Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 126 of 198
Found at i:40314241 original size:40 final size:40
Alignment explanation
Indices: 40314183--40314287 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
40314173 GAAAGAAATC
* **
40314183 TAAATGAGTAAGATCATAGATGAAAGATGTTATGGTATCA
1 TAAATGAGTAAGAACATAGATGAAAGATGTTATGACATCA
** *
40314223 TAAATGAGTAAGAACATAGCCGACAGATGTTATGACATCA
1 TAAATGAGTAAGAACATAGATGAAAGATGTTATGACATCA
* * *
40314263 AAAATAAGTAA-AACCATAGTTGAAA
1 TAAATGAGTAAGAA-CATAGATGAAA
40314288 ACCACTATGA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 2 0.04
40 51 0.96
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.25
Consensus pattern (40 bp):
TAAATGAGTAAGAACATAGATGAAAGATGTTATGACATCA
Found at i:40314962 original size:40 final size:40
Alignment explanation
Indices: 40314902--40315004 Score: 161
Period size: 40 Copynumber: 2.6 Consensus size: 40
40314892 AATTTAAATG
** * *
40314902 TGAGTAAGATTATAGTTGAAAGAGGTTATGGCATCATAAA
1 TGAGTAAGACCATAGCTGAAAGAGGTTATGACATCATAAA
*
40314942 TGAGTAAGACCATAGCTGAAAGATGTTATGACATCATAAA
1 TGAGTAAGACCATAGCTGAAAGAGGTTATGACATCATAAA
40314982 TGAGTAAGACCATAGCTGAAAGA
1 TGAGTAAGACCATAGCTGAAAGA
40315005 CACTATAGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (40 bp):
TGAGTAAGACCATAGCTGAAAGAGGTTATGACATCATAAA
Found at i:40315536 original size:715 final size:717
Alignment explanation
Indices: 40313467--40316352 Score: 3273
Period size: 715 Copynumber: 4.0 Consensus size: 717
40313457 GCTATACACC
* * *
40313467 AAATATGAGTAAAATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACTATAGTTGAA
1 AAATATGAGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
* * * * *
40313532 AGATGTTATGACATCTTAAATGAGTAAGACAATAGTTAAAAG-GCACTATA-ACATCCTTTGATA
66 AGATGTTATGACATCATAAATGAGTAAGACCATAGCTGAAAGACCACTATAGACATCCTTTGATA
* * * * * ** * * *
40313595 GTCCGTCGAAAAAGTAAACACCAGATTATATCGTGTAAGACCATAGATGAAAGATACTACAACAT
131 GTCCGTCGAGACAGTAAACACGAGGTTATATCGTGTAAGACCATAGCTGAAAGACGCCATAGCAT
* * * * * * * *
40313660 TGTAGATAGTTCGTCGGGACAACAAACATGGGATATTCCACCAAGATAATAATCACGGGACAATT
196 CGTAGATAGTTCGTCAGGACAACAAACACGGGATAATCCACTAAAACAATAATCACGGGGCAATT
* *
40313725 TGCCAATACAGAAAGCATGGTAACATCCACCAAGACAATTAG-TATGGAAAGAAAGAGTGAAAGA
261 CGCCAAGACAGAAAGCATGGTAACATCCACCAAGACAATTAGCT-TGGAAAGAAAGAGTGAAAGA
* * ** *
40313789 CCATAAATCGGTTATGACATCAAGAAGACTCAATTGATAAGGTAAACATGAGAGTTTAAAAGGTG
325 CCATAAATCGGTTATGAAATCATGAAGACTCAACCGATAAGGTGAACATGAGAGTTTAAAAGGTG
* *
40313854 TAAATTTTGGGCTCGGTGATGGAGGTTGGTAAAGATCAGCGAATGGAGTGAATTCTAAGGCTTAT
390 TAAATTCTGGGCTCGGTGATGGAGGTTGGTAAAGATC-GCGAATGGAGTGGATTCTAAGGCTTAT
* * * * *
40313919 TGAATAAGAGGATGTATTTAATCAAGGATCGGGACTTGAGGGTCTGCAGACAAATGGGGAAATTA
454 TGAACAAGAGGATGTATTTAATTAAGGA-CGAGACTTAAGGGTCCGCAGACAAATGGGGAAATTA
* * *
40313984 AGGGCGATTATGTTCATCGAGGTTATACGGGGCTAAGTCACTCGGGTTGGAAAAAGAATG-AATC
518 AGGGGGATTATGTCCATCGAGGTTATACGGGGCTAAGTCACCCGGGTTGGAAAAAGAA-GAAATC
* * * *
40314048 CGTTAAGGACTAACCTAGGGCGGGCAGTCCACTAGGAAATATGAGGGATAAAAATTTGAAACCTA
582 CGTTAAGGACTAACCTAGGGCGGGTAGTCCACCAAGAAATAAGAGGGATAAAAATTTGAAACCTA
*
40314113 AGGAAATAAATGTCAGACAACCAATGACCGAAATTGGGTCTCCCATTCAAGGTTGTGAGAGAAAG
647 AGGAAATAAATGTCAGACAACCAATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAAAG
*
40314178 AAATCT
712 AAATTT
* * * * *
40314184 -AA-ATGAGTAAGATCATAGATGAAAGATGTTATGGTATCATAAATGAGTAAGAACATAGCCGAC
1 AAATATGAGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
* * * * *
40314247 AGATGTTATGACATCAAAAATAAGTAAAACCATAGTTGAAA-ACCACTAT-GACATCCTTTAATA
66 AGATGTTATGACATCATAAATGAGTAAGACCATAGCTGAAAGACCACTATAGACATCCTTTGATA
* * * *
40314310 GTCCGTCGAGACAGTAAACATGAGGTTATATCGTGTAAGACCATAGTTAAAAGATGCCATAGCAT
131 GTCCGTCGAGACAGTAAACACGAGGTTATATCGTGTAAGACCATAGCTGAAAGACGCCATAGCAT
* * * * * *** *
40314375 GGTAGATAGTCCGCCAAGACAACAAACACGGGATAATCTACTGAAAA-AATAATCATAAGGCAAA
196 CGTAGATAGTTCGTCAGGACAACAAACACGGGATAATCCACT-AAAACAATAATCACGGGGCAAT
* * ** * * *
40314439 TCACCAAGACAGAAAGCGTGGTAA-ATTTTACCAATATAATTAGCTTGGAAATAAAGAGTGAAAG
260 TCGCCAAGACAGAAAGCATGGTAACA-TCCACCAAGACAATTAGCTTGGAAAGAAAGAGTGAAAG
* *
40314503 A-CATAAATCGGTTATGAAATCATGAAGACTCAACCGATAAGGTTAACA-AAGAGTTTAAAAGGT
324 ACCATAAATCGGTTATGAAATCATGAAGACTCAACCGATAAGGTGAACATGAGAGTTTAAAAGGT
* ** *
40314566 GTAAATTCTGGGCTCGGTGATGGAGGTTGGTAAAGATTGCTGAATAAAGTGGATTCTAAGGTTTA
389 GTAAATTCTGGGCTCGGTGATGGAGGTTGGTAAAGATCGC-GAATGGAGTGGATTCTAAGGCTTA
*
40314631 TTGAACAAGAGGATGTATTTAATGAAGGACTGAGACTTAAGGGTCCGCAGACAAA-GGAGGAAAT
453 TTGAACAAGAGGATGTATTTAATTAAGGAC-GAGACTTAAGGGTCCGCAGACAAATGG-GGAAAT
* * * * *
40314695 TAAGGGAGATTATGTCCATCGAGGTTATACGGGGATAAGTCACCTGGGTTGGCAAAAGAAGGAAT
516 TAAGGGGGATTATGTCCATCGAGGTTATACGGGGCTAAGTCACCCGGGTTGGAAAAAGAAGAAAT
* * * *
40314760 CCGTTAATGACTAACCT-GAGGCGGGTAGTCCATCAAGAAATAAGGGGGATAAAACTTTGAAACC
581 CCGTTAAGGACTAACCTAG-GGCGGGTAGTCCACCAAGAAATAAGAGGGATAAAAATTTGAAACC
*
40314824 TAAAGAAATAAATGTCAGACAACCAATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAA
645 TAAGGAAATAAATGTCAGACAACCAATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAA
40314889 AGAAATTT
710 AGAAATTT
* * * *
40314897 AAATGTGAGTAAGATTATAGTTGAAAGAGGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
1 AAATATGAGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
40314962 AGATGTTATGACATCATAAATGAGTAAGACCATAGCTGAAAGA-CACTATAG-CATCCTTTGATA
66 AGATGTTATGACATCATAAATGAGTAAGACCATAGCTGAAAGACCACTATAGACATCCTTTGATA
* *
40315025 GTCCG-CTGAGATAGTAAACACGAGGTTATATCGTGTAAGACCATAGCTGAAAGACGTCATAGCA
131 GTCCGTC-GAGACAGTAAACACGAGGTTATATCGTGTAAGACCATAGCTGAAAGACGCCATAGCA
* * * * *
40315089 TCATAGATAGTTCGTCAGGACAATAAACACGAGATAATCTACTAAAACAATAATCACGGGGTAAT
195 TCGTAGATAGTTCGTCAGGACAACAAACACGGGATAATCCACTAAAACAATAATCACGGGGCAAT
* *
40315154 TCGCCAAGACAGAAAGCGTGGTAACATCTACCAAGACAATTAGCTTGGAAAGAAAGAGTGAAAGA
260 TCGCCAAGACAGAAAGCATGGTAACATCCACCAAGACAATTAGCTTGGAAAGAAAGAGTGAAAGA
*
40315219 CCATAAATCAGTTATGAAATCATGAAGACTCAACCGATAAGGTGAACATGAGAGTTTAAAAGGTG
325 CCATAAATCGGTTATGAAATCATGAAGACTCAACCGATAAGGTGAACATGAGAGTTTAAAAGGTG
* * * * *
40315284 TAAATTCTGGGCTCGATGATGCATGTTGGTAAAGATCGTCAAATGGAGTGGATTCGAAGGCTTAT
390 TAAATTCTGGGCTCGGTGATGGAGGTTGGTAAAGATCG-CGAATGGAGTGGATTCTAAGGCTTAT
* * * *
40315349 TGAACAAGAGGATGTATTTAATTAAGGACAGGGACTTAAGGGTCCACGGACAAA-GGGGCAATTA
454 TGAACAAGAGGATGTATTTAATTAAGGAC-GAGACTTAAGGGTCCGCAGACAAATGGGGAAATTA
* * *
40315413 AGGGGGATTATGTCCATCGAGGTTATACGGGGCTAAGTCACCCAGGTTGGAAAAAGAATAAATTC
518 AGGGGGATTATGTCCATCGAGGTTATACGGGGCTAAGTCACCCGGGTTGGAAAAAGAAGAAATCC
* * *
40315478 GTTAAGAACTAATCTGGGGCGGGTAGTCCACCAAGAAATAAGAGGGAT-AAAATTTGAAACCTAA
583 GTTAAGGACTAACCTAGGGCGGGTAGTCCACCAAGAAATAAGAGGGATAAAAATTTGAAACCTAA
* * *
40315542 GGAAACAAATGTCAGACAACCAATGACCGACATTGGGTCTCCCATTCAATGTTGTGAGAGACAGA
648 GGAAATAAATGTCAGACAACCAATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAAAGA
40315607 AATTT
713 AATTT
*
40315612 AAATATAAGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
1 AAATATGAGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
* *** * *
40315677 AGATGTTATGACATTATAAATGAGTAAGACCATAGCTGAAAGA-TGTTAT-GACATCATAAATGA
66 AGATGTTATGACATCATAAATGAGTAAGACCATAGCTGAAAGACCACTATAGACATCCT--TTGA
* * * ** ** * * *
40315740 GTAAGACCATAGCTGAAAGACACTATGTCATC--TTTTGATAGTTCGTCGAGACAGTAAACACGA
129 -T-AGTCCGT--C-G--AGACAGTA-AACA-CGAGGTT-ATA--TCGT-G-TA-AG--ACCA-TA
* * ** ** * * * *
40315803 GGTTATATCATGTAAAACCATAGCTGAAAG-ATGCCATAGCATCGTAGATAGTTCGTCAGGATAA
176 GCTGA-A--A-G--ACGCCATAGC--ATCGTA-G--ATAG-TTCGT---CAG---GACA--ACAA
* ** * * *
40315867 TAAACACGGGATAATCCACCT-AGACAATAATCACGGGGCAGTTCCCCAAGACAGAAAGCATGGT
221 -ACACGGG--ATAATCCA-CTAAAACAATAATCACGGGGCAATTCGCCAAGACAGAAAGCATGGT
* * *
40315931 AACATCCACCAAGACAATTAGCTTGGAAAGAAAGAGTGAAATACCATAAAT-GGTAATGACATCA
282 AACATCCACCAAGACAATTAGCTTGGAAAGAAAGAGTGAAAGACCATAAATCGGTTATGAAATCA
* * *
40315995 TGAAGACTCAACCAATAAGGTGAACGTGAGAGTTTAAAAGGTGTAAATTTTGGGCTCGGTGATGG
347 TGAAGACTCAACCGATAAGGTGAACATGAGAGTTTAAAAGGTGTAAATTCTGGGCTCGGTGATGG
* * * *
40316060 AGGTTGGTAAAGATTGTTGAATGGAGTAGATTTTAAGGCTTATTGAAC-A-A-GATG--------
412 AGGTTGGTAAAGATCG-CGAATGGAGTGGATTCTAAGGCTTATTGAACAAGAGGATGTATTTAAT
* * * * * * * *
40316114 --A--CCGAGACTTAAGGGTCCGCGGAAAAATGGGGTAACTAAGGGCGG-TTATGTTCGTCGAGA
476 TAAGGACGAGACTTAAGGGTCCGCAGACAAATGGGGAAATTAAGGG-GGATTATGTCCATCGAGG
* * *
40316174 TTATACGGGGCTAAGTCACCCGAGTTGGCAAAAGAAGAAATCCGTTAAGGATTAACCTAGGGCGG
540 TTATACGGGGCTAAGTCACCCGGGTTGGAAAAAGAAGAAATCCGTTAAGGACTAACCTAGGGCGG
* *
40316239 GTAGTGCACCAAGAAATAGAGGGGGATAAAAATTTGAAACCTAAGGAAATAAATGTCAGACAACC
605 GTAGTCCACCAAGAAATA-AGAGGGATAAAAATTTGAAACCTAAGGAAATAAATGTCAGACAACC
*
40316304 AATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAAATAAATTT
669 AATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAAAGAAATTT
40316353 GGTTGAGGTG
Statistics
Matches: 1859, Mismatches: 240, Indels: 116
0.84 0.11 0.05
Matches are distributed among these distances:
712 7 0.00
713 305 0.16
714 51 0.03
715 717 0.39
716 159 0.09
717 124 0.07
718 2 0.00
719 4 0.00
722 3 0.00
724 8 0.00
725 5 0.00
726 1 0.00
727 4 0.00
728 1 0.00
729 1 0.00
730 2 0.00
732 3 0.00
733 4 0.00
734 1 0.00
736 1 0.00
737 1 0.00
738 21 0.01
739 105 0.06
740 10 0.01
741 85 0.05
743 4 0.00
744 4 0.00
747 2 0.00
750 3 0.00
751 4 0.00
752 5 0.00
753 5 0.00
754 111 0.06
755 94 0.05
756 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (717 bp):
AAATATGAGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATGAGTAAGACCATAGCTGAA
AGATGTTATGACATCATAAATGAGTAAGACCATAGCTGAAAGACCACTATAGACATCCTTTGATA
GTCCGTCGAGACAGTAAACACGAGGTTATATCGTGTAAGACCATAGCTGAAAGACGCCATAGCAT
CGTAGATAGTTCGTCAGGACAACAAACACGGGATAATCCACTAAAACAATAATCACGGGGCAATT
CGCCAAGACAGAAAGCATGGTAACATCCACCAAGACAATTAGCTTGGAAAGAAAGAGTGAAAGAC
CATAAATCGGTTATGAAATCATGAAGACTCAACCGATAAGGTGAACATGAGAGTTTAAAAGGTGT
AAATTCTGGGCTCGGTGATGGAGGTTGGTAAAGATCGCGAATGGAGTGGATTCTAAGGCTTATTG
AACAAGAGGATGTATTTAATTAAGGACGAGACTTAAGGGTCCGCAGACAAATGGGGAAATTAAGG
GGGATTATGTCCATCGAGGTTATACGGGGCTAAGTCACCCGGGTTGGAAAAAGAAGAAATCCGTT
AAGGACTAACCTAGGGCGGGTAGTCCACCAAGAAATAAGAGGGATAAAAATTTGAAACCTAAGGA
AATAAATGTCAGACAACCAATGACCGACATTGGGTCTCCCATTCAAGGTTGTGAGAGAAAGAAAT
TT
Found at i:40315671 original size:40 final size:40
Alignment explanation
Indices: 40315619--40315759 Score: 255
Period size: 40 Copynumber: 3.5 Consensus size: 40
40315609 TTTAAATATA
* *
40315619 AGTAAGATCATAGCTGAAAGATGTTATGGCATCATAAATG
1 AGTAAGACCATAGCTGAAAGATGTTATGACATCATAAATG
*
40315659 AGTAAGACCATAGCTGAAAGATGTTATGACATTATAAATG
1 AGTAAGACCATAGCTGAAAGATGTTATGACATCATAAATG
40315699 AGTAAGACCATAGCTGAAAGATGTTATGACATCATAAATG
1 AGTAAGACCATAGCTGAAAGATGTTATGACATCATAAATG
40315739 AGTAAGACCATAGCTGAAAGA
1 AGTAAGACCATAGCTGAAAGA
40315760 CACTATGTCA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (40 bp):
AGTAAGACCATAGCTGAAAGATGTTATGACATCATAAATG
Found at i:40318365 original size:6 final size:6
Alignment explanation
Indices: 40318356--40318403 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
40318346 CAAAAATCAA
* *
40318356 AAAAAT AAAAGT AAAAGT AAAAGT AAAAGT AAAAATT AAAAGTT AAAA
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT -AAAAGT AAAAG-T AAAA
40318404 AAATTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (6 bp):
AAAAGT
Found at i:40318957 original size:20 final size:20
Alignment explanation
Indices: 40318920--40318957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40318910 AGTTAAAACA
* *
40318920 TAAAAAAATTCAATAATTAT
1 TAAAAAAATCCAAAAATTAT
40318940 TAAAAAAATCCAAAAATT
1 TAAAAAAATCCAAAAATT
40318958 TGTTTAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAAATCCAAAAATTAT
Found at i:40319013 original size:28 final size:29
Alignment explanation
Indices: 40318967--40319035 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
40318957 TTGTTTAAGA
**
40318967 AATTATAAAATTA-TTAAAATAGAAAAAG
1 AATTATAAAATTACAAAAAATAGAAAAAG
* *
40318995 AATTATAAAGTTACAAAAAATATAAAAA-
1 AATTATAAAATTACAAAAAATAGAAAAAG
40319023 AATATACTAAAAT
1 AAT-TA-TAAAAT
40319036 ATTAAAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 15 0.45
29 13 0.39
30 5 0.15
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (29 bp):
AATTATAAAATTACAAAAAATAGAAAAAG
Found at i:40319036 original size:20 final size:20
Alignment explanation
Indices: 40319011--40319048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40319001 AAAGTTACAA
40319011 AAAATATAAAAAAATATACT
1 AAAATATAAAAAAATATACT
* *
40319031 AAAATATTAAAATATATA
1 AAAATATAAAAAAATATA
40319049 TTATAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATATAAAAAAATATACT
Found at i:40320001 original size:42 final size:42
Alignment explanation
Indices: 40319937--40320017 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
40319927 AGGTACTCAT
*
40319937 CCAACTTCTATAAGTTTGCATTTTAGATACCAAAGTTTAGAC
1 CCAACTTCTATAAGTTTACATTTTAGATACCAAAGTTTAGAC
* *
40319979 CCAACTT-TCATAATTTTACATTTTAGGTACCAAAGTTTA
1 CCAACTTCT-ATAAGTTTACATTTTAGATACCAAAGTTTA
40320018 AATCTGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (42 bp):
CCAACTTCTATAAGTTTACATTTTAGATACCAAAGTTTAGAC
Found at i:40323497 original size:2 final size:2
Alignment explanation
Indices: 40323490--40323524 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40323480 NNNTAAGTAT
40323490 TA TA 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 TA TA T
40323525 CTTTTTGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40325069 original size:19 final size:19
Alignment explanation
Indices: 40325045--40325083 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40325035 CTAATTTTAC
40325045 TTTTAA-ACAAATTTAATCA
1 TTTTAAGACAAA-TTAATCA
*
40325064 TTTTAAGTCAAATTAATCA
1 TTTTAAGACAAATTAATCA
40325083 T
1 T
40325084 GATTTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (19 bp):
TTTTAAGACAAATTAATCA
Found at i:40325609 original size:16 final size:16
Alignment explanation
Indices: 40325584--40325626 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40325574 ATAATTGTTA
*
40325584 TGTTTAGAACAATTTT
1 TGTTTAGAACAACTTT
*
40325600 TGTTTGGAACAACTTT
1 TGTTTAGAACAACTTT
*
40325616 TATTTAGAACA
1 TGTTTAGAACA
40325627 GTTGTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (16 bp):
TGTTTAGAACAACTTT
Found at i:40336083 original size:28 final size:27
Alignment explanation
Indices: 40336045--40336132 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 27
40336035 ATTAAATAAA
*
40336045 GGAAAAGGCATTAATACATTAAATGTAG
1 GGAAAAAGCATTAA-ACATTAAATGTAG
* *
40336073 GGAAAAAGCATTAAGATATTAAATGCA-
1 GGAAAAAGCATTAA-ACATTAAATGTAG
* *
40336100 TGAAAAAGTCATTAAGCATTAAATGTAG
1 GGAAAAAG-CATTAAACATTAAATGTAG
40336128 GGAAA
1 GGAAA
40336133 TGACTTATTG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 16 0.33
28 33 0.67
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (27 bp):
GGAAAAAGCATTAAACATTAAATGTAG
Found at i:40344409 original size:13 final size:14
Alignment explanation
Indices: 40344393--40344423 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
40344383 AATGTTTGAG
40344393 ATTAATTGAA-ATA
1 ATTAATTGAATATA
40344406 ATTAATTGAATATA
1 ATTAATTGAATATA
40344420 ATTA
1 ATTA
40344424 TTTATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTAATTGAATATA
Found at i:40344781 original size:41 final size:41
Alignment explanation
Indices: 40344615--40344799 Score: 203
Period size: 41 Copynumber: 4.5 Consensus size: 41
40344605 ATTATTGTCT
* * *
40344615 AATTGTACATATGTGCCCATGTTTGTACTTCGATACCCCTG
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * *
40344656 AATTGCACGTATGTACTCCTGTTTATACTTCGGTACCCCTG
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * *
40344697 AATTGCATATATGTTCCCCTATTTGTACTTCGGTACCCCTG
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * * *
40344738 AATTGCACATACGTGCCTCTGTTTGTACTTCAGTACTCTTG
1 AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTG
*
40344779 AA-TGCAC-TTTCGTGCCCCTGT
1 AATTGCACATAT-GTGCCCCTGT
40344800 ATTAGACCTG
Statistics
Matches: 119, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 14 0.12
41 104 0.87
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.37
Consensus pattern (41 bp):
AATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:40354329 original size:16 final size:17
Alignment explanation
Indices: 40354308--40354346 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
40354298 ATTCAGAAAT
*
40354308 ATAAAAGAAAATTAA-A
1 ATAAAAGAAAATAAAGA
*
40354324 ATAAAATAAAATAAAGA
1 ATAAAAGAAAATAAAGA
40354341 ATAAAA
1 ATAAAA
40354347 AATCAATCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
ATAAAAGAAAATAAAGA
Found at i:40359382 original size:22 final size:22
Alignment explanation
Indices: 40359340--40359383 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40359330 AATAAATATT
* *
40359340 AATATATATAGTATTTTAGATC
1 AATATATATAGTATATCAGATC
40359362 AATATGATATAG-ATATCAGATC
1 AATAT-ATATAGTATATCAGATC
40359384 GATTCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (22 bp):
AATATATATAGTATATCAGATC
Found at i:40360827 original size:21 final size:21
Alignment explanation
Indices: 40360801--40360842 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40360791 CCAATTATCA
*
40360801 TATTATTAAATTAATATATAT
1 TATTATCAAATTAATATATAT
* *
40360822 TATTATCAAATTTATTTATAT
1 TATTATCAAATTAATATATAT
40360843 AAATTTAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATCAAATTAATATATAT
Found at i:40362196 original size:2 final size:2
Alignment explanation
Indices: 40362189--40362222 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40362179 TGGAATTGGA
40362189 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
40362223 TCCCACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40367097 original size:27 final size:26
Alignment explanation
Indices: 40367067--40367160 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
40367057 AGTTCACTTA
*
40367067 GACAGTAAACACAAGATGGTTCATGGG
1 GACAGTAAACACAAGA-GGTTCATCGG
* * ** *
40367094 GACACTAAACACAGGACGGTTTGTCGA
1 GACAGTAAACACAAGA-GGTTCATCGG
* * *
40367121 GACATTAAACACGAAGAAGTTCATTGG
1 GACAGTAAACAC-AAGAGGTTCATCGG
*
40367148 GATAGTAAACACA
1 GACAGTAAACACA
40367161 GGGCGGTCCG
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
26 1 0.02
27 46 0.92
28 3 0.06
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.19
Consensus pattern (26 bp):
GACAGTAAACACAAGAGGTTCATCGG
Found at i:40367184 original size:54 final size:54
Alignment explanation
Indices: 40367066--40367184 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
40367056 GAGTTCACTT
* * **
40367066 AGACAGTAAACACAAGATGGTTCATGGGGACACTAAACACAGGACGGTTTGTCG
1 AGACACTAAACACAAGATAGTTCATGGGGACACTAAACACAGGACGGTCCGTCG
* * * * *
40367120 AGACATTAAACACGAAGA-AGTTCATTGGGATAGTAAACACAGGGCGGTCCGTCG
1 AGACACTAAACAC-AAGATAGTTCATGGGGACACTAAACACAGGACGGTCCGTCG
*
40367174 GGACACTAAAC
1 AGACACTAAAC
40367185 TGGGGTAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 50 0.93
55 4 0.07
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (54 bp):
AGACACTAAACACAAGATAGTTCATGGGGACACTAAACACAGGACGGTCCGTCG
Found at i:40381888 original size:60 final size:59
Alignment explanation
Indices: 40381728--40381896 Score: 193
Period size: 60 Copynumber: 2.8 Consensus size: 59
40381718 TTAATTTATA
*
40381728 ATATAATTTATTTCAATTATTAGCCTCAATTTTTATATTCTATTCAATTAGATTAAATTC
1 ATATAATTTATTTCAATTATTAGCCTCAA-TTTTATATTCTATTCAATTAAATTAAATTC
* * * *
40381788 ATATAA-TTCTTT-AAGTGTATT--CATATAATTCATATAATTCTATTCAATTAAATTAAATTC
1 ATATAATTTATTTCAA-T-TATTAGCCT-CAATT-TTAT-ATTCTATTCAATTAAATTAAATTC
*
40381848 ATATAATTTATTTCGATTATTAGCCTCAATTTTCATATTCTATTCAATT
1 ATATAATTTATTTCAATTATTAGCCTCAATTTT-ATATTCTATTCAATT
40381897 CCCCCCACAT
Statistics
Matches: 89, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
58 6 0.07
59 11 0.12
60 57 0.64
61 12 0.13
62 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.49
Consensus pattern (59 bp):
ATATAATTTATTTCAATTATTAGCCTCAATTTTATATTCTATTCAATTAAATTAAATTC
Found at i:40388052 original size:39 final size:39
Alignment explanation
Indices: 40387987--40388080 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 39
40387977 AACATGTTTT
* * *
40387987 TGAGTATTGTGACATATACTTGAATGTTATACGATTATA
1 TGAGTATTGTGATATACACTTAAATGTTATACGATTATA
* **
40388026 TGAGTATTGTGATATACGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATACACTTAAATGTTATACGATTATA
* * *
40388065 TGTGTAATGTGGTATA
1 TGAGTATTGTGATATA
40388081 TGTTTAAAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (39 bp):
TGAGTATTGTGATATACACTTAAATGTTATACGATTATA
Found at i:40394285 original size:510 final size:509
Alignment explanation
Indices: 40393078--40394614 Score: 2772
Period size: 510 Copynumber: 3.0 Consensus size: 509
40393068 TCAGTAGTAT
*
40393078 CCTCATCTATTCGGATCAGGTAAATTTCAAGGCCGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
1 CCTCTTCTATTCGGATCAGGTAAATTTCAAGGCCGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
40393143 CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAGACACAAGTGTGTATCTGCTTCAATGGTTAA
66 CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAGACACAAGTGTGTATCTGCTTCAATGGTTAA
* * * * *
40393208 GTGTTCTGGTATGGGTAAGGGGTCTTGGGTTCAACTTCCACTTTCGGTAAAACTTTTTTATTTTA
131 GTGTTCTGGTATGGGTAAGAGGTCTTGGGTTCAACTCCCACTTTTGGCAAAACTTTGTTATTTTA
40393273 GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAATTGTTTGTTAATCCAAATCAGAATGA
196 GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAATTGTTTGTTAATCCAAATCAGAATGA
* *
40393338 GTCTGCTGGTTCGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCTTGTGTTCGAGCCCTTGCGTGAG
261 GTCTGCTGGTTCGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCCTATGTTCGAGCCCTTGCGTGAG
*
40393403 TGTCAATGTTAATTTTTACTCGGTTGTCTGATAGAGTTTCGGTAGAGCTAAAATTCTGAAATAGT
326 TGTCGATGTTAATTTTTACTCGGTTGTCTGATAGAGTTTCGGTAGAGCTAAAATTCTGAAATAGT
*
40393468 TGTGAATTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATATCTTTTATTTTTCTTAT
391 TGTGAGTTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATA--TTTTATTTTTCTTAT
40393533 TTTTTTCAAATTTTTATTTTCTTCCCCAATTTCTAACGTCAATTTTTTTCTCTTTTC
454 TTTTTTCAAATTTTTATTTTCTT-CCCAATTTCTAACGTCAATTTTTTTCTCTTTTC
* *
40393590 CCTCTTCTATTCGGATCACGTAAATTTCAAGGCTGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
1 CCTCTTCTATTCGGATCAGGTAAATTTCAAGGCCGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
40393655 CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAGACACAAGTGTGTATCTGCTTCAATGGTTAA
66 CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAGACACAAGTGTGTATCTGCTTCAATGGTTAA
40393720 GTGTTCTGGTATGGGTAAGAGGTCTTGGGTTCAACTCCCACTTTTGGCAAAACTTTGTTATTTTA
131 GTGTTCTGGTATGGGTAAGAGGTCTTGGGTTCAACTCCCACTTTTGGCAAAACTTTGTTATTTTA
*
40393785 GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAATTGTTTGTTAATCCAAATCATAATGA
196 GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAATTGTTTGTTAATCCAAATCAGAATGA
*
40393850 GTCTGCTGGTTCGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCCTATGTTTGAGCCCTTGCGTGAG
261 GTCTGCTGGTTCGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCCTATGTTCGAGCCCTTGCGTGAG
* * *
40393915 TGTCGATGTTAATTTTTACTCGGTTGTTTGGTAGAGTTTCGGTAGAGCTAAAATTCTAAAATAGT
326 TGTCGATGTTAATTTTTACTCGGTTGTCTGATAGAGTTTCGGTAGAGCTAAAATTCTGAAATAGT
40393980 TGTGAGTTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATATTTTATTTTTCTTATTT
391 TGTGAGTTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATATTTTATTTTTCTTATTT
40394045 TTTTCAAATTTTTATTTTCTTCCCTAATTTCTAACGTCAATTTTTTTCTCTTTTC
456 TTTTCAAATTTTTATTTTCTTCCC-AATTTCTAACGTCAATTTTTTTCTCTTTTC
*
40394100 CCTCTTCTATTTGGATCAGGTAAATTTCAAGGCCGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
1 CCTCTTCTATTCGGATCAGGTAAATTTCAAGGCCGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
* * *
40394165 CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAAACACAAGTATGTATCTGTTTCAATGGTTAA
66 CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAGACACAAGTGTGTATCTGCTTCAATGGTTAA
*
40394230 GTGTTCTGATATGGGTAAGAGGTCTTGGGTTCAACTCCCACTTTTGGCAAAACTTTGTTATTTTA
131 GTGTTCTGGTATGGGTAAGAGGTCTTGGGTTCAACTCCCACTTTTGGCAAAACTTTGTTATTTTA
* *
40394295 GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAACTGTTTGTTAATCTAAATCAGAATGA
196 GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAATTGTTTGTTAATCCAAATCAGAATGA
*
40394360 GTCTGCTGGTTTGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCCTATGTTCGAGCCCTTGCGTGAG
261 GTCTGCTGGTTCGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCCTATGTTCGAGCCCTTGCGTGAG
*
40394425 AGTCGATGTTAATTTTTACTCGGTTGTCTGATAGAGTTTCGGTAGAGCTAAAATTCTGAAATAGT
326 TGTCGATGTTAATTTTTACTCGGTTGTCTGATAGAGTTTCGGTAGAGCTAAAATTCTGAAATAGT
*
40394490 TATGAGTTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATATTTTATTTTTCTTATTT
391 TGTGAGTTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATATTTTATTTTTCTTATTT
*
40394555 TTTTCAAATTTTTATTTTC--CCCAATTTCTAACGTCAAATTTTTTCTCTTTTC
456 TTTTCAAATTTTTATTTTCTTCCCAATTTCTAACGTCAATTTTTTTCTCTTTTC
40394607 CCTCTTCT
1 CCTCTTCT
40394615 GATATTTTTC
Statistics
Matches: 989, Mismatches: 35, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
507 37 0.04
508 3 0.00
509 3 0.00
510 525 0.53
512 421 0.43
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (509 bp):
CCTCTTCTATTCGGATCAGGTAAATTTCAAGGCCGAAATTTCTTTTAGGGGGTAGAGTTGTGATA
CCCTAAGTAACTTATTTCTGTTTTTGTGAAATCAGACACAAGTGTGTATCTGCTTCAATGGTTAA
GTGTTCTGGTATGGGTAAGAGGTCTTGGGTTCAACTCCCACTTTTGGCAAAACTTTGTTATTTTA
GATCCAAGCTTTACTCTTATTGAGTGGGCTTATATTAAATTGTTTGTTAATCCAAATCAGAATGA
GTCTGCTGGTTCGAGTGGTAAGGAGTTAGTGTGTTGGAGTTCCTATGTTCGAGCCCTTGCGTGAG
TGTCGATGTTAATTTTTACTCGGTTGTCTGATAGAGTTTCGGTAGAGCTAAAATTCTGAAATAGT
TGTGAGTTAGTGGGTCAGTAGGAGAAAAATAGGGGATACGTTGTCATATTTTATTTTTCTTATTT
TTTTCAAATTTTTATTTTCTTCCCAATTTCTAACGTCAATTTTTTTCTCTTTTC
Found at i:40396977 original size:2 final size:2
Alignment explanation
Indices: 40396970--40396996 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40396960 TCCATAAAAT
40396970 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
40396997 CCCTACCAAA
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:40400608 original size:21 final size:21
Alignment explanation
Indices: 40400582--40400623 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40400572 AGGATTTCGG
40400582 TATGTGATTTCGTGTAAGACC
1 TATGTGATTTCGTGTAAGACC
40400603 TATGTGATTTCGTGTAAGACC
1 TATGTGATTTCGTGTAAGACC
40400624 ACGTCTGGGA
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:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (21 bp):
TATGTGATTTCGTGTAAGACC
Found at i:40400674 original size:44 final size:43
Alignment explanation
Indices: 40400607--40400771 Score: 167
Period size: 43 Copynumber: 3.8 Consensus size: 43
40400597 AAGACCTATG
40400607 TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TT
1 TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT
* * ** *
40400649 GAGATTTACGTGTAAGACCATGTCTGGGAAATTGGCATCG-TGTT
1 -TGATTT-CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT
* *
40400693 TGACTTCGTGTAATACC-CTGTCTGGGACAG-TGGCATCGATATT
1 TGATTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATT
* * * *
40400736 TGATTACATGTAAGACCACGTCTAGGACGATGGCAT
1 TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
40400772 TGTGCGAGCT
Statistics
Matches: 99, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 27 0.27
43 40 0.40
44 32 0.32
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT
Found at i:40403018 original size:13 final size:13
Alignment explanation
Indices: 40403002--40403045 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
40402992 TCGTAGGTCA
40403002 AATAAATTATACT
1 AATAAATTATACT
*
40403015 AATAAATGATA--
1 AATAAATTATACT
*
40403026 AATATATTATACT
1 AATAAATTATACT
40403039 AATAAAT
1 AATAAAT
40403046 ACTAAATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (13 bp):
AATAAATTATACT
Found at i:40403467 original size:22 final size:22
Alignment explanation
Indices: 40403442--40403525 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
40403432 TTCGACTCCA
* * *
40403442 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
40403464 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
**
40403486 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
*
40403508 TCACGTACTAAGCTCTCA
1 TAACGTACTAAGCTCTCA
40403526 GCCCCACAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:40405789 original size:9 final size:9
Alignment explanation
Indices: 40405772--40405808 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40405762 TGAGTTTTCG
40405772 AATTCGAAT
1 AATTCGAAT
*
40405781 AACTCGAAT
1 AATTCGAAT
40405790 AATTCGAAT
1 AATTCGAAT
40405799 AATTCGAAT
1 AATTCGAAT
40405808 A
1 A
40405809 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40406114 original size:7 final size:7
Alignment explanation
Indices: 40406079--40406112 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
40406069 ATTCTCTTCT
40406079 CCTCCCA
1 CCTCCCA
*
40406086 CCTCCTA
1 CCTCCCA
40406093 CCTCCCA
1 CCTCCCA
*
40406100 CCTCCCC
1 CCTCCCA
40406107 CCTCCC
1 CCTCCC
40406113 CCAAACTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.09, C:0.74, G:0.00, T:0.18
Consensus pattern (7 bp):
CCTCCCA
Found at i:40407529 original size:17 final size:17
Alignment explanation
Indices: 40407507--40407539 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40407497 TTTCAACTTG
40407507 CTTCTATAATTTACTCA
1 CTTCTATAATTTACTCA
40407524 CTTCTATAATTTACTC
1 CTTCTATAATTTACTC
40407540 TGACTTGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (17 bp):
CTTCTATAATTTACTCA
Found at i:40408385 original size:16 final size:18
Alignment explanation
Indices: 40408352--40408410 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
40408342 ATAGAAAATA
40408352 ATATTTTAAAATTATAAT
1 ATATTTTAAAATTATAAT
* *
40408370 ATATTTTTAAATTAATAGAAG
1 ATATTTTAAAATT-AT--AAT
40408391 ATAATTTTAAAATTATAAT
1 AT-ATTTTAAAATTATAAT
40408410 A
1 A
40408411 ATTAGATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
21 6 0.18
22 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTTTAAAATTATAAT
Found at i:40408409 original size:40 final size:43
Alignment explanation
Indices: 40408330--40408410 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 43
40408320 TATATCCATT
40408330 TTTTTATAATTAATAGAAAATAATATTTTAAAATTATAATATA
1 TTTTTATAATTAATAGAAAATAATATTTTAAAATTATAATATA
*
40408373 TTTTTA-AATTAATAGAAGAT-A-ATTTTAAAATTATAATA
1 TTTTTATAATTAATAGAAAATAATATTTTAAAATTATAATA
40408411 ATTAGATGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 17 0.46
41 1 0.03
42 13 0.35
43 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (43 bp):
TTTTTATAATTAATAGAAAATAATATTTTAAAATTATAATATA
Found at i:40410186 original size:20 final size:20
Alignment explanation
Indices: 40410141--40410186 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
40410131 GGTAAGATTT
40410141 TATA-ATTTTATTATTTTAA
1 TATATATTTTATTATTTTAA
40410160 -ATAATATTTTATTATTTTAA
1 TAT-ATATTTTATTATTTTAA
40410180 TATATAT
1 TATATAT
40410187 GATAATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 1 0.04
20 19 0.79
21 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATATTTTATTATTTTAA
Found at i:40415901 original size:18 final size:18
Alignment explanation
Indices: 40415878--40415923 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
40415868 CTTATCCTAT
* *
40415878 ACCCAATACCAACCCAAA
1 ACCCAAAACAAACCCAAA
*
40415896 ACCCAAAACAAACCCAATT
1 ACCCAAAACAAACCCAA-A
40415915 ACCCAAAAC
1 ACCCAAAAC
40415924 CCAAACAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.52, C:0.41, G:0.00, T:0.07
Consensus pattern (18 bp):
ACCCAAAACAAACCCAAA
Found at i:40415936 original size:25 final size:26
Alignment explanation
Indices: 40415889--40415937 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
40415879 CCCAATACCA
40415889 ACCCAAAACCCAAAACAAACCCAATT
1 ACCCAAAACCCAAAACAAACCCAATT
*
40415915 ACCCAAAACCC-AAACAAGCCCAA
1 ACCCAAAACCCAAAACAAACCCAA
40415938 CTAAACCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.53, C:0.41, G:0.02, T:0.04
Consensus pattern (26 bp):
ACCCAAAACCCAAAACAAACCCAATT
Found at i:40421783 original size:14 final size:14
Alignment explanation
Indices: 40421764--40421793 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40421754 ATGAAGGGGG
40421764 ATATGAAGTGTTGC
1 ATATGAAGTGTTGC
40421778 ATATGAAGTGTTGC
1 ATATGAAGTGTTGC
40421792 AT
1 AT
40421794 TAACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (14 bp):
ATATGAAGTGTTGC
Found at i:40423428 original size:8 final size:7
Alignment explanation
Indices: 40423406--40423434 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40423396 TCCAAATTTC
40423406 ATAAAAT
1 ATAAAAT
40423413 ATAAAAT
1 ATAAAAT
40423420 ATAAAA-
1 ATAAAAT
40423426 ATAAAAT
1 ATAAAAT
40423433 AT
1 AT
40423435 TTTTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAAAAT
Found at i:40423431 original size:13 final size:14
Alignment explanation
Indices: 40423406--40423434 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40423396 TCCAAATTTC
40423406 ATAAAATATAAAAT
1 ATAAAATATAAAAT
40423420 ATAAAA-ATAAAAT
1 ATAAAATATAAAAT
40423433 AT
1 AT
40423435 TTTTAACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAATATAAAAT
Found at i:40423479 original size:27 final size:27
Alignment explanation
Indices: 40423449--40423511 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
40423439 AACATTTTAA
40423449 TATAATTTAATATAAAATAAAAAATCT
1 TATAATTTAATATAAAATAAAAAATCT
* * * * *
40423476 TATAATATAATTTAATATAAAATATTT
1 TATAATTTAATATAAAATAAAAAATCT
40423503 TAT-ATTTAA
1 TATAATTTAA
40423512 ATATTGTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAATTTAATATAAAATAAAAAATCT
Found at i:40423515 original size:32 final size:32
Alignment explanation
Indices: 40423426--40423515 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
40423416 AAATATAAAA
*
40423426 ATAAAATATTTTTAACATTTTAATATAATTTAAT
1 ATAAAATA-TTTTAA-ATTTAAATATAATTTAAT
**
40423460 ATAAAATA--AAAAATCTTATAATATAATTTAAT
1 ATAAAATATTTTAAAT-TTA-AATATAATTTAAT
*
40423492 ATAAAATATTTTATATTTAAATAT
1 ATAAAATATTTTAAATTTAAATAT
40423516 TGTTCTTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
30 2 0.04
31 4 0.09
32 26 0.57
33 3 0.07
34 11 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAAAATATTTTAAATTTAAATATAATTTAAT
Found at i:40423978 original size:114 final size:114
Alignment explanation
Indices: 40423793--40425045 Score: 1877
Period size: 114 Copynumber: 11.0 Consensus size: 114
40423783 AAAATAAGCA
*** * * *** *
40423793 TTAGCGGCGTTTTCCAGAAAGCGCCGC-AAAGTACCTAATCCCAACGATGTCATTTT-TCGAGCT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCT-GAGCT
* * * * * *
40423856 TTCAGGGATTTAGCGGCGTTTTTAA-TAAATCGCTGCTAATGCTGAGGCCT
65 TTCGGGGATTTAGTGGCGTTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
* * * *
40423906 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAATCCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
* *
40423971 TCGGGGATTTAGTGGCATTTTTAAGCAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
*
40424020 TTCGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCG-TTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
40424084 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
*
40424133 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
*
40424198 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCATGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
40424247 TTAGCGGCGTCTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
* * *
40424312 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGTTTAAGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
*
40424361 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
* *
40424426 TCGGGGATTTTGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCATGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* ** *
40424475 TTAGCGGCGTTTTTGGGAAAGCACCGCAAAAATATTTAAGCCCAACGACACCGTTTTCTAAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
* * * *
40424540 TCGGGGATTTAGTGACATTTTTAAATAAGCACCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
40424589 TTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
*
40424654 TCAGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * *
40424703 TTAGTGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
* * * *
40424768 TCGGGAATTTAGTGGCGTTTTTAAGTAAACGTCGCTAATGCTCAGTGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * **
40424817 TTAGCGGCGTTTTTGGGAAATCGCCGCAAAAATACCTAAGCCCAACAACACAATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
* *
40424882 TCGGGAATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGAT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * ** *
40424931 TTAGCGGCGTTTTTGAGAAAGCGCCG-AGAAAAAACCTAAGCCCAACGACGTCGTTTTCTTAGCT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCA-AAAATACCTAAGCCCAACGACACCGTTTTCTGAGCT
* *
40424995 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
40425045 T
1 T
40425046 AAAATAATTT
Statistics
Matches: 1042, Mismatches: 93, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
113 134 0.13
114 907 0.87
115 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACACCGTTTTCTGAGCTT
TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
Found at i:40425623 original size:14 final size:15
Alignment explanation
Indices: 40425595--40425627 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40425585 AAGTTTTATA
40425595 GATTATGGAATTAGG
1 GATTATGGAATTAGG
40425610 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
40425624 GATT
1 GATT
40425628 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:40425884 original size:82 final size:83
Alignment explanation
Indices: 40425714--40425932 Score: 242
Period size: 89 Copynumber: 2.6 Consensus size: 83
40425704 TTAGGTTAGA
* *
40425714 GTTTAGGGTTTAGATTAATTAGTGTGTTTTAA-TTATATATTAAATAAGGTTTAGGGGTTAGGGA
1 GTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGA
* **
40425778 TTCGGGGTCGAGTTTAAG
66 TTAGGGGTCGAGGGTAAG
* *
40425796 GTTTAGGGTTTAGATCAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGG
1 GTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGA
* * * *
40425861 TTAGGGATTTGGGGTCGTGTTAGG
66 TTAGGG--GTCGAG--G-G-TAAG
* * **
40425885 GTTTAAGATTTAGATTAATTAGTACTTTTTAATTTATATATTAAATAA
1 GTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA
40425933 GTTCTTTATA
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
82 30 0.26
83 35 0.31
85 3 0.03
89 46 0.40
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (83 bp):
GTTTAGGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGA
TTAGGGGTCGAGGGTAAG
Found at i:40425919 original size:89 final size:90
Alignment explanation
Indices: 40425764--40425932 Score: 259
Period size: 89 Copynumber: 1.9 Consensus size: 90
40425754 TAAATAAGGT
* * **
40425764 TTAGGGGTTAGGGATTCGGGGTCGAGTTTAAGGTTTAGGGTTTAGATCAATTAGTGTTTTTTAAT
1 TTAGGGGTTAGGGATTCGGGGTCGAGTTTAAGGTTTAAGATTTAGATCAATTAGTACTTTTTAAT
40425829 TTATATATTAAATAAAGTTTAGGGG
66 TTATATATTAAATAAAGTTTAGGGG
* * * *
40425854 TTAGGGGTTAGGGATTTGGGGTCGTG-TTAGGGTTTAAGATTTAGATTAATTAGTACTTTTTAAT
1 TTAGGGGTTAGGGATTCGGGGTCGAGTTTAAGGTTTAAGATTTAGATCAATTAGTACTTTTTAAT
40425918 TTATATATTAAATAA
66 TTATATATTAAATAA
40425933 GTTCTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 47 0.66
90 24 0.34
ACGTcount: A:0.28, C:0.03, G:0.27, T:0.43
Consensus pattern (90 bp):
TTAGGGGTTAGGGATTCGGGGTCGAGTTTAAGGTTTAAGATTTAGATCAATTAGTACTTTTTAAT
TTATATATTAAATAAAGTTTAGGGG
Found at i:40426012 original size:21 final size:21
Alignment explanation
Indices: 40425959--40426012 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
40425949 TAAAGATTAT
40425959 TAATTTAAAA-TTGATATGAA
1 TAATTTAAAATTTGATATGAA
*
40425979 -ATATATAATAATTTGAATAT-AA
1 TA-ATTTAA-AATTTG-ATATGAA
40426001 TAATTTAAAATT
1 TAATTTAAAATT
40426013 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 6 0.22
22 10 0.37
23 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATGAA
Found at i:40426027 original size:8 final size:8
Alignment explanation
Indices: 40426002--40426045 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
40425992 TGAATATAAT
40426002 AATT-TAA
1 AATTGTAA
40426009 AATTGTAAA
1 AATTGT-AA
40426018 AATTGTAA
1 AATTGTAA
40426026 AATTGTAAAA
1 AATTGT--AA
40426036 AATTGTAA
1 AATTGTAA
40426044 AA
1 AA
40426046 ATTATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 4 0.12
8 13 0.39
9 8 0.24
10 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (8 bp):
AATTGTAA
Found at i:40426039 original size:10 final size:9
Alignment explanation
Indices: 40426007--40426055 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
40425997 ATAATAATTT
40426007 AAAATTGTA
1 AAAATTGTA
40426016 AAAATTGT-
1 AAAATTGTA
40426024 AAAATTGTAA
1 AAAATTGT-A
40426034 AAAATTGTA
1 AAAATTGTA
*
40426043 AAAATTATA
1 AAAATTGTA
40426052 AAAA
1 AAAA
40426056 ATAAAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.22
9 21 0.57
10 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (9 bp):
AAAATTGTA
Found at i:40426157 original size:47 final size:48
Alignment explanation
Indices: 40426085--40426175 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
40426075 GAAAAAGAAA
** *
40426085 TAAAAACACTAAAATTTTTATTTTTACCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACT
*
40426133 TAAAAA-ACTAAAATTGATAATTTTATCTAATTTTTATAAATAT
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATAT
40426176 GACCTAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 33 0.85
48 6 0.15
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (48 bp):
TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATATTACT
Found at i:40427473 original size:21 final size:21
Alignment explanation
Indices: 40427430--40427476 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40427420 TTAAATTTGA
* *
40427430 AATTTTACAATTTAATCATCT
1 AATTTTACAATATAATCAACT
* *
40427451 AATTTTACAATATCATTAACT
1 AATTTTACAATATAATCAACT
40427472 AATTT
1 AATTT
40427477 AAATAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTACAATATAATCAACT
Found at i:40428776 original size:41 final size:41
Alignment explanation
Indices: 40428731--40428877 Score: 111
Period size: 41 Copynumber: 3.4 Consensus size: 41
40428721 AAAAAATGTC
40428731 CAACTTAATAACTTATATAATTCACATAATAACTTACATAA
1 CAACTTAATAACTTATATAATTCACATAATAACTTACATAA
* * * * *
40428772 CAACTTAACAACTCACATAATTTACATAATACATATATATATGTCATACCATA
1 CAACTTAATAACTTATATAATTCACATAAT--A-A-CT-TA---CAT---A-A
*
40428825 TAACTTAATAACTTATATAATTCACATAATAACTTACAT--
1 CAACTTAATAACTTATATAATTCACATAATAACTTACATAA
40428864 -AACTTAATAACTTA
1 CAACTTAATAACTTA
40428878 ACAACTTACA
Statistics
Matches: 83, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
38 14 0.17
41 26 0.31
43 1 0.01
44 1 0.01
45 4 0.05
46 2 0.02
48 2 0.02
49 4 0.05
50 1 0.01
51 1 0.01
52 1 0.01
53 26 0.31
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.35
Consensus pattern (41 bp):
CAACTTAATAACTTATATAATTCACATAATAACTTACATAA
Found at i:40428837 original size:8 final size:8
Alignment explanation
Indices: 40428824--40428907 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
40428814 GTCATACCAT
40428824 ATAACTTA
1 ATAACTTA
40428832 ATAACTTA
1 ATAACTTA
*
40428840 TATAA-TTC
1 -ATAACTTA
*
40428848 A-CA-T-A
1 ATAACTTA
40428853 ATAACTTA
1 ATAACTTA
40428861 CATAACTTA
1 -ATAACTTA
40428870 ATAACTTA
1 ATAACTTA
*
40428878 ACAACTTA
1 ATAACTTA
*
40428886 CATAATTTA
1 -ATAACTTA
*
40428895 CATAACTAA
1 -ATAACTTA
40428904 ATAA
1 ATAA
40428908 TTTTAAAACA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 2 0.03
8 30 0.49
9 25 0.41
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAACTTA
Found at i:40428844 original size:17 final size:17
Alignment explanation
Indices: 40428824--40428907 Score: 64
Period size: 17 Copynumber: 4.7 Consensus size: 17
40428814 GTCATACCAT
*
40428824 ATAACTTAATAACTTAT
1 ATAACTTAATAACTTAC
40428841 ATAA-TTCACATAATAACTTAC
1 ATAACTT-A-AT---AACTTAC
40428862 ATAACTTAATAACTTA-
1 ATAACTTAATAACTTAC
* *
40428878 ACAACTTACATAATTTAC
1 ATAACTTA-ATAACTTAC
*
40428896 ATAACTAAATAA
1 ATAACTTAATAA
40428908 TTTTAAAACA
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
16 9 0.17
17 22 0.41
18 8 0.15
20 2 0.04
21 11 0.20
22 2 0.04
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAACTTAATAACTTAC
Found at i:40428856 original size:29 final size:29
Alignment explanation
Indices: 40428732--40428873 Score: 112
Period size: 32 Copynumber: 4.7 Consensus size: 29
40428722 AAAAATGTCC
40428732 AACTTAATAACTTATATAATTCACATAAT
1 AACTTAATAACTTATATAATTCACATAAT
* *
40428761 AACTTACATAACAACTTA-ACAACTCACATAATT
1 AACTTA-AT---AACTTATATAATTCACATAA-T
* * *
40428794 TACATAAT-ACATATATATATGTCATACCAT-AT
1 AACTTAATAACTTATATA-AT-TC--A-CATAAT
40428826 AACTTAATAACTTATATAATTCACATAAT
1 AACTTAATAACTTATATAATTCACATAAT
40428855 AACTTACATAACTTA-ATAA
1 AACTTA-ATAACTTATATAA
40428874 CTTAACAACT
Statistics
Matches: 89, Mismatches: 10, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
28 7 0.08
29 21 0.24
30 11 0.12
31 4 0.04
32 22 0.25
33 21 0.24
34 3 0.03
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.35
Consensus pattern (29 bp):
AACTTAATAACTTATATAATTCACATAAT
Found at i:40428865 original size:9 final size:9
Alignment explanation
Indices: 40428853--40428901 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
40428843 AATTCACATA
40428853 ATAACTTAC
1 ATAACTTAC
40428862 ATAACTTA-
1 ATAACTTAC
40428870 ATAACTTA-
1 ATAACTTAC
*
40428878 ACAACTTAC
1 ATAACTTAC
*
40428887 ATAATTTAC
1 ATAACTTAC
40428896 ATAACT
1 ATAACT
40428902 AAATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 15 0.43
9 20 0.57
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40429025 original size:17 final size:17
Alignment explanation
Indices: 40429003--40429074 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
40428993 ATAACTCACA
40429003 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
40429020 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
40429037 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
40429053 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
40429071 TAAT
1 TAAT
40429075 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:40429047 original size:25 final size:26
Alignment explanation
Indices: 40429011--40429074 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
40429001 CATAATAACT
*
40429011 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
40429036 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
40429062 TACATAACTTAAT
1 TACATAACTTAAT
40429075 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:40429619 original size:43 final size:43
Alignment explanation
Indices: 40429553--40429701 Score: 217
Period size: 43 Copynumber: 3.5 Consensus size: 43
40429543 CACCAAACAA
* * *
40429553 TAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGAACATGGCCTT
1 TAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTT
*
40429596 TAGCAGCATTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTT
* * * *
40429639 TAGCGGCGTTTGTGGGAAAAGCACCGCTAATGAACATGGCCTT
1 TAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTT
*
40429682 TAGCAGCGTTTGTAGAAAAA
1 TAGCAGCGTTTGTGGAAAAA
40429702 AATGCCGCAA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.23
Consensus pattern (43 bp):
TAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTT
Found at i:40441288 original size:23 final size:22
Alignment explanation
Indices: 40441262--40441306 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40441252 AAGTAAATAT
40441262 ACTAAATTCCTTAAA-ATAAAAAA
1 ACTAAATT--TTAAATATAAAAAA
*
40441285 ACTAAGTTTTAAATATAAAAAA
1 ACTAAATTTTAAATATAAAAAA
40441307 TACACGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (22 bp):
ACTAAATTTTAAATATAAAAAA
Found at i:40441852 original size:20 final size:20
Alignment explanation
Indices: 40441814--40441851 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40441804 TCAATTAAGT
*
40441814 TAAATTTAAATAGTTTTTTA
1 TAAATTAAAATAGTTTTTTA
40441834 TAAATTAAAATA-TTTTTT
1 TAAATTAAAATAGTTTTTT
40441852 TGTTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TAAATTAAAATAGTTTTTTA
Found at i:40451190 original size:28 final size:28
Alignment explanation
Indices: 40451146--40451199 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40451136 TTGATTTTTA
* * *
40451146 ATTTTTTATTTTCAATTGTCAATTCTCG
1 ATTTTTTATTCTAAATTGTAAATTCTCG
*
40451174 ATTTTTTATTCTAAATTTTAAATTCT
1 ATTTTTTATTCTAAATTGTAAATTCT
40451200 AAAATCTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (28 bp):
ATTTTTTATTCTAAATTGTAAATTCTCG
Found at i:40451197 original size:7 final size:7
Alignment explanation
Indices: 40451181--40451225 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
40451171 TCGATTTTTT
40451181 ATTCTAA
1 ATTCTAA
*
40451188 ATTTTAA
1 ATTCTAA
40451195 ATTCTAA
1 ATTCTAA
*
40451202 AATCTAA
1 ATTCTAA
*
40451209 AATCTAA
1 ATTCTAA
40451216 ATTCTCAA
1 ATTCT-AA
40451224 AT
1 AT
40451226 CTTTTCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
7 29 0.88
8 4 0.12
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (7 bp):
ATTCTAA
Found at i:40451207 original size:21 final size:21
Alignment explanation
Indices: 40451183--40451227 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40451173 GATTTTTTAT
* *
40451183 TCTAAATTTTAAATTCTAAAA
1 TCTAAAATCTAAATTCTAAAA
*
40451204 TCTAAAATCTAAATTCTCAAA
1 TCTAAAATCTAAATTCTAAAA
40451225 TCT
1 TCT
40451228 TTTCTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (21 bp):
TCTAAAATCTAAATTCTAAAA
Found at i:40451389 original size:51 final size:52
Alignment explanation
Indices: 40451328--40451427 Score: 159
Period size: 51 Copynumber: 1.9 Consensus size: 52
40451318 AAATGGTAAT
*
40451328 AAAATATTATTAAATTATTAAAT-TATAATTAGTTAATTATTATGTTGTTAAG
1 AAAATATTATTAAATTATTAAATCT-TAAATAGTTAATTATTATGTTGTTAAG
*
40451380 AAAAT-TTATTAAATTATTTAATCTTAAATAGTTAATTATTATGTTGTT
1 AAAATATTATTAAATTATTAAATCTTAAATAGTTAATTATTATGTTGTT
40451428 TAGATTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 39 0.87
52 6 0.13
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (52 bp):
AAAATATTATTAAATTATTAAATCTTAAATAGTTAATTATTATGTTGTTAAG
Found at i:40461379 original size:28 final size:28
Alignment explanation
Indices: 40461335--40461456 Score: 172
Period size: 28 Copynumber: 4.4 Consensus size: 28
40461325 CAGTACAGTA
40461335 TGGGCCTTAGCCCAATACAACAACAATG
1 TGGGCCTTAGCCCAATACAACAACAATG
* *
40461363 TGGGTCTTAGCCGAATACAACAACAATG
1 TGGGCCTTAGCCCAATACAACAACAATG
**
40461391 TGGGCCTTAGCCCAATACAGTAACAATG
1 TGGGCCTTAGCCCAATACAACAACAATG
* * **
40461419 TGGGCCTTAGCCTAAAACATTAACAATG
1 TGGGCCTTAGCCCAATACAACAACAATG
40461447 TGGGCCTTAG
1 TGGGCCTTAG
40461457 GCCTAAGCAG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 85 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATACAACAACAATG
Found at i:40461617 original size:26 final size:26
Alignment explanation
Indices: 40461576--40461652 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
40461566 AATACACCAA
*
40461576 TATCTCAGCAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCTAGTAACAG
* *
40461602 TATTGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCTAGTAACAG
* *
40461628 TATCGCAACAAAACTG-TCAGTAACA
1 TATCGCAGCAAAGCTGCT-AGTAACA
40461653 ATATACTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCTAGTAACAG
Found at i:40461824 original size:27 final size:28
Alignment explanation
Indices: 40461775--40461879 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 28
40461765 AAAGCCATAT
* * * *
40461775 AGTCATTTCATCTTCTAGTGGTATAAT-
1 AGTCATTTTATCCTATAGGGGTATAATC
*
40461802 AGTCATTTTATCCTATAGGGGTAT-TTC
1 AGTCATTTTATCCTATAGGGGTATAATC
* * *
40461829 GGTCATTTTACCCTATAGGGGTA-ATTC
1 AGTCATTTTATCCTATAGGGGTATAATC
* *
40461856 AGTCATTTTAACCTATAGAGGTAT
1 AGTCATTTTATCCTATAGGGGTAT
40461880 TTCGATCATT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 64 0.98
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (28 bp):
AGTCATTTTATCCTATAGGGGTATAATC
Found at i:40461864 original size:54 final size:53
Alignment explanation
Indices: 40461802--40462343 Score: 336
Period size: 54 Copynumber: 10.2 Consensus size: 53
40461792 GTGGTATAAT
*
40461802 AGTCATTTTATCCTATAGGGGTATTTCGGTCATTTTACCCTATAG-GGGTAATTC
1 AGTCATTTTA-CCTATAGGGGTATTTCGGTCATTTTACCCT-TAGAGGGTATTTC
* *
40461856 AGTCATTTTAACCTATAGAGGTATTTCGATCA-TTT---C----A-GGTATTTC
1 AGTCATTTT-ACCTATAGGGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
* * * **
40461901 -GATCATTTTACCTTTTA-GAGTATTTTGGTCATTTTACCC-TATGAGGGTAACTC
1 AG-TCATTTTACC-TATAGGGGTATTTCGGTCATTTTACCCTTA-GAGGGTATTTC
* * * * *
40461954 GGTCATTTTACCATATGGGGGTATTTTGGTCATTTTTA-CCTTCGGGGGTATTTC
1 AGTCATTTTACC-TATAGGGGTATTTCGGTCA-TTTTACCCTTAGAGGGTATTTC
* * * * * * *
40462008 AGTTATTTCACCCTTTGGGGGTATTTCGGTTATTTTACCCTTTGGGGGTATTTC
1 AGTCATTTTA-CCTATAGGGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
* * * * * *
40462062 -GATCATTTTACCCATCGAGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTT
1 AG-TCATTTTACCTATAG-GGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
* * * * *
40462116 AGTCATTTTACCCAGTAGGGGTATTTTGATTATTTTACCCTTTGAGGGTATTTC
1 AGTCATTTTACCTA-TAGGGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
* * *
40462170 -GCTCATTTTACCCT-TCAAGGGTATTTTAGGTCATTTTACCCTTCGAGGGTATTTC
1 AG-TCATTTTA-CCTAT-AGGGGTA-TTTCGGTCATTTTACCCTTAGAGGGTATTTC
* * * *
40462225 -GATTATTTTATCCT-TCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTC
1 AG-TCATTTTA-CCTATAG-GGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
* * * **
40462279 TA-TCATTTTACCCT-TCGAAGGCATTTCGGTCATTTTACCCTCCGAGGGTATTTC
1 -AGTCATTTTA-CCTATAG-GGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
40462333 -GATCATTTTAC
1 AG-TCATTTTAC
40462344 TCGTCAGGGG
Statistics
Matches: 401, Mismatches: 55, Indels: 65
0.77 0.11 0.12
Matches are distributed among these distances:
44 14 0.03
45 20 0.05
48 1 0.00
50 1 0.00
52 1 0.00
53 34 0.08
54 272 0.68
55 58 0.14
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.44
Consensus pattern (53 bp):
AGTCATTTTACCTATAGGGGTATTTCGGTCATTTTACCCTTAGAGGGTATTTC
Found at i:40461888 original size:27 final size:26
Alignment explanation
Indices: 40461804--40462343 Score: 246
Period size: 27 Copynumber: 20.3 Consensus size: 26
40461794 GGTATAATAG
* * *
40461804 TCATTTTATCCTATAGGGGTATTTCGG
1 TCATTTTACCCT-TAGAGGTATTTCGA
* *
40461831 TCATTTTACCCTATAGGGGTAATTC-A
1 TCATTTTACCCT-TAGAGGTATTTCGA
*
40461857 GTCATTTTAACCTATAGAGGTATTTCGA
1 -TCATTTTACCCT-TAGAGGTATTTCGA
40461885 TCA-TTT---C----AGGTATTTCGA
1 TCATTTTACCCTTAGAGGTATTTCGA
* * *
40461903 TCATTTTACCTTTTAGA-GTATTTTGG
1 TCATTTTACC-CTTAGAGGTATTTCGA
** *
40461929 TCATTTTACCC-TATGAGGGTAACTCGG
1 TCATTTTACCCTTA-GA-GGTATTTCGA
* * * * *
40461956 TCATTTTACCATATGGGGGTATTTTGG
1 TCATTTTACCCT-TAGAGGTATTTCGA
* *
40461983 TCATTTTTA-CCTTCGGGGGTATTTC-A
1 TCA-TTTTACCCTT-AGAGGTATTTCGA
* * * * *
40462009 GTTATTTCACCCTTTGGGGGTATTTCGG
1 -TCATTTTACCC-TTAGAGGTATTTCGA
* * *
40462037 TTATTTTACCCTTTGGGGGTATTTCGA
1 TCATTTTACCC-TTAGAGGTATTTCGA
* * * *
40462064 TCATTTTACCCATCGAGGGTATTTTGG
1 TCATTTTACCCTTAGA-GGTATTTCGA
* * *
40462091 TTATTTTACCCTTTGAGGGTATTT-TA
1 TCATTTTACCCTTAGA-GGTATTTCGA
* * *
40462117 GTCATTTTACCCAGTAGGGGTATTTTGA
1 -TCATTTTACCC-TTAGAGGTATTTCGA
* * *
40462145 TTATTTTACCCTTTGAGGGTATTTCGC
1 TCATTTTACCCTTAGA-GGTATTTCGA
* *
40462172 TCATTTTACCCTTCA-AGGGTATTTTAGG
1 TCATTTTACCCTT-AGA-GGTA-TTTCGA
*
40462200 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTAGA-GGTATTTCGA
* * * *
40462227 TTATTTTATCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTAGA-GGTATTTCGA
* * *
40462254 TTATTTTACCCTTCGAGGGTATTTCTA
1 TCATTTTACCCTTAGA-GGTATTTCGA
* * *
40462281 TCATTTTACCCTTCGAAGGCATTTCGG
1 TCATTTTACCCTTAG-AGGTATTTCGA
**
40462308 TCATTTTACCCTCCGAGGGTATTTCGA
1 TCATTTTACCCTTAGA-GGTATTTCGA
40462335 TCATTTTAC
1 TCATTTTAC
40462344 TCGTCAGGGG
Statistics
Matches: 412, Mismatches: 69, Indels: 64
0.76 0.13 0.12
Matches are distributed among these distances:
18 14 0.03
19 3 0.01
23 1 0.00
24 2 0.00
25 2 0.00
26 30 0.07
27 323 0.78
28 36 0.09
29 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.44
Consensus pattern (26 bp):
TCATTTTACCCTTAGAGGTATTTCGA
Found at i:40461895 original size:18 final size:18
Alignment explanation
Indices: 40461874--40461908 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40461864 TAACCTATAG
40461874 AGGTATTTCGATCATTTC
1 AGGTATTTCGATCATTTC
40461892 AGGTATTTCGATCATTT
1 AGGTATTTCGATCATTT
40461909 TACCTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (18 bp):
AGGTATTTCGATCATTTC
Found at i:40461960 original size:71 final size:72
Alignment explanation
Indices: 40461821--40461961 Score: 160
Period size: 71 Copynumber: 2.0 Consensus size: 72
40461811 ATCCTATAGG
* * **
40461821 GGTATTTCGGTCATTTTACCCTATAGGGGTAATTCAGTCATTTTAACCTATAGAGGTATTTCGAT
1 GGTATTTCGATCATTTTACCCTATAGGAGTAATTCAGTCATTTTAACCTATAGAGGTAACTCGAT
40461886 CATTTCA
66 CATTTCA
* * * ** * *
40461893 GGTATTTCGATCATTTTACCTTTTA-GAGTATTTTGGTCATTTTACCCTAT-GAGGGTAACTCGG
1 GGTATTTCGATCATTTTACCCTATAGGAGTAATTCAGTCATTTTAACCTATAGA-GGTAACTCGA
40461956 TCATTT
65 TCATTT
40461962 TACCATATGG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
70 2 0.04
71 33 0.58
72 22 0.39
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (72 bp):
GGTATTTCGATCATTTTACCCTATAGGAGTAATTCAGTCATTTTAACCTATAGAGGTAACTCGAT
CATTTCA
Found at i:40462333 original size:81 final size:81
Alignment explanation
Indices: 40461893--40462368 Score: 444
Period size: 81 Copynumber: 5.9 Consensus size: 81
40461883 GATCATTTCA
** * * * ** **
40461893 GGTATTTCGATCATTTTA-CCTTTTAGAGTATTTTGGTCATTTTACCCTAT-GAGGGTAACTCGG
1 GGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCT-TCGAGGGTATTTTAG
* *
40461956 TCATTTTACCATAT-GGG
65 TCATTTTACCCT-TCGAG
* * * * * * * **
40461973 GGTATTTTGGTCATTTTTA-CCTTCGGGGGTATTTCAGTTATTTCACCCTTTGGGGGTATTTCGG
1 GGTATTTCGATCA-TTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTTAG
* * *
40462037 TTATTTTACCCTTTGGG
65 TCATTTTACCCTTCGAG
* * *
40462054 GGTATTTCGATCATTTTACCCATCGAGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTTAGT
1 GGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTTAGT
* *
40462119 CATTTTACCCAGTAG-G
66 CATTTTACCC-TTCGAG
* * * * * *
40462135 GGTATTTTGATTATTTTACCCTTTGAGGGTATTTCGCTCATTTTACCCTTCAAGGGTATTTTAGG
1 GGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTTA-G
40462200 TCATTTTACCCTTCGAG
65 TCATTTTACCCTTCGAG
* *
40462217 GGTATTTCGATTATTTTATCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTCTA-
1 GGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTT-TAG
*
40462281 TCATTTTACCCTTCGAA
65 TCATTTTACCCTTCGAG
* * * * * * *
40462298 GGCATTTCGGTCATTTTACCCTCCGAGGGTATTTCGATCATTTTACTCGTC-AGGGGTATTTTAG
1 GGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGA-GGGTATTTTAG
40462362 TCATTTT
65 TCATTTT
40462369 CCCACAAATC
Statistics
Matches: 331, Mismatches: 55, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
80 21 0.06
81 238 0.72
82 70 0.21
83 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (81 bp):
GGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTTAGT
CATTTTACCCTTCGAG
Found at i:40462358 original size:27 final size:27
Alignment explanation
Indices: 40461893--40462343 Score: 385
Period size: 27 Copynumber: 16.7 Consensus size: 27
40461883 GATCATTTCA
**
40461893 GGTATTTCGATCATTTTA-CCTTTTAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* * *
40461919 AGTATTTTGGTCATTTTACCCTAT-GAG
1 GGTATTTCGATCATTTTACCCT-TCGAG
** * * *
40461946 GGTAACTCGGTCATTTTACCATAT-GGG
1 GGTATTTCGATCATTTTACCCT-TCGAG
* * *
40461973 GGTATTTTGGTCATTTTTA-CCTTCGGG
1 GGTATTTCGATCA-TTTTACCCTTCGAG
* * * *
40462000 GGTATTTC-AGTTATTTCACCCTTTGGG
1 GGTATTTCGA-TCATTTTACCCTTCGAG
* * * *
40462027 GGTATTTCGGTTATTTTACCCTTTGGG
1 GGTATTTCGATCATTTTACCCTTCGAG
*
40462054 GGTATTTCGATCATTTTACCCATCGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* * * *
40462081 GGTATTTTGGTTATTTTACCCTTTGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* * *
40462108 GGTATTT-TAGTCATTTTACCCAGTAG-G
1 GGTATTTCGA-TCATTTTACCC-TTCGAG
* * *
40462135 GGTATTTTGATTATTTTACCCTTTGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* *
40462162 GGTATTTCGCTCATTTTACCCTTCAAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* *
40462189 GGTATTTTAGGTCATTTTACCCTTCGAG
1 GGTA-TTTCGATCATTTTACCCTTCGAG
* *
40462217 GGTATTTCGATTATTTTATCCTTCGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* *
40462244 GGTATTTCGGTTATTTTACCCTTCGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* *
40462271 GGTATTTCTATCATTTTACCCTTCGAA
1 GGTATTTCGATCATTTTACCCTTCGAG
* * *
40462298 GGCATTTCGGTCATTTTACCCTCCGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
40462325 GGTATTTCGATCATTTTAC
1 GGTATTTCGATCATTTTAC
40462344 TCGTCAGGGG
Statistics
Matches: 348, Mismatches: 65, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
26 22 0.06
27 293 0.84
28 33 0.09
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
GGTATTTCGATCATTTTACCCTTCGAG
Found at i:40462365 original size:54 final size:54
Alignment explanation
Indices: 40461893--40462368 Score: 441
Period size: 54 Copynumber: 8.8 Consensus size: 54
40461883 GATCATTTCA
* * *
40461893 GGTATTTCGATCATTTTACCTTTTA-GAGTATTTTGGTCATTTTACCCTAT-GAG
1 GGTATTTCGATCATTTTACCCTTCAGGGGTATTTTGGTCATTTTACCCT-TCGAG
** * * * *
40461946 GGTAACTCGGTCATTTTACCATAT-GGGGGTATTTTGGTCATTTTTA-CCTTCGGG
1 GGTATTTCGATCATTTTACCCT-TCAGGGGTATTTTGGTCA-TTTTACCCTTCGAG
* * ** * * * *
40462000 GGTATTTC-AGTTATTTCACCCTTTGGGGGTATTTCGGTTATTTTACCCTTTGGG
1 GGTATTTCGA-TCATTTTACCCTTCAGGGGTATTTTGGTCATTTTACCCTTCGAG
* * *
40462054 GGTATTTCGATCATTTTACCCATC-GAGGGTATTTTGGTTATTTTACCCTTTGAG
1 GGTATTTCGATCATTTTACCCTTCAG-GGGTATTTTGGTCATTTTACCCTTCGAG
* * * * *
40462108 GGTATTT-TAGTCATTTTACCCAGT-AGGGGTATTTTGATTATTTTACCCTTTGAG
1 GGTATTTCGA-TCATTTTACCC-TTCAGGGGTATTTTGGTCATTTTACCCTTCGAG
* *
40462162 GGTATTTCGCTCATTTTACCCTTCAAGGGTATTTTAGGTCATTTTACCCTTCGAG
1 GGTATTTCGATCATTTTACCCTTCAGGGGTATTTT-GGTCATTTTACCCTTCGAG
* * * *
40462217 GGTATTTCGATTATTTTATCCTTC-GAGGGTATTTCGGTTATTTTACCCTTCGAG
1 GGTATTTCGATCATTTTACCCTTCAG-GGGTATTTTGGTCATTTTACCCTTCGAG
* * * * *
40462271 GGTATTTCTATCATTTTACCCTTC-GAAGGCATTTCGGTCATTTTACCCTCCGAG
1 GGTATTTCGATCATTTTACCCTTCAG-GGGTATTTTGGTCATTTTACCCTTCGAG
* * *
40462325 GGTATTTCGATCATTTTACTCGTCAGGGGTATTTTAGTCATTTT
1 GGTATTTCGATCATTTTACCCTTCAGGGGTATTTTGGTCATTTT
40462369 CCCACAAATC
Statistics
Matches: 354, Mismatches: 52, Indels: 33
0.81 0.12 0.08
Matches are distributed among these distances:
53 28 0.08
54 272 0.77
55 54 0.15
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (54 bp):
GGTATTTCGATCATTTTACCCTTCAGGGGTATTTTGGTCATTTTACCCTTCGAG
Found at i:40463288 original size:68 final size:68
Alignment explanation
Indices: 40463200--40463334 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
40463190 TCAACTCCCT
*
40463200 CTATGACCAGCTCAAACTCCATTTAACAGTGTTCTATTCCAACTCTACCACCTACCCAGCTCAAG
1 CTATGACCAGCTCAAACTCCATTTAACAGTGTTCTATTCCAACTCCACCACCTACCCAGCTCAAG
40463265 CAA
66 CAA
* * *
40463268 CTATGACCGGTTCAAACTCCATTTAACAGTGTTCTATTCCAACTCCACCATCTACCCAGCTCAAG
1 CTATGACCAGCTCAAACTCCATTTAACAGTGTTCTATTCCAACTCCACCACCTACCCAGCTCAAG
40463333 CA
66 CA
40463335 GCAAAATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.26
Consensus pattern (68 bp):
CTATGACCAGCTCAAACTCCATTTAACAGTGTTCTATTCCAACTCCACCACCTACCCAGCTCAAG
CAA
Found at i:40464734 original size:28 final size:28
Alignment explanation
Indices: 40464685--40464848 Score: 222
Period size: 28 Copynumber: 5.9 Consensus size: 28
40464675 CTATTCAGTA
* *
40464685 ACAGT-ACAGTGTGGACCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* * *
40464712 ATAGCAACAATGTGAGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
**
40464740 ACAACAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* * *
40464768 ACAGTAACAATGTGGGTCTTATCCTAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
40464796 ATAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
40464824 ACAGTAACAATGTGGGCCTTAGCCC
1 ACAGTAACAATGTGGGCCTTAGCCC
40464849 TAAACAATAT
Statistics
Matches: 118, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 3 0.03
28 115 0.97
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:40464998 original size:26 final size:26
Alignment explanation
Indices: 40464969--40465071 Score: 154
Period size: 26 Copynumber: 4.0 Consensus size: 26
40464959 CACCAATATT
* *
40464969 GCAGCAAAGCTGTCAGTAATAGAATC
1 GCAGCAAAGCTGTCAGTAACAGTATC
40464995 GCAGCAAAGCTG-CTAGTAACAGTATC
1 GCAGCAAAGCTGTC-AGTAACAGTATC
*
40465021 GCAGCAAAGTTGTCAGTAACAGTATC
1 GCAGCAAAGCTGTCAGTAACAGTATC
*
40465047 GCAGCAAAGCTGCCAGTAACAGTAT
1 GCAGCAAAGCTGTCAGTAACAGTAT
40465072 ACTTCCTCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
25 1 0.01
26 68 0.97
27 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (26 bp):
GCAGCAAAGCTGTCAGTAACAGTATC
Found at i:40465026 original size:52 final size:52
Alignment explanation
Indices: 40464969--40465071 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
40464959 CACCAATATT
* *
40464969 GCAGCAAAGCTGTCAGTAATAGAATCGCAGCAAAGCTGCTAGTAACAGTATC
1 GCAGCAAAGCTGTCAGTAACAGAATCGCAGCAAAGCTGCCAGTAACAGTATC
* *
40465021 GCAGCAAAGTTGTCAGTAACAGTATCGCAGCAAAGCTGCCAGTAACAGTAT
1 GCAGCAAAGCTGTCAGTAACAGAATCGCAGCAAAGCTGCCAGTAACAGTAT
40465072 ACTTCCTCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (52 bp):
GCAGCAAAGCTGTCAGTAACAGAATCGCAGCAAAGCTGCCAGTAACAGTATC
Found at i:40465721 original size:27 final size:26
Alignment explanation
Indices: 40465216--40465734 Score: 359
Period size: 27 Copynumber: 19.3 Consensus size: 26
40465206 GGGGTATAAA
* * *
40465216 GTCATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTACCCT-TCGGGGTATTTCG
* * * *
40465243 ATCATTTTATCCTAT-GGGGTAATTCA
1 GTCATTTTACCCT-TCGGGGTATTTCG
**
40465269 GTCATTTTACCCTAT-GAGGGTATTTTA
1 GTCATTTTACCCT-TCG-GGGTATTTCG
*
40465296 GTCATTTTACCCTTTGGGGTATTTCG
1 GTCATTTTACCCTTCGGGGTATTTCG
* * *
40465322 ATCATTTCACCCTTCGGGGTATTTTG
1 GTCATTTTACCCTTCGGGGTATTTCG
40465348 GTCATTTTACCCTAT-GGGAGTAATTT-G
1 GTCATTTTACCCT-TCGGG-GT-ATTTCG
* *
40465375 GTCATTTGACCCTATGGGGGTATTTCG
1 GTCATTTTACCCT-TCGGGGTATTTCG
*
40465402 GTCATTTCTTA--CTTCAAGGGTATTTCG
1 GTCA-TT-TTACCCTTC-GGGGTATTTCG
* * * *
40465429 GTTATTTCACCTTTTGGGGGTATTTCG
1 GTCATTTTACC-CTTCGGGGTATTTCG
* *
40465456 ATCATTTTA-CCTATCGAGGGTATTTTG
1 GTCATTTTACCCT-TCG-GGGTATTTCG
* *
40465483 GTCATTTTACCCTTTGAGGGTATTTCA
1 GTCATTTTACCCTTCG-GGGTATTTCG
* *
40465510 GTCACTTTACCCTGTAGGGGTATTTCG
1 GTCATTTTACCCT-TCGGGGTATTTCG
* ** *
40465537 ATTGTTTTACCCTTCGAGGGTATTTTTG
1 GTCATTTTACCCTTCG-GGGTA-TTTCG
* * *
40465565 GTTATTTTACCCTTTGAGGGCATTTCG
1 GTCATTTTACCCTTCG-GGGTATTTCG
* *
40465592 GTCATTTTTCCCTTCGAGGGTATTTTTG
1 GTCATTTTACCCTTCG-GGGTA-TTTCG
* * *
40465620 ATCATTTTACCTTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCG-GGGTATTTCG
* * * *
40465647 ATCATTTTACCCTTCGAAGGCATTTCA
1 GTCATTTTACCCTTCG-GGGTATTTCG
*
40465674 GTCATTTTACCCTCCGAGGGTATTTCG
1 GTCATTTTACCCTTCG-GGGTATTTCG
* *
40465701 GTCATTTTACCCTGTAGGGGTATTTCA
1 GTCATTTTACCCT-TCGGGGTATTTCG
40465728 GTCATTT
1 GTCATTT
40465735 GCCCACAAAT
Statistics
Matches: 401, Mismatches: 70, Indels: 42
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.01
26 79 0.20
27 255 0.64
28 62 0.15
29 2 0.00
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCCTTCGGGGTATTTCG
Found at i:40475475 original size:5 final size:5
Alignment explanation
Indices: 40475465--40475508 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
40475455 GATAGAAGAA
* *
40475465 AAAAG AAAAG AGAAG AAAAG AAAAG AAAAG AAAATG CAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG AAA
40475509 GGGGAGAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:40475485 original size:15 final size:15
Alignment explanation
Indices: 40475461--40475498 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
40475451 ACAGGATAGA
40475461 AGAA-AAAAGAAAAG
1 AGAAGAAAAGAAAAG
40475475 AGAAGAAAAGAAAAG
1 AGAAGAAAAGAAAAG
*
40475490 AAAAGAAAA
1 AGAAGAAAA
40475499 TGCAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAGAAAAG
Found at i:40475585 original size:10 final size:11
Alignment explanation
Indices: 40475548--40475583 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40475538 TTATAGGGAA
40475548 AAATAAAAATG
1 AAATAAAAATG
40475559 AAATAAAAATG
1 AAATAAAAATG
*
40475570 AAATTAAAA-G
1 AAATAAAAATG
40475580 AAAT
1 AAAT
40475584 TATCCTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (11 bp):
AAATAAAAATG
Found at i:40476246 original size:27 final size:29
Alignment explanation
Indices: 40476206--40476281 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 29
40476196 ATAAAATTCT
40476206 TAAAATTTA-A-AAAAACTA-AAATATTA
1 TAAAATTTATATAAAAACTATAAATATTA
*
40476232 -AAAATTTATAT-AAAATTATAAATATTA
1 TAAAATTTATATAAAAACTATAAATATTA
*
40476259 TAAAA-ATATAT-AAAACTTATAAA
1 TAAAATTTATATAAAAAC-TATAAA
40476282 AAATTCATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 8 0.19
26 7 0.17
27 17 0.40
28 10 0.24
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAATTTATATAAAAACTATAAATATTA
Found at i:40476248 original size:11 final size:9
Alignment explanation
Indices: 40476171--40476314 Score: 73
Period size: 10 Copynumber: 15.6 Consensus size: 9
40476161 TTTTCTCATA
*
40476171 AAAAATCAT
1 AAAAATTAT
*
40476180 AAAAAGTATT
1 AAAAATTA-T
*
40476190 AAAAA-AAT
1 AAAAATTAT
*
40476198 -AAAATTCT
1 AAAAATTAT
*
40476206 TAAAATT-T
1 AAAAATTAT
*
40476214 AAAAA-AACT
1 AAAAATTA-T
40476223 AAAATATTA-
1 AAAA-ATTAT
*
40476232 AAAATTTAT
1 AAAAATTAT
40476241 ATAAAATTAT
1 A-AAAATTAT
*
40476251 AAATATTAT
1 AAAAATTAT
40476260 AAAAATATAT
1 AAAAAT-TAT
*
40476270 AAAACTTAT
1 AAAAATTAT
40476279 AAAAAATTCAT
1 -AAAAATT-AT
* *
40476290 AATAAGTTCT
1 AA-AAATTAT
40476300 AATAAATTAT
1 AA-AAATTAT
40476310 AAAAA
1 AAAAA
40476315 AATTATAATT
Statistics
Matches: 104, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
7 4 0.04
8 10 0.10
9 41 0.39
10 42 0.40
11 7 0.07
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40476253 original size:28 final size:29
Alignment explanation
Indices: 40476222--40476348 Score: 104
Period size: 28 Copynumber: 4.4 Consensus size: 29
40476212 TTAAAAAAAC
*
40476222 TAAAATATTA-AAAATTTATATAAAATTA
1 TAAAAAATTATAAAATTTATATAAAATTA
* *
40476250 T-AAATATTATAAAA-ATATATAAAACTTA
1 TAAAAAATTATAAAATTTATATAAAA-TTA
40476278 TAAAAAATTCATAATAAGTTCTA-AT-AAATTA
1 TAAAAAATT-ATAA-AA-TT-TATATAAAATTA
**
40476309 TAAAAAAATTATAATTTTTA-ATAAAATTA
1 T-AAAAAATTATAAAATTTATATAAAATTA
*
40476338 TAAAACATTAT
1 TAAAAAATTAT
40476349 CGATTCCTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
27 17 0.20
28 22 0.27
29 15 0.18
30 4 0.05
31 10 0.12
32 11 0.13
33 2 0.02
34 2 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (29 bp):
TAAAAAATTATAAAATTTATATAAAATTA
Found at i:40476270 original size:19 final size:19
Alignment explanation
Indices: 40476223--40476283 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
40476213 TAAAAAAACT
*
40476223 AAAATAT-TAAAAATTTATA
1 AAAATATAT-AAAACTTATA
40476242 TAAAAT-TATAAATA-TTATA
1 -AAAATATATAAA-ACTTATA
40476261 AAAATATATAAAACTTATA
1 AAAATATATAAAACTTATA
40476280 AAAA
1 AAAA
40476284 ATTCATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.16
19 24 0.65
20 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATATAAAACTTATA
Found at i:40476279 original size:9 final size:8
Alignment explanation
Indices: 40476240--40476282 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
40476230 TAAAAATTTA
40476240 TATAAAAT
1 TATAAAAT
40476248 TATAAATAT
1 TATAAA-AT
40476257 TATAAAAAT
1 TAT-AAAAT
40476266 ATATAAAACT
1 -TATAAAA-T
40476276 TATAAAA
1 TATAAAA
40476283 AATTCATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.19
9 18 0.58
10 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
TATAAAAT
Found at i:40477176 original size:9 final size:9
Alignment explanation
Indices: 40477164--40477257 Score: 66
Period size: 10 Copynumber: 9.9 Consensus size: 9
40477154 GTTAAATACG
40477164 TTTTATTAAT
1 TTTTA-TAAT
40477174 TTTTATAATTT
1 TTTTATAA--T
40477185 TTTTATAAT
1 TTTTATAAT
40477194 TTTTATGAAT
1 TTTTAT-AAT
40477204 TTTTATAA-
1 TTTTATAAT
**
40477212 -TACATAAGT
1 TTTTATAA-T
*
40477221 TTTTATGATT
1 TTTTAT-AAT
*
40477231 TTTTTTATAT
1 TTTTATA-AT
*
40477241 TTTTATACT
1 TTTTATAAT
40477250 TTTTATAA
1 TTTTATAA
40477258 GTGTGAAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
7 5 0.08
9 21 0.32
10 30 0.45
11 10 0.15
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40477189 original size:11 final size:11
Alignment explanation
Indices: 40477173--40477197 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40477163 GTTTTATTAA
40477173 TTTTTATAATT
1 TTTTTATAATT
40477184 TTTTTATAATT
1 TTTTTATAATT
40477195 TTT
1 TTT
40477198 ATGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:40478885 original size:18 final size:17
Alignment explanation
Indices: 40478864--40478925 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
40478854 TTTTGGTTAA
*
40478864 AAATTAACCGAATTACC
1 AAATTAATCGAATTACC
40478881 TAAATTAATCGAATTAACC
1 -AAATTAATCGAATT-ACC
*
40478900 GAATTAATCGAATTAACC
1 AAATTAATCGAATT-ACC
*
40478918 GAATTAAT
1 AAATTAAT
40478926 TGAAGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 38 0.93
19 3 0.07
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (17 bp):
AAATTAATCGAATTACC
Found at i:40478895 original size:9 final size:9
Alignment explanation
Indices: 40478883--40478925 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
40478873 GAATTACCTA
40478883 AATTAATCG
1 AATTAATCG
*
40478892 AATTAACCG
1 AATTAATCG
40478901 AATTAATCG
1 AATTAATCG
*
40478910 AATTAACCG
1 AATTAATCG
40478919 AATTAAT
1 AATTAAT
40478926 TGAAGTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (9 bp):
AATTAATCG
Found at i:40478913 original size:27 final size:27
Alignment explanation
Indices: 40478865--40478924 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
40478855 TTTGGTTAAA
*
40478865 AATTAACCGAATTACCTAAATTAATCG
1 AATTAACCGAATTACCTAAATTAACCG
* *
40478892 AATTAACCGAATTA-ATCGAATTAACCG
1 AATTAACCGAATTACCT-AAATTAACCG
40478919 AATTAA
1 AATTAA
40478925 TTGAAGTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTACCTAAATTAACCG
Found at i:40479076 original size:18 final size:18
Alignment explanation
Indices: 40479053--40479124 Score: 99
Period size: 18 Copynumber: 3.9 Consensus size: 18
40479043 AATTTTTATG
40479053 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
40479071 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
* *
40479089 ATTGGGCTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
40479107 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
40479125 TTAGGTGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 39 0.83
19 8 0.17
ACGTcount: A:0.11, C:0.03, G:0.47, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:40482153 original size:20 final size:20
Alignment explanation
Indices: 40482130--40482186 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
40482120 TAATTTATCC
40482130 ATTTTAATTTTAATTTTAAT
1 ATTTTAATTTTAATTTTAAT
** *
40482150 ATTTTTGTTTTAAATTTAAT
1 ATTTTAATTTTAATTTTAAT
*
40482170 -TTTTACATTCTAATTTT
1 ATTTTA-ATTTTAATTTT
40482187 TCTTTAGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTAATTTTAATTTTAAT
Found at i:40482186 original size:26 final size:26
Alignment explanation
Indices: 40482130--40482186 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
40482120 TAATTTATCC
* * * *
40482130 ATTTTAATTTTAATTTTAATATTTTT
1 ATTTTAAATTTAATTTTAACATTCTA
* *
40482156 GTTTTAAATTTAATTTTTACATTCTA
1 ATTTTAAATTTAATTTTAACATTCTA
40482182 ATTTT
1 ATTTT
40482187 TCTTTAGTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTTAAATTTAATTTTAACATTCTA
Found at i:40485738 original size:40 final size:40
Alignment explanation
Indices: 40485686--40485882 Score: 214
Period size: 40 Copynumber: 4.9 Consensus size: 40
40485676 AAGGCGATAA
* * *
40485686 CACATACATTTCAGTGGAATCGGTAGGTATAGCTCGAAAG
1 CACATACATTTCAGTAGATTCAGTAGGTATAGCTCGAAAG
* * * *
40485726 CGCATACGTTTCAGTAGATTCAGTAAGTATGGCTCGAAAG
1 CACATACATTTCAGTAGATTCAGTAGGTATAGCTCGAAAG
* * * * *
40485766 CACATACATTTCAGTGGATTCAGTAGCTGTGGTTCGAAAAG
1 CACATACATTTCAGTAGATTCAGTAGGTATAGCTCG-AAAG
* *
40485807 CACATACATTTTAGTAGATTCAGTAGGTATAGCTCAAAAG
1 CACATACATTTCAGTAGATTCAGTAGGTATAGCTCGAAAG
* * * * *
40485847 AATATACATTTCAGTAGATTCAATAGATATCGCTCG
1 CACATACATTTCAGTAGATTCAGTAGGTATAGCTCG
40485883 TCTGAGCACC
Statistics
Matches: 128, Mismatches: 28, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
40 95 0.74
41 33 0.26
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (40 bp):
CACATACATTTCAGTAGATTCAGTAGGTATAGCTCGAAAG
Found at i:40485854 original size:81 final size:80
Alignment explanation
Indices: 40485687--40485882 Score: 221
Period size: 81 Copynumber: 2.4 Consensus size: 80
40485677 AGGCGATAAC
* * * * *
40485687 ACATACATTTCAGTGGAATCGGTAGGTATAGCTCGAAAGCGCATACGTTTCAGTAGATTCAGTAA
1 ACATACATTTCAGTGGATTCAGTAGCTATAGCTCGAAAGCACATACATTTCAGTAGATTCAGTAA
* * *
40485752 GTATGGCTCGAAAGC
66 GTATAGCTCAAAAGA
* * * *
40485767 ACATACATTTCAGTGGATTCAGTAGCTGTGGTTCGAAAAGCACATACATTTTAGTAGATTCAGTA
1 ACATACATTTCAGTGGATTCAGTAGCTATAGCTCG-AAAGCACATACATTTCAGTAGATTCAGTA
*
40485832 GGTATAGCTCAAAAGA
65 AGTATAGCTCAAAAGA
* * * * *
40485848 ATATACATTTCAGTAGATTCAATAGATATCGCTCG
1 ACATACATTTCAGTGGATTCAGTAGCTATAGCTCG
40485883 TCTGAGCACC
Statistics
Matches: 95, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
80 29 0.31
81 66 0.69
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (80 bp):
ACATACATTTCAGTGGATTCAGTAGCTATAGCTCGAAAGCACATACATTTCAGTAGATTCAGTAA
GTATAGCTCAAAAGA
Found at i:40490498 original size:59 final size:59
Alignment explanation
Indices: 40490431--40490551 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 59
40490421 CAATGAAACA
* * * * *
40490431 TAAGTTAGATTAGACCAATCAATATCATACTATTACAGGTTTATATGGCATGTCCATTC
1 TAAGTTAGATCAGACCAATCAATATCACACTATCACAGGTTCATATGGCATGTACATTC
* *
40490490 TAAGTTAGATCAGACCAATCAATATCACAGTATCACAGGTTCATATGGCATGTACTTTC
1 TAAGTTAGATCAGACCAATCAATATCACACTATCACAGGTTCATATGGCATGTACATTC
40490549 TAA
1 TAA
40490552 TCTTTCAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (59 bp):
TAAGTTAGATCAGACCAATCAATATCACACTATCACAGGTTCATATGGCATGTACATTC
Found at i:40493415 original size:12 final size:11
Alignment explanation
Indices: 40493390--40493422 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40493380 GGGCCCGGTG
40493390 TAATTGGG-TT
1 TAATTGGGTTT
40493400 TAATTTGGGTTT
1 TAA-TTGGGTTT
40493412 TAATTGGGTTT
1 TAATTGGGTTT
40493423 GGTATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 13 0.62
12 5 0.24
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (11 bp):
TAATTGGGTTT
Found at i:40493509 original size:9 final size:8
Alignment explanation
Indices: 40493480--40493528 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
40493470 GTTTTCATTA
40493480 TTTATATTT
1 TTTAT-TTT
*
40493489 TGTATTTT
1 TTTATTTT
40493497 TTTATTTT
1 TTTATTTT
*
40493505 GTTTATTTA
1 -TTTATTTT
*
40493514 TTTAATTT
1 TTTATTTT
40493522 TTTATTT
1 TTTATTT
40493529 GATTTGATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 22 0.67
9 11 0.33
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:40493533 original size:17 final size:16
Alignment explanation
Indices: 40493477--40493533 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
40493467 TTGGTTTTCA
*
40493477 TTATTTATATTTTGTAT
1 TTATTTA-ATTTTTTAT
* *
40493494 TTTTTTATTTTGTTTAT
1 TTATTTAATTT-TTTAT
40493511 TTATTTAATTTTTTAT
1 TTATTTAATTTTTTAT
40493527 TTGATTT
1 TT-ATTT
40493534 GATTCAGTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 10 0.30
17 23 0.70
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.75
Consensus pattern (16 bp):
TTATTTAATTTTTTAT
Found at i:40493591 original size:40 final size:40
Alignment explanation
Indices: 40493534--40493713 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
40493524 TATTTGATTT
*
40493534 GATTCAGTAGGTATGGCTCGAAAGCACATATGTTTCAGTA
1 GATTCAGTAGGTATGGCTCGAAAGCACATACGTTTCAGTA
* * *
40493574 GATTCGGTAGGTGTGGCTCGAAAGCACTTACGTTTCAGTA
1 GATTCAGTAGGTATGGCTCGAAAGCACATACGTTTCAGTA
* * * *
40493614 AATTTAGTAGGTATGGCTGGAAAGCACATACGTTTCAATA
1 GATTCAGTAGGTATGGCTCGAAAGCACATACGTTTCAGTA
*
40493654 GATTCTA-TAGGTATGGCTCGAAAGCACATAAGTTTCAGTA
1 GATTC-AGTAGGTATGGCTCGAAAGCACATACGTTTCAGTA
* * *
40493694 GATTCAATAGATATCGCTCG
1 GATTCAGTAGGTATGGCTCG
40493714 TCTGAGCACT
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 118 0.98
41 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (40 bp):
GATTCAGTAGGTATGGCTCGAAAGCACATACGTTTCAGTA
Found at i:40494487 original size:14 final size:14
Alignment explanation
Indices: 40494468--40494502 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
40494458 AACCCAAGTG
40494468 TTTTTATTT-ATTT
1 TTTTTATTTCATTT
40494481 ATTTTTATTTCATTT
1 -TTTTTATTTCATTT
40494496 TTTTTAT
1 TTTTTAT
40494503 GTTGCATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTATTTCATTT
Found at i:40495259 original size:5 final size:5
Alignment explanation
Indices: 40495249--40495340 Score: 109
Period size: 5 Copynumber: 18.4 Consensus size: 5
40495239 TCTATTAGCA
* * *
40495249 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT-TC TCATT AGTATTT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT -TTA-TT
40495300 TTACTT TTA-T TT-TT TTATT TTATT TTATT TTATT TTATT TT
1 TTA-TT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
40495341 TTCCTTATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
4 8 0.11
5 57 0.76
6 8 0.11
7 2 0.03
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:40499343 original size:6 final size:6
Alignment explanation
Indices: 40499317--40499389 Score: 89
Period size: 6 Copynumber: 12.3 Consensus size: 6
40499307 AGTGACTTTA
*
40499317 TTTAGT TTTATGT TTTA-- TTTATT TTTATT TTTATT TTTATT TTTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
40499364 TTTATT TTTATT TGTACTT TTT-TT TT
1 TTTATT TTTATT TTTA-TT TTTATT TT
40499390 GTTATGTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 43 0.72
7 9 0.15
ACGTcount: A:0.15, C:0.01, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:40502339 original size:3 final size:3
Alignment explanation
Indices: 40502331--40502375 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
40502321 ACATTGTCCT
*
40502331 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40502376 ATATTATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40502383 original size:3 final size:3
Alignment explanation
Indices: 40502377--40502421 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
40502367 TAATAATAAA
40502377 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40502422 ATTGGTACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40507416 original size:24 final size:24
Alignment explanation
Indices: 40507357--40507406 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
40507347 ACCAAATTAT
* *
40507357 AATT-ATATGAATTAATTTAACCG
1 AATTAATATTAATTAAATTAACCG
*
40507380 AATTAATATTAATTAAATTAATCG
1 AATTAATATTAATTAAATTAACCG
40507404 AAT
1 AAT
40507407 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (24 bp):
AATTAATATTAATTAAATTAACCG
Found at i:40507437 original size:24 final size:24
Alignment explanation
Indices: 40507410--40507455 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
40507400 ATCGAATATA
**
40507410 TTTTAATAGTTAATTGAATTGAGT
1 TTTTAATAAATAATTGAATTGAGT
**
40507434 TTTTTTTAAATAATTGAATTGA
1 TTTTAATAAATAATTGAATTGA
40507456 AATATTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTTAATAAATAATTGAATTGAGT
Found at i:40508408 original size:14 final size:14
Alignment explanation
Indices: 40508387--40508420 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40508377 TGGTATGGGT
40508387 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
40508400 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
40508414 TTATAGG
1 TTATAGG
40508421 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:40508902 original size:28 final size:29
Alignment explanation
Indices: 40508871--40508933 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
40508861 AATGTCGATA
*
40508871 TTTTTTAATATTTGTAGGAGTAGGTC-TT
1 TTTTTTAATATTTATAGGAGTAGGTCGTT
* * *
40508899 TTTTTGAATATTTATGGGATTAGGTCGTT
1 TTTTTTAATATTTATAGGAGTAGGTCGTT
40508928 TTTTTT
1 TTTTTT
40508934 TTAAAACCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.19, C:0.03, G:0.21, T:0.57
Consensus pattern (29 bp):
TTTTTTAATATTTATAGGAGTAGGTCGTT
Found at i:40509097 original size:21 final size:23
Alignment explanation
Indices: 40509073--40509121 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
40509063 CCTGAACCAA
* *
40509073 TTTAGGGT-TTTCTTTTA-AGGT
1 TTTAGGGTATTTATTTTAGAGCT
40509094 TTTAGGGTATTTATTTTAGAGCT
1 TTTAGGGTATTTATTTTAGAGCT
40509117 TTTAG
1 TTTAG
40509122 AAGACATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.18, C:0.04, G:0.22, T:0.55
Consensus pattern (23 bp):
TTTAGGGTATTTATTTTAGAGCT
Found at i:40512505 original size:22 final size:25
Alignment explanation
Indices: 40512477--40512527 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
40512467 TTTTAGACTG
40512477 TTATTTT-ATTTG-GTTTTTATTT-
1 TTATTTTAATTTGAGTTTTTATTTA
*
40512499 TTATTTTAATTTGATTTTTTATTTA
1 TTATTTTAATTTGAGTTTTTATTTA
40512524 TTAT
1 TTAT
40512528 GGGCCGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 5 0.20
24 9 0.36
25 4 0.16
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (25 bp):
TTATTTTAATTTGAGTTTTTATTTA
Found at i:40516558 original size:29 final size:31
Alignment explanation
Indices: 40516497--40516561 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
40516487 AAGCGTTTTC
*
40516497 AAAAATAGGTCTAATCCCATAAATATTCAAA
1 AAAAATAGGTCTAATCCAATAAATATTCAAA
*
40516528 AAAAAT-GGTCTAATCCAATAAATATTTAAA
1 AAAAATAGGTCTAATCCAATAAATATTCAAA
40516558 AAAA
1 AAAA
40516562 TCGATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.26
Consensus pattern (31 bp):
AAAAATAGGTCTAATCCAATAAATATTCAAA
Found at i:40518116 original size:124 final size:123
Alignment explanation
Indices: 40517895--40518268 Score: 606
Period size: 124 Copynumber: 3.0 Consensus size: 123
40517885 TTAGGGTTTT
* ** * *
40517895 TAGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCACTTCTAGC
1 TAGGTCATGGAAGAAATAATTT--TTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
40517960 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAG
64 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
40518020 TAGGTCATGGAAGAAATAAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAAT-AATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
40518085 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
65 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
40518144 TCGATCATGGAAGAAAT-ATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGATTCTAGCAG
1 TAGGTCATGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
* *
40518208 GATGCTATTTGAGAAGAATTTGTAAAATCGCACCCTCGTGGATGCGCTTTTGCTACAG
66 GATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
40518266 TAG
1 TAG
40518269 CATGTTTGGG
Statistics
Matches: 235, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
122 104 0.44
124 110 0.47
125 16 0.07
126 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (123 bp):
TAGGTCATGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
GATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:40523589 original size:20 final size:20
Alignment explanation
Indices: 40523552--40523589 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40523542 TTTATTTTTA
*
40523552 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
40523572 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
40523590 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:40524547 original size:11 final size:11
Alignment explanation
Indices: 40524531--40524561 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40524521 AAAAAGGGAG
40524531 TTAAGAGAAAC
1 TTAAGAGAAAC
*
40524542 TTAAGAGTAAC
1 TTAAGAGAAAC
40524553 TTAAGAGAA
1 TTAAGAGAA
40524562 TTTTTGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:40525753 original size:164 final size:161
Alignment explanation
Indices: 40525477--40525888 Score: 526
Period size: 164 Copynumber: 2.5 Consensus size: 161
40525467 TTTCCACCAT
* *
40525477 CTATTATTGTTTTTTTATTTCCAAATGAATATTAAAACTAAT-AAATCTGTTTCCGGATTTTTCC
1 CTATTTTTGTTTTTTTATTTCCAAATGAATATTAAAACTAATAAAATC-GTTTCGGGATTTTTCC
* * *
40525541 CGTCGTTTAATAGATTTTAATCGATTTTGTTTCCAAATTAAAAGTAAATAAAATTCGTTTCGGGA
65 CGTCGTTTAACAGATTTTATTCGATTTTGTTTCCAAATTAAAAGTAAATAAAATCCGTTTCGGGA
* * *
40525606 TTTATTCCTGCTGTTCAACAAATTTCTTTTTCCA
130 TTTATTCCCGCCGTTCAACAAATTTC-ATTT-CA
*
40525640 CTATTTTTGTTTTTTTATTTCCAAATGAATATTAAAACTAATAAAATACGTTTTGGGATTTTTCC
1 CTATTTTTGTTTTTTTATTTCCAAATGAATATTAAAACTAATAAAAT-CGTTTCGGGATTTTTCC
*
40525705 CGTCGTTTAACAGATTTTATTCGATTTTGTTTCCAAATTAAAAGTAAATAAAATCCGTTTTGGGA
65 CGTCGTTTAACAGATTTTATTCGATTTTGTTTCCAAATTAAAAGTAAATAAAATCCGTTTCGGGA
**
40525770 TTTATTCCCGCCGTTCAACGGATTTCATTTCA
130 TTTATTCCCGCCGTTCAACAAATTTCATTTCA
* * * * ** *
40525802 TTA-TTTTG--ATTTTATTTCCAAATGAAAAAATAAAGGTAAATAAAATTCGTTTCGGGATTGAT
1 CTATTTTTGTTTTTTTATTTCCAAATG-AATATTAAAACT-AATAAAA-TCGTTTCGGGATT-TT
* * *
40525864 TCCCGCCGTTCAACGGATTTTATTC
62 TCCCGTCGTTTAACAGATTTTATTC
40525889 CAAATTTTGT
Statistics
Matches: 220, Mismatches: 23, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
159 15 0.07
160 8 0.04
161 23 0.10
162 28 0.13
163 44 0.20
164 101 0.46
165 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (161 bp):
CTATTTTTGTTTTTTTATTTCCAAATGAATATTAAAACTAATAAAATCGTTTCGGGATTTTTCCC
GTCGTTTAACAGATTTTATTCGATTTTGTTTCCAAATTAAAAGTAAATAAAATCCGTTTCGGGAT
TTATTCCCGCCGTTCAACAAATTTCATTTCA
Found at i:40525929 original size:75 final size:74
Alignment explanation
Indices: 40525842--40525990 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
40525832 TAAAGGTAAA
* *
40525842 TAAAATTCGTTTCGGGATTGATTCCCGCCGTTCAACGGATTTTATTCCAAATTTTGTTTTATTTC
1 TAAAATTAGTTTCGGGATTGATTCCCGCCATTCAAC-GATTTTATTCCAAATTTTGTTTTATTTC
40525907 CAAAAACGAG
65 CAAAAACGAG
*
40525917 TAAAATTAGTTTCGGGATTGATTCCCGCTATTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
1 TAAAATTAGTTTCGGGATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
*
40525982 AAAATCGAG
66 AAAAACGAG
40525991 CATTAAAACT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 37 0.53
75 33 0.47
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (74 bp):
TAAAATTAGTTTCGGGATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
AAAAACGAG
Done.