTTAATCTTTTTTGAAAATG
130 CACATGAATTTCAAAAACA-AGAAAGCGATTTTCAAAATTTCCCATTTAATATTTTCAGAAAATG
* * ***
689863 AAATTTTCGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTCAGT-AAGTCA-TTCGCTCTAT
194 AAATTTTCGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCCAGTAAACT-ATTTC-CAAAAT
* * * *
689926 CAG-TAAGTCATTCG-GTCCATCAGTAAGTCTTTCGAGCATGATTATTAAATCCTTCGGGTCATT
257 -AGTTAAGTCATTCGAG-CCATCAATAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATC
* ** * * *
689989 TGTCAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATCTATAAGACCTTTAGGCATAATGTT
320 TGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGCAGAATGTT
* * *
690054 TTCACATGATATTTAAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATATAGTGTTTTAATAA
385 TTCACATGATATTT-AAAAAAATGAGAAAGCGATTTCCAAAGTTTCCCATATAATCTTTTAATAA
** * *
690119 AATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGATTCTTAC
449 AATGAAATTTTCAAAAAGTAAGAAAACAATTTCCAAAGATTCTTAC
690165 CTATTAAACT
Statistics
Matches: 414, Mismatches: 71, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
493 8 0.02
494 197 0.48
495 128 0.31
497 80 0.19
498 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (496 bp):
AGTAAGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCAGGTCATCTGT
AAGGCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCTATAAGACATTCGGGCAGGATATTTTC
ACATGAATTTCAAAAACAAGAAAGCGATTTTCAAAATTTCCCATTTAATATTTTCAGAAAATGAA
ATTTTCGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATAGTT
AAGTCATTCGAGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTGTAAG
TCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCATAAGACCTTCAGGCAGAATGTTTTCACA
TGATATTTAAAAAAATGAGAAAGCGATTTCCAAAGTTTCCCATATAATCTTTTAATAAAATGAAA
TTTTCAAAAAGTAAGAAAACAATTTCCAAAGATTCTTACTT
Found at i:690289 original size:41 final size:42
Alignment explanation
Indices: 690211--690290 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
690201 GCCATCAGTA
** *
690211 AGTCTTTTGAGCATGATGATTAAATCATTTGGATCATCTGTC
1 AGTCTTTCAAGCAAGATGATTAAATCATTTGGATCATCTGTC
* *
690253 AGTCTTTCAAGCAAGATGA-TAAGTCATTTGGGTCATCT
1 AGTCTTTCAAGCAAGATGATTAAATCATTTGGATCATCT
690291 ATAAGACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (42 bp):
AGTCTTTCAAGCAAGATGATTAAATCATTTGGATCATCTGTC
Found at i:690398 original size:21 final size:20
Alignment explanation
Indices: 690368--690415 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
690358 CTCATTTAAA
*
690368 AAAAAAGAGAAAAAAAGAAAG
1 AAAAATGAG-AAAAAAGAAAG
*
690389 AAAAATGAGAAGAAAGAAAG
1 AAAAATGAGAAAAAAGAAAG
690409 AATAAAT
1 AA-AAAT
690416 AAAAATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (20 bp):
AAAAATGAGAAAAAAGAAAG
Found at i:694507 original size:17 final size:19
Alignment explanation
Indices: 694485--694522 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
694475 AAAGACATAT
*
694485 TGATATG-AT-GAAACTAC
1 TGATATGTATGGAAAATAC
694502 TGATATGTATGGAAAATAC
1 TGATATGTATGGAAAATAC
694521 TG
1 TG
694523 GTTTTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 2 0.11
19 9 0.50
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (19 bp):
TGATATGTATGGAAAATAC
Found at i:695828 original size:24 final size:24
Alignment explanation
Indices: 695800--695898 Score: 110
Period size: 24 Copynumber: 4.2 Consensus size: 24
695790 ATTTTCGATT
*
695800 TGAATTCTGTTATGATACCTGACC
1 TGAATTCTGATATGATACCTGACC
* * *
695824 TGAATTCTGATCTGAT-TCTGACA
1 TGAATTCTGATATGATACCTGACC
* *
695847 TGGATTCTGATATGATACATGACC
1 TGAATTCTGATATGATACCTGACC
* * *
695871 TGGATTCTAATATGATACTTGACC
1 TGAATTCTGATATGATACCTGACC
695895 TGAA
1 TGAA
695899 ATATGTTTTG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
23 19 0.31
24 43 0.69
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (24 bp):
TGAATTCTGATATGATACCTGACC
Found at i:700225 original size:24 final size:24
Alignment explanation
Indices: 700198--700296 Score: 112
Period size: 24 Copynumber: 4.2 Consensus size: 24
700188 GATTTCGATT
* * *
700198 TGAATTCTGTTATGATACCTGACC
1 TGAATTCTGATCTGATACTTGACC
*
700222 TGAATTCTGATCTGATA-TTGACA
1 TGAATTCTGATCTGATACTTGACC
* *
700245 TGGATTCTGATTTGATACATT-ACC
1 TGAATTCTGATCTGATAC-TTGACC
*
700269 TGGATTCTGATCTGATACTTGACC
1 TGAATTCTGATCTGATACTTGACC
700293 TGAA
1 TGAA
700297 ATATGTTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
23 21 0.33
24 40 0.63
25 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TGAATTCTGATCTGATACTTGACC
Found at i:700252 original size:47 final size:48
Alignment explanation
Indices: 700201--700291 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
700191 TTCGATTTGA
*
700201 ATTCTG-TTATGATACCTGACCTGAATTCTGATCTGATA-TTGACATGG
1 ATTCTGATT-TGATACATGACCTGAATTCTGATCTGATACTTGACATGG
* *
700248 ATTCTGATTTGATACATTACCTGGATTCTGATCTGATACTTGAC
1 ATTCTGATTTGATACATGACCTGAATTCTGATCTGATACTTGAC
700292 CTGAAATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 32 0.82
48 7 0.18
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (48 bp):
ATTCTGATTTGATACATGACCTGAATTCTGATCTGATACTTGACATGG
Found at i:704745 original size:24 final size:23
Alignment explanation
Indices: 704717--704814 Score: 76
Period size: 23 Copynumber: 4.2 Consensus size: 23
704707 ATTTTTTATT
* *
704717 TGAATTCTGTTACGATACCTGACC
1 TGAATTCTGATACGATA-CTGACA
*
704741 TGAATTCTGATATGATACTGACA
1 TGAATTCTGATACGATACTGACA
*
704764 TGGATTCTGAT-CTGATACATGACA
1 TGAATTCTGATAC-GATAC-TGACA
* *
704788 TGGA-TCTGAT-CTGATACTTGACC
1 TGAATTCTGATAC-GATAC-TGACA
704811 TGAA
1 TGAA
704815 ATATGTTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
23 40 0.62
24 24 0.38
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (23 bp):
TGAATTCTGATACGATACTGACA
Found at i:704800 original size:28 final size:23
Alignment explanation
Indices: 704720--704805 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
704710 TTTTATTTGA
* * * *
704720 ATTCTGTTACGATACCTGACCTGA
1 ATTCTGATATGATA-CTGACATGG
704744 ATTCTGATATGATACTGACATGG
1 ATTCTGATATGATACTGACATGG
*
704767 ATTCTGATCTGATACATGACATGG
1 ATTCTGATATGATAC-TGACATGG
*
704791 A-TCTGATCTGATACT
1 ATTCTGATATGATACT
704806 TGACCTGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 1 0.02
23 34 0.61
24 21 0.38
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (23 bp):
ATTCTGATATGATACTGACATGG
Found at i:704809 original size:23 final size:23
Alignment explanation
Indices: 704730--704805 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
704720 ATTCTGTTAC
* * *
704730 GATACCTGACCTGAATTCTGATAT
1 GATA-CTGACATGGATTCTGATCT
704754 GATACTGACATGGATTCTGATCT
1 GATACTGACATGGATTCTGATCT
704777 GATACATGACATGGA-TCTGATCT
1 GATAC-TGACATGGATTCTGATCT
704800 GATACT
1 GATACT
704806 TGACCTGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
22 1 0.02
23 34 0.71
24 13 0.27
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (23 bp):
GATACTGACATGGATTCTGATCT
Found at i:708007 original size:118 final size:119
Alignment explanation
Indices: 707798--708037 Score: 322
Period size: 118 Copynumber: 2.0 Consensus size: 119
707788 ACTGGGAGAA
* **
707798 TCACTCATGACTTAAACTTTTTGTAACAAAAAAAAAACTCGTCAATTAATCAATGTCGACCCAAT
1 TCACTCATGACCTAAACTTTTTGTAACAAAAAAAAAACAAGTCAATTAATCAATGTCGACCCAAT
*
707863 AATCATATGTATTTATCACTCGACCTCAACATTTTGATCTTCTGCTC-ATGACCC
66 AATCATATCTATTTATCACTCGACCTCAACATTTTGATCTTCTGCTCGA-GACCC
* * * * *
707917 TCACTCCTGACCTAAAC-TTTTGTATCAAAAAAAAAACAATTCAATTCATCATTGTCGACCCAAT
1 TCACTCATGACCTAAACTTTTTGTAACAAAAAAAAAACAAGTCAATTAATCAATGTCGACCCAAT
* * * ** *
707981 AATCTTATCTATTTCTCCCTCGACCTCAACATTTTTTTCTTTTGCTCGAGACCC
66 AATCATATCTATTTATCACTCGACCTCAACATTTTGATCTTCTGCTCGAGACCC
708035 TCA
1 TCA
708038 ATTAGTAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
118 89 0.85
119 16 0.15
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.34
Consensus pattern (119 bp):
TCACTCATGACCTAAACTTTTTGTAACAAAAAAAAAACAAGTCAATTAATCAATGTCGACCCAAT
AATCATATCTATTTATCACTCGACCTCAACATTTTGATCTTCTGCTCGAGACCC
Found at i:708782 original size:43 final size:43
Alignment explanation
Indices: 708727--709066 Score: 217
Period size: 43 Copynumber: 7.9 Consensus size: 43
708717 TTTTTGTTAA
* *
708727 AAAAATGCCGCAATAGGTGTTGTTATTTAGCGGCGTTTGTCAC-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCACT
** * * ** *
708770 AAAAACTTCGCAATAGGTTTTGATGTTTAGCGGTATTTTCCCT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCACT
* * *
708813 ACAAACGCCGCAGTAGGTGTTGATATTTAGCGGCGTTTTCCCT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCACT
* * * * * **
708856 ACAAACGCCGTAGTAGGTGTTGATATTTTGCGGTGTTTTTTC-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCACT
* * *
708898 AACAAACGCCGCAATAGGTGATGATGTTTAGTGGCGTTTCTTC-C-
1 AA-AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TT-TTCACT
* * * * * * * *
708942 ATAAACGTCGCAGTAGGTTTTCAGATTAAGCGGCATTTGT-A-T
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCACT
* * * * * * *
708984 CGAAAATGACGCAATAAGG-GTTGAGAATTAGCGGCGTTTTTATT
1 -AAAAACGCCGCAAT-AGGTGTTGATATTTAGCGGCGTTTTCACT
**
709028 AAAAACGCCGCAATAGGTGTTGAGCTTTAGCGGCGTTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTT
709067 TTTATAAAAA
Statistics
Matches: 228, Mismatches: 57, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
41 1 0.00
42 11 0.05
43 206 0.90
44 8 0.04
45 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCACT
Found at i:709456 original size:21 final size:21
Alignment explanation
Indices: 709431--709515 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
709421 ATTCTTCACA
709431 TCTCTGCTGATAT-GTTGCTTC
1 TCTCTG-TGATATCGTTGCTTC
*
709452 TCTCTGTGCTATCGTTGCTTC
1 TCTCTGTGATATCGTTGCTTC
* * ** *
709473 TCTTTGTGCTGCCGCTGCTTC
1 TCTCTGTGATATCGTTGCTTC
* * *
709494 TCTCTGTGCTACCGCTGCTTC
1 TCTCTGTGATATCGTTGCTTC
709515 T
1 T
709516 TTCTCTTCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 5 0.09
21 51 0.91
ACGTcount: A:0.05, C:0.31, G:0.20, T:0.45
Consensus pattern (21 bp):
TCTCTGTGATATCGTTGCTTC
Found at i:709530 original size:42 final size:42
Alignment explanation
Indices: 709446--709569 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
709436 GCTGATATGT
* * * *
709446 TGCTTCTCTCTGTGCTATCGTTGCTTCTCTT-TGTGCTGCCGC
1 TGCTTCTCTCTGTGCTACCGCTGCTTCT-TTCTCTGCTTCCGC
*
709488 TGCTTCTCTCTGTGCTACCGCTGCTTCTTTCTCTTCTTCCGC
1 TGCTTCTCTCTGTGCTACCGCTGCTTCTTTCTCTGCTTCCGC
* * * * *
709530 TGCTGCTCT-GGCTGCTTCCGCTGCTGCTCTCTCTGCTTCC
1 TGCTTCTCTCTG-TGCTACCGCTGCTTCTTTCTCTGCTTCC
709570 CTTGCTTTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.04
42 66 0.96
ACGTcount: A:0.02, C:0.36, G:0.19, T:0.43
Consensus pattern (42 bp):
TGCTTCTCTCTGTGCTACCGCTGCTTCTTTCTCTGCTTCCGC
Found at i:709575 original size:21 final size:21
Alignment explanation
Indices: 709479--709569 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
709469 CTTCTCTTTG
* * *
709479 TGCTGCCGCTGCTTCTCTCTG
1 TGCTTCCGCTGCTGCTCTCTC
* * *
709500 TGCTACCGCTGCTTCTTTCTC
1 TGCTTCCGCTGCTGCTCTCTC
* **
709521 TTCTTCCGCTGCTGCTCTGGC
1 TGCTTCCGCTGCTGCTCTCTC
709542 TGCTTCCGCTGCTGCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
709563 TGCTTCC
1 TGCTTCC
709570 CTTGCTTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.01, C:0.40, G:0.20, T:0.40
Consensus pattern (21 bp):
TGCTTCCGCTGCTGCTCTCTC
Found at i:717830 original size:41 final size:41
Alignment explanation
Indices: 717772--717881 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
717762 TACTATTATA
* * *
717772 GCATTTTAATATAAACGCCACTAAAGTACG-AGTCTATAGCG
1 GCATTTTCATACAAACGCCACTAAAATA-GAAGTCTATAGCG
* *
717813 GCGTTTTCATACGAACGCCACTAAAATAGAAGTCTATAGCG
1 GCATTTTCATACAAACGCCACTAAAATAGAAGTCTATAGCG
*
717854 GTATTTTCATACAAACGCCACTAAAATA
1 GCATTTTCATACAAACGCCACTAAAATA
717882 CAAATATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (41 bp):
GCATTTTCATACAAACGCCACTAAAATAGAAGTCTATAGCG
Found at i:717936 original size:42 final size:41
Alignment explanation
Indices: 717890--717998 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 41
717880 TACAAATATT
717890 TTGCGGCGTTTGTTATAAAAACGCCACTATATAATAC-AC-CTA
1 TTGCGGCGTTTGTTATAAAAACGCCACTAT-T-ATACTACTC-A
* *
717932 TTGCGGCGTTTG-TAAAAAAACGCCGCTATTATACTACTCA
1 TTGCGGCGTTTGTTATAAAAACGCCACTATTATACTACTCA
* *
717972 TTAGCGGCGTTTATATCTAAAAACGCC
1 TT-GCGGCGTTTGT-TATAAAAACGCC
717999 GTAAAATGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 4 0.07
40 6 0.11
41 25 0.44
42 12 0.21
43 10 0.18
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (41 bp):
TTGCGGCGTTTGTTATAAAAACGCCACTATTATACTACTCA
Found at i:721110 original size:37 final size:35
Alignment explanation
Indices: 721055--721137 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 35
721045 TGGCAACCAA
721055 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAAT-TTT
* *
721092 CTTTGAAAAATGATTTTTCAAAGTTTGGTAGATTTT
1 CTTTGAAAAATG-GTTTTCAAAGTTTGGTAAATTTT
*
721128 -GTTGAAAAAT
1 CTTTGAAAAAT
721138 TATAATGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 9 0.21
36 10 0.24
37 23 0.55
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (35 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATTTT
Found at i:725724 original size:37 final size:35
Alignment explanation
Indices: 725625--725743 Score: 159
Period size: 35 Copynumber: 3.3 Consensus size: 35
725615 TGGCAACCAA
*
725625 CTTTGAAAAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTG-AAAAAT-GTTTTCAAAGTTTGGTAAATGTTT
*
725662 CTTTGAAAATTGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTT
*
725697 CTTTGAAAAATGATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATG--TTTTCAAAGTTTGGTAAATGTTT
*
725734 -GTTGAAAAAT
1 CTTTGAAAAAT
725744 TGTAATGGGG
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 14 0.19
37 27 0.36
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.45
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTT
Found at i:730269 original size:35 final size:35
Alignment explanation
Indices: 730223--730343 Score: 120
Period size: 35 Copynumber: 3.4 Consensus size: 35
730213 AAAGTATTAG
*
730223 TTCAAAGTTTGG-CAA-CTAACTTTGAAAAAATGGTT
1 TTCAAAGTTTGGTAAATCTAACTTTG--AAAATGGTT
* **
730258 TTCAAAGTTTGGTAAATGTTCCTTTGAAAATGGTT
1 TTCAAAGTTTGGTAAATCTAACTTTGAAAATGGTT
* ** *
730293 TTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGATTT
1 TTCAAAGTTTGGTAAATCTAACTTTG-AAAATG-GTT
730330 TTCAAAGTTTGGTA
1 TTCAAAGTTTGGTA
730344 GATGTTTGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 46 0.61
36 8 0.11
37 22 0.29
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (35 bp):
TTCAAAGTTTGGTAAATCTAACTTTGAAAATGGTT
Found at i:730274 original size:21 final size:21
Alignment explanation
Indices: 730250--730310 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
730240 AACTTTGAAA
730250 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
* *
730271 AAAT-G--TTC---CTTT-GA
1 AAATGGTTTTCAAAGTTTGGT
730285 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
730306 AAATG
1 AAATG
730311 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.14
17 3 0.10
18 3 0.10
20 4 0.14
21 10 0.34
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:730341 original size:37 final size:36
Alignment explanation
Indices: 730242--730360 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
730232 TGGCAACTAA
*
730242 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTC
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
730279 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
730314 CTTTGAAAAATGATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATG-GTTTTCAAAGTTTGGTAAATGTTT
*
730351 -GTTGAAAAAT
1 CTTTGAAAAAT
730361 TATAATGGGG
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 15 0.20
37 27 0.36
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:737244 original size:20 final size:20
Alignment explanation
Indices: 737201--737246 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
737191 TATAAATCCT
*
737201 AAATATGAAATATGTCACTG
1 AAATATGAAATATGTCACTA
*
737221 AAATATGAAATATGTCATTA
1 AAATATGAAATATGTCACTA
737241 AAATAT
1 AAATAT
737247 ATGTGGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (20 bp):
AAATATGAAATATGTCACTA
Found at i:740338 original size:2 final size:2
Alignment explanation
Indices: 740286--740319 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
740276 CTAAAAATTA
740286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
740320 TATTTTAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:740880 original size:11 final size:10
Alignment explanation
Indices: 740861--740917 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
740851 CTTTTAAAAG
*
740861 TTATAAAATAA
1 TTATTAAAT-A
*
740872 TTATTAAATT
1 TTATTAAATA
740882 TTATTAAACTA
1 TTATTAAA-TA
*
740893 TTATAAAATAA
1 TTATTAAAT-A
740904 TTATTAAAT-
1 TTATTAAATA
740913 TTATT
1 TTATT
740918 GAATTTTACA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.13
10 9 0.23
11 25 0.64
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (10 bp):
TTATTAAATA
Found at i:741036 original size:55 final size:56
Alignment explanation
Indices: 740932--741040 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
740922 TTTACACTTA
*
740932 TTATAACTAAAAAAGTTAACACTTGAAACAATTATTTAAAAAGTAATTTAATGATT
1 TTATAACTAAAAAAGTTAACACTTGAAAAAATTATTTAAAAAGTAATTTAATGATT
*
740988 TTATAACTAAAAAATTTAACACTT-ACAAAAATTATTT-AAAAGTAATTTAATGA
1 TTATAACTAAAAAAGTTAACACTTGA-AAAAATTATTTAAAAAGTAATTTAATGA
741041 CTATTTTACC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
55 17 0.34
56 33 0.66
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (56 bp):
TTATAACTAAAAAAGTTAACACTTGAAAAAATTATTTAAAAAGTAATTTAATGATT
Found at i:743335 original size:2 final size:2
Alignment explanation
Indices: 743328--743371 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
743318 TTGTTTAACA
743328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
743370 AT
1 AT
743372 GTTTTATCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:755721 original size:4 final size:4
Alignment explanation
Indices: 755712--755741 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
755702 TCCTTGAACC
755712 TACG TACG TACG TACG TACG TACG TACG TA
1 TACG TACG TACG TACG TACG TACG TACG TA
755742 TGTATGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (4 bp):
TACG
Found at i:755746 original size:4 final size:4
Alignment explanation
Indices: 755739--755802 Score: 128
Period size: 4 Copynumber: 16.0 Consensus size: 4
755729 ACGTACGTAC
755739 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
755787 GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT
755803 ATTCATATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:757673 original size:6 final size:6
Alignment explanation
Indices: 757664--757736 Score: 110
Period size: 6 Copynumber: 12.0 Consensus size: 6
757654 AGGGGGCTGG
757664 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT
1 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT
* * *
757712 GATTTT GATTTT GATTTT GGGTTTT
1 GGTTTT GGTTTT GGTTTT -GGTTTT
757737 ATTTAATTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
6 59 0.92
7 5 0.08
ACGTcount: A:0.04, C:0.00, G:0.30, T:0.66
Consensus pattern (6 bp):
GGTTTT
Found at i:758033 original size:38 final size:37
Alignment explanation
Indices: 757984--758098 Score: 185
Period size: 37 Copynumber: 3.1 Consensus size: 37
757974 TCGAATATGT
*
757984 ATTCTGATTTTCCCTTTCTTTAATTTGGTCACTATTA
1 ATTCTAATTTTCCCTTTCTTTAATTTGGTCACTATTA
*
758021 ATTCTAATTTTTCCCTTTCTTTAATTTGGTCTCTATTA
1 ATTCTAA-TTTTCCCTTTCTTTAATTTGGTCACTATTA
* *
758059 ATTCTAATTTTCTCTTTCTTTAATTTGGTTACTATTA
1 ATTCTAATTTTCCCTTTCTTTAATTTGGTCACTATTA
758096 ATT
1 ATT
758099 TTGCTTTTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
37 36 0.50
38 36 0.50
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (37 bp):
ATTCTAATTTTCCCTTTCTTTAATTTGGTCACTATTA
Found at i:758108 original size:37 final size:37
Alignment explanation
Indices: 757990--758100 Score: 161
Period size: 38 Copynumber: 3.0 Consensus size: 37
757980 ATGTATTCTG
* *
757990 ATTTTCCCTTTCTTTAATTTGGTCACTATTAATTCTA
1 ATTTTCCCTTTCTTTAATTTGGTTACTATTAATTTTA
*
758027 ATTTTTCCCTTTCTTTAATTTGGTCT-CTATTAATTCTA
1 A-TTTTCCCTTTCTTTAATTTGGT-TACTATTAATTTTA
*
758065 ATTTTCTCTTTCTTTAATTTGGTTACTATTAATTTT
1 ATTTTCCCTTTCTTTAATTTGGTTACTATTAATTTT
758101 GCTTTTCTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
36 1 0.01
37 32 0.47
38 35 0.51
ACGTcount: A:0.20, C:0.16, G:0.05, T:0.59
Consensus pattern (37 bp):
ATTTTCCCTTTCTTTAATTTGGTTACTATTAATTTTA
Found at i:760931 original size:38 final size:38
Alignment explanation
Indices: 760880--760961 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
760870 AGCAAATAAA
* *
760880 AAGGCAAGGAAAAAGTTCCAAAATAGTCGGACTACAGT
1 AAGGCAAGGAAAAAATTCCAAAATAATCGGACTACAGT
* *
760918 AAGGCAAGGAAAAAATTCTAGAATAATCGGACTACAGT
1 AAGGCAAGGAAAAAATTCCAAAATAATCGGACTACAGT
760956 AAGGCA
1 AAGGCA
760962 TAATAGTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.16
Consensus pattern (38 bp):
AAGGCAAGGAAAAAATTCCAAAATAATCGGACTACAGT
Found at i:761965 original size:3 final size:3
Alignment explanation
Indices: 761957--762016 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
761947 ATTTGAAACG
761957 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
762005 TTA TTA TGTA TT
1 TTA TTA T-TA TT
762017 TGAAGAATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:766958 original size:35 final size:35
Alignment explanation
Indices: 766912--766979 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
766902 GTTTTAAAGA
766912 TGGTATCGATACCATCCTTAAGGTATCGATACCCT
1 TGGTATCGATACCATCCTTAAGGTATCGATACCCT
** * *
766947 TGGTATCGATACTGTTCTTCAGGTATCGATACC
1 TGGTATCGATACCATCCTTAAGGTATCGATACC
766980 TCATGAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (35 bp):
TGGTATCGATACCATCCTTAAGGTATCGATACCCT
Found at i:777389 original size:15 final size:15
Alignment explanation
Indices: 777369--777403 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
777359 ATTAAAGAAT
*
777369 TTATTTTTATTTTTC
1 TTATTTTTATTTTTA
777384 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
777399 TTATT
1 TTATT
777404 CATGGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:782557 original size:26 final size:25
Alignment explanation
Indices: 782515--782567 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
782505 TTTTGTCAAA
*
782515 GTCAACGGTCTACGGTC-GATCAACG
1 GTCAACGGTCAACGGTCAG-TCAACG
*
782540 GTCAACAGGTCAATGGTCAGTCAACG
1 GTCAAC-GGTCAACGGTCAGTCAACG
782566 GT
1 GT
782568 TGGTCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 17 0.71
27 1 0.04
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (25 bp):
GTCAACGGTCAACGGTCAGTCAACG
Found at i:784548 original size:22 final size:23
Alignment explanation
Indices: 784505--784552 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
784495 GCTGTTGTTT
*
784505 TTATTTTTTTTTCAAAATTTTAA
1 TTATTTATTTTTCAAAATTTTAA
784528 TTATTTATTTTT-AATAA-TTTAA
1 TTATTTATTTTTCAA-AATTTTAA
784550 TTA
1 TTA
784553 AAATTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTTATTTTTCAAAATTTTAA
Found at i:786680 original size:30 final size:30
Alignment explanation
Indices: 786623--786683 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
786613 CTCAACAATA
* *
786623 CTTAATCGATCGAACGGTTCGGTTTTAATT
1 CTTAATCGACCGAACGGTTAGGTTTTAATT
*
786653 CTTAATTCGACCGATCGGTTAGG-TTTAATT
1 CTTAA-TCGACCGAACGGTTAGGTTTTAATT
786683 C
1 C
786684 AACGGTGAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (30 bp):
CTTAATCGACCGAACGGTTAGGTTTTAATT
Found at i:790810 original size:2 final size:2
Alignment explanation
Indices: 790803--790833 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
790793 ATAATAAACA
790803 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
790834 TGGTTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:791313 original size:63 final size:63
Alignment explanation
Indices: 791181--791300 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
791171 GCATTTCGCA
* * * **
791181 TTGCGATAGTTGAAAATCGCGTTGCGTTTTTCCATTTCGCGTTGTGATAGTTGGAGATCGCGT
1 TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGT
*
791244 TTGCGATAGTTGAAAACCGCTTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
1 TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TACAG
791301 TTGTCGTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
63 47 0.94
64 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (63 bp):
TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGT
Found at i:791417 original size:6 final size:6
Alignment explanation
Indices: 791406--791448 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
791396 CACACGTATT
791406 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
791449 CGAGACGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.30, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:791954 original size:6 final size:6
Alignment explanation
Indices: 791943--791973 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
791933 TCGTCTCGTC
791943 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
791974 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:792113 original size:42 final size:41
Alignment explanation
Indices: 792066--792164 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
792056 ACAACGAATT
*
792066 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACACGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTAACGCAACACGAAA
* * * *
792108 TGGAAAATCGCAACGCGATTTTCAACTAACGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTAACGCAACACGAAA
*
792149 TGAAAAATCGCAACGC
1 TGGAAAATCGCAACGC
792165 GATTTTGTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 34 0.68
42 16 0.32
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.15
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTAACGCAACACGAAA
Found at i:792156 original size:41 final size:41
Alignment explanation
Indices: 792091--792170 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
792081 ACAACTGTAG
* *
792091 ACTATCGCAACACGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTAACGCAACACGAAATGAAAAATCGCAACGCGATTTTCA
*
792132 ACTAACGCAACGCGAAATGAAAAATCGCAACGCGATTTT
1 ACTAACGCAACACGAAATGAAAAATCGCAACGCGATTTT
792171 GTTAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (41 bp):
ACTAACGCAACACGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:792162 original size:20 final size:20
Alignment explanation
Indices: 792094--792166 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
792084 ACTGTAGACT
* *
792094 ATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * *
792114 ATCGCAACGCGATTTTCAACTA
1 ATCGCAACGCGA-AATGAA-AA
792136 A-CGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
792155 ATCGCAACGCGA
1 ATCGCAACGCGA
792167 TTTTGTTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 24 0.60
21 12 0.30
22 2 0.05
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:792807 original size:13 final size:13
Alignment explanation
Indices: 792789--792814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
792779 ACAACGGCAA
792789 AAAAACTATGGTT
1 AAAAACTATGGTT
792802 AAAAACTATGGTT
1 AAAAACTATGGTT
792815 CCTAGTCTGG
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAAAACTATGGTT
Found at i:792923 original size:2 final size:2
Alignment explanation
Indices: 792918--792957 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
792908 TTTAACACAC
792918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
792958 TCACTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:794153 original size:20 final size:21
Alignment explanation
Indices: 794109--794164 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
794099 CAGTTTCCAA
* *
794109 ATTCGCAACGCGAATATCCAG
1 ATTCGCAACGCGATTATCAAG
*
794130 ATTCGCAACGCGATTGT-AAG
1 ATTCGCAACGCGATTATCAAG
* *
794150 ATTCGTAACGTGATT
1 ATTCGCAACGCGATT
794165 CTGAAAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (21 bp):
ATTCGCAACGCGATTATCAAG
Found at i:794193 original size:19 final size:19
Alignment explanation
Indices: 794169--794206 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
794159 GTGATTCTGA
*
794169 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGAGAGTT
794188 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGAGAGTT
794207 TGAAAAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (19 bp):
AAAATGTGTTGCGAGAGTT
Found at i:794780 original size:41 final size:41
Alignment explanation
Indices: 794723--794841 Score: 175
Period size: 41 Copynumber: 2.9 Consensus size: 41
794713 CATTGCGATT
* * *
794723 TTATCGCGTTGTGATAGTCAGAATCGCGTTGTGATTTTGTA
1 TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTGTA
* * *
794764 TTATCGCGTTACGATAGTCAGAATCGCCTTACGATTTTGTA
1 TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTGTA
*
794805 TTATCCCGTTGCGATAGTCAGAATCGCATTGCGATTT
1 TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTT
794842 ACATATTCGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTGTA
Found at i:794928 original size:20 final size:19
Alignment explanation
Indices: 794905--794950 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
794895 GGAAACTGAT
* *
794905 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
794925 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
794944 TTGCGAT
1 TTGCGAT
794951 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:794940 original size:19 final size:19
Alignment explanation
Indices: 794916--794952 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
794906 TGCGATACTG
*
794916 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
794935 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
794953 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:796837 original size:18 final size:17
Alignment explanation
Indices: 796804--796837 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
796794 GAACAATTAA
796804 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
796821 ATAAAATTATTAAAATA
1 ATAAAA-TATCAAAATA
796838 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:799397 original size:29 final size:30
Alignment explanation
Indices: 799342--799402 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
799332 ATTTTGGGTC
*
799342 CTAAACTTTTCAAAGTTCATACTTTAGCCA
1 CTAAACTTTTCAAACTTCATACTTTAGCCA
* *
799372 CTAAAC-TTTCTAAACTT-ATATTTTAGTCA
1 CTAAACTTTTC-AAACTTCATACTTTAGCCA
799401 CT
1 CT
799403 GGTCAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAACTTCATACTTTAGCCA
Found at i:803054 original size:21 final size:21
Alignment explanation
Indices: 803029--803081 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
803019 CACAACGGAA
803029 ACAAGCTCCAGTCTTCATTCT
1 ACAAGCTCCAGTCTTCATTCT
803050 ACAAGCTCCAGTCTTCATTCT
1 ACAAGCTCCAGTCTTCATTCT
*
803071 ACAAACTCCAG
1 ACAAGCTCCAG
803082 GGTGATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.28
Consensus pattern (21 bp):
ACAAGCTCCAGTCTTCATTCT
Found at i:804271 original size:18 final size:17
Alignment explanation
Indices: 804238--804273 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
804228 GAACAATTAA
804238 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
804255 ATAAAATTATTAAAATAT
1 ATAAAA-TATCAAAATAT
804273 A
1 A
804274 ACAGACTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:806833 original size:29 final size:30
Alignment explanation
Indices: 806778--806838 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
806768 ATTTTGGGTC
*
806778 CTAAACTTTTCAAAGTTCATACTTTAGCCA
1 CTAAACTTTTCAAACTTCATACTTTAGCCA
* *
806808 CTAAAC-TTTCTAAACTT-ATATTTTAGTCA
1 CTAAACTTTTC-AAACTTCATACTTTAGCCA
806837 CT
1 CT
806839 GGTCAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAACTTCATACTTTAGCCA
Found at i:823230 original size:24 final size:21
Alignment explanation
Indices: 823179--823232 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
823169 AAAATTTTTA
*
823179 TTATTTTAAATATATAAAAAT
1 TTATTATAAATATATAAAAAT
* *
823200 ATGTTATAGAATATATAATAAGAT
1 TTATTATA-AATATATAA-AA-AT
823224 TTATTATAA
1 TTATTATAA
823233 GAAAGTGCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
23 3 0.12
24 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TTATTATAAATATATAAAAAT
Found at i:824187 original size:3 final size:3
Alignment explanation
Indices: 824179--824213 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
824169 TCATAGTGTT
824179 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
824214 TTCTTCTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:825831 original size:9 final size:9
Alignment explanation
Indices: 825785--825842 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
825775 AGTAAAAAAC
825785 AAAT-AATA
1 AAATAAATA
825793 AAATATATATA
1 AAATA-A-ATA
**
825804 AAA-AAGGA
1 AAATAAATA
825812 AAA-AAAT-
1 AAATAAATA
825819 AAATAAATA
1 AAATAAATA
825828 AAATAAATA
1 AAATAAATA
825837 AAATAA
1 AAATAA
825843 TAATAACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 3 0.07
8 14 0.34
9 16 0.39
10 2 0.05
11 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:825839 original size:22 final size:22
Alignment explanation
Indices: 825780--825906 Score: 64
Period size: 22 Copynumber: 5.6 Consensus size: 22
825770 TAGTAAGTAA
825780 AAAACAAAT-AATAAAATATATAT
1 AAAA-AAATAAATAAAATA-ATAT
**
825803 AAAAAAGGAAA-AAAATAA-AT
1 AAAAAAATAAATAAAATAATAT
825823 AAATAAAATAAATAAAATAATAAT
1 AAA-AAAATAAATAAAATAAT-AT
* * *
825847 AACAAAGTACGAATAATATATATAT
1 AAAAAAATA--AATAAAATA-ATAT
* * * * *
825872 ATATATATATATATAATAA-AT
1 AAAAAAATAAATAAAATAATAT
825893 AAAAAAAGTAAATA
1 AAAAAAA-TAAATA
825907 TATATAAATT
Statistics
Matches: 76, Mismatches: 19, Indels: 19
0.67 0.17 0.17
Matches are distributed among these distances:
20 5 0.07
21 13 0.17
22 21 0.28
23 17 0.22
24 4 0.05
25 14 0.18
26 2 0.03
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAAAAATAAATAAAATAATAT
Found at i:825869 original size:2 final size:2
Alignment explanation
Indices: 825862--825886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
825852 AGTACGAATA
825862 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 A
825887 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:826206 original size:2 final size:2
Alignment explanation
Indices: 826158--826190 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
826148 CTTGTTTAGA
826158 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
826191 GTAAAATGTA
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:826287 original size:2 final size:2
Alignment explanation
Indices: 826280--826312 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
826270 AAATTAATAA
826280 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
826313 AAATATAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:826317 original size:10 final size:11
Alignment explanation
Indices: 826238--826319 Score: 57
Period size: 10 Copynumber: 7.6 Consensus size: 11
826228 AAAAGAAAAT
826238 AAATATA-ATA
1 AAATATATATA
*
826248 TAATGATA-ATA
1 AAAT-ATATATA
* *
826259 AAAAATATAGA
1 AAATATATATA
826270 AAAT-TA-ATA
1 AAATATATATA
826279 AATATATATATA
1 AA-ATATATATA
*
826291 TATATATATATA
1 -AAATATATATA
*
826303 TAATAT-TATA
1 AAATATATATA
826313 AAATATA
1 AAATATA
826320 GCACTTAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
9 4 0.07
10 19 0.35
11 19 0.35
12 12 0.22
13 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AAATATATATA
Found at i:826441 original size:12 final size:11
Alignment explanation
Indices: 826413--826459 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
826403 ATAAAAAATA
* *
826413 AATAATATAAA
1 AATAATACAAG
826424 AATAATACAAG
1 AATAATACAAG
826435 TAATAATACAAG
1 -AATAATACAAG
*
826447 AATAATAAAAG
1 AATAATACAAG
826458 AA
1 AA
826460 ATAGAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATACAAG
Found at i:826450 original size:23 final size:23
Alignment explanation
Indices: 826403--826462 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
826393 GCATATATAT
* *
826403 ATAA-AAAATAAATAATATAAAA
1 ATAATAAAAGAAATAATACAAAA
* * *
826425 ATAATACAAGTAATAATACAAGA
1 ATAATAAAAGAAATAATACAAAA
826448 ATAATAAAAGAAATA
1 ATAATAAAAGAAATA
826463 GAAAGTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (23 bp):
ATAATAAAAGAAATAATACAAAA
Found at i:826510 original size:22 final size:23
Alignment explanation
Indices: 826468--826516 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
826458 AAATAGAAAG
826468 TAAAAAATATAATAATAATAATA
1 TAAAAAATATAATAATAATAATA
826491 TAAAAAATATACAT-AT-ATAATA
1 TAAAAAATATA-ATAATAATAATA
826513 TAAA
1 TAAA
826517 TAAGTAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.40
23 13 0.52
24 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAAAATATAATAATAATAATA
Found at i:826582 original size:9 final size:9
Alignment explanation
Indices: 826405--826582 Score: 55
Period size: 9 Copynumber: 18.7 Consensus size: 9
826395 ATATATATAT
826405 AAAA-AATA
1 AAAATAATA
826413 AATAAT-ATA
1 AA-AATAATA
826422 AAAATAATA
1 AAAATAATA
826431 CAAGTAATAATA
1 -AA--AATAATA
826443 CAAGAATAATA
1 -AA-AATAATA
826454 AAAGA-AATA
1 AAA-ATAATA
*
826463 GAAAGTAA-A
1 -AAAATAATA
826472 AAATATAATA
1 AAA-ATAATA
*
826482 ATAATAATA
1 AAAATAATA
826491 TAAAA-AATA
1 -AAAATAATA
826500 TACATATATAATA
1 -A-A-A-ATAATA
*
826513 TAAATAAGTA
1 AAAATAA-TA
**
826523 GAATAA-AAGG
1 -AA-AATAATA
826533 AAAAT-ATA
1 AAAATAATA
* * *
826541 ATAGTAAAA
1 AAAATAATA
826550 AAAATAATA
1 AAAATAATA
*
826559 AATATAATA
1 AAAATAATA
**
826568 GTAATAATA
1 AAAATAATA
826577 AAAATA
1 AAAATA
826583 CAAAGAAAAT
Statistics
Matches: 126, Mismatches: 23, Indels: 41
0.66 0.12 0.22
Matches are distributed among these distances:
8 14 0.11
9 63 0.50
10 20 0.16
11 12 0.10
12 13 0.10
13 4 0.03
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:826582 original size:15 final size:14
Alignment explanation
Indices: 826470--826582 Score: 52
Period size: 15 Copynumber: 7.5 Consensus size: 14
826460 ATAGAAAGTA
826470 AAAAATATAATAAT
1 AAAAATATAATAAT
* *
826484 AATAATATAAAAAAT
1 AAAAATAT-AATAAT
*
826499 ATACATATATAAT-AT
1 A-A-AAATATAATAAT
* *
826514 AAATAAGTAGAATAAA
1 AAA-AA-TATAATAAT
*
826530 AGGAAAATATAATAGT
1 A--AAAATATAATAAT
826546 AAAAA-A-AATAAT
1 AAAAATATAATAAT
826558 AAATATAATAGTAATAAT
1 -AA-A-AATA-TAATAAT
826576 AAAAATA
1 AAAAATA
826583 CAAAGAAAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 27
0.65 0.11 0.24
Matches are distributed among these distances:
12 5 0.07
13 4 0.05
14 14 0.19
15 20 0.27
16 14 0.19
17 8 0.11
18 8 0.11
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (14 bp):
AAAAATATAATAAT
Found at i:828260 original size:106 final size:106
Alignment explanation
Indices: 827953--829003 Score: 1435
Period size: 106 Copynumber: 10.0 Consensus size: 106
827943 ATTGTTCTGA
* * ** * *
827953 GTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 GTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* * * *
828017 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * * *
828059 GTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAATC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
* * * * *
828118 AGCCGCCCCTTCGTCGCGAAGTTGAGCTTGTGTTGTCTTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * *
828159 GTCCAAGATCCTTCCCTGAGAAGTTGAAATTGGCTCTGGAATTGGGAAGTTGTTTATTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
* *
828224 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * *
828265 GTCCAATATCCTACGCTGTGAAGTTGAAATTGTCTCTGAAATTGAGAAATTGTTTATTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
*
828330 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTC-TGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
828370 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* * *
828435 CAGCGATCCCTTTGTCGTGAAGCTGAACTTGCGTTGT-TTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
828476 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
*
828541 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * *
828583 GTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGTAATTGGGAAATTTTTTATTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
828648 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
828688 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
*
828753 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTC-TGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* *
828794 AGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* *
828859 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* ** * *
828901 GTCCAATATCATTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
* *
828966 AGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 AG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
829004 CGAGTGGCAC
Statistics
Matches: 848, Mismatches: 83, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
99 1 0.00
100 78 0.09
101 3 0.00
102 4 0.00
104 3 0.00
105 7 0.01
106 746 0.88
107 6 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
Found at i:828588 original size:318 final size:316
Alignment explanation
Indices: 827950--829008 Score: 1596
Period size: 318 Copynumber: 3.3 Consensus size: 316
827940 AGCATTGTTC
* * ** * *
827950 TGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
* * * *
828015 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGA
65 ACCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGA
* * * *
828080 AGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAATCAGCCGCCCCTTCGTCGCGAAG
130 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG-CGTCCCTTCGTCGTGAAG
* * * *
828139 TTGAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCCCTGAGAAGTTGAAATTGGCTCTGGAATTG
194 TTGAACTTGTGTTGT-TTGGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTG
*
828203 GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
258 GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
828262 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGTCTCTGAAATTGAGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
* *
828327 ACCAG-CGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
65 ACCAGTC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTG
*
828391 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGATCCCTTTGTCGTGAA
129 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG-TCCCTTCGTCGTGAA
* * *
828456 GCTGAACTTGCGTTGTTTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
193 GTTGAACTTGTGTTGTTTGGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTG
828521 GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
258 GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
828580 TGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGTAATTGGGAAATTTTTTATTGACA
1 TGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
*
828645 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
65 ACCAGTC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTG
828709 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
129 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGC-GTCCCTTCGTCGTGAA
* * *
828774 GTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTAAAATTG
193 GTTGAACTTGTGTTGTTTGGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTG
828839 GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
258 GGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
828898 AGAGTCCAATATCATTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTC-GTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
* *
828963 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
65 ACCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGT
829009 GGCACGATAT
Statistics
Matches: 684, Mismatches: 50, Indels: 20
0.91 0.07 0.03
Matches are distributed among these distances:
311 1 0.00
312 129 0.19
313 3 0.00
314 3 0.00
315 2 0.00
317 7 0.01
318 537 0.79
319 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (316 bp):
TGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
CCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGTCCCTTCGTCGTGAAGTT
GAACTTGTGTTGTTTGGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGA
AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:829949 original size:22 final size:22
Alignment explanation
Indices: 829923--829975 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
829913 GTGTTTGGTT
829923 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
829945 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
829967 AAAGGTTTG
1 AAAGGTTTG
829976 ATGGGGTAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTC
Found at i:830617 original size:20 final size:19
Alignment explanation
Indices: 830583--830661 Score: 56
Period size: 20 Copynumber: 4.2 Consensus size: 19
830573 TTTGTCCCTT
*
830583 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTA-TTTTGTTC
*
830603 TTTCTTTTTTCTTTTG-T-
1 TTTCTTTTTTATTTTGTTC
*
830620 TTTCTTCTTT-TTTTGCTTC
1 TTTCTTTTTTATTTTG-TTC
* * *
830639 TTTTCCTTTTTGTTTTTTTC
1 -TTTCTTTTTTATTTTGTTC
830659 TTT
1 TTT
830662 TTGTTCTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.10
17 9 0.19
18 2 0.04
19 8 0.17
20 20 0.42
21 4 0.08
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTTATTTTGTTC
Found at i:830624 original size:21 final size:20
Alignment explanation
Indices: 830583--830632 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
830573 TTTGTCCCTT
*
830583 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTATTTTTGTTC
* *
830603 TTTCTTTTTT-CTTTTGTTT
1 TTTCTTTTTTATTTTTGTTC
830622 TCTTCTTTTTT
1 T-TTCTTTTTT
830633 TGCTTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTATTTTTGTTC
Found at i:830625 original size:17 final size:16
Alignment explanation
Indices: 830603--830663 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
830593 ATTTTTGTTC
*
830603 TTTCTTTTTTCTTTTGT
1 TTTCTTCTTT-TTTTGT
830620 TTTCTTCTTTTTTTGCT
1 TTTCTTCTTTTTTTG-T
*
830637 TCTT-TTC-CTTTTTGT
1 T-TTCTTCTTTTTTTGT
*
830652 TTTTTTCTTTTT
1 TTTCTTCTTTTT
830664 GTTCTGATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.05
15 5 0.14
16 14 0.38
17 14 0.38
18 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTCTTCTTTTTTTGT
Found at i:834432 original size:26 final size:24
Alignment explanation
Indices: 834396--834465 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
834386 ATGAAGAAAG
*
834396 CAAAGATAAAATAGTA-AGTAAAAAA
1 CAAAAATAAAATA-TATA-TAAAAAA
834421 CAAATAATAAAATATATATAAAAAA
1 CAAA-AATAAAATATATATAAAAAA
* *
834446 GAAAAAGAAAATA-A-ATAAAA
1 CAAAAATAAAATATATATAAAA
834466 CAAATAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.15
23 1 0.03
24 8 0.20
25 16 0.40
26 9 0.22
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (24 bp):
CAAAAATAAAATATATATAAAAAA
Found at i:834478 original size:22 final size:21
Alignment explanation
Indices: 834417--834491 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 21
834407 TAGTAAGTAA
*
834417 AAAACAAATAATAAAATATATAT
1 AAAACAAATAA-AAAA-ATAAAT
*
834440 AAAA-AAGAAAAAGAAAATAAAT
1 AAAACAA-ATAAA-AAAATAAAT
834462 AAAACAAATAAACAAAAT-AAT
1 AAAACAAATAAA-AAAATAAAT
834483 AATAACAAA
1 AA-AACAAA
834492 GTACGAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 5 0.11
22 27 0.61
23 12 0.27
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (21 bp):
AAAACAAATAAAAAAATAAAT
Found at i:834840 original size:2 final size:2
Alignment explanation
Indices: 834785--834821 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
834775 CTTGTTTAGA
834785 AT AT 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 AT AT A
834822 ATAGTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:835022 original size:2 final size:2
Alignment explanation
Indices: 835015--835067 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
835005 GAACATACGC
835015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
835057 AT AT AT AT AT A
1 AT AT AT AT AT A
835068 AAAACAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:835107 original size:12 final size:11
Alignment explanation
Indices: 835079--835125 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
835069 AAACAAAATA
* *
835079 AATAATATAAA
1 AATAATACAAG
835090 AATAATACAAG
1 AATAATACAAG
835101 TAATAATACAAG
1 -AATAATACAAG
*
835113 AATAATAAAAG
1 AATAATACAAG
835124 AA
1 AA
835126 AGAGAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATACAAG
Found at i:835163 original size:25 final size:26
Alignment explanation
Indices: 835134--835185 Score: 83
Period size: 23 Copynumber: 2.1 Consensus size: 26
835124 AAAGAGAAAG
835134 TAAAAAATATA-ATA-ATAATA-AAA
1 TAAAAAATATACATATATAATATAAA
835157 TAAAAAATATACATATATAATATAAA
1 TAAAAAATATACATATATAATATAAA
835183 TAA
1 TAA
835186 GTAGAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.42
24 3 0.12
25 6 0.23
26 6 0.23
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAAAAATATACATATATAATATAAA
Found at i:835221 original size:12 final size:12
Alignment explanation
Indices: 835199--835243 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
835189 GAATAAAAGG
835199 AAAATATAATAGT
1 AAAA-ATAATAGT
*
835212 AAAAATAATAAT
1 AAAAATAATAGT
*
835224 AAATATAATAGT
1 AAAAATAATAGT
*
835236 AATAATAA
1 AAAAATAA
835244 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:835863 original size:37 final size:37
Alignment explanation
Indices: 835822--835918 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
835812 GGATCCTATC
835822 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
* * * * * * *
835859 TTTAGGAGTTTGAATCCTAGCAAAATTTTATCTTATT
1 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
*
835896 TTTAGGAGTTTAAATCTTAGTAG
1 TTTAGGAGTTTAAATCATAGTAG
835919 TACGAAAAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.43
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
Found at i:852662 original size:15 final size:15
Alignment explanation
Indices: 852638--852669 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
852628 CCCCCTTACT
852638 TTAACACTACTCCTC
1 TTAACACTACTCCTC
*
852653 TTAACTCTACTCCTC
1 TTAACACTACTCCTC
852668 TT
1 TT
852670 TAAAACGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAACACTACTCCTC
Found at i:854998 original size:21 final size:20
Alignment explanation
Indices: 854957--855001 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
854947 AAAACCAGAA
*
854957 CCCC-AGGGGGGTATCGATT
1 CCCCTAGGGGGGAATCGATT
*
854976 CCCCTAGGGGAGGAATCGGTT
1 CCCCTAGGGG-GGAATCGATT
854997 CCCCT
1 CCCCT
855002 TCAAAGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.20
Consensus pattern (20 bp):
CCCCTAGGGGGGAATCGATT
Found at i:858897 original size:22 final size:21
Alignment explanation
Indices: 858855--858894 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
858845 GAGTTTATTT
*
858855 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
858876 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
858895 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:866825 original size:29 final size:29
Alignment explanation
Indices: 866790--866871 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
866780 AAACTAAATT
* *
866790 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
866819 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
866848 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
866872 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:875560 original size:3 final size:3
Alignment explanation
Indices: 875549--875589 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
875539 TTTTTTATCG
875549 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
875590 ATTACATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:875577 original size:19 final size:18
Alignment explanation
Indices: 875553--875589 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
875543 TTATCGTTAT
875553 TTTATTATTATTATTATTA
1 TTTATTATTATTA-TATTA
875572 TTTATTATTATTATATTA
1 TTTATTATTATTATATTA
875590 ATTACATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTATTATATTA
Found at i:875599 original size:19 final size:19
Alignment explanation
Indices: 875558--875600 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
875548 GTTATTTTAT
* *
875558 TATTATTATTATTATTTAT
1 TATTATTATTATTAATTAA
875577 TATTATTA-TATTAATTACA
1 TATTATTATTATTAATTA-A
875596 TATTA
1 TATTA
875601 CATATTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTATTATTAATTAA
Found at i:875599 original size:22 final size:22
Alignment explanation
Indices: 875554--875600 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
875544 TATCGTTATT
**
875554 TTATTATTATTATTATTATTTA
1 TTATTATTATTATTATTACATA
875576 TTATTATTA-TATTAATTACATA
1 TTATTATTATTATT-ATTACATA
875598 TTA
1 TTA
875601 CATATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTATTATTATTATTACATA
Found at i:882156 original size:26 final size:25
Alignment explanation
Indices: 882128--882199 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
882118 TTTTTGACGT
882128 TCTATCTCTTTCAGACCTTG-AA-A
1 TCTATCTCTTTCAGACCTTGAAACA
*
882151 TAT-TCT-TTTC-GACCTTGAAACGA
1 TCTATCTCTTTCAGACCTTGAAAC-A
*
882174 TCTATCTCTTTGAGACCTTGAAACA
1 TCTATCTCTTTCAGACCTTGAAACA
882199 T
1 T
882200 TCTTTCCACC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.17
21 6 0.15
22 3 0.08
23 5 0.12
24 3 0.08
25 5 0.12
26 11 0.28
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (25 bp):
TCTATCTCTTTCAGACCTTGAAACA
Found at i:882195 original size:46 final size:45
Alignment explanation
Indices: 882128--882216 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 45
882118 TTTTTGACGT
* *
882128 TCTATCTCTTTCAGACCTTGAAATATTCTTTTCGACCTTGAAACGA
1 TCTATCTCTTTCAGACCTTGAAACATTC-TTTCCACCTTGAAACGA
*
882174 TCTATCTCTTTGAGACCTTGAAACATTCTTTCCACCTTGAAAC
1 TCTATCTCTTTCAGACCTTGAAACATTCTTTCCACCTTGAAAC
882217 ACTGCATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 14 0.35
46 26 0.65
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (45 bp):
TCTATCTCTTTCAGACCTTGAAACATTCTTTCCACCTTGAAACGA
Found at i:882856 original size:19 final size:20
Alignment explanation
Indices: 882832--882877 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
882822 AATCAAAGAG
882832 CAAAGAGCA-AAGAA-AAAAA
1 CAAAGAGCAGAA-AACAAAAA
882851 CAAAGAGCAGAAAAGCAAAAA
1 CAAAGAGCAGAAAA-CAAAAA
882872 CAAAGA
1 CAAAGA
882878 AAAATCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 11 0.46
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (20 bp):
CAAAGAGCAGAAAACAAAAA
Found at i:882911 original size:56 final size:57
Alignment explanation
Indices: 882810--882920 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 57
882800 GATCCAATCG
*
882810 AAAACAAAGAAAAATCAAAGAGCAAAGAGCAAAGAAAAAAACAAAGAGCAGAAAAGCA
1 AAAACAAAGAAAAATCAAAGAGCAAAGAGCAAAGAAAAAAACAAAGAACA-AAAAGCA
*
882868 AAAACAAAGAAAAATC-AA-AGCAAA-AGTCAAAGAAAAAAGCAAAGAACAAAAAG
1 AAAACAAAGAAAAATCAAAGAGCAAAGAG-CAAAGAAAAAAACAAAGAACAAAAAG
882921 AGGACAAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
55 7 0.14
56 25 0.50
57 2 0.04
58 16 0.32
ACGTcount: A:0.70, C:0.12, G:0.15, T:0.03
Consensus pattern (57 bp):
AAAACAAAGAAAAATCAAAGAGCAAAGAGCAAAGAAAAAAACAAAGAACAAAAAGCA
Found at i:884098 original size:4 final size:4
Alignment explanation
Indices: 884089--884169 Score: 94
Period size: 4 Copynumber: 20.8 Consensus size: 4
884079 AAGAGTATAC
* * * *
884089 ACAT ACAT ACAT ACGT ATAC ACAT ACAT ACAT ATAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
884137 ACAT ACAT ATAT ACAT ACAC ACAT --AT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
884170 CGATACATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
4 61 0.97
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:884719 original size:71 final size:72
Alignment explanation
Indices: 884633--884773 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 72
884623 TGAGAATTTT
** * **
884633 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGACAT
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTGCGTCTCGATTGAGACAT
884698 TTTTCTA
66 TTTTCTA
* *
884705 AAAACAAA-TTTTGTCTCGTTTGAGACAATTTCTTGAAAAACAAATTGCGTCTCGCTTGAGACAT
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTGCGTCTCGATTGAGACAT
884769 TTTTC
66 TTTTC
884774 CTTTGAGATA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 54 0.87
72 8 0.13
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTGCGTCTCGATTGAGACAT
TTTTCTA
Found at i:884720 original size:35 final size:36
Alignment explanation
Indices: 884633--884767 Score: 175
Period size: 36 Copynumber: 3.8 Consensus size: 36
884623 TGAGAATTTT
*
884633 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTTTA
* *
884670 AAAGCAAATTTTGTCTCGATTGAGAC-ATTT-TTCTA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTT-TA
* *
884705 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTTA
**
884741 AAAACAAATTGCGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
884768 TTTTTCCTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.02
35 29 0.34
36 46 0.53
37 9 0.10
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTTA
Found at i:884917 original size:105 final size:101
Alignment explanation
Indices: 884740--884978 Score: 259
Period size: 105 Copynumber: 2.3 Consensus size: 101
884730 CAATTTCTTG
** * *
884740 AAAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTGGATTCAC
1 AAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTGGATTCAC
*
884805 TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC
66 TAAAAACAAAATTAATCTCA-CTTGAGA---TCGTTTC--TC
* * * * *
884846 -AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCAC
1 AAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTGGATTCAC
* * *
884910 -ATTAAACAAAGTTGATCTCACTTGAGATCGTTTCTC
66 TA-AAAACAAAATTAATCTCACTTGAGATCGTTTCTC
* *
884946 AAAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACATTTTC
884979 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
100 2 0.02
101 29 0.25
102 6 0.05
104 4 0.04
105 73 0.64
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (101 bp):
AAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTGGATTCAC
TAAAAACAAAATTAATCTCACTTGAGATCGTTTCTC
Found at i:884952 original size:35 final size:36
Alignment explanation
Indices: 884925--885008 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
884915 ACAAAGTTGA
*
884925 TCTCACTTGAGATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
884960 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
884996 TCTCATTTGAGAC
1 TCTCACTTGAGAC
885009 TATATCTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.02
35 17 0.40
36 24 0.57
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:884996 original size:36 final size:36
Alignment explanation
Indices: 884940--885044 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
884930 CTTGAGATCG
*
884940 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
884975 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
885011 TATCT-T-AAAGCAAATTTTTGTCTCGCCTGAGACA
1 TTTCTCTAAAAACAAA-TTTTGTCTCGCTTGAGACA
885045 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
34 7 0.12
35 22 0.38
36 29 0.50
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:885341 original size:29 final size:27
Alignment explanation
Indices: 885296--885366 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
885286 CAGTTTCTCG
* *
885296 TGAAAAAATCTTGGAGTTTGTTCCTTT
1 TGAAAAAATCTTTGAGTTCGTTCCTTT
*
885323 TGAATAAATATCTTTGAG-TCGTTTCTTT
1 TGAA-AAA-ATCTTTGAGTTCGTTCCTTT
885351 TG-AAAAATCTTTGAGT
1 TGAAAAAATCTTTGAGT
885367 CTATTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 9 0.24
26 3 0.08
27 5 0.13
28 13 0.34
29 8 0.21
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (27 bp):
TGAAAAAATCTTTGAGTTCGTTCCTTT
Found at i:885364 original size:25 final size:25
Alignment explanation
Indices: 885299--885381 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 25
885289 TTTCTCGTGA
* * *
885299 AAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAATCTTTGAG-TCGTTTCTTTTG
885325 AATAAATATCTTTGAGTCGTTTCTTTTG
1 -A-AAA-ATCTTTGAGTCGTTTCTTTTG
* *
885353 AAAAATCTTTGAGTCTATTTATTTTG
1 AAAAATCTTTGAGTC-GTTTCTTTTG
885379 AAA
1 AAA
885382 CAAAGTTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
25 11 0.23
26 14 0.29
27 2 0.04
28 13 0.27
29 8 0.17
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (25 bp):
AAAAATCTTTGAGTCGTTTCTTTTG
Found at i:885505 original size:28 final size:27
Alignment explanation
Indices: 885467--885524 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
885457 ATTTTGTGAA
*
885467 AAAAAATCTTTGAGATTGTTTCTTTTGG
1 AAAAAATCTTTGAGATTGTTT-ATTTGG
*
885495 AAAAAATCTTTGAGTTTGTTTATTTGG
1 AAAAAATCTTTGAGATTGTTTATTTGG
885522 AAA
1 AAA
885525 CAAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (27 bp):
AAAAAATCTTTGAGATTGTTTATTTGG
Done.