Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 8 of 14
Found at i:3708828 original size:26 final size:26
Alignment explanation
Indices: 3708798--3708850 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3708788 GAAGTACGGT
3708798 AGTTAAAAAATAACAAATATCTTGAC
1 AGTTAAAAAATAACAAATATCTTGAC
*
3708824 AGTTAAAAATTAACAAATATCTTGAC
1 AGTTAAAAAATAACAAATATCTTGAC
3708850 A
1 A
3708851 TTTTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (26 bp):
AGTTAAAAAATAACAAATATCTTGAC
Found at i:3717636 original size:2 final size:2
Alignment explanation
Indices: 3717619--3717655 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3717609 CAAAGAAGGG
* *
3717619 GA GA GG GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3717656 TTCTCTACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3725985 original size:57 final size:57
Alignment explanation
Indices: 3725922--3726036 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
3725912 ATTCTACATC
3725922 TGTTTATCTTAATCTGTCAATAGCATAAATTATATATACTCTCTCATTTATTAATAT
1 TGTTTATCTTAATCTGTCAATAGCATAAATTATATATACTCTCTCATTTATTAATAT
3725979 TGTTTATCTTAATCTGTCAATAGCATAAATTATATATACTCTCTCATTTATTAATAT
1 TGTTTATCTTAATCTGTCAATAGCATAAATTATATATACTCTCTCATTTATTAATAT
3726036 T
1 T
3726037 TTATTATACA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (57 bp):
TGTTTATCTTAATCTGTCAATAGCATAAATTATATATACTCTCTCATTTATTAATAT
Found at i:3735190 original size:117 final size:117
Alignment explanation
Indices: 3734978--3735192 Score: 331
Period size: 117 Copynumber: 1.8 Consensus size: 117
3734968 TCTTGATTGG
* ** *
3734978 TATTTAATTGTTTCCTCTAATAGTCACAAAAAAATTTTATATTTTGATAAAGTTTATTGCTTTTA
1 TATTTAATTATTTCCTCTAATAGTCACAAAAAAATTTTATATTAGGATAAACTTTATTGCTTTTA
*
3735043 TTCACCTACTACATTTAAAGATTATAATAAATATGTATTAGAGTGAATAGGT
66 CTCACCTACTACATTTAAAGATTATAATAAATATGTATTAGAGTGAATAGGT
* *
3735095 TATTTAATTATTTCCTCTAGTAGTCACAAATAAATTTTATATTAGGATAAACTTTATTGCTTTTA
1 TATTTAATTATTTCCTCTAATAGTCACAAAAAAATTTTATATTAGGATAAACTTTATTGCTTTTA
* * * *
3735160 CTCACCTACTGCCTTTAAAGATTTTGATAAATA
66 CTCACCTACTACATTTAAAGATTATAATAAATA
3735193 ATTATTAAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 87 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (117 bp):
TATTTAATTATTTCCTCTAATAGTCACAAAAAAATTTTATATTAGGATAAACTTTATTGCTTTTA
CTCACCTACTACATTTAAAGATTATAATAAATATGTATTAGAGTGAATAGGT
Found at i:3735934 original size:767 final size:768
Alignment explanation
Indices: 3734607--3738883 Score: 3654
Period size: 767 Copynumber: 5.6 Consensus size: 768
3734597 ATGAGTTCAT
* * * * * * *
3734607 ATTTTCAA-TCCAAAATATATTCTTATTAAGTGGAAGAAGATGTTTATTTATAAA-CTCAAGATT
1 ATTTTCAACTCTAAAATACATGCTTGTTAGGTGGAAGAAGGTGCTTATTTATAAACCT-AAGATT
* ** ** * * * * * *
3734670 T-AGAATTTGATTCTTGGCCTCAAAATGAACACAACCGTTA-AGCAGGTTCTTTAAAGAATAGGA
65 TAAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGA-TAGGTTCTTT-AAGAAGAGGA
* * * * * *
3734733 AGACATCTTTTGTGCAAATCTATCTTGTTGTTTTTAATCATGCTAACTAAG--TGAAAAATTGTA
128 AGACATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGATTGAAAAATTGTA
* * * * ** * *
3734796 AAGAAAGGTATAATATTTATAGTACTTA-T-GTTTTTATATGTAAATTTGGTAAATAAGTTGTTG
193 TAGAAAGGTATGATATTTATAGTACTCATTCTTTTTTATACATAAATTTGGTAAATAAGTTATTA
* * *
3734859 AGTTTCTCAAATCAAAGCAATATATATTGTATTTTACAAGATTTGTGTAATTAAAATTATAACTG
258 AGTTTTTCAAATCAAAGCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATTG
* * * * * * *
3734924 ATCA-CATCTTGTCAATAATATATAACATTTAACTATT-TGTCAATTCTTGATTGGTATTTAATT
323 ATCACCTTC-TATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTTATTGGCATTCAATT
* * * * ** *
3734987 GTTTCCTCTAATAGTCACAAAAAAATTTTATATTTTGATAAAGTTTATTGCTTTTATTCACCTA-
387 GTTTTCTCTAATAGTGACAAATAAATTTTATACTAAGATAAACTTTATTGCTTTTATTCACCTAT
* * * * * * * * * *
3735051 CTACATTTAAAGATTATAATAAATATGTATTAGAGTGAATAGGTTATTTAATTATTTCCTCTAGT
452 CGACCTTTAAAGATTTTAATAAATAAGTATTAAAATGAATAAGTTATTCAATTGTTTCCTCTAAT
* * * * *
3735116 AGTCACAAATAAATTTTATATTAGGATAAACTTTATTGCTTTTACTCACCTACTGCCTTTAAAGA
517 AGTCACAAATAAATTTTATACTAAGATAAATTTTATTGCTTTTATTCACCTACAGCCTTTAAAGA
* * * * * * *
3735181 TTTTGATAAATAATTATTAAAGTAAATATGTTGTATTTCTGAGTGAAAAATTTGGTGAAAGTTAT
582 TTTTAATAAATAAGTATTAAAGTGAATAGGTTTTATTTCTGAGTGAAAAATATGGTGAAAGTTCT
* * * * *
3735246 TTATACAACTTAG-TGGACGC-TGTTATCACTCATAAAGGGTTGACCTCGACTTGATATCTCTCA
647 TTATACTACTTAGATCGAC-CTTGGTATCTCTCAT--AGGGTTGACCTCGACTTGGTATCTCTCA
* * * * * * * * * * * *
3735309 TTAAAGTCAT-ACATTATTAAAAATTT-GAGTATACTTTAATACCACTTATCAAGGTTTAC
709 TTAAGGTCCTCACATTAGTGAAGATTTAG-GTTTGCTCTAATACCACATGTTAAGGCTTAC
* * * * **
3735368 ATTTTTAACTC-AAAATAAATGCTTGTTAGATTGAAGAAGGTAATTATTTATAAA-CTCAAGATT
1 ATTTTCAACTCTAAAATACATGCTTGTTAGGTGGAAGAAGGTGCTTATTTATAAACCT-AAGATT
* * * * * *
3735431 TAAGAACTTGATTCTTCATCTTGATATAGACACGACAATTAGATAGATTCTTTAAAGAAGAGAAA
65 TAAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGATAGGTTCTTT-AAGAAGAGGAA
* * * * * *
3735496 GACATATTTTGTACAAATTTATTTTTTTGTTTAACATTATACTAGCTAAAATTGAAAAATTGTAT
129 GACATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGATTGAAAAATTGTAT
* * *
3735561 CGAAAGGTATGATATTTATAATACTCATTCTTTTTTATACATAAATTTGGTAAATAAAGTT-TTC
194 AGAAAGGTATGATATTTATAGTACTCATTCTTTTTTATACATAAATTTGGTAAAT-AAGTTATTA
* * * * *
3735625 AGTTTTTCTAATCAAAGCAATAGATATTATATTTTGCAAGATTCATGTAATTAAAATTATAATTG
258 AGTTTTTCAAATCAAAGCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATTG
* *
3735690 ATCTCCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTTGTTGGCATTCAATTG
323 ATCACCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTTATTGGCATTCAATTG
* * * * *
3735755 TTTTCTCTAATAATGACAAATAAATTTTATACTAATATAAACTTTATCGCTTTTATTTACCTATT
388 TTTTCTCTAATAGTGACAAATAAATTTTATACTAAGATAAACTTTATTGCTTTTATTCACCTATC
* *
3735820 GA-ATTTAAAGATTTTAAGAAATAAGTATTAAAATGAATAAGTTATTCAATTGTTTCCTCTAATA
453 GACCTTTAAAGATTTTAATAAATAAGTATTAAAATGAATAAGTTATTCAATTGTTTCCTCTAATA
* * ** * * *
3735884 GTCATAAATAAATTTTATATTAAGATAAATTTTATCACTTTTGTTCACCTACTGCCTTTCAAGAT
518 GTCACAAATAAATTTTATACTAAGATAAATTTTATTGCTTTTATTCACCTACAGCCTTTAAAGAT
* * *
3735949 TTTAATAAGTAAGTATTAAAGTGAATAGATTTTATTTCTAAGTGAAAAATATGGTGAAAGTTCTT
583 TTTAATAAATAAGTATTAAAGTGAATAGGTTTTATTTCTGAGTGAAAAATATGGTGAAAGTTCTT
* * * * * * * * *
3736014 TACACTA-TTTGATCGACCTTGGTGTTTCTCAT-GGGTTATTGACTTCAACCTGGTATCCCTTA-
648 TATACTACTTAGATCGACCTTGGTATCTCTCATAGGG---TTGACCTCGACTTGGTATCTCTCAT
* * ** * * * * *
3736076 TGAGGGCCTCACAGCAGTGAAAATTTAGGTCTGCTATAATGA-TAC-TAGTCAAGGGCTTAC
710 TAAGGTCCTCACATTAGTGAAGATTTAGGTTTGCTCTAAT-ACCACAT-GTTAA-GGCTTAC
* * * * *
3736136 ATTTTCAAC-CTAAAATATATGTTTGCTAGGTGGCAA-AATGTGCTTATTTATAAACCGAAGA-T
1 ATTTTCAACTCTAAAATACATGCTTGTTAGGTGG-AAGAAGGTGCTTATTTATAAACCTAAGATT
* * * * * * * * **
3736198 TCAGAACCTAATTTTTTATCTTGATATGGACACAACCCTTAGGCAGGTTCTTTAAGAAAGAGGAA
65 TAAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGATAGGTTCTTTAAG-AAGAGGAA
* * * * * * *
3736263 GAAATTTTTTATGCAAGTCTATCTCTTTGTTCATCATTATGCTAGCTAAGATTTG-AAAATTGTA
129 GACATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGA-TTGAAAAATTGTA
* * * * * * * * *
3736327 TAGAATGGTATGATATTTATAGTATTTATTGTTTTTTACATATAACTTTAGTAAATTAGTTATTA
193 TAGAAAGGTATGATATTTATAGTACTCATTCTTTTTTATACATAAATTTGGTAAATAAGTTATTA
* ** * *
3736392 AGTTTTTCAGATCAAAGCTCTATATATTTTACTTTACAAG-TATCGTGTAATTAAAATTATAATT
258 AGTTTTTCAAATCAAAGCAATATATATTGTATTTTACAAGAT-TCGTGTAATTAAAATTATAATT
* * *
3736456 GATCACCTTTTATCAATACTATATAAAGTTTAATTATTGTGTCAATTCTTCGT-TTGGCATTCAA
322 GATCACCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTT--TATTGGCATTCAA
** * *
3736520 TT-TTTTCCTCTAATAGTGACAAATAAATTTTATACTAATCTAAACTTTATCGTTTTTATTCACC
385 TTGTTTT-CTCTAATAGTGACAAATAAATTTTATACTAAGATAAACTTTATTGCTTTTATTCACC
* * * * * * *
3736584 -AACCATCTTTAAAGATTTTAATATATAATTATTCAAATGAAT-AGATTATTCAATTGTTTTCTC
449 TATCGACCTTTAAAGATTTTAATAAATAAGTATTAAAATGAATAAG-TTATTCAATTGTTTCCTC
** * * * * * *
3736647 TTGTAATCATAAATAAATTTTATACTAAGATAAATTTTATTGTTTTTATTTACTTATCAG-CTTC
513 TAATAGTCACAAATAAATTTTATACTAAGATAAATTTTATTGCTTTTATTCACCTA-CAGCCTTT
* * * *
3736711 AAAGATTTTAATAAATAAGTATTAAAGTAAATAGGCTTTATTTCTAAGTGAAAAATATGGTAAAA
577 AAAGATTTTAATAAATAAGTATTAAAGTGAATAGGTTTTATTTCTGAGTGAAAAATATGGTGAAA
* * *** * * * * *
3736776 GTTCTTTACACTACTT-GGTCGACCCAAGTGTCTCCCATGGGGGTTTAACTCGACTTGGTATCTC
642 GTTCTTTATACTACTTAGATCGACCTTGGTATCTCTCAT-AGGGTTGACCTCGACTTGGTATCTC
* * * * *
3736840 TCATT-AGGGCCTTATATTAGTGAAGATTTAGGTTTGCTCTAATACCACATGTTATGGGCTCAC
706 TCATTAAGGTCCTCACATTAGTGAAGATTTAGGTTTGCTCTAATACCACATGTTA-AGGCTTAC
* * * * * * *
3736903 -GTTTCAACT-TAAAATATATG-TCCGGTAGGTAGAAGAAAGTGCTTATTTATAAACCTAAGA-G
1 ATTTTCAACTCTAAAATACATGCT-TGTTAGGTGGAAGAAGGTGCTTATTTATAAACCTAAGATT
* * * * * *
3736964 TCAGAACCTGATTTTTAACCTTGATATCGACATGACCATTAGTTAGGTTCTTTAAGTAAGAGGAA
65 TAAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGATAGGTTCTTTAAG-AAGAGGAA
* * * ** * *
3737029 GATATCTTTTGTACGAATCTATC-TTGTGTTTATCATTATTTTAGTTAAGATTGAAAAATAGTAT
129 GACATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGATTGAAAAATTGTAT
* * *
3737093 AGAAAGGTATGCTATTTATAGTTCTCATTCTTTTTTTATACATAACTTTGGTAAATAAGTTATTA
194 AGAAAGGTATGATATTTATAGTACTCATTC-TTTTTTATACATAAATTTGGTAAATAAGTTATTA
* * ** *
3737158 AGTTTCTT-AAATTAAAGCAATATATATTGTATTTTACAAGATTCATGTCGTTAAAATTATAACT
258 AGTTT-TTCAAATCAAAGCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATT
* * * ***
3737222 AATCACCTTCTATCAATATTATATAAAATTTAACTATTGTGTTAATT-TTTCATTGGTGCTCAAT
322 GATCACCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTT-ATTGGCATTCAAT
* * * *
3737286 TG-TTTCATCTAATTGTGATAAATAAATTTTATACTAAGATAAATTTTATTGCTTTAATTCACCT
386 TGTTTTC-TCTAATAGTGACAAATAAATTTTATACTAAGATAAACTTTATTGCTTTTATTCACCT
* * * * *
3737350 A-CCACCTTTAAAGATTTTAAAAAATTACTATTAAAATG----A---A-T-AA--GTTTCCTCAA
450 ATCGACCTTTAAAGATTTTAATAAATAAGTATTAAAATGAATAAGTTATTCAATTGTTTCCTCTA
* * * * * *
3737403 ATAGTTACAAAAAAATTTTATAGTAAGATAAATTTTATCGCTTTTATTCCCCTACAACCTTTAAA
515 ATAGTCACAAATAAATTTTATACTAAGATAAATTTTATTGCTTTTATTCACCTACAGCCTTTAAA
* * *
3737468 GATTTTAATAAATAAGTATTAAAATGAATAGGTTTTATTTTTGAGTGAAAAATATGGTGAAAATT
580 GATTTTAATAAATAAGTATTAAAGTGAATAGGTTTTATTTCTGAGTGAAAAATATGGTGAAAGTT
* * * * * * * *
3737533 CTTTATAGTACTTAG-TTGGCCCTAGTATCTCTCATGGGGTTGACCTTGACTTCGTATCTCTCA-
645 CTTTATACTACTTAGATCGACCTTGGTATCTCTCATAGGGTTGACCTCGACTTGGTATCTCTCAT
* * * * * ** * *
3737596 CAAGGACCTCACATCAGTGAAGATTTAGGTTTTCTCTGATATTACATGTTATGG-TCCAC
710 TAAGGTCCTCACATTAGTGAAGATTTAGGTTTGCTCTAATACCACATGTTAAGGCT-TAC
* * * *
3737655 ATTTTCAA-TCTAAATTACATACTTGTTAGGTGGAAGAATGTGCTTATTTGTAAACCTAAGATTT
1 ATTTTCAACTCTAAAATACATGCTTGTTAGGTGGAAGAAGGTGCTTATTTATAAACCTAAGATTT
* * * **
3737719 -AGAACTTAATTCTTAACCTTGATATAGATATAACCA-T---TA-G-TC---------A-G--G-
66 AAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGATAGGTTCTTTAAGAAGAGGAAGA
* * * *
3737764 ------TTCTACAAATCTATCTTGTTGTTTATCATTACGCTAACTAAGATTGAAAAATTGTATAA
131 CATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGATTGAAAAATTGTAT-A
* * * * ** *
3737823 AAAAGGTATGATATTTATATTACTCATTCTTGTCTATACATAGCTTTGGTAAATAAGTTATTAAC
195 GAAAGGTATGATATTTATAGTACTCATTCTTTTTTATACATAAATTTGGTAAATAAGTTATTAAG
* * * **
3737888 TTTCTCAAATAAAAGCAATATTTATTGCGTTTTACAAGATTCGTGTAATTAAAATTATAATT-AT
260 TTTTTCAAATCAAAGCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATTGA-
* * * *
3737952 TCACCTTCTATGAATACTGTATAAAATTTAACTATTGTGTTAATTCTTCATTGGCATTCAATTGT
324 TCACCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTTATTGGCATTCAATTGT
* * * * * * *
3738017 TTTATCTAATAGTGATAAAT-AATATTTACAGTAAGATAAATTTTATTACTTTTATTCACCTATT
389 TTTCTCTAATAGTGACAAATAAAT-TTTATACTAAGATAAACTTTATTGCTTTTATTCACCTATC
* * * * **
3738081 G-TCTTTAAAGATTTTAAGAAATAAGTATTAAAATTAATAAATTATTCAATCATTTCCT-TCAAT
453 GACCTTTAAAGATTTTAATAAATAAGTATTAAAATGAATAAGTTATTCAATTGTTTCCTCT-AAT
* * * *
3738144 AATCACAAATAAATTGTATCCTAAGATAAATTTTATTGCTTTTATTCACCTACAACCTTTAAAGA
517 AGTCACAAATAAATTTTATACTAAGATAAATTTTATTGCTTTTATTCACCTACAGCCTTTAAAGA
* * * * * *
3738209 TATTAATAAATAATTATTAAACTGAATAGGTTTTATTTTTGAGTGAAAAATATAGTAAAAGTT-T
582 TTTTAATAAATAAGTATTAAAGTGAATAGGTTTTATTTCTGAGTGAAAAATATGGTGAAAGTTCT
* * *
3738273 TTAATAGTACTT-GATCGACCTTGGTGTCTCTTAT-GAGGTTGGATCCT-GACTTGGTATCTCTC
647 TT-ATACTACTTAGATCGACCTTGGTATCTCTCATAG-GGTT-GA-CCTCGACTTGGTATCTCTC
* * * * * * * * * * *
3738335 ATGAGGGT-CTCACATTAATAAAGATTT-GAGTTTGTTTTGATATCA-TTGTTAGGGGCTCAC
708 ATTAAGGTCCTCACATTAGTGAAGATTTAG-GTTTGCTCTAATACCACATGTTA-AGGCTTAC
* * * * * * *
3738395 ATTTTCAA-TCAAAAATACATTCCTATTAGGTGGAAGAAGATGATTATTTATATTTA-C-AAGAT
1 ATTTTCAACTCTAAAATACATGCTTGTTAGGTGGAAGAAGGTGCTTATTTATA--AACCTAAGAT
* * * * * * *
3738457 TCAA-AAATTGATTCTTAACCTTGATATGGGCATGACTATTAGGTAGGTTCATTAAGGAAGAGGA
64 TTAAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGATAGGTTCTTTAA-GAAGAGGA
* * * ** * ** * * *
3738521 AGACATCTTTCGTTCAAATCAATCTCGTTGTTTATCATTATGTTAATTTAGACTGAAAAATTATA
128 AGACATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGATTGAAAAATTGTA
* * * *
3738586 TAGATAGGTATGATATTTATAGTACTCATTCATTATTATACATAAATTTGGTAAATAAGTTGTTG
193 TAGAAAGGTATGATATTTATAGTACTCATTCTTTTTTATACATAAATTTGGTAAATAAGTTATT-
* *
3738651 AA-TTTTTCAAATAAAATCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATT
257 AAGTTTTTCAAATCAAAGCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATT
* * * * * * * *
3738715 TATTACATTCTACCAATATTATATAAAATTTAACTATTGTGTCATTTCATAATTGGCATTCAATT
322 GATCACCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTTATTGGCATTCAATT
* * * * * *
3738780 GTTTCCTTTAATAGTCACAAATAAATTTTTTAATAAGATAAA-TTT-TTAG-TTTTATTCACCTG
387 GTTTTCTCTAATAGTGACAAATAAATTTTATACTAAGATAAACTTTATT-GCTTTTATTCACCTA
* * *
3738842 TCG-CCTTTAAAAAATTTTAATAAATAAGTACTAAAGTGAATA
451 TCGACCTTT-AAAGATTTTAATAAATAAGTATTAAAATGAATA
3738884 GGTTTTATTT
Statistics
Matches: 2859, Mismatches: 533, Indels: 245
0.79 0.15 0.07
Matches are distributed among these distances:
727 18 0.01
728 248 0.09
729 31 0.01
732 1 0.00
734 1 0.00
735 1 0.00
736 2 0.00
737 3 0.00
738 5 0.00
739 156 0.05
740 126 0.04
741 10 0.00
742 1 0.00
744 2 0.00
745 1 0.00
746 2 0.00
747 2 0.00
748 1 0.00
749 2 0.00
751 1 0.00
752 7 0.00
753 144 0.05
754 142 0.05
755 1 0.00
756 3 0.00
757 2 0.00
758 1 0.00
759 1 0.00
761 51 0.02
762 86 0.03
763 22 0.01
764 73 0.03
765 345 0.12
766 421 0.15
767 626 0.22
768 309 0.11
769 8 0.00
770 3 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (768 bp):
ATTTTCAACTCTAAAATACATGCTTGTTAGGTGGAAGAAGGTGCTTATTTATAAACCTAAGATTT
AAGAACTTGATTCTTAACCTTGATATGGACACGACCATTAGATAGGTTCTTTAAGAAGAGGAAGA
CATCTTTTGTACAAATCTATCTTTTTGTTTATCATTATGCTAGCTAAGATTGAAAAATTGTATAG
AAAGGTATGATATTTATAGTACTCATTCTTTTTTATACATAAATTTGGTAAATAAGTTATTAAGT
TTTTCAAATCAAAGCAATATATATTGTATTTTACAAGATTCGTGTAATTAAAATTATAATTGATC
ACCTTCTATCAATACTATATAAAATTTAACTATTGTGTCAATTCTTTATTGGCATTCAATTGTTT
TCTCTAATAGTGACAAATAAATTTTATACTAAGATAAACTTTATTGCTTTTATTCACCTATCGAC
CTTTAAAGATTTTAATAAATAAGTATTAAAATGAATAAGTTATTCAATTGTTTCCTCTAATAGTC
ACAAATAAATTTTATACTAAGATAAATTTTATTGCTTTTATTCACCTACAGCCTTTAAAGATTTT
AATAAATAAGTATTAAAGTGAATAGGTTTTATTTCTGAGTGAAAAATATGGTGAAAGTTCTTTAT
ACTACTTAGATCGACCTTGGTATCTCTCATAGGGTTGACCTCGACTTGGTATCTCTCATTAAGGT
CCTCACATTAGTGAAGATTTAGGTTTGCTCTAATACCACATGTTAAGGCTTAC
Found at i:3735952 original size:117 final size:117
Alignment explanation
Indices: 3735746--3735975 Score: 307
Period size: 117 Copynumber: 2.0 Consensus size: 117
3735736 CTTTGTTGGC
* * * *
3735746 ATTCAATTGTTTTCTCTAATAATGACAAATAAATTTTATACTAATATAAACTTTATCGCTTTTAT
1 ATTCAATTGTTTCCTCTAATAATCACAAATAAATTTTATACTAAGATAAACTTTATCACTTTTAT
* *
3735811 TTACCTATTGAATTTAAAGATTTTAAGAAATAAGTATTAAAATGAATAAGTT
66 TCACCTACTGAATTTAAAGATTTTAAGAAATAAGTATTAAAATGAATAAGTT
* * * * *
3735863 ATTCAATTGTTTCCTCTAATAGTCATAAATAAATTTTATATTAAGATAAATTTTATCACTTTTGT
1 ATTCAATTGTTTCCTCTAATAATCACAAATAAATTTTATACTAAGATAAACTTTATCACTTTTAT
** * * * *
3735928 TCACCTACTGCCTTTCAAGATTTTAATAAGTAAGTATTAAAGTGAATA
66 TCACCTACTGAATTTAAAGATTTTAAGAAATAAGTATTAAAATGAATA
3735976 GATTTTATTT
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
117 96 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (117 bp):
ATTCAATTGTTTCCTCTAATAATCACAAATAAATTTTATACTAAGATAAACTTTATCACTTTTAT
TCACCTACTGAATTTAAAGATTTTAAGAAATAAGTATTAAAATGAATAAGTT
Found at i:3737457 original size:106 final size:106
Alignment explanation
Indices: 3737309--3737502 Score: 307
Period size: 106 Copynumber: 1.8 Consensus size: 106
3737299 TGTGATAAAT
* *
3737309 AAATTTTATACTAAGATAAATTTTATTGCTTTAATTCACCTACCACCTTTAAAGATTTTAAAAAA
1 AAATTTTATACTAAGATAAATTTTATCGCTTTAATTCACCTACAACCTTTAAAGATTTTAAAAAA
*
3737374 TTACTATTAAAATGAATAAGTTTCCTCAAATAGTTACAAAA
66 TAACTATTAAAATGAATAAGTTTCCTCAAATAGTTACAAAA
* * * *
3737415 AAATTTTATAGTAAGATAAATTTTATCGCTTTTATTCCCCTACAACCTTTAAAGATTTTAATAAA
1 AAATTTTATACTAAGATAAATTTTATCGCTTTAATTCACCTACAACCTTTAAAGATTTTAAAAAA
* *
3737480 TAAGTATTAAAATGAATAGGTTT
66 TAACTATTAAAATGAATAAGTTT
3737503 TATTTTTGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 79 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (106 bp):
AAATTTTATACTAAGATAAATTTTATCGCTTTAATTCACCTACAACCTTTAAAGATTTTAAAAAA
TAACTATTAAAATGAATAAGTTTCCTCAAATAGTTACAAAA
Found at i:3739670 original size:23 final size:22
Alignment explanation
Indices: 3739644--3739692 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
3739634 ATTTAGTTGA
3739644 AAGA-AAATTATCTTTGAGTATAT
1 AAGAGAAATTATC-TTGAGTAT-T
3739667 AAGAGGAAATTATCTTGAGTATT
1 AAGA-GAAATTATCTTGAGTATT
3739690 AAG
1 AAG
3739693 TCTTTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 8 0.33
25 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (22 bp):
AAGAGAAATTATCTTGAGTATT
Found at i:3742569 original size:91 final size:91
Alignment explanation
Indices: 3742407--3742585 Score: 286
Period size: 91 Copynumber: 2.0 Consensus size: 91
3742397 ATCATAGTGA
* * * * *
3742407 GATTTTAGCAGTCTACACAATCTAAATTTAAATATATTTATTTAAACCTAGTAATTAATTTTCAT
1 GATTTTAACAGTCTACACAATCCAAATTCAAATATATTTATTTAAACCTAGTAATTAATTTCCAC
*
3742472 AGCACTGAAAATGTAATTAAAACAAG
66 AACACTGAAAATGTAATTAAAACAAG
3742498 GATTTTAACAGTCTACACAATCCAAATTCAAATATATTTATTTAAACCTAGTAATTAATTTCCAC
1 GATTTTAACAGTCTACACAATCCAAATTCAAATATATTTATTTAAACCTAGTAATTAATTTCCAC
* *
3742563 AACACTGGAAATGTGATTAAAAC
66 AACACTGAAAATGTAATTAAAAC
3742586 TAGGCAATAG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (91 bp):
GATTTTAACAGTCTACACAATCCAAATTCAAATATATTTATTTAAACCTAGTAATTAATTTCCAC
AACACTGAAAATGTAATTAAAACAAG
Found at i:3749566 original size:32 final size:30
Alignment explanation
Indices: 3749530--3749590 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
3749520 TCATAAAGAT
*
3749530 TTATTTGATTCAAAATAAAAGTAAAAAAAAAC
1 TTATTTAATTCAAAA-AAAA-TAAAAAAAAAC
*
3749562 TTATTTAATTCAAAAAAAATATAAAAAAA
1 TTATTTAATTCAAAAAAAATAAAAAAAAA
3749591 GATTGAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 9 0.33
31 4 0.15
32 14 0.52
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (30 bp):
TTATTTAATTCAAAAAAAATAAAAAAAAAC
Found at i:3757630 original size:17 final size:17
Alignment explanation
Indices: 3757590--3757632 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3757580 TGCAAATATT
*
3757590 TTTAAATATAATTATAAC
1 TTTAAAT-TAAATATAAC
3757608 TTTAAATTAAAT-TAAC
1 TTTAAATTAAATATAAC
3757624 ATTTAAATT
1 -TTTAAATT
3757633 TTTTGGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAAATATAAC
Found at i:3758320 original size:20 final size:19
Alignment explanation
Indices: 3758295--3758368 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
3758285 ATATTTAATG
3758295 AATATTAATATTTAACTTAA
1 AATATTAATATTTAA-TTAA
* *
3758315 AATATTAAAAAATTAA--AA
1 AATATT-AATATTTAATTAA
3758333 ATATATTAATATTTAATTTAA
1 A-ATATTAATATTTAA-TTAA
3758354 AATATTAATATTTAA
1 AATATTAATATTTAA
3758369 ATTATTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 10 0.22
19 5 0.11
20 20 0.44
21 10 0.22
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTAATATTTAATTAA
Found at i:3758368 original size:15 final size:17
Alignment explanation
Indices: 3758346--3758389 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
3758336 TATTAATATT
3758346 TAATTTAAAATATT-AA
1 TAATTTAAAATATTCAA
*
3758362 T-ATTTAAATTATTCAA
1 TAATTTAAAATATTCAA
3758378 TAATATTAAAAT
1 TAAT-TTAAAAT
3758390 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 2 0.09
18 6 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTAAAATATTCAA
Found at i:3758384 original size:45 final size:41
Alignment explanation
Indices: 3758286--3758386 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 41
3758276 TAGGAATATA
*
3758286 TATTTAATGAATATTAATATTTAACTTAAAATATTAAAAAAT
1 TATTAAAT-AATATTAATATTTAACTTAAAATATTAAAAAAT
* *
3758328 TA-AAAAT-ATATTAATATTTAATTTAAAATATTAATATTTAAAT
1 TATTAAATAATATTAATATTTAACTTAAAATATTAA-A---AAAT
*
3758371 TATTCAATAATATTAA
1 TATTAAATAATATTAA
3758387 AATTAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
39 26 0.54
40 1 0.02
41 3 0.06
42 2 0.04
43 6 0.12
44 3 0.06
45 7 0.15
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (41 bp):
TATTAAATAATATTAATATTTAACTTAAAATATTAAAAAAT
Found at i:3758398 original size:19 final size:19
Alignment explanation
Indices: 3758339--3758398 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
3758329 AAAAATATAT
* *
3758339 TAATATTTAATTTAAAATAT
1 TAATATTTAAATTAAAA-AA
***
3758359 TAATATTTAAATTATTCAA
1 TAATATTTAAATTAAAAAA
*
3758378 TAATATTAAAATTAAAAAA
1 TAATATTTAAATTAAAAAA
3758397 TA
1 TA
3758399 TTTTTTAATG
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATATTTAAATTAAAAAA
Found at i:3758582 original size:63 final size:61
Alignment explanation
Indices: 3758510--3758684 Score: 201
Period size: 63 Copynumber: 2.8 Consensus size: 61
3758500 ATGAATATAT
* * * *
3758510 ATAATTATAAATTTTGGATGTTTTACACAATTGATAAATATTGATATTTTATGGTGAATTCAC
1 ATAAATATAAGTTTTGGATGTTTTACACAATTGATAAATATTGATATTTTATAGT-AA-ACAC
* * *
3758573 GTAAATATAAGTTTTGAATGTTTTATC-CAATTGATAAATAATGATAATTTTTATAGTAAACAC
1 ATAAATATAAGTTTTGGATGTTTTA-CACAATTGATAAATATTGAT-A-TTTTATAGTAAACAC
* * *
3758636 ATAAATATAGGTTTTGGAT-TCTTACACAATTAATAAATATTGATATTTT
1 ATAAATATAAGTTTTGGATGTTTTACACAATTGATAAATATTGATATTTT
3758685 TATAATATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
60 4 0.04
61 2 0.02
62 20 0.21
63 57 0.60
64 4 0.04
65 8 0.08
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.43
Consensus pattern (61 bp):
ATAAATATAAGTTTTGGATGTTTTACACAATTGATAAATATTGATATTTTATAGTAAACAC
Found at i:3758842 original size:19 final size:19
Alignment explanation
Indices: 3758815--3758854 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3758805 ATCTCTTAAC
*
3758815 ACCCGTTAACT-GAATCCAA
1 ACCCATTAACTGGAAT-CAA
3758834 ACCCATTAACTGGAATCAA
1 ACCCATTAACTGGAATCAA
3758853 AC
1 AC
3758855 AACTTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (19 bp):
ACCCATTAACTGGAATCAA
Found at i:3761190 original size:22 final size:23
Alignment explanation
Indices: 3761147--3761193 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3761137 TACATATTGC
*
3761147 TTTTATTTCTTTTCTTTCCTCTT
1 TTTTATTTATTTTCTTTCCTCTT
* *
3761170 TTTTTTTTATTTTTTTTCTCTCTT
1 TTTTATTTATTTTCTTTC-CTCTT
3761194 AAAGATCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTATTTATTTTCTTTCCTCTT
Found at i:3763167 original size:2 final size:2
Alignment explanation
Indices: 3763154--3763184 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3763144 ACCTTTACTA
*
3763154 AT AT AA 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 A
3763185 CACAGCTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3765596 original size:2 final size:2
Alignment explanation
Indices: 3765589--3765622 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3765579 TTACCCCATC
*
3765589 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3765623 GCTGGATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3782013 original size:16 final size:16
Alignment explanation
Indices: 3781992--3782026 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3781982 TATAAAAAAA
3781992 AATGAAACACAGTAAG
1 AATGAAACACAGTAAG
3782008 AATGAAACACAGTAAG
1 AATGAAACACAGTAAG
3782024 AAT
1 AAT
3782027 AGAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (16 bp):
AATGAAACACAGTAAG
Found at i:3790047 original size:2 final size:2
Alignment explanation
Indices: 3790040--3790067 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3790030 TACTTCGTAC
3790040 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
3790068 TCGATGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3801571 original size:2 final size:2
Alignment explanation
Indices: 3801566--3801594 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3801556 GTACGCACAC
3801566 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 A
3801595 GTTTCAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3814957 original size:34 final size:35
Alignment explanation
Indices: 3814905--3814974 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
3814895 TAACGAAATT
*
3814905 CCCCCTCCCCTCCCACGAGTCC-GACCTGATTCCCC
1 CCCCCCCCCCTCCCACGAGTCCAGACCT-ATTCCCC
*
3814940 CCCCCCCCCCT-CGACGAGTCCAGGACCTATTCCCC
1 CCCCCCCCCCTCCCACGAGTCCA-GACCTATTCCCC
3814975 TCCCGGCGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 9 0.29
35 17 0.55
36 5 0.16
ACGTcount: A:0.13, C:0.59, G:0.13, T:0.16
Consensus pattern (35 bp):
CCCCCCCCCCTCCCACGAGTCCAGACCTATTCCCC
Found at i:3821758 original size:64 final size:64
Alignment explanation
Indices: 3821617--3821807 Score: 211
Period size: 64 Copynumber: 3.0 Consensus size: 64
3821607 CATTTGATAA
* * * * * * * *
3821617 ATACATATAATTATAGGTTTTGGATGTTTTATACAATTAATAAATATTGACATTTTTATAGTGAA
1 ATACATA-AA-TATAGGTTTTGAATGTCTTACACAATTGATAAATATTAATATTTTTATAATAAA
3821682 T
64 T
* ** * *
3821683 ACATTTGAATATAGGTTTTGAATGCCTTACACAATTGATAAATATTAATATTTTTATAATAAAT
1 ATACATAAATATAGGTTTTGAATGTCTTACACAATTGATAAATATTAATATTTTTATAATAAAT
* ** *
3821747 ATACATAAATATAGGTTTTGAATTTCTTACGTAATTGATAAATATTTATATTTTTATAATA
1 ATACATAAATATAGGTTTTGAATGTCTTACACAATTGATAAATATTAATATTTTTATAATA
3821808 TTACGATAAA
Statistics
Matches: 103, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
64 98 0.95
65 2 0.02
66 3 0.03
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (64 bp):
ATACATAAATATAGGTTTTGAATGTCTTACACAATTGATAAATATTAATATTTTTATAATAAAT
Found at i:3821997 original size:19 final size:19
Alignment explanation
Indices: 3821962--3822001 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3821952 GTCTGTAAAT
*
3821962 ACCCATTAATCGGATCCAA
1 ACCCATTAATCGAATCCAA
3821981 ACCCATTAA-CTGAATCCAA
1 ACCCATTAATC-GAATCCAA
3822000 AC
1 AC
3822002 AACTTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (19 bp):
ACCCATTAATCGAATCCAA
Found at i:3823716 original size:15 final size:15
Alignment explanation
Indices: 3823698--3823735 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3823688 TCCACCATAT
3823698 CCACCTCCGCCGCCG
1 CCACCTCCGCCGCCG
*
3823713 CCACCACCGCCGCCG
1 CCACCTCCGCCGCCG
*
3823728 CCGCCTCC
1 CCACCTCC
3823736 TCCTCCTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.68, G:0.18, T:0.05
Consensus pattern (15 bp):
CCACCTCCGCCGCCG
Found at i:3823725 original size:18 final size:18
Alignment explanation
Indices: 3823698--3823732 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3823688 TCCACCATAT
*
3823698 CCACCTCCGCCGCCGCCA
1 CCACCGCCGCCGCCGCCA
3823716 CCACCGCCGCCGCCGCC
1 CCACCGCCGCCGCCGCC
3823733 TCCTCCTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.69, G:0.20, T:0.03
Consensus pattern (18 bp):
CCACCGCCGCCGCCGCCA
Found at i:3825741 original size:21 final size:21
Alignment explanation
Indices: 3825715--3825754 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3825705 CTTCCACTGG
*
3825715 TGGTGGAGGTGGTGGTAGTAC
1 TGGTGGAGGTGGCGGTAGTAC
*
3825736 TGGTGGTGGTGGCGGTAGT
1 TGGTGGAGGTGGCGGTAGT
3825755 GGTTCATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.05, G:0.55, T:0.30
Consensus pattern (21 bp):
TGGTGGAGGTGGCGGTAGTAC
Found at i:3858260 original size:42 final size:42
Alignment explanation
Indices: 3858123--3858248 Score: 200
Period size: 42 Copynumber: 3.0 Consensus size: 42
3858113 AATTAATTGT
* *
3858123 GCTAGCTGTGACCCACCATTGCTAAGATCATGATATACGTAA
1 GCTAGCTGTGACCCACCATTGCCAAGATCATGATATACATAA
*
3858165 GCTAGCTGTGACCCACCATTGCCAAGCTCAT-ATTATACATAA
1 GCTAGCTGTGACCCACCATTGCCAAGATCATGA-TATACATAA
*
3858207 GCTAGCTGTGACCCATCATTGCCAAGATCATGATATACATAA
1 GCTAGCTGTGACCCACCATTGCCAAGATCATGATATACATAA
3858249 ATCAGCTGTG
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 75 0.97
43 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
GCTAGCTGTGACCCACCATTGCCAAGATCATGATATACATAA
Found at i:3871516 original size:23 final size:22
Alignment explanation
Indices: 3871486--3871537 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3871476 CATTTATCCA
3871486 TTTA-TTTTTCT-CTTTATTTAT
1 TTTATTTTTTCTGCTTTA-TTAT
* *
3871507 TTTGTTTTTTCTGGTTTATTAT
1 TTTATTTTTTCTGCTTTATTAT
3871529 TTTATTTTT
1 TTTATTTTT
3871538 GGTATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 19 0.73
23 4 0.15
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTATTTTTTCTGCTTTATTAT
Found at i:3889647 original size:24 final size:23
Alignment explanation
Indices: 3889610--3889654 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3889600 GTAAAATCGA
*
3889610 ATAAAAAGATTTAATCAATAAAT
1 ATAAAAAGAATTAATCAATAAAT
*
3889633 ATAATAAAGAATTAATTAATAA
1 ATAA-AAAGAATTAATCAATAA
3889655 GCAAGAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
ATAAAAAGAATTAATCAATAAAT
Found at i:3891605 original size:29 final size:29
Alignment explanation
Indices: 3891520--3891606 Score: 165
Period size: 29 Copynumber: 3.0 Consensus size: 29
3891510 TGTTTGTCGC
*
3891520 AAGGAAGACTTCATTATTCAATACCTACT
1 AAGGAAGACTTCATTATTCAATACCTATT
3891549 AAGGAAGACTTCATTATTCAATACCTATT
1 AAGGAAGACTTCATTATTCAATACCTATT
3891578 AAGGAAGACTTCATTATTCAATACCTATT
1 AAGGAAGACTTCATTATTCAATACCTATT
3891607 CATCATTCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (29 bp):
AAGGAAGACTTCATTATTCAATACCTATT
Found at i:3899772 original size:27 final size:28
Alignment explanation
Indices: 3899707--3899773 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
3899697 ATTGTTTACT
** *
3899707 CATGGTGCATAATAATTAAATTTTTTAA
1 CATGGTGTGTAATAATTAAATTCTTTAA
* *
3899735 CATGATATGTAATAATTAAA-TCTTTAA
1 CATGGTGTGTAATAATTAAATTCTTTAA
3899762 CATGGTGTGTAA
1 CATGGTGTGTAA
3899774 CAACTACATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (28 bp):
CATGGTGTGTAATAATTAAATTCTTTAA
Found at i:3899940 original size:111 final size:110
Alignment explanation
Indices: 3899795--3900307 Score: 310
Period size: 109 Copynumber: 4.7 Consensus size: 110
3899785 TTCAACCATA
* * * * * * * *
3899795 CATATAACAACTATATTTTTTAACATGACGTGTAACAATTACATTTTTCAACATGACGTATGATA
1 CATATAACAATTATATTTTTCAACATGACATGTAACAACTAAATTTTT-AACATAACGTATAACA
* *
3899860 ACTATA-TTTTCAAT-ATAGCATATAATAACTAAATATTTAACAT-G
65 ACTACATTTTTC-ATCATAACATATAATAACTAAATATTTAACATCG
* * *
3899904 -ATGCATAGCAATTATATTTTTCAATATTGACATGTAACAACTAAATTTTTAACATAACGTGTAA
1 CAT--ATAACAATTATATTTTTCAACA-TGACATGTAACAACTAAATTTTTAACATAACGTATAA
* * * *
3899968 CAATTACATTTTTCGTCATAACATGTAATAACTAAATTTTTAACATCG
63 CAACTACATTTTTCATCATAACATATAATAACTAAATATTTAACATCG
* * * * * *
3900016 CATATAACAATTATATTTTTCAACATGACATGTAATAAGTGAATTTTCAACATAACGTAAAATAA
1 CATATAACAATTATATTTTTCAACATGACATGTAACAACTAAATTTTTAACATAACGTATAACAA
* * * * * * * * *
3900081 TTAAATTTTT-AACATAACGTGTAATAACTACATCTTTCAATAT-A
66 CTACATTTTTCATCATAACATATAATAACTAAATATTT-AACATCG
* * * * * * * * * * * *
3900125 AAGTGTAACAACTAAATTTTT-AATAT-AGCATGTAACAACTAAATCTTCAATATAGCATTTAAT
1 CA-TATAACAATTATATTTTTCAACATGA-CATGTAACAACTAAATTTTTAACATAACGTATAAC
* * ** * *
3900188 AACTA-AATTTTCAAT-TTGGCATATAACAACTAAATTTTTAACAT-G
64 AACTACATTTTTC-ATCATAACATATAATAACTAAATATTTAACATCG
* * * * * * * * *
3900233 ACATGTAACAATTACATTTTTCAACATGTCGTTTAACAATTAAATTTTCAACATGACATATAACA
1 -CATATAACAATTATATTTTTCAACATGACATGTAACAACTAAATTTTTAACATAACGTATAACA
* *
3900298 ATTATATTTT
65 ACTACATTTT
3900308 CAATGTAATT
Statistics
Matches: 311, Mismatches: 77, Indels: 31
0.74 0.18 0.07
Matches are distributed among these distances:
108 28 0.09
109 108 0.35
110 101 0.32
111 71 0.23
112 1 0.00
113 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (110 bp):
CATATAACAATTATATTTTTCAACATGACATGTAACAACTAAATTTTTAACATAACGTATAACAA
CTACATTTTTCATCATAACATATAATAACTAAATATTTAACATCG
Found at i:3900009 original size:55 final size:55
Alignment explanation
Indices: 3899769--3900307 Score: 280
Period size: 55 Copynumber: 9.8 Consensus size: 55
3899759 TAACATGGTG
* * * * * * * *
3899769 TGTAACAACTACATTTTTCAACCAT-ACATATAACAACTATATTTTTTAACATGACG
1 TGTAATAACTA-AATTTTCAA-CATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * * * * * * *
3899825 TGTAACAATTACATTTTTCAACATGACGTATGATAACTATA-TTTTCAATATAGCA
1 TGTAATAACTA-AATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * * * * *
3899880 TATAATAACTAAATATTT-AACATGATGCATAGCAATTATATTTTTCAATATTGACA
1 TGTAATAACTAAAT-TTTCAACATAACGTATAACAATTAAATTTTTCAACA-TAACA
* * * * **
3899936 TGTAACAACTAAATTTTTAACATAACGTGTAACAATTACATTTTTCGTCATAACA
1 TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* ** * * *
3899991 TGTAATAACTAAATTTTTAACATCGCATATAACAATTATATTTTTCAACATGACA
1 TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * *
3900046 TGTAATAAGTGAATTTTCAACATAACGTAAAATAATTAAATTTTT-AACATAACG
1 TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * * * *
3900100 TGTAATAACTACATCTTTCAATATAAAGTGTAACAACTAAATTTTT-AATATAGCA
1 TGTAATAACTAAAT-TTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * * * * * ** **
3900155 TGTAACAACTAAATCTTCAATATAGCATTTAATAACTAAA-TTTTCAATTTGGCA
1 TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * * * * ** *
3900209 TATAACAACTAAATTTTTAACATGACATGTAACAATTACATTTTTCAACATGTCG
1 TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
* * * * * *
3900264 TTTAACAATTAAATTTTCAACATGACATATAACAATTATATTTT
1 TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTT
3900308 CAATGTAATT
Statistics
Matches: 381, Mismatches: 94, Indels: 17
0.77 0.19 0.03
Matches are distributed among these distances:
53 4 0.01
54 93 0.24
55 213 0.56
56 71 0.19
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (55 bp):
TGTAATAACTAAATTTTCAACATAACGTATAACAATTAAATTTTTCAACATAACA
Found at i:3900241 original size:27 final size:27
Alignment explanation
Indices: 3899723--3900307 Score: 268
Period size: 27 Copynumber: 21.3 Consensus size: 27
3899713 GCATAATAAT
* * *
3899723 TAAATTTTTTAACATGATATGTAATAAT
1 TAAA-TTTTTAACATGACATGTAACAAC
* ***
3899751 TAAATCTTTAACATGGTGTGTAACAAC
1 TAAATTTTTAACATGACATGTAACAAC
* *
3899778 TACATTTTTCAACCAT-ACATATAACAAC
1 TAAATTTTT-AA-CATGACATGTAACAAC
* * *
3899806 TATATTTTTTAACATGACGTGTAACAAT
1 TA-AATTTTTAACATGACATGTAACAAC
* * * * *
3899834 TACATTTTTCAACATGACGTATGATAAC
1 TAAATTTTT-AACATGACATGTAACAAC
* * * * *
3899862 TATATTTTCAATAT-AGCATATAATAAC
1 TAAATTTTTAACATGA-CATGTAACAAC
* * *
3899889 TAAATATTTAACATG--ATGCATAGCAAT
1 TAAATTTTTAACATGACATG--TAACAAC
* *
3899916 TATATTTTTCAATATTGACATGTAACAAC
1 TAAATTTTT-AACA-TGACATGTAACAAC
* * *
3899945 TAAATTTTTAACATAACGTGTAACAAT
1 TAAATTTTTAACATGACATGTAACAAC
* ** * *
3899972 TACATTTTTCGTCATAACATGTAATAAC
1 TAAATTTTT-AACATGACATGTAACAAC
* *
3900000 TAAATTTTTAACATCG-CATATAACAAT
1 TAAATTTTTAACAT-GACATGTAACAAC
* * *
3900027 TATATTTTTCAACATGACATGTAATAAG
1 TAAATTTTT-AACATGACATGTAACAAC
* * * * ** * *
3900055 TGAATTTTCAACATAACGTAAAATAAT
1 TAAATTTTTAACATGACATGTAACAAC
* * *
3900082 TAAATTTTTAACATAACGTGTAATAAC
1 TAAATTTTTAACATGACATGTAACAAC
* * * *
3900109 TACATCTTTCAATAT-AAAGTGTAACAAC
1 TAAAT-TTTTAACATGACA-TGTAACAAC
*
3900137 TAAATTTTTAATAT-AGCATGTAACAAC
1 TAAATTTTTAACATGA-CATGTAACAAC
* * * * *
3900164 TAAATCTTCAATAT-AGCATTTAATAAC
1 TAAATTTTTAACATGA-CATGTAACAAC
* ** * *
3900191 TAAATTTTCAATTTGGCATATAACAAC
1 TAAATTTTTAACATGACATGTAACAAC
*
3900218 TAAATTTTTAACATGACATGTAACAAT
1 TAAATTTTTAACATGACATGTAACAAC
* * * * *
3900245 TACATTTTTCAACATGTCGTTTAACAAT
1 TAAATTTTT-AACATGACATGTAACAAC
* * *
3900273 TAAATTTTCAACATGACATATAACAAT
1 TAAATTTTTAACATGACATGTAACAAC
*
3900300 TATATTTT
1 TAAATTTT
3900308 CAATGTAATT
Statistics
Matches: 426, Mismatches: 109, Indels: 45
0.73 0.19 0.08
Matches are distributed among these distances:
25 2 0.00
26 1 0.00
27 259 0.61
28 138 0.32
29 23 0.05
31 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (27 bp):
TAAATTTTTAACATGACATGTAACAAC
Found at i:3900295 original size:82 final size:81
Alignment explanation
Indices: 3899723--3900307 Score: 342
Period size: 82 Copynumber: 7.1 Consensus size: 81
3899713 GCATAATAAT
* * * ** *
3899723 TAAATTTTTTAACATGATATGTAATAATTAAATCTTT-AACATGGTGTGTAACAACTACATTTTT
1 TAAA-TTTTTAACATGACATGTAACAATTAAATTTTTCAACATGACGTGTAACAACTA-AATTTT
3899787 CAACCATACATATAACAAC
64 CAA-CATACATATAACAAC
* * * * * * *
3899806 TATATTTTTTAACATGACGTGTAACAATTACATTTTTCAACATGACGTATGATAACTATATTTTC
1 TA-AATTTTTAACATGACATGTAACAATTAAATTTTTCAACATGACGTGTAACAACTAAATTTTC
* *
3899871 AATATAGCATATAATAAC
65 AACATA-CATATAACAAC
* * * * *
3899889 TAAATATTTAACATG--ATGCATAGCAATTATATTTTTCAATATTGACATGTAACAACTAAATTT
1 TAAATTTTTAACATGACATG--TAACAATTAAATTTTTCAACA-TGACGTGTAACAACTAAATTT
* * * *
3899952 TTAACATAACGTGTAACAAT
63 TCAACAT-ACATATAACAAC
* ** * * * * * * *
3899972 TACATTTTTCGTCATAACATGTAATAACTAAATTTTT-AACATCG-CATATAACAATTATATTTT
1 TAAATTTTT-AACATGACATGTAACAATTAAATTTTTCAACAT-GACGTGTAACAACTA-AATTT
* * *
3900035 TCAACATGACATGTAATAAG
63 TCAACAT-ACATATAACAAC
* * * * ** * * * *
3900055 TGAATTTTCAACATAACGTAAAATAATTAAATTTTT-AACATAACGTGTAATAACTACATCTTTC
1 TAAATTTTTAACATGACATGTAACAATTAAATTTTTCAACATGACGTGTAACAACTAAAT-TTTC
* * *
3900119 AATATAAAGTGTAACAAC
65 AACATACA-TATAACAAC
* * * * * * *
3900137 TAAATTTTTAATAT-AGCATGTAACAACTAAA-TCTTCAATAT-AGCATTTAATAACTAAATTTT
1 TAAATTTTTAACATGA-CATGTAACAATTAAATTTTTCAACATGA-CGTGTAACAACTAAATTTT
** *
3900199 CAATTTGGCATATAACAAC
64 CAACAT-ACATATAACAAC
* * * *
3900218 TAAATTTTTAACATGACATGTAACAATTACATTTTTCAACATGTCGTTTAACAATTAAATTTTCA
1 TAAATTTTTAACATGACATGTAACAATTAAATTTTTCAACATGACGTGTAACAACTAAATTTTCA
*
3900283 ACATGACATATAACAAT
66 ACAT-ACATATAACAAC
*
3900300 TATATTTT
1 TAAATTTT
3900308 CAATGTAATT
Statistics
Matches: 379, Mismatches: 101, Indels: 45
0.72 0.19 0.09
Matches are distributed among these distances:
80 2 0.01
81 50 0.13
82 180 0.47
83 112 0.30
84 32 0.08
86 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (81 bp):
TAAATTTTTAACATGACATGTAACAATTAAATTTTTCAACATGACGTGTAACAACTAAATTTTCA
ACATACATATAACAAC
Found at i:3904951 original size:14 final size:15
Alignment explanation
Indices: 3904924--3904961 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3904914 ATTTGTTTAA
3904924 TTTTTATATAAAATT
1 TTTTTATATAAAATT
*
3904939 TTTTTAT-TTAAATT
1 TTTTTATATAAAATT
*
3904953 ATTTTATAT
1 TTTTTATAT
3904962 TTTTATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTATATAAAATT
Found at i:3905991 original size:11 final size:11
Alignment explanation
Indices: 3905971--3906009 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3905961 ACCAGATAGC
*
3905971 TTCTTATCTTT
1 TTCTTTTCTTT
3905982 TTCTTTTC-TT
1 TTCTTTTCTTT
3905992 TTCTTTTCTTT
1 TTCTTTTCTTT
*
3906003 TTGTTTT
1 TTCTTTT
3906010 TGACCATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:3907851 original size:2 final size:2
Alignment explanation
Indices: 3907840--3907899 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
3907830 TTGTTTTTAT
3907840 TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3907881 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
3907900 TTTAATGGGG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3919790 original size:101 final size:100
Alignment explanation
Indices: 3919574--3919968 Score: 649
Period size: 101 Copynumber: 4.0 Consensus size: 100
3919564 GAGATTGAAA
*
3919574 TCACCTTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAA-C----AAAAAAAA
1 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAACCAAAAAAAAAAAA
*
3919634 -AATCAATCATAAATGTTATTCAGTGATCGAACGG
66 TAATCAATCATAAATGTTATTCAGTGATCGAATGG
*
3919668 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAAAATAGTATAAGAACCAAAAAAAAGAAA
1 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAACCAAAAAAAA-AAA
**
3919733 ATAATCAATCATAAATGTTATTCAGCAATCGAATGG
65 ATAATCAATCATAAATGTTATTCAGTGATCGAATGG
*
3919769 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAATCAAAAAAAAGAAA
1 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAACCAAAAAAAA-AAA
3919834 ATAATCAATCATAAATGTTATTCAGTGATCGAATGG
65 ATAATCAATCATAAATGTTATTCAGTGATCGAATGG
3919870 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAACCAGAAAAAAAAAG
1 TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAACCA-AAAAAAAAA-
*
3919935 AATAATCAAACATAAATGTTATTCAGTGATCGAA
64 AATAATCAATCATAAATGTTATTCAGTGATCGAA
3919969 CGGTTGAAAA
Statistics
Matches: 281, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
94 49 0.17
95 1 0.00
99 4 0.01
100 4 0.01
101 183 0.65
102 40 0.14
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (100 bp):
TCACCGTTTTATATTTATTTTACAATAAATTAAAATAGAATAGTATAAGAACCAAAAAAAAAAAA
TAATCAATCATAAATGTTATTCAGTGATCGAATGG
Found at i:3950130 original size:21 final size:21
Alignment explanation
Indices: 3950089--3950130 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3950079 CAAATAAAAA
* *
3950089 ATATTAATTTTAATTTATTTT
1 ATATTAAATTTAAATTATTTT
3950110 ATATTAAAATTTAAATT-TTTT
1 ATATT-AAATTTAAATTATTTT
3950131 GTAATATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTAAATTTAAATTATTTT
Found at i:3955042 original size:2 final size:2
Alignment explanation
Indices: 3955037--3955061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3955027 CTTTACCGAA
3955037 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
3955062 ATCTCTTAGG
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:3955939 original size:2 final size:2
Alignment explanation
Indices: 3955932--3955963 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3955922 ACATACATAC
3955932 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
3955964 GTCATATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3997664 original size:30 final size:31
Alignment explanation
Indices: 3997601--3997664 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
3997591 TCATAAGGGT
* * *
3997601 TTATTTGACTTAAAATTAAAATACAATAGAC
1 TTATTTGACTCAAAATAAAAATACAATAAAC
* *
3997632 TTATTTGGCTCAAAATAAAAATATAA-AAAC
1 TTATTTGACTCAAAATAAAAATACAATAAAC
3997662 TTA
1 TTA
3997665 ATTAAATGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (31 bp):
TTATTTGACTCAAAATAAAAATACAATAAAC
Found at i:4001853 original size:29 final size:30
Alignment explanation
Indices: 4001817--4001887 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
4001807 AATCATTAGT
* *
4001817 TATAAAAATTTATTTAGTTTAAAATAAAAA
1 TATAAAAATTTATTTAATTCAAAATAAAAA
*
4001847 TATAAAAACTTATTTAATTCAAAATAAAAA
1 TATAAAAATTTATTTAATTCAAAATAAAAA
4001877 TAT-AAAATTTA
1 TATAAAAATTTA
4001888 ATTTGATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 7 0.19
30 30 0.81
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (30 bp):
TATAAAAATTTATTTAATTCAAAATAAAAA
Found at i:4002215 original size:24 final size:26
Alignment explanation
Indices: 4002179--4002231 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
4002169 TATTTATTTT
*
4002179 AAATTAAATTAATTTTTA-TAATTAA
1 AAATTAAATTAATTATTATTAATTAA
4002204 AAATT-AATTAATTATTATTAATTAA
1 AAATTAAATTAATTATTATTAATTAA
4002229 AAA
1 AAA
4002232 ATTTATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTAAATTAATTATTATTAATTAA
Found at i:4002252 original size:25 final size:26
Alignment explanation
Indices: 4002188--4002254 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
4002178 TAAATTAAAT
4002188 TAATTTTTATAATT-AAAAATTAATTAA
1 TAATTTTT-T-ATTAAAAAATTAATTAA
* * * *
4002215 TTATTATTAATTAAAAAATTTATT-A
1 TAATTTTTTATTAAAAAATTAATTAA
4002240 TAATTTTTTATTAAA
1 TAATTTTTTATTAAA
4002255 TATAATACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
25 16 0.50
26 10 0.31
27 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTTTTTATTAAAAAATTAATTAA
Found at i:4006364 original size:175 final size:168
Alignment explanation
Indices: 4006049--4006396 Score: 473
Period size: 175 Copynumber: 2.0 Consensus size: 168
4006039 CCTAAACACC
* ** * *
4006049 ATCTTGTATCTGTCGGGTGCATGTTGGAGTAAGGTGTGGTTAGATTGGAGGATTGGATTGTGTAT
1 ATCTGGTATCTGTCGGGTGCATGCCGGAGTAAGGTGTGGTTAGATTGGAGGATTGAATTGTATAT
* *
4006114 CAAAAGGCAAGGAGTAGCCTCCTGAGGATTTCACTTATGATGCACTGTTTCAGGTTTGAAGAATA
66 CAAAAGACAAGGAGTAGCCTCCTGAGGATTTCACTTATGATGCACTGTTTCAGATTTGAAGAATA
4006179 ATGACATGTT-GTCTTCTTAGAGACAAGCAAATAGTAAT
131 ATGACATGTTGGT-TTCTTAGAGACAAGCAAATAGTAAT
* *
4006217 ATCTGGTATCTGTGGGGTGCATGCCGGAGTAAGGTGTGGTTAGGTTGGAGGATTCGTAAGTTCGT
1 ATCTGGTATCTGTCGGGTGCATGCCGGAGTAAGGTGTGGTTAGATTGGAGGATT-G-AA-TT-GT
* * **
4006282 ATATCAAAAGACAAGGAGAAGTAGCCTCCTGAGGATTTTACTTGTTTTGCACTGTTTCAGATTTG
62 ATATCAAAAGACAA-G-G-AGTAGCCTCCTGAGGATTTCACTTATGATGCACTGTTTCAGATTTG
* * *
4006347 AAGACTAATGGCATGTTGGTTTCTTAGAGACGAGCAAATAGTAAT
124 AAGAATAATGACATGTTGGTTTCTTAGAGACAAGCAAATAGTAAT
4006392 ATCTG
1 ATCTG
4006397 CTGAAAGATT
Statistics
Matches: 156, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
168 49 0.31
169 1 0.01
170 1 0.01
171 2 0.01
172 14 0.09
173 1 0.01
174 1 0.01
175 85 0.54
176 2 0.01
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32
Consensus pattern (168 bp):
ATCTGGTATCTGTCGGGTGCATGCCGGAGTAAGGTGTGGTTAGATTGGAGGATTGAATTGTATAT
CAAAAGACAAGGAGTAGCCTCCTGAGGATTTCACTTATGATGCACTGTTTCAGATTTGAAGAATA
ATGACATGTTGGTTTCTTAGAGACAAGCAAATAGTAAT
Found at i:4021347 original size:26 final size:25
Alignment explanation
Indices: 4021317--4021365 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
4021307 ATTATATAAA
4021317 TAAATTTTAA-AAATTATTCTAAAAAT
1 TAAA-TTTAATAAATTATT-TAAAAAT
*
4021343 TAAATTTAATAATTTATTTAAAA
1 TAAATTTAATAAATTATTTAAAA
4021366 GAATTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TAAATTTAATAAATTATTTAAAAAT
Found at i:4021441 original size:17 final size:19
Alignment explanation
Indices: 4021419--4021454 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4021409 TTAGATCAAT
4021419 TTAAC-AATA-AATAAAAA
1 TTAACAAATATAATAAAAA
4021436 TTAACAAATATAATAAAAA
1 TTAACAAATATAATAAAAA
4021455 AATCTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (19 bp):
TTAACAAATATAATAAAAA
Found at i:4021712 original size:69 final size:67
Alignment explanation
Indices: 4021615--4021750 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 67
4021605 TTGTTTATAT
*
4021615 GAATCTAAATAAAAAAATATAAAAAATTTATAGAAAAGTAATCAAGTAATCCTCAAATAAATAAA
1 GAATCTAAATAAAAAAATATAAAAAATTTATAAAAAAGTAATCAAGTAATCCTCAAATAAATAAA
4021680 TA
66 TA
* *
4021682 GAATCTAAATTAAAAAAA-ATACAAAGAATTTATAAAAAAGTAATCAAGTAATCTTTAAATAAAT
1 GAATCTAAA-TAAAAAAATATA-AAA-AATTTATAAAAAAGTAATCAAGTAATCCTCAAATAAAT
4021746 AAATA
63 AAATA
4021751 ATAACTAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
67 12 0.19
68 11 0.17
69 40 0.63
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.26
Consensus pattern (67 bp):
GAATCTAAATAAAAAAATATAAAAAATTTATAAAAAAGTAATCAAGTAATCCTCAAATAAATAAA
TA
Found at i:4021862 original size:15 final size:15
Alignment explanation
Indices: 4021839--4021876 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4021829 TCAAAATCAC
4021839 AAATAAAAAT-TATAA
1 AAATAAAAATAT-TAA
*
4021854 AATTAAAAATATTAA
1 AAATAAAAATATTAA
4021869 AAATAAAA
1 AAATAAAA
4021877 TAAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAAAATATTAA
Found at i:4033843 original size:2 final size:2
Alignment explanation
Indices: 4033836--4033863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4033826 TTCAAAAATA
4033836 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
4033864 CACAAACCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4037075 original size:10 final size:10
Alignment explanation
Indices: 4037060--4037085 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4037050 GTCCACCTGT
4037060 TTTTTTTTTC
1 TTTTTTTTTC
4037070 TTTTTTTTTC
1 TTTTTTTTTC
4037080 TTTTTT
1 TTTTTT
4037086 CTTATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:4043116 original size:23 final size:23
Alignment explanation
Indices: 4043086--4043139 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
4043076 NNNNNNNNNN
4043086 ACCCTAAAACCGGTTTAACAGAA
1 ACCCTAAAACCGGTTTAACAGAA
4043109 ACCCTAAAACCGGTTTAACAGAA
1 ACCCTAAAACCGGTTTAACAGAA
4043132 ACCCTAAA
1 ACCCTAAA
4043140 CCCCCGACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (23 bp):
ACCCTAAAACCGGTTTAACAGAA
Found at i:4079807 original size:2 final size:2
Alignment explanation
Indices: 4079800--4079830 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4079790 CAGATCTAAT
4079800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4079831 TTCCTCTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4087704 original size:3 final size:3
Alignment explanation
Indices: 4087696--4087724 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4087686 GCATGTTATA
4087696 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4087725 CCCTTGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4119075 original size:2 final size:2
Alignment explanation
Indices: 4119070--4119094 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4119060 TAGAGAACTG
4119070 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
4119095 AATTCTGACA
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:4120933 original size:23 final size:22
Alignment explanation
Indices: 4120902--4120945 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
4120892 TCTGCATCGA
4120902 CAAATGAAATTCAAATGTAAAG
1 CAAATGAAATTCAAATGTAAAG
4120924 CAAATTGAAATTCAAATGTAAA
1 CAAA-TGAAATTCAAATGTAAA
4120946 AGAGTCGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (22 bp):
CAAATGAAATTCAAATGTAAAG
Found at i:4126217 original size:36 final size:36
Alignment explanation
Indices: 4126170--4126243 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
4126160 ATGGCCGAAG
*
4126170 TCATAGTCAAGCGTTACAACATCACCATTTGATCCA
1 TCATAGTCAAGCGTTACAACATCACCATTGGATCCA
*
4126206 TCATAGTCAAGCGTTACAACATCACGATTGGATCCA
1 TCATAGTCAAGCGTTACAACATCACCATTGGATCCA
4126242 TC
1 TC
4126244 GGAATCCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (36 bp):
TCATAGTCAAGCGTTACAACATCACCATTGGATCCA
Found at i:4128109 original size:30 final size:30
Alignment explanation
Indices: 4128073--4128129 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
4128063 TCGAATCCAT
* *
4128073 AATAGAATGAGAAATACGGATGAGACCTTG
1 AATAGAAAGAGAAACACGGATGAGACCTTG
4128103 AATAGAAAGAGAAACACGGATGAGACC
1 AATAGAAAGAGAAACACGGATGAGACC
4128130 CCATCGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.26, T:0.14
Consensus pattern (30 bp):
AATAGAAAGAGAAACACGGATGAGACCTTG
Found at i:4134700 original size:13 final size:14
Alignment explanation
Indices: 4134687--4134725 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4134677 ATTAAAATTA
4134687 TTTGATAAATTTAT
1 TTTGATAAATTTAT
* *
4134701 TTTTATAAATTTTT
1 TTTGATAAATTTAT
*
4134715 TTTAATAAATT
1 TTTGATAAATT
4134726 ATAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTGATAAATTTAT
Found at i:4134710 original size:14 final size:14
Alignment explanation
Indices: 4134691--4134725 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
4134681 AAATTATTTG
4134691 ATAAATTTATTTTT-
1 ATAAATTT-TTTTTA
4134705 ATAAATTTTTTTTA
1 ATAAATTTTTTTTA
4134719 ATAAATT
1 ATAAATT
4134726 ATAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATAAATTTTTTTTA
Found at i:4146354 original size:5 final size:5
Alignment explanation
Indices: 4146344--4146368 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4146334 CCCTACCCCC
4146344 CAGAT CAGAT CAGAT CAGAT CAGAT
1 CAGAT CAGAT CAGAT CAGAT CAGAT
4146369 TACAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
CAGAT
Found at i:4163677 original size:2 final size:2
Alignment explanation
Indices: 4163670--4163696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4163660 ATTTCTAAAT
4163670 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4163697 TATGGCTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4164741 original size:13 final size:13
Alignment explanation
Indices: 4164723--4164758 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
4164713 AAAGAACCCC
4164723 TTTTCATTTTCCT
1 TTTTCATTTTCCT
4164736 TTTTCATTTTCCT
1 TTTTCATTTTCCT
*
4164749 TTTTCCTTTT
1 TTTTCATTTT
4164759 TCTGGTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCATTTTCCT
Found at i:4180777 original size:2 final size:2
Alignment explanation
Indices: 4180770--4180831 Score: 92
Period size: 2 Copynumber: 31.5 Consensus size: 2
4180760 TCAGTTATCA
4180770 AT AT AT AT AT A- 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
*
4180811 AT AT A- AT GAT AT AG AT AT AT A
1 AT AT AT AT -AT AT AT AT AT AT A
4180832 GATACCCCCG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4185289 original size:13 final size:14
Alignment explanation
Indices: 4185267--4185309 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
4185257 TTCAAGAATC
*
4185267 TTTATTCTTTCTCT
1 TTTATCCTTTCTCT
*
4185281 TTT-TCCTTTCCCT
1 TTTATCCTTTCTCT
4185294 TTTATCCTTTCT-T
1 TTTATCCTTTCTCT
4185307 TTT
1 TTT
4185310 GATTATTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATCCTTTCTCT
Found at i:4192821 original size:28 final size:27
Alignment explanation
Indices: 4192724--4192831 Score: 91
Period size: 28 Copynumber: 4.1 Consensus size: 27
4192714 AACAAATATG
* *
4192724 TTAAATTCAAT-TA-AAAATTAAAAAA
1 TTAAATACAATATATAAAATTAAATAA
*
4192749 TTGATAATAGAA-ATATAAAATTAAATAA
1 TT-A-AATACAATATATAAAATTAAATAA
* * * *
4192777 -AAAATATAATGTGTAAAATATAAATAA
1 TTAAATACAATATATAAAAT-TAAATAA
4192804 TTAAATACAATATATAAAATT-AATAA
1 TTAAATACAATATATAAAATTAAATAA
4192830 TT
1 TT
4192832 TTTTCTTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
25 8 0.12
26 16 0.25
27 15 0.23
28 26 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (27 bp):
TTAAATACAATATATAAAATTAAATAA
Found at i:4194783 original size:32 final size:32
Alignment explanation
Indices: 4194743--4194809 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
4194733 GATAGTGGAT
*
4194743 ATAAGTTTTGAGTAATAGAGTAGTAGCATTTA
1 ATAAGTTTTGAGTAATAGAGTAGTAACATTTA
4194775 ATAAGTTTTGAGTAATAGAGTAGTAACATTTA
1 ATAAGTTTTGAGTAATAGAGTAGTAACATTTA
4194807 ATA
1 ATA
4194810 GTACACCACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (32 bp):
ATAAGTTTTGAGTAATAGAGTAGTAACATTTA
Found at i:4212235 original size:27 final size:26
Alignment explanation
Indices: 4212205--4212255 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
4212195 ACACTCTTAA
* *
4212205 GCACTTCCTTGCTTGGAACAACCTTGG
1 GCACTTCCATGCTTAGAAC-ACCTTGG
*
4212232 GCACTTGCATGCTTAGAACACCTT
1 GCACTTCCATGCTTAGAACACCTT
4212256 AATATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (26 bp):
GCACTTCCATGCTTAGAACACCTTGG
Found at i:4218293 original size:217 final size:217
Alignment explanation
Indices: 4217910--4218343 Score: 742
Period size: 217 Copynumber: 2.0 Consensus size: 217
4217900 AGTATTAGAT
* * ** *
4217910 CATGTCTTGCCAATAGGTGGGCTCACCTTTTTCATAACCTTTGTCTTTTTATGCTTCACATGGAC
1 CATGTCTTGCCAATAGGTGGGCTCAACTTTTTCATAACCTTTGACCATATATGCTTCACATGGAC
* * *
4217975 TGTAGGGTATGCCCGCAGATATAAGTTCCTGTTTTTCAGGAATATTTTATCGGTTAAAGTTTGTT
66 TGTAGGGTATGCCCACAGATATAAGTTCCTGTTTTCCAGGAATATATTATCGGTTAAAGTTTGTT
* * *
4218040 AGCTGAACAGTGGATGATAGTGCTATCATGCTGTTGGTTGTGAAGTGAATGACTTAAAGTTCCAA
131 AGCTGAACAGTGGATCATAGTGCTATAATGCTGTTGGTTGTGAAGTGAATGACTTAAAGCTCCAA
4218105 ATCTGTTAACTTGTATTGTTTG
196 ATCTGTTAACTTGTATTGTTTG
* *
4218127 CATGTCTTGCCAATAGGTGGGCTCAACTTTTTCATCACCTTTGACCATATATGCTTCACATGGGC
1 CATGTCTTGCCAATAGGTGGGCTCAACTTTTTCATAACCTTTGACCATATATGCTTCACATGGAC
4218192 TGTAGGGTATGCCCACAGATATAAGTTCCTGTTTTCCAGGAATATATTATCGGTTAAAGTTTGTT
66 TGTAGGGTATGCCCACAGATATAAGTTCCTGTTTTCCAGGAATATATTATCGGTTAAAGTTTGTT
*
4218257 AGCTGAACAGTGGATCATAGTGCTATAATTCTGTTGGTTGTGAAGTGAATGACTTAAAGCTCCAA
131 AGCTGAACAGTGGATCATAGTGCTATAATGCTGTTGGTTGTGAAGTGAATGACTTAAAGCTCCAA
4218322 ATCTGTTAACTTGTATTGTTTG
196 ATCTGTTAACTTGTATTGTTTG
4218344 TGCTAAACAA
Statistics
Matches: 203, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 203 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (217 bp):
CATGTCTTGCCAATAGGTGGGCTCAACTTTTTCATAACCTTTGACCATATATGCTTCACATGGAC
TGTAGGGTATGCCCACAGATATAAGTTCCTGTTTTCCAGGAATATATTATCGGTTAAAGTTTGTT
AGCTGAACAGTGGATCATAGTGCTATAATGCTGTTGGTTGTGAAGTGAATGACTTAAAGCTCCAA
ATCTGTTAACTTGTATTGTTTG
Found at i:4228077 original size:12 final size:12
Alignment explanation
Indices: 4228062--4228133 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 12
4228052 ATGACTTCAG
4228062 TGATGATGATTA
1 TGATGATGATTA
*
4228074 TGATGACTTGGATGA
1 TGATGA--T-GATTA
*
4228089 TGATTATGATCTTGA
1 TGATGATGA--TT-A
*
4228104 TGATGATGAATA
1 TGATGATGATTA
*
4228116 TGATGATGAATA
1 TGATGATGATTA
4228128 TGATGA
1 TGATGA
4228134 CCCTCATCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 27 0.55
13 2 0.04
14 2 0.04
15 18 0.37
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (12 bp):
TGATGATGATTA
Found at i:4228087 original size:21 final size:22
Alignment explanation
Indices: 4228063--4228121 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
4228053 TGACTTCAGT
4228063 GATGATGATTATGATGACTTG-
1 GATGATGATTATGATGACTTGA
4228084 GATGATGATTATGAT--CTTGA
1 GATGATGATTATGATGACTTGA
*
4228104 TGATGATGAATATGATGA
1 -GATGATGATTATGATGA
4228122 TGAATATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.12
21 29 0.88
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.37
Consensus pattern (22 bp):
GATGATGATTATGATGACTTGA
Found at i:4228307 original size:6 final size:6
Alignment explanation
Indices: 4228296--4228323 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4228286 AAGGAGGTAA
4228296 TGGCGG TGGCGG TGGCGG TGGCGG TGGC
1 TGGCGG TGGCGG TGGCGG TGGCGG TGGC
4228324 AATGCTGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.64, T:0.18
Consensus pattern (6 bp):
TGGCGG
Found at i:4228762 original size:6 final size:6
Alignment explanation
Indices: 4228751--4228777 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4228741 CTGCCATGAA
4228751 CGGTGG CGGTGG CGGTGG CGGTGG CGG
1 CGGTGG CGGTGG CGGTGG CGGTGG CGG
4228778 GTACTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.67, T:0.15
Consensus pattern (6 bp):
CGGTGG
Found at i:4233652 original size:65 final size:65
Alignment explanation
Indices: 4233563--4233684 Score: 172
Period size: 65 Copynumber: 1.9 Consensus size: 65
4233553 AAGCTTGTAG
* * *
4233563 TTGAAAGTGAACCATACAATTGATTGAACGCATTTATTTTTAAACTAAATCAGCTATAAACAAGC
1 TTGAAAGTGAACCATACAACTGATTAAACGCATTTAGTTTTAAACTAAATCAGCTATAAACAAGC
* * ** *
4233628 TTGATAGTGAACCATACAACTGATTAAACGCGTTTAGTTTTGGACTAAATCGGCTAT
1 TTGAAAGTGAACCATACAACTGATTAAACGCATTTAGTTTTAAACTAAATCAGCTAT
4233685 CAACCTCAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 49 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (65 bp):
TTGAAAGTGAACCATACAACTGATTAAACGCATTTAGTTTTAAACTAAATCAGCTATAAACAAGC
Found at i:4239240 original size:21 final size:21
Alignment explanation
Indices: 4239214--4239255 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4239204 CTAGTGATCA
4239214 GCACTCACATGTAAACAAAAT
1 GCACTCACATGTAAACAAAAT
4239235 GCACTCACATGTAAACAAAAT
1 GCACTCACATGTAAACAAAAT
4239256 AAAGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.10, T:0.19
Consensus pattern (21 bp):
GCACTCACATGTAAACAAAAT
Found at i:4241951 original size:16 final size:19
Alignment explanation
Indices: 4241919--4241958 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
4241909 CGCCCTTTCT
4241919 TATATTTATATACTTTT-A
1 TATATTTATATACTTTTAA
4241937 TATATTTAT-TA-TTTTAA
1 TATATTTATATACTTTTAA
4241954 TATAT
1 TATAT
4241959 ATTTCGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 9 0.43
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTTATATACTTTTAA
Found at i:4247244 original size:2 final size:2
Alignment explanation
Indices: 4247239--4247264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4247229 AAAAAAAAAG
4247239 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
4247265 AAAGCCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4254429 original size:52 final size:53
Alignment explanation
Indices: 4254367--4254481 Score: 205
Period size: 54 Copynumber: 2.2 Consensus size: 53
4254357 AGCAAATCCA
4254367 GTTGGAAACTAACTACAAAAATCAAAAG-ATAATTGCAGAGCTATTTTGTTAG
1 GTTGGAAACTAACTACAAAAATCAAAAGAATAATTGCAGAGCTATTTTGTTAG
4254419 GTTGGAAACTAACTACAAAAATCAAAAGATATAATTGCAGAGCTATTTTGTTAG
1 GTTGGAAACTAACTACAAAAATCAAAAGA-ATAATTGCAGAGCTATTTTGTTAG
*
4254473 GTTGAAAAC
1 GTTGGAAAC
4254482 AAACAACTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 28 0.47
54 32 0.53
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (53 bp):
GTTGGAAACTAACTACAAAAATCAAAAGAATAATTGCAGAGCTATTTTGTTAG
Found at i:4261966 original size:2 final size:2
Alignment explanation
Indices: 4261959--4261998 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4261949 AGGAAACCAA
4261959 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
4261999 TTGTACTATT
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:4262926 original size:23 final size:23
Alignment explanation
Indices: 4262894--4262945 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
4262884 TCCTAGGCCA
*
4262894 GGTTGCACCAACCAAACTTGTGC
1 GGTTGTACCAACCAAACTTGTGC
4262917 GGTTGTACCAACCAAACTTGTGC
1 GGTTGTACCAACCAAACTTGTGC
4262940 GGTTGT
1 GGTTGT
4262946 CCTCTCTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (23 bp):
GGTTGTACCAACCAAACTTGTGC
Found at i:4269450 original size:6 final size:7
Alignment explanation
Indices: 4269432--4269473 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
4269422 TCTCTTCTTC
4269432 TTTTTTCA
1 TTTTTT-A
4269440 TTTTTTA
1 TTTTTTA
4269447 TTTTTTA
1 TTTTTTA
4269454 TTTTTTA
1 TTTTTTA
4269461 TTTTTTA
1 TTTTTTA
*
4269468 CTTTTT
1 TTTTTT
4269474 GAGACTGGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:4272064 original size:18 final size:19
Alignment explanation
Indices: 4272031--4272068 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4272021 TTGTTTATCT
4272031 ATTTCCATATTAAACTTGA
1 ATTTCCATATTAAACTTGA
*
4272050 ATTTCC-TATTTAACTTGA
1 ATTTCCATATTAAACTTGA
4272068 A
1 A
4272069 ATAGTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTCCATATTAAACTTGA
Found at i:4280406 original size:44 final size:43
Alignment explanation
Indices: 4280328--4280418 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
4280318 TAGTTAAAAT
* *
4280328 TTTTTTTAAAGTATTATGATATAAAATAAGAAAAAAAT-ACTAA
1 TTTTTTTAAAATATTATGACATAAAATAAGAAAAAAATAACT-A
*
4280371 TTTTTTTAAAATATTATGACATAAAATATGAAAAAAAATAACTA
1 TTTTTTTAAAATATTATGACATAAAATAAG-AAAAAAATAACTA
4280415 TTTT
1 TTTT
4280419 GCGTCACTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 27 0.63
44 13 0.30
45 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (43 bp):
TTTTTTTAAAATATTATGACATAAAATAAGAAAAAAATAACTA
Found at i:4281392 original size:15 final size:15
Alignment explanation
Indices: 4281372--4281401 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4281362 TTTTGTTGAG
*
4281372 AAAAAGATAATAAAT
1 AAAAAGATAAAAAAT
4281387 AAAAAGATAAAAAAT
1 AAAAAGATAAAAAAT
4281402 TGATATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAAGATAAAAAAT
Found at i:4283501 original size:32 final size:32
Alignment explanation
Indices: 4283447--4283637 Score: 112
Period size: 32 Copynumber: 5.8 Consensus size: 32
4283437 TTTATAATGT
4283447 TATAAT-TAAAATAAAAATATTAAA-ATAAAATA
1 TATAATATAAAAT-AAAA-ATTAAATATAAAATA
4283479 TATAATATAAGAATAAAAATTAAATATAAAATA
1 TATAATATAA-AATAAAAATTAAATATAAAATA
*
4283512 -A-AATATAACAATTAAAAATTAGATAATATAAGTAAAA
1 TATAATATAA-AA-TAAAAATT--A-AATATAA--AATA
* * *
4283549 TA-AAT-TAAAATAAAATATAAAAAATAAAAAA
1 TATAATATAAAATAAAA-ATTAAATATAAAATA
* * * *
4283580 TTATATTA-AAAATAAAAATAAAAAATATAAATT
1 -TATAATATAAAATAAAAATTAAATATA-AAATA
* *
4283613 TATAATA-ATAA-AAAAATAAAATATA
1 TATAATATAAAATAAAAATTAAATATA
4283638 TGAGATTCAA
Statistics
Matches: 134, Mismatches: 10, Indels: 31
0.77 0.06 0.18
Matches are distributed among these distances:
31 26 0.19
32 42 0.31
33 35 0.26
34 5 0.04
35 12 0.09
36 4 0.03
37 6 0.04
38 4 0.03
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.29
Consensus pattern (32 bp):
TATAATATAAAATAAAAATTAAATATAAAATA
Found at i:4283576 original size:19 final size:19
Alignment explanation
Indices: 4283453--4283602 Score: 69
Period size: 19 Copynumber: 7.5 Consensus size: 19
4283443 ATGTTATAAT
*
4283453 TAAAATAAAA-ATATTAAAA
1 TAAAATAAAATATA-AAAAA
*
4283472 TAAAATATATAATAT-AAGAA
1 TAAAATA-A-AATATAAAAAA
*
4283492 TAAAAATTAAATATAAAATAA
1 T-AAAATAAAATATAAAA-AA
* *
4283513 -AATATAACAAT-TAAAAAT
1 TAAAATAA-AATATAAAAAA
*
4283531 TAGATAATATAAGTA-AAATAAA
1 TA-A-AATA-AAATATAAA-AAA
4283553 TTAAAATAAAATATAAAAAA
1 -TAAAATAAAATATAAAAAA
* *
4283573 TAAAA-AATTATATTAAAAA
1 TAAAATAA-AATATAAAAAA
4283592 TAAAAATAAAA
1 T-AAAATAAAA
4283603 AATATAAATT
Statistics
Matches: 99, Mismatches: 14, Indels: 35
0.67 0.09 0.24
Matches are distributed among these distances:
18 3 0.03
19 38 0.38
20 24 0.24
21 26 0.26
22 6 0.06
23 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAATAAAATATAAAAAA
Found at i:4283596 original size:5 final size:5
Alignment explanation
Indices: 4283453--4283577 Score: 53
Period size: 5 Copynumber: 25.0 Consensus size: 5
4283443 ATGTTATAAT
* * * *
4283453 TAAAA TAAAA -ATAT TAAAA TAAAA T-ATA TAATA TAAGAA TAAAAA TTAAATA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA T-AAAA -TAAA-A
* * * * * * * *
4283505 TAAAA TAAAA TATAA -CAAT TAAAAA TTAGA TAATA T-AAG TAAAA TAAAT
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA
*
4283554 TAAAA TAAAA TATAA -AAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
4283578 AATTATATTA
Statistics
Matches: 87, Mismatches: 23, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
4 11 0.13
5 58 0.67
6 14 0.16
7 4 0.05
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:4283611 original size:19 final size:19
Alignment explanation
Indices: 4283454--4283597 Score: 55
Period size: 21 Copynumber: 7.2 Consensus size: 19
4283444 TGTTATAATT
*
4283454 AAAATAAAAATATTAAAATAA
1 AAAATATAAATA--AAAATAA
* *
4283475 AATATATAATATAAGAAT-A
1 AAAATATAA-ATAAAAATAA
4283494 AAAAT-TAAATATAAAATAA
1 AAAATATAAATA-AAAATAA
* *
4283513 AATATA-ACAATTAAAAATTAG
1 AAAATATA-AA-TAAAAA-TAA
* *
4283534 ATAATATAAGT-AAAATAAA
1 AAAATATAAATAAAAAT-AA
*
4283553 TTAAAATAAAATATAAAAAATAA
1 --AAAATATAA-AT-AAAAATAA
*
4283576 AAAAT-TATATTAAAAATAA
1 AAAATATA-AATAAAAATAA
4283595 AAA
1 AAA
4283598 TAAAAAATAT
Statistics
Matches: 92, Mismatches: 16, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
17 3 0.03
18 8 0.09
19 27 0.29
20 13 0.14
21 29 0.32
22 5 0.05
23 2 0.02
24 5 0.05
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATATAAATAAAAATAA
Found at i:4283890 original size:15 final size:15
Alignment explanation
Indices: 4283871--4283909 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
4283861 CATTGCTTAC
*
4283871 AATCACATTACCTG-
1 AATCACATTAACTGT
4283885 ATATCACATTAACTGT
1 A-ATCACATTAACTGT
4283901 AATCACATT
1 AATCACATT
4283910 GTATTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (15 bp):
AATCACATTAACTGT
Found at i:4290144 original size:2 final size:2
Alignment explanation
Indices: 4290139--4290192 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
4290129 ATTGTGTGTG
* * * *
4290139 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TG TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4290181 TA TA TA TA TA TA
1 TA TA TA TA TA TA
4290193 AATCTAAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4300701 original size:77 final size:75
Alignment explanation
Indices: 4300574--4300797 Score: 279
Period size: 77 Copynumber: 2.9 Consensus size: 75
4300564 ATGCTCACCG
*
4300574 TCCATTCTTTTTGTGGCTAACCAAGTATGAAAGACTTTCAGGATGAGATCTCACCCTGATTATAC
1 TCCATTCTTTTTGTGGCTAACCAAGTA-GAAAGACTTTCAGGATAAGATCTCACCCTG-TTATAC
*
4300639 ATCCATTTACAT
64 ATCCATTCACAT
* * * *
4300651 TCCATTCTTTTCGTGGCTAACGAAATAGGAAAGACTCTCAGGATAAGATCTCAACCCCT-TTATA
1 TCCATTCTTTTTGTGGCTAACCAAGTA-GAAAGACTTTCAGGATAAGATCTC-A-CCCTGTTATA
* *
4300715 CATCTATTCGCAT
63 CATCCATTCACAT
* * *
4300728 TCCATTCTTTTTGTGGTTAACCAAGTAGAATAGGCTTTCAGGATAACATCTCACCCTCGTTATAC
1 TCCATTCTTTTTGTGGCTAACCAAGTAGAA-AGACTTTCAGGATAAGATCTCACCCT-GTTATAC
4300793 ATCCA
64 ATCCA
4300798 CATGAAAAGG
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
75 4 0.03
76 4 0.03
77 112 0.90
78 1 0.01
79 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (75 bp):
TCCATTCTTTTTGTGGCTAACCAAGTAGAAAGACTTTCAGGATAAGATCTCACCCTGTTATACAT
CCATTCACAT
Found at i:4317084 original size:71 final size:71
Alignment explanation
Indices: 4316972--4317107 Score: 209
Period size: 71 Copynumber: 1.9 Consensus size: 71
4316962 AGTGTGATAC
* * * *
4316972 GGAGAAGATATCATCTTCTAGCTTATTCTTTTGCATTGAATTTGCTAGTTGAGAGACCAAGATTG
1 GGAGAAGATATAACCTTCTAGCTTATTCTTTTGCATAGAATTCGCTAGTTGAGAGACCAAGATTG
4317037 TGACAT
66 TGACAT
* * *
4317043 GGAGAAGATCTAACCTTCTGGCTTATTCTTTTGCATAGAATTCGCTGGTTGAGAGACCAAGATTG
1 GGAGAAGATATAACCTTCTAGCTTATTCTTTTGCATAGAATTCGCTAGTTGAGAGACCAAGATTG
4317108 AATCTGCAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (71 bp):
GGAGAAGATATAACCTTCTAGCTTATTCTTTTGCATAGAATTCGCTAGTTGAGAGACCAAGATTG
TGACAT
Found at i:4318816 original size:12 final size:13
Alignment explanation
Indices: 4318785--4318816 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4318775 TTTTTTTAAA
4318785 AAATAAATTATTT
1 AAATAAATTATTT
4318798 AAA-AAATT-TTT
1 AAATAAATTATTT
4318809 AAATAAAT
1 AAATAAAT
4318817 CATTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 9 0.50
13 3 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATAAATTATTT
Found at i:4323613 original size:14 final size:15
Alignment explanation
Indices: 4323558--4323615 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 15
4323548 TAAAATCACT
4323558 AAATGAAAACTATTAA
1 AAATGAAAA-TATTAA
* *
4323574 ATAAAGAAAAAATTTAA
1 A-AATGAAAATA-TTAA
*
4323591 AATTGAAAATATTAA
1 AAATGAAAATATTAA
4323606 AAAT-AAAATA
1 AAATGAAAATA
4323616 ACAATAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 9 0.26
17 12 0.35
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (15 bp):
AAATGAAAATATTAA
Found at i:4331267 original size:25 final size:23
Alignment explanation
Indices: 4331235--4331282 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4331225 GATTTTGTTA
4331235 AAATTTTATATATTAATAATATTT
1 AAATTTTATATATT-ATAATATTT
* *
4331259 AAATATTTATTTATTATATTATTT
1 AAAT-TTTATATATTATAATATTT
4331283 TTTAGAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AAATTTTATATATTATAATATTT
Found at i:4331427 original size:16 final size:16
Alignment explanation
Indices: 4331397--4331438 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4331387 TAATAATATT
* *
4331397 TAAATATTATCAAAAAG
1 TAAAT-TTATAAAAAAA
4331414 TAAATTTATAAAAAAA
1 TAAATTTATAAAAAAA
4331430 T-AATTTATA
1 TAAATTTATA
4331439 TATTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAATTTATAAAAAAA
Found at i:4332019 original size:42 final size:43
Alignment explanation
Indices: 4331972--4332057 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
4331962 ATGATTGTTA
** * *
4331972 AGTGATAAGTGAATGA-TGGTAGGTGACATATGATAGTATTTG
1 AGTGATAAGTGAATGATTGGTAAATGACATATGACAGCATTTG
*
4332014 AGTGATAAGTGAATGATTGTTAAATGACATATGACAGCATTTG
1 AGTGATAAGTGAATGATTGGTAAATGACATATGACAGCATTTG
4332057 A
1 A
4332058 CGGTGTTTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 16 0.42
43 22 0.58
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (43 bp):
AGTGATAAGTGAATGATTGGTAAATGACATATGACAGCATTTG
Found at i:4334486 original size:13 final size:13
Alignment explanation
Indices: 4334470--4334494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4334460 AATAGTAAAA
4334470 ATATTATTATATT
1 ATATTATTATATT
4334483 ATATTATTATAT
1 ATATTATTATAT
4334495 ATCAACAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:4338834 original size:22 final size:20
Alignment explanation
Indices: 4338802--4338842 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
4338792 TACTTTACCT
*
4338802 TTTTCTCTCTCTTTCTTTTC
1 TTTTCTCTCTCTATCTTTTC
4338822 TTTTCTCCTTCTCTATCTTTT
1 TTTTCT-C-TCTCTATCTTTT
4338843 TCCCCGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCTCTCTCTATCTTTTC
Found at i:4339872 original size:3 final size:3
Alignment explanation
Indices: 4339864--4339896 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4339854 TGAAATCCTT
4339864 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
4339897 ATGTATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:4348159 original size:27 final size:25
Alignment explanation
Indices: 4348125--4348208 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 25
4348115 TAACATGTTG
4348125 TATA-ATAATTAATTTTTTAATATAA
1 TATATATAATT-ATTTTTTAATATAA
4348150 TATATTATAATTATATTTTT-A-AT--
1 TATA-TATAATTAT-TTTTTAATATAA
4348173 TATA-ATAATTA-TTTTTAATATAA
1 TATATATAATTATTTTTTAATATAA
4348196 TATATAATAATTA
1 TATAT-ATAATTA
4348209 AATTTTAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
19 5 0.10
20 1 0.02
21 9 0.18
23 8 0.16
25 13 0.26
26 3 0.06
27 11 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATAATTATTTTTTAATATAA
Found at i:4348174 original size:18 final size:18
Alignment explanation
Indices: 4348153--4348200 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
4348143 AATATAATAT
4348153 ATTATAATTATATTTTTA
1 ATTATAATTATATTTTTA
*
4348171 ATTATAATAATTATTTTTA
1 ATTATAATTA-TATTTTTA
4348190 A-TATAA-TATAT
1 ATTATAATTATAT
4348201 AATAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 1 0.04
18 14 0.52
19 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATAATTATATTTTTA
Found at i:4348199 original size:46 final size:48
Alignment explanation
Indices: 4348125--4348214 Score: 148
Period size: 46 Copynumber: 1.9 Consensus size: 48
4348115 TAACATGTTG
* *
4348125 TATAATAATTAATTTTTTAATATAATATATTATAATTATATTTTTAAT
1 TATAATAATTAATTTTTTAATATAATATATAATAATTAAATTTTTAAT
4348173 TATAATAATT-A-TTTTTAATATAATATATAATAATTAAATTTT
1 TATAATAATTAATTTTTTAATATAATATATAATAATTAAATTTT
4348215 AAAATATACT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 29 0.73
47 1 0.03
48 10 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (48 bp):
TATAATAATTAATTTTTTAATATAATATATAATAATTAAATTTTTAAT
Found at i:4348220 original size:28 final size:27
Alignment explanation
Indices: 4348125--4348222 Score: 95
Period size: 21 Copynumber: 3.9 Consensus size: 27
4348115 TAACATGTTG
*
4348125 TATAATAATTAATTTTTTAATATAATA
1 TATAATAATTAATTTTTAAATATAATA
* *
4348152 TATTATAATT-ATATTT---T-TAAT-
1 TATAATAATTAATTTTTAAATATAATA
4348173 TATAATAATT-ATTTTT-AATATAATA
1 TATAATAATTAATTTTTAAATATAATA
*
4348198 TATAATAATTAAATTTTAAAATATA
1 TATAATAATT-AATTTTTAAATATA
4348223 CTAAATAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
21 14 0.24
22 4 0.07
23 2 0.03
24 4 0.07
25 10 0.17
26 5 0.08
27 14 0.24
28 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATAATTAATTTTTAAATATAATA
Found at i:4348230 original size:25 final size:25
Alignment explanation
Indices: 4348125--4348220 Score: 85
Period size: 26 Copynumber: 3.9 Consensus size: 25
4348115 TAACATGTTG
*
4348125 TATAATAATTAATTTTTTAATATAATA
1 TATAATAATTAA--TTTTAAAATAATA
*
4348152 TATTATAATTATATTTT----TAAT-
1 TATAATAATTA-ATTTTAAAATAATA
* *
4348173 TATAATAATTATTTTTAATATAATA
1 TATAATAATTAATTTTAAAATAATA
4348198 TATAATAATTAAATTTTAAAATA
1 TATAATAATT-AATTTTAAAATA
4348221 TACTAAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
20 4 0.07
21 10 0.18
22 4 0.07
24 4 0.07
25 10 0.18
26 14 0.25
27 10 0.18
28 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATAATAATTAATTTTAAAATAATA
Found at i:4348230 original size:28 final size:25
Alignment explanation
Indices: 4348174--4348230 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 25
4348164 ATTTTTAATT
* *
4348174 ATAATAATTATTTTTAATATAATAT
1 ATAATAATTATTTTAAATATAATAA
*
4348199 ATAATAATTAAATTTTAAAATATACTAA
1 ATAATAATT--ATTTT-AAATATAATAA
4348227 ATAA
1 ATAA
4348231 CACCACATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.35
27 5 0.19
28 12 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAATAATTATTTTAAATATAATAA
Found at i:4364554 original size:3 final size:3
Alignment explanation
Indices: 4364546--4364576 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4364536 TGTCTTGGTT
4364546 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
4364577 ACTCTGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:4375822 original size:2 final size:2
Alignment explanation
Indices: 4375815--4375839 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4375805 TCTTCCAAAA
4375815 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
4375840 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4377612 original size:2 final size:2
Alignment explanation
Indices: 4377605--4377633 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4377595 TCCTTTGGAC
4377605 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 A
4377634 GATGAATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4378497 original size:10 final size:10
Alignment explanation
Indices: 4378482--4378506 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4378472 TATGATAATA
4378482 CACATCTCCT
1 CACATCTCCT
4378492 CACATCTCCT
1 CACATCTCCT
4378502 CACAT
1 CACAT
4378507 GGCCAGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (10 bp):
CACATCTCCT
Found at i:4381306 original size:16 final size:16
Alignment explanation
Indices: 4381270--4381308 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4381260 GAAATTCAAT
*
4381270 AGGAAAAAAAGGGGGG
1 AGGACAAAAAGGGGGG
*
4381286 A-GACAAAAAGGGTGG
1 AGGACAAAAAGGGGGG
4381301 AGGACAAA
1 AGGACAAA
4381309 CTAAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.41, T:0.03
Consensus pattern (16 bp):
AGGACAAAAAGGGGGG
Found at i:4381533 original size:6 final size:6
Alignment explanation
Indices: 4381522--4381560 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4381512 ATCCACTGTA
* * *
4381522 TTCCTC TTCCTC TGCCTC TTCCTC TTCTTC TTCTTC TTC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTC
4381561 TTCGGCTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.54
Consensus pattern (6 bp):
TTCCTC
Found at i:4394301 original size:73 final size:74
Alignment explanation
Indices: 4394164--4394304 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 74
4394154 ATAAATGAAA
* *
4394164 TAAATTTTACTTATAACTATAATAAAAAATATTTCAATAATTATCATTTAATAAACACACATTTA
1 TAAATCTTACTAATAACTATAATAAAAAATATTTCAATAATTATCATTTAATAAACACACATTTA
4394229 TAATACGTT
66 TAATACGTT
* * * *
4394238 TAAATCTTACTAATAATTATAAT-AAAAATATTTCAATAATTATCATTTAATGAATACATATTTA
1 TAAATCTTACTAATAACTATAATAAAAAATATTTCAATAATTATCATTTAATAAACACACATTTA
4394302 TAA
66 TAA
4394305 GTATAGGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 41 0.67
74 20 0.33
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.41
Consensus pattern (74 bp):
TAAATCTTACTAATAACTATAATAAAAAATATTTCAATAATTATCATTTAATAAACACACATTTA
TAATACGTT
Found at i:4421521 original size:44 final size:44
Alignment explanation
Indices: 4421428--4421525 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
4421418 ACATGCGTAT
* * ** **
4421428 GTATGTATCTTTTTACATACATACATTCATACATGTGTATGTAA
1 GTATGTATCTTTTCACATACATACATGCATACATGCATACATAA
4421472 GTATGTATCTTTTCACATACATACATGCATACATGCATACATACA
1 GTATGTATCTTTTCACATACATACATGCATACATGCATACATA-A
4421517 -TATGTATCT
1 GTATGTATCT
4421526 ATGCATCGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (44 bp):
GTATGTATCTTTTCACATACATACATGCATACATGCATACATAA
Found at i:4421521 original size:52 final size:52
Alignment explanation
Indices: 4421441--4421544 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 52
4421431 TGTATCTTTT
* *** * * *
4421441 TACATACATACATTCATACATGTGTATGTAAGTATGTATCTTTTCACATACA
1 TACATACATACATGCATACATACATATGTAACTATGCATCGTTTCACATACA
* *
4421493 TACATGCATACATGCATACATACATATGTATCTATGCATCGTTTCACATACA
1 TACATACATACATGCATACATACATATGTAACTATGCATCGTTTCACATACA
4421545 AATGCACAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (52 bp):
TACATACATACATGCATACATACATATGTAACTATGCATCGTTTCACATACA
Done.