Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 147 of 427
Found at i:40232482 original size:55 final size:57
Alignment explanation
Indices: 40232388--40232510 Score: 148
Period size: 55 Copynumber: 2.2 Consensus size: 57
40232378 TACCATTTTA
* ** *
40232388 CCCTCGATTTATAAAATTACTAAAATACCTCTGGTTTGT-AAAATTACTAAAATACC
1 CCCTCGATTTATAAAATCACTAAAATACCTCTGACTTGTAAAAATTACCAAAATACC
* *
40232444 CCCT-GATTTGTAAAATCACTAAAATACC-CTTGACTTGTAAAAATTACCAAAGTA--
1 CCCTCGATTTATAAAATCACTAAAATACCTC-TGACTTGTAAAAATTACCAAAATACC
40232498 CCCTCGATTTATA
1 CCCTCGATTTATA
40232511 GAATTATTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
54 5 0.09
55 35 0.61
56 17 0.30
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (57 bp):
CCCTCGATTTATAAAATCACTAAAATACCTCTGACTTGTAAAAATTACCAAAATACC
Found at i:40232554 original size:54 final size:53
Alignment explanation
Indices: 40232305--40232587 Score: 192
Period size: 54 Copynumber: 5.2 Consensus size: 53
40232295 ATTACTAAAG
* * * * *
40232305 TACCCCCGATTTACAGAATTA-TCGTTCTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTA-AGAATTACT-ATTTTACCCTCGATTTATAAAATTACTATTT
* ***
40232359 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAAAATTACTAAAA
1 TACCCTCGATTTA-AGAATTACTATTTTACCCTCGATTTATAAAATTACTATTT
* * *** * * * ***
40232413 TACCTCTGGTTTGTAA-AATTACTAAAATACCCCCTGATTTGTAAAATCACTAAAA
1 TACC-CTCGATT-TAAGAATTACTATTTTACCCTC-GATTTATAAAATTACTATTT
* * * *** * *
40232468 TACCCTTGACTTGTAAAAATTACCAAAGTACCCTCGATTTATAGAATTATTATTT
1 TACCCTCGA-TT-TAAGAATTACTATTTTACCCTCGATTTATAAAATTACTATTT
* * *
40232523 TACCCTCGATTTACAGAATTACTATTTTACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTA-AGAATTACTATTTTACCCTCGATTTATAAAATTACTATTT
40232577 TACCCTCGATT
1 TACCCTCGATT
40232588 GTGAAATTAC
Statistics
Matches: 180, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
53 2 0.01
54 106 0.59
55 55 0.31
56 17 0.09
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (53 bp):
TACCCTCGATTTAAGAATTACTATTTTACCCTCGATTTATAAAATTACTATTT
Found at i:40232721 original size:27 final size:27
Alignment explanation
Indices: 40232619--40232770 Score: 137
Period size: 27 Copynumber: 5.6 Consensus size: 27
40232609 TATAGGGTAG
* *
40232619 AATTACCAAAACACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* ** *
40232646 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
*
40232673 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AATTTGTAA
**
40232700 AATTACCAAAATACCCCTAATTTACAAA
1 AATTACCAAAATACCCCTAATTT-GTAA
* * *
40232728 AATTA-CAGAAATACCCTTGATTTGTAG
1 AATTACCA-AAATACCCCTAATTTGTAA
* *
40232755 ATTTACCAAAACACCC
1 AATTACCAAAATACCC
40232771 TTGTAAGATG
Statistics
Matches: 101, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
26 3 0.03
27 72 0.71
28 26 0.26
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:40232751 original size:55 final size:54
Alignment explanation
Indices: 40232639--40232770 Score: 147
Period size: 55 Copynumber: 2.4 Consensus size: 54
40232629 ACACCCCTAG
* ** *** *
40232639 TTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACCCCTAATTTCAAAAATTACAGAAATACCCTCAA
**
40232693 TTTGTAAAATTACCAAAATACCCCTAATTTACAAAAATTACAGAAATACCCTTGA
1 TTTGTAAAATTACCAAAATACCCCTAATTT-CAAAAATTACAGAAATACCCTCAA
* * *
40232748 TTTGTAGATTTACCAAAACACCC
1 TTTGTAAAATTACCAAAATACCC
40232771 TTGTAAGATG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
54 27 0.42
55 38 0.58
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCCCTAATTTCAAAAATTACAGAAATACCCTCAA
Found at i:40233218 original size:20 final size:22
Alignment explanation
Indices: 40233180--40233221 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
40233170 GTGCACGATG
40233180 GTAAGTTGGGCCTCAATGGGCT
1 GTAAGTTGGGCCTCAATGGGCT
40233202 GTAA-TTGGGCC-CAATGGGCT
1 GTAAGTTGGGCCTCAATGGGCT
40233222 TTCGAGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (22 bp):
GTAAGTTGGGCCTCAATGGGCT
Found at i:40233600 original size:20 final size:20
Alignment explanation
Indices: 40233575--40233661 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
40233565 GATATGATAT
*
40233575 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
40233595 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
*
40233615 ATATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
40233635 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
40233655 ACATGAT
1 ACATGAT
40233662 GTATTCATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:40233740 original size:26 final size:26
Alignment explanation
Indices: 40233711--40233899 Score: 269
Period size: 26 Copynumber: 7.3 Consensus size: 26
40233701 GAGGTAGTGC
*
40233711 AAAAGGGCTTATGCCCCGGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40233737 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
40233763 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
40233789 AAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40233815 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
40233841 AAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40233866 AAAAAGGGCTT-TGCCCCAG-TTATT-
1 -AAAAGGGCTTATGCCCCAGTTTATTG
40233890 AAAAGAGGCT
1 AAAAG-GGCT
40233900 AGGCCTCCAG
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
23 5 0.03
24 4 0.03
25 15 0.10
26 126 0.84
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40233840 original size:78 final size:78
Alignment explanation
Indices: 40233711--40233886 Score: 302
Period size: 78 Copynumber: 2.3 Consensus size: 78
40233701 GAGGTAGTGC
* *
40233711 AAAAGGGCTTATGCCCCGGTTTATTGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
1 AAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TG
*
40233776 CCCCAGTTTACCG-
65 CCCCAATTTACCGA
40233789 AAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGC
1 AAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGC
40233854 CCCAATTTACCGA
66 CCCAATTTACCGA
40233867 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40233887 ATTAAAAGAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
77 24 0.26
78 70 0.74
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (78 bp):
AAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGC
CCCAATTTACCGA
Found at i:40234097 original size:42 final size:42
Alignment explanation
Indices: 40234032--40234123 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
40234022 TAGTCTCCCC
* * ** *
40234032 AAATAGGCTTGCATACATTCATTGGTATTTCATATAATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATAATATTG
* * *
40234074 AAATGGGCTTGCATAGATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATAATATTG
40234116 AAATGGGC
1 AAATGGGC
40234124 CTATGGGCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATAATATTG
Found at i:40234182 original size:31 final size:31
Alignment explanation
Indices: 40234147--40234225 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
40234137 CGTTTACAGT
40234147 AAAGGCTTCGGCCCAGTGAAAGGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAAGGATTTATGA
* *
40234178 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAAGGATTTATGA
40234209 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
40234226 ATATGTCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAAGGATTTATGA
Found at i:40237252 original size:26 final size:26
Alignment explanation
Indices: 40237216--40237268 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40237206 GGTCGAAACG
40237216 ATTGTATGAACATAGTTAACATTCTT
1 ATTGTATGAACATAGTTAACATTCTT
40237242 ATTGTATGAACATAGTTAACATTCTT
1 ATTGTATGAACATAGTTAACATTCTT
40237268 A
1 A
40237269 CACATTCGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTGTATGAACATAGTTAACATTCTT
Found at i:40240794 original size:24 final size:24
Alignment explanation
Indices: 40240743--40240884 Score: 207
Period size: 24 Copynumber: 5.9 Consensus size: 24
40240733 GCTTTATCAT
*
40240743 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
40240768 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
40240792 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
40240815 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40240839 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
40240863 ATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTT
40240885 CACTTCCTCC
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 75 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40240822 original size:47 final size:48
Alignment explanation
Indices: 40240743--40240886 Score: 211
Period size: 47 Copynumber: 3.0 Consensus size: 48
40240733 GCTTTATCAT
* *
40240743 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
40240792 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
40240839 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
40240887 CTTCCTCCAT
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:40240843 original size:71 final size:72
Alignment explanation
Indices: 40240742--40240884 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 72
40240732 TGCTTTATCA
*
40240742 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
40240807 GCCCTTT
66 GCCCTTT
* * **
40240814 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
40240877 AGCCCTTT
65 AGCCCTTT
40240885 CACTTCCTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 52 0.80
72 13 0.20
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:40240959 original size:20 final size:20
Alignment explanation
Indices: 40240934--40240993 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
40240924 TATGATTACC
40240934 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
40240954 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
40240974 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
40240994 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:40240964 original size:11 final size:11
Alignment explanation
Indices: 40240934--40240988 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40240924 TATGATTACC
40240934 TCATGTGCATA
1 TCATGTGCATA
*
40240945 TCA--TACATA
1 TCATGTGCATA
40240954 TCATGTGCATA
1 TCATGTGCATA
* *
40240965 TCA--TACATT
1 TCATGTGCATA
40240974 TCATGTGCATA
1 TCATGTGCATA
40240985 TCAT
1 TCAT
40240989 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40241068 original size:25 final size:25
Alignment explanation
Indices: 40241036--40241083 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40241026 ATACATAAAC
* * *
40241036 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40241061 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40241084 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40242337 original size:27 final size:27
Alignment explanation
Indices: 40242317--40242602 Score: 330
Period size: 27 Copynumber: 10.6 Consensus size: 27
40242307 AGGGTATTTT
*
40242317 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40242344 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
40242371 AGTAATTCTGTAAATCGAGGGTAAAA-
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
40242397 TGATAATTATGTAAATCG-GGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
40242424 GGTAATTATGTAAAT-TAGGGGTAAAAC
1 AGTAATTCTGTAAATCGA-GGGTAAAAC
* * *
40242451 GGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40242478 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
40242505 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
40242532 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40242559 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
40242586 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
40242603 GGAGTACTTT
Statistics
Matches: 226, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
26 24 0.11
27 199 0.88
28 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:40242404 original size:81 final size:81
Alignment explanation
Indices: 40242316--40242601 Score: 382
Period size: 81 Copynumber: 3.5 Consensus size: 81
40242306 AAGGGTATTT
* * * *
40242316 TAGTAATTTTGTAAA-TCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCT
1 TAGTAATTCTATAAACT-GAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCT
*
40242380 GTAAATCGAGGGTAAAA
65 ATAAATCGAGGGTAAAA
* * * * * *
40242397 T-GATAATTATGTAAA-TCG-GGGTAAAATGGTAATTATGTAAATTAGGGGTAAAACGGTAATTC
1 TAG-TAATTCTATAAACT-GAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTC
40242459 TATAAATCGAGGGTAAAA
64 TATAAATCGAGGGTAAAA
* *
40242477 TAGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTA
1 TAGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTA
*
40242542 CAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
*
40242558 CAGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATC
1 TAGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATC
40242602 GGGAGTACTT
Statistics
Matches: 183, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
80 68 0.37
81 115 0.63
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (81 bp):
TAGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTA
TAAATCGAGGGTAAAA
Found at i:40245677 original size:24 final size:24
Alignment explanation
Indices: 40245626--40245768 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
40245616 GCTTTATCAT
*
40245626 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
40245651 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
40245675 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
40245698 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40245722 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
40245746 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40245769 CACTTCCTCC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40245705 original size:47 final size:48
Alignment explanation
Indices: 40245626--40245767 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
40245616 GCTTTATCAT
* *
40245626 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
40245675 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
40245722 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
40245768 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:40245726 original size:71 final size:72
Alignment explanation
Indices: 40245625--40245768 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
40245615 TGCTTTATCA
*
40245625 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
40245690 GCCCTTT
66 GCCCTTT
* * **
40245697 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
40245760 AGCCCTTT
65 AGCCCTTT
40245768 T
1 T
40245769 CACTTCCTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:40245848 original size:11 final size:11
Alignment explanation
Indices: 40245818--40245871 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40245808 TATGATTACC
40245818 TCATGTGCATA
1 TCATGTGCATA
*
40245829 TCA--TACATA
1 TCATGTGCATA
40245838 TCATGTGCATA
1 TCATGTGCATA
*
40245849 TCA--TACAT-
1 TCATGTGCATA
40245857 TCATGTGCATA
1 TCATGTGCATA
40245868 TCAT
1 TCAT
40245872 ACATACCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 3 0.09
9 12 0.35
10 4 0.12
11 15 0.44
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40245862 original size:19 final size:20
Alignment explanation
Indices: 40245818--40245876 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
40245808 TATGATTACC
40245818 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
40245838 TCATGTGCATATCATACAT-
1 TCATGTGCATATCATACATA
40245857 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
40245877 CCATATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:40245951 original size:25 final size:25
Alignment explanation
Indices: 40245919--40245966 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40245909 ATACATAAAC
* * *
40245919 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40245944 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40245967 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40247223 original size:27 final size:27
Alignment explanation
Indices: 40247203--40247488 Score: 339
Period size: 27 Copynumber: 10.6 Consensus size: 27
40247193 AGGGTATTTT
*
40247203 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40247230 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
40247257 AGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
40247284 -GATAATTATGTAAATCG-GGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
40247310 GGTAATTATGTAAAT-TAGGGGTAAAAC
1 AGTAATTCTGTAAATCGA-GGGTAAAAC
* * *
40247337 GGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40247364 AGTAATTCTGTAAA-CTGAAGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
40247391 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
40247418 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40247445 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
40247472 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
40247489 GGAGTACTTT
Statistics
Matches: 225, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
26 24 0.11
27 198 0.88
28 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:40247290 original size:81 final size:81
Alignment explanation
Indices: 40247203--40247487 Score: 380
Period size: 81 Copynumber: 3.5 Consensus size: 81
40247193 AGGGTATTTT
* * * *
40247203 AGTAATTTTGTAAA-TCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTG
1 AGTAATTCTGTAAACT-GAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTA
40247267 TAAATCGAGGGTAAAAC
65 TAAATCGAGGGTAAAAC
* * * * *
40247284 -GATAATTATGTAAA-TCG-GGGTAAAATGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCT
1 AG-TAATTCTGTAAACT-GAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCT
*
40247346 ATAAATCGAGGGTAAAAT
64 ATAAATCGAGGGTAAAAC
* * * *
40247364 AGTAATTCTGTAAACTGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAC
1 AGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTAT
40247429 AAATCGAGGGTAAAAC
66 AAATCGAGGGTAAAAC
*
40247445 AGTAATTCTATAAACTGAGGGTAAAACGGTAATTCTGTAAATC
1 AGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATC
40247488 GGGAGTACTT
Statistics
Matches: 179, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
80 68 0.38
81 111 0.62
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (81 bp):
AGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTAT
AAATCGAGGGTAAAAC
Found at i:40247532 original size:81 final size:81
Alignment explanation
Indices: 40247222--40247521 Score: 304
Period size: 81 Copynumber: 3.7 Consensus size: 81
40247212 GTAAATCGAG
* * * * ** *
40247222 GGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAAC-GA
1 GGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGCAAAACAG-
* * *
40247286 TAATTATGTAAA-TCG-G
65 TAATTCTATAAACT-GAA
* * * * * * *
40247302 GGTAAAATGGTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATAG
1 GGTAAAACGGTAATTCTGTAAATCGA-GGGTAAAACGGTAATTTTACAAATCGAGGGCAAAACAG
*
40247366 TAATTCTGTAAACTGAA
65 TAATTCTATAAACTGAA
*
40247383 GGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAACAGT
1 GGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGCAAAACAGT
*
40247448 AATTCTATAAACTGAG
66 AATTCTATAAACTGAA
**** *
40247464 GGTAAAACGGTAATTCTGTAAATCG-GGAGTACTTTGGTAATTTTACAAGTCGAGGGCA
1 GGTAAAACGGTAATTCTGTAAATCGAGG-GTAAAACGGTAATTTTACAAATCGAGGGCA
40247522 TTTCAGTAAT
Statistics
Matches: 191, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 67 0.35
81 122 0.64
82 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (81 bp):
GGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGCAAAACAGT
AATTCTATAAACTGAA
Found at i:40251961 original size:20 final size:20
Alignment explanation
Indices: 40251936--40251974 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40251926 ATGATAGGGT
40251936 TTGTTTTAAATGTGAATCAC
1 TTGTTTTAAATGTGAATCAC
*
40251956 TTGTTTTAAATGTGGATCA
1 TTGTTTTAAATGTGAATCA
40251975 TTATATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (20 bp):
TTGTTTTAAATGTGAATCAC
Found at i:40254709 original size:31 final size:31
Alignment explanation
Indices: 40254666--40254729 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40254656 CCTTTTCATA
40254666 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
40254697 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
40254728 TT
1 TT
40254730 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:40254969 original size:24 final size:24
Alignment explanation
Indices: 40254922--40255042 Score: 174
Period size: 24 Copynumber: 5.0 Consensus size: 24
40254912 GCTTTATCAT
*
40254922 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
40254947 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
40254972 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40254996 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
40255020 ATAACTGGGGCATAGGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40255043 GCACTTCCTC
Statistics
Matches: 90, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
23 1 0.01
24 58 0.64
25 25 0.28
26 6 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40255119 original size:20 final size:20
Alignment explanation
Indices: 40255096--40255158 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
40255086 GAACATCTCG
40255096 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
40255116 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
40255136 TGTGCATATTATACATATCA
1 TGTGCATATCATACATATCA
40255156 TGT
1 TGT
40255159 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:40255223 original size:25 final size:25
Alignment explanation
Indices: 40255195--40255242 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40255185 ATATATAAAC
* *
40255195 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
40255220 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
40255243 CATACTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:40261672 original size:53 final size:53
Alignment explanation
Indices: 40261494--40261700 Score: 225
Period size: 53 Copynumber: 3.8 Consensus size: 53
40261484 ATTAGGGTTT
* * * * *
40261494 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTGACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * *
40261548 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * * *
40261603 AAAGATCCCATGTAAGACCATGCCAAGGCATGGAAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
*
40261656 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
40261701 TAAAAAGGAA
Statistics
Matches: 123, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 46 0.37
54 38 0.31
55 39 0.32
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:40269863 original size:41 final size:40
Alignment explanation
Indices: 40269728--40269951 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
40269718 AACCCAAGTA
* * * *
40269728 CCTTCGGGATTTA-ACCGGATATAG-CAAATCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
40269767 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40269807 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-AAATG
* * *
40269848 CCTTCGGGTCATAGCCCGGATATTGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40269888 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAGTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAA-TG
*
40269929 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
40269952 CATCCGAATA
Statistics
Matches: 166, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 12 0.07
40 94 0.57
41 60 0.36
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40269863 original size:81 final size:80
Alignment explanation
Indices: 40269728--40269951 Score: 317
Period size: 81 Copynumber: 2.8 Consensus size: 80
40269718 AACCCAAGTA
* * * * *
40269728 CCTTCGGGATTTAACCGGATATAG-CAAATCGCAC-AAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTACCCGGATATAGTC-ACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATATA
*
40269791 GTAACTCGCACAAATG
65 GTAACTAGCACAAATG
* *
40269807 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCATAGCCCGGATATT
1 CCTTCGGGACTTA-CCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATATA
*
40269872 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
*
40269888 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAGTGCCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTT-ACCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATAT
40269952 CATCCGAATA
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
79 12 0.09
80 16 0.12
81 101 0.78
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTACCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATATAG
TAACTAGCACAAATG
Found at i:40271375 original size:14 final size:14
Alignment explanation
Indices: 40271353--40271395 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
40271343 TTTCATTTTG
40271353 TAACATAAAATTAT
1 TAACATAAAATTAT
*
40271367 TAGCATAAAA-TAT
1 TAACATAAAATTAT
* *
40271380 TAACACAAAATAAT
1 TAACATAAAATTAT
40271394 TA
1 TA
40271396 TAATATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (14 bp):
TAACATAAAATTAT
Found at i:40271389 original size:13 final size:13
Alignment explanation
Indices: 40271353--40271391 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
40271343 TTTCATTTTG
40271353 TAACATAAAATTAT
1 TAACATAAAA-TAT
*
40271367 TAGCATAAAATAT
1 TAACATAAAATAT
*
40271380 TAACACAAAATA
1 TAACATAAAATA
40271392 ATTATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (13 bp):
TAACATAAAATAT
Found at i:40273416 original size:39 final size:40
Alignment explanation
Indices: 40273369--40273512 Score: 202
Period size: 39 Copynumber: 3.6 Consensus size: 40
40273359 AATGTTCGAG
40273369 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
*
40273408 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
40273447 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
** * *
40273487 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAGTCCCGAAGGC
40273513 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 53 0.56
40 41 0.44
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (40 bp):
TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
Found at i:40273548 original size:79 final size:79
Alignment explanation
Indices: 40273385--40273550 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 79
40273375 CCGGGCTAAG
** * ** *
40273385 CCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGA
1 CCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGA
* * *
40273450 TATCCGGGTTAAGT
66 TATCCGGATAAACT
* * * **
40273464 CCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT
1 CCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-T
40273529 -ATATCCGGATAAACT
64 GATATCCGGATAAACT
40273544 -CCGAAGG
1 CCCGAAGG
40273551 TATGTGATTC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
79 40 0.56
80 30 0.42
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (79 bp):
CCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGA
TATCCGGATAAACT
Found at i:40280664 original size:41 final size:40
Alignment explanation
Indices: 40280561--40280754 Score: 307
Period size: 40 Copynumber: 4.8 Consensus size: 40
40280551 ATAGCAAATC
* *
40280561 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
40280601 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
* *
40280641 GCACAAAATGCCTTCGGGTCTTAGCCCGGATATCGTCACTA
1 GCAC-AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
*
40280682 GCACAAATGCCTTCGGGACTTAACCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
* *
40280722 GCACAAAGTGCCTTCGAGTCTTAGCCCGGATAT
1 GCACAAA-TGCCTTCGGGACTTAGCCCGGATAT
40280755 CATCCGAATA
Statistics
Matches: 142, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
40 82 0.58
41 60 0.42
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
Found at i:40280755 original size:81 final size:80
Alignment explanation
Indices: 40280531--40280755 Score: 319
Period size: 81 Copynumber: 2.8 Consensus size: 80
40280521 AACCCAAGTA
* * * * * *
40280531 CCTTCGGGATTTAA-CTGGATATAG-CAAATCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATC
*
40280594 GTAACTCGCACAAATG
65 GTAACTAGCACAAATG
*
40280610 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATATC
1 CCTTCGGGACTTAACCCGGATATAGTCACTAGCAC-AAATGCCTTCGGGTCTTAGCCCGGATATC
*
40280675 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
*
40280691 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAAGTGCCTTCGAGTCTTAGCCCGGATATC
1 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAA-TGCCTTCGGGTCTTAGCCCGGATATC
40280756 ATCCGAATAA
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
79 12 0.09
80 18 0.14
81 101 0.77
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATCG
TAACTAGCACAAATG
Found at i:40283245 original size:53 final size:53
Alignment explanation
Indices: 40283070--40283273 Score: 131
Period size: 53 Copynumber: 3.8 Consensus size: 53
40283060 AGGGTTTAAG
* * * * * * * *
40283070 GATACCAAGTAAGACCATGTCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAG
1 GATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGAAAA
* * * * * ** ** * *
40283124 GAAATCATGTAAAACCATGTCAAGACATGGCTTTAATAAACTATGATAAGGAAAA
1 GATACCACGTAAGACCATGCCAAGACATGGCAATGGT-AAGT-TCATAAGGAAAA
* * * * *
40283179 GATCCCATGTAAGACCATGCCAACG-CATGGCAATGGTGAGTTCATAAGGCAAG
1 GATACCACGTAAGACCATGCCAA-GACATGGCAATGGTAAGTTCATAAGGAAAA
* *
40283232 GATACCACGTAAGATCATGTCAAGACATGGCAATGGTAAGTT
1 GATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
40283274 TAAAAAGGAA
Statistics
Matches: 114, Mismatches: 32, Indels: 9
0.74 0.21 0.06
Matches are distributed among these distances:
52 1 0.01
53 44 0.39
54 32 0.28
55 36 0.32
56 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (53 bp):
GATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGAAAA
Found at i:40286010 original size:46 final size:46
Alignment explanation
Indices: 40285957--40286132 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40285947 TATTTGGGCA
40285957 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
40286003 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
40286050 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
40286096 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40286133 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:40286112 original size:93 final size:93
Alignment explanation
Indices: 40285953--40286124 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40285943 GGGATATTTG
* *
40285953 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40286018 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
40286046 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40286111 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
40286125 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:40290183 original size:26 final size:26
Alignment explanation
Indices: 40290152--40290259 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
40290142 TGAAATGCCC
*
40290152 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
40290178 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
40290204 ATCATGGAATATTTACCTAATCTATT
1 ATCATGGAACATTTACCTAACCCATT
40290230 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40290256 ATCA
1 ATCA
40290260 ATTTATACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40296525 original size:19 final size:19
Alignment explanation
Indices: 40296498--40296538 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40296488 TTATAGCCTA
*
40296498 ATTTGCATGATAGAATCAG
1 ATTTACATGATAGAATCAG
*
40296517 ATTTACATGCTAGAATCAG
1 ATTTACATGATAGAATCAG
40296536 ATT
1 ATT
40296539 GATACAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (19 bp):
ATTTACATGATAGAATCAG
Found at i:40297437 original size:20 final size:20
Alignment explanation
Indices: 40297365--40297437 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 20
40297355 TTGGTAGAAC
*
40297365 TTTTATATATTTATTTC-CAT
1 TTTTATATATTT-TTTCAAAT
* * *
40297385 TTTTATA-ATCTTCT-AAAA
1 TTTTATATATTTTTTCAAAT
* *
40297403 TTATATATAACTTTTTCAAAT
1 TTTTATAT-ATTTTTTCAAAT
40297424 TTTTATATATTTTT
1 TTTTATATATTTTT
40297438 ATTTCCATTT
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
18 9 0.24
19 3 0.08
20 16 0.42
21 10 0.26
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATATTTTTTCAAAT
Found at i:40297749 original size:2 final size:2
Alignment explanation
Indices: 40297744--40297782 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
40297734 GCCAAAAAAG
*
40297744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40297783 GTTTTGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40298023 original size:27 final size:28
Alignment explanation
Indices: 40297981--40298039 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
40297971 ATTAGTAAAA
40297981 AGGGCCACTTTAAAAAAAATAGCGATTT
1 AGGGCCACTTTAAAAAAAATAGCGATTT
40298009 AGGGCCACTTTAAAAAAAATAGCGATTT
1 AGGGCCACTTTAAAAAAAATAGCGATTT
40298037 AGG
1 AGG
40298040 TTATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (28 bp):
AGGGCCACTTTAAAAAAAATAGCGATTT
Found at i:40299012 original size:19 final size:17
Alignment explanation
Indices: 40298976--40299032 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
40298966 CCCGAGATTG
40298976 AAAATATATAATACTAA
1 AAAATATATAATACTAA
**
40298993 AAAATATATAAATA-TTT
1 AAAATATAT-AATACTAA
*
40299010 AAAATATAATAATGCTAA
1 AAAATAT-ATAATACTAA
40299028 AAAAT
1 AAAAT
40299033 CATTTCAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 20 0.62
18 12 0.38
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATATATAATACTAA
Found at i:40299318 original size:69 final size:67
Alignment explanation
Indices: 40299241--40299371 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 67
40299231 TTATGTACTC
* * *
40299241 AAAAATAATTATATTTGAACTAATTGATTGACTTTAT-ATATTAG-ATTTACCATACCCACGATG
1 AAAAATAATGATATTTGAAATAATT-ATT---TTTATAATATTAGAATTTACCATACCCACAATG
40299304 TAGGTG
62 TAGGTG
*
40299310 AAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATTTACCATACTCACAATGT
1 AAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATTTACCATACCCACAATGT
40299372 GTATGAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
65 5 0.09
66 7 0.12
67 18 0.32
68 3 0.05
69 23 0.41
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (67 bp):
AAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATTTACCATACCCACAATGTAGG
TG
Found at i:40299394 original size:12 final size:12
Alignment explanation
Indices: 40299377--40299405 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40299367 AATGTGTATG
40299377 AAAAATATATCA
1 AAAAATATATCA
40299389 AAAAATATATCA
1 AAAAATATATCA
40299401 AAAAA
1 AAAAA
40299406 ATTAGTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATATATCA
Found at i:40301283 original size:6 final size:6
Alignment explanation
Indices: 40301272--40301312 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
40301262 ATACAATTTT
*
40301272 AGATTC AGATTC AGATATC AGATTC AGATTC AAATTC AGAT
1 AGATTC AGATTC AGAT-TC AGATTC AGATTC AGATTC AGAT
40301313 AGGAGATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (6 bp):
AGATTC
Found at i:40301296 original size:19 final size:18
Alignment explanation
Indices: 40301272--40301312 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
40301262 ATACAATTTT
*
40301272 AGATTCAGATTCAGATATC
1 AGATTCAGATTCAAAT-TC
40301291 AGATTCAGATTCAAATTC
1 AGATTCAGATTCAAATTC
40301309 AGAT
1 AGAT
40301313 AGGAGATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (18 bp):
AGATTCAGATTCAAATTC
Found at i:40301319 original size:25 final size:25
Alignment explanation
Indices: 40301272--40301319 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40301262 ATACAATTTT
* *
40301272 AGATTCAGATTCAGATATCAGATTC
1 AGATTCAAATTCAGATAGCAGATTC
*
40301297 AGATTCAAATTCAGATAGGAGAT
1 AGATTCAAATTCAGATAGCAGAT
40301320 ATGCAAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (25 bp):
AGATTCAAATTCAGATAGCAGATTC
Found at i:40312492 original size:10 final size:10
Alignment explanation
Indices: 40312477--40312501 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40312467 TCCTTACACG
40312477 TCTCTCCCTC
1 TCTCTCCCTC
40312487 TCTCTCCCTC
1 TCTCTCCCTC
40312497 TCTCT
1 TCTCT
40312502 GATTTGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (10 bp):
TCTCTCCCTC
Found at i:40313381 original size:17 final size:17
Alignment explanation
Indices: 40313359--40313400 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
40313349 GGTTGGGCCG
40313359 TGTGGGCCACATGAGCA
1 TGTGGGCCACATGAGCA
40313376 TGTGGGCCACATGAGCA
1 TGTGGGCCACATGAGCA
*
40313393 TGTAGGCC
1 TGTGGGCC
40313401 CATTTTCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (17 bp):
TGTGGGCCACATGAGCA
Found at i:40316456 original size:18 final size:18
Alignment explanation
Indices: 40316430--40316465 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40316420 GGAATTAAAT
*
40316430 TTAAATAAAAATATTTTG
1 TTAAATAAAAATAATTTG
*
40316448 TTAATTAAAAATAATTTG
1 TTAAATAAAAATAATTTG
40316466 AATCAAACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTAAATAAAAATAATTTG
Found at i:40319177 original size:22 final size:24
Alignment explanation
Indices: 40319136--40319179 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
40319126 TAAAATGATG
*
40319136 ATAATTTTTCTTTTTTAAAATACA
1 ATAATTTTTCTTTTTGAAAATACA
40319160 ATAA-TTTT-TTTTTGAAAATA
1 ATAATTTTTCTTTTTGAAAATA
40319180 ATGGAGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (24 bp):
ATAATTTTTCTTTTTGAAAATACA
Found at i:40320577 original size:9 final size:9
Alignment explanation
Indices: 40320565--40320700 Score: 66
Period size: 9 Copynumber: 14.9 Consensus size: 9
40320555 AAATATTAAA
40320565 AAAAATTAT
1 AAAAATTAT
** *
40320574 AAAAACCAG
1 AAAAATTAT
*
40320583 AAAAATTTTT
1 AAAAA-TTAT
*
40320593 AAAAATTTT
1 AAAAATTAT
**
40320602 TTAAA-TATT
1 AAAAATTA-T
40320611 AAAAA-TATT
1 AAAAATTA-T
*
40320620 AAAATTTAT
1 AAAAATTAT
*
40320629 ATAAACTTAT
1 A-AAAATTAT
40320639 AAAAATTAT
1 AAAAATTAT
40320648 AAAAA--AT
1 AAAAATTAT
*
40320655 AAAAGCTTAT
1 AAAA-ATTAT
* *
40320665 AAATATAAT
1 AAAAATTAT
40320674 AATAAATTAT
1 AA-AAATTAT
40320684 AAAAA-TAT
1 AAAAATTAT
40320692 AATAAATTA
1 AA-AAATTA
40320701 ATATCAACCA
Statistics
Matches: 96, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
7 6 0.06
8 6 0.06
9 55 0.57
10 29 0.30
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40321122 original size:10 final size:9
Alignment explanation
Indices: 40321067--40321277 Score: 63
Period size: 10 Copynumber: 22.0 Consensus size: 9
40321057 GACTTTTTCG
40321067 TAATTTTTAA
1 TAATTTTT-A
*
40321077 TATTTTTTTA
1 TA-ATTTTTA
40321087 TAATTTATTA
1 TAATTT-TTA
*
40321097 GAATTTATTA
1 TAATTT-TTA
40321107 T-ATTTTTA
1 TAATTTTTA
40321115 TAAGTTTTTTA
1 TAA--TTTTTA
**
40321126 TAAAAATTTA
1 T-AATTTTTA
*
40321136 AATATATTTTA
1 TA-AT-TTTTA
40321147 TTAA-TTTTA
1 -TAATTTTTA
*
40321156 TATATTTTAA
1 TA-ATTTTTA
*
40321166 TACTTTATTAA
1 TAATTT-TT-A
* *
40321177 AAATTATTA
1 TAATTTTTA
*
40321186 -GATTTTTA
1 TAATTTTTA
*
40321194 TAATATTTA
1 TAATTTTTA
* *
40321203 TAGGTTTCTA
1 TA-ATTTTTA
*
40321213 TTATTTTTTTA
1 -TA-ATTTTTA
40321224 TAATTTTTA
1 TAATTTTTA
*
40321233 TACATTTATA
1 TA-ATTTTTA
*
40321243 TCAATTTTGA
1 T-AATTTTTA
*
40321253 -GATTTTT-
1 TAATTTTTA
*
40321260 TAATATTTA
1 TAATTTTTA
40321269 TAATTTTTA
1 TAATTTTTA
40321278 ATATTTATAA
Statistics
Matches: 146, Mismatches: 35, Indels: 41
0.66 0.16 0.18
Matches are distributed among these distances:
8 22 0.15
9 43 0.29
10 49 0.34
11 29 0.20
12 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (9 bp):
TAATTTTTA
Found at i:40321232 original size:9 final size:9
Alignment explanation
Indices: 40321218--40321277 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
40321208 TTCTATTATT
40321218 TTTTTATAA
1 TTTTTATAA
40321227 TTTTTATACA
1 TTTTTATA-A
*
40321237 TTTATATCAA
1 TTTTTAT-AA
* *
40321247 TTTTGA-GA
1 TTTTTATAA
40321255 TTTTT-TAA
1 TTTTTATAA
*
40321263 TATTTATAA
1 TTTTTATAA
40321272 TTTTTA
1 TTTTTA
40321278 ATATTTATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
8 10 0.26
9 16 0.41
10 12 0.31
11 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40321277 original size:16 final size:16
Alignment explanation
Indices: 40321256--40321294 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40321246 ATTTTGAGAT
40321256 TTTTTAATATTTATAA
1 TTTTTAATATTTATAA
40321272 TTTTTAATATTTATAA
1 TTTTTAATATTTATAA
*
40321288 GTTTTAA
1 TTTTTAA
40321295 AGAATTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTAATATTTATAA
Found at i:40321419 original size:8 final size:8
Alignment explanation
Indices: 40321408--40321474 Score: 59
Period size: 7 Copynumber: 8.0 Consensus size: 8
40321398 TTTTTTATTT
40321408 TTTTATAA
1 TTTTATAA
40321416 TTTTATATAAA
1 -TTT-TAT-AA
40321427 TTTTA-AA
1 TTTTATAA
40321434 TTTTA-AA
1 TTTTATAA
40321441 TTTTA-AA
1 TTTTATAA
40321448 TTTTTAATAA
1 -TTTT-ATAA
40321458 TTTTTATAA
1 -TTTTATAA
40321467 TTTTATAA
1 TTTTATAA
40321475 ATGTTTCTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
7 16 0.30
8 12 0.23
9 10 0.19
10 13 0.25
11 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTATAA
Found at i:40321436 original size:29 final size:29
Alignment explanation
Indices: 40321378--40321437 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
40321368 ATTTATTAGA
** **
40321378 TTTTTATAATATTTATAAGTTTTTTTATT
1 TTTTTATAATATTTATAAAATTTTAAATT
40321407 TTTTTATAAT-TTTATATAAATTTTAAATT
1 TTTTTATAATATTTATA-AAATTTTAAATT
40321436 TT
1 TT
40321438 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTTATAATATTTATAAAATTTTAAATT
Found at i:40323626 original size:17 final size:17
Alignment explanation
Indices: 40323604--40323677 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
40323594 ATTTTAATAG
40323604 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
*
40323621 TTTAATACTT--ATCATAA
1 TTTAATA-TTAAAT-TTAA
* **
40323638 --TAGTATTTTAT-TAA
1 TTTAATATTAAATTTAA
*
40323652 TTTAATATTAAATTTAT
1 TTTAATATTAAATTTAA
40323669 TTTAATATT
1 TTTAATATT
40323678 TATCTTATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.11
15 4 0.09
16 12 0.27
17 21 0.48
18 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:40324721 original size:2 final size:2
Alignment explanation
Indices: 40324714--40324751 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
40324704 TATAATTATG
40324714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40324752 GAGACGATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40331411 original size:3 final size:3
Alignment explanation
Indices: 40331403--40331435 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40331393 AAAAAGATAT
40331403 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40331436 ATTAGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40331897 original size:23 final size:21
Alignment explanation
Indices: 40331863--40331909 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
40331853 GGAAATTGAA
40331863 TAGAAATGAAGTATGAATTGAGT
1 TAGAAATGAAG--TGAATTGAGT
*
40331886 TAGAAA-GTAAGTGAATTTAGT
1 TAGAAATG-AAGTGAATTGAGT
40331907 TAG
1 TAG
40331910 GATTAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.55
22 1 0.05
23 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.32
Consensus pattern (21 bp):
TAGAAATGAAGTGAATTGAGT
Found at i:40338587 original size:93 final size:93
Alignment explanation
Indices: 40338475--40338646 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
40338465 GCCCATAAGT
* *
40338475 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40338540 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
40338568 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40338633 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40338647 CAAATATCCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40338642 original size:46 final size:46
Alignment explanation
Indices: 40338467--40338645 Score: 238
Period size: 46 Copynumber: 3.9 Consensus size: 46
40338457 TGTAACCCGC
* ** *
40338467 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
*
40338513 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-CTCG---CAT
* *
40338563 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
40338606 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
40338646 CCAAATATCC
Statistics
Matches: 116, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
Found at i:40340455 original size:28 final size:27
Alignment explanation
Indices: 40340403--40340455 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
40340393 CTATTCAGAA
* *
40340403 ATCAGTGTTAACTAGGCCTTAGCCCAT
1 ATCAGTATTAACTAGGCCATAGCCCAT
*
40340430 ATCAGTATTAATCTGGGCCATAGCCC
1 ATCAGTATTAA-CTAGGCCATAGCCC
40340456 CTTACAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAACTAGGCCATAGCCCAT
Found at i:40340540 original size:60 final size:59
Alignment explanation
Indices: 40340417--40340551 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 59
40340407 GTGTTAACTA
* *
40340417 GGCCTTAGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTATACTG
1 GGCC-TAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGT-ACAGAGTATACTG
* * *
40340478 GGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACAAGT-C-GAGATATATTG
1 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTACAGAG-TATACTG
*
40340538 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
40340552 TAACACAGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 51 0.78
61 8 0.12
62 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (59 bp):
GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTACAGAGTATACTG
Found at i:40340587 original size:19 final size:20
Alignment explanation
Indices: 40340544--40340589 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40340534 ATTGGGCCTT
40340544 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
40340564 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
40340583 GCCCATA
1 GCCCATA
40340590 ATAAAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:40348228 original size:3 final size:3
Alignment explanation
Indices: 40348222--40348255 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
40348212 TATAATAATA
40348222 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
40348256 ATTAATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:40349531 original size:26 final size:25
Alignment explanation
Indices: 40349502--40349583 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 25
40349492 TGATACAAAT
40349502 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
*
40349528 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
40349554 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
40349580 TGAT
1 TGAT
40349584 GGGAATTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
26 50 0.96
27 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:40363219 original size:23 final size:23
Alignment explanation
Indices: 40363193--40363237 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40363183 AAAGATGAAG
40363193 AAAA-AAATAAGAAAAAAAGGGAA
1 AAAATAAAT-AGAAAAAAAGGGAA
* *
40363216 AAAATAAATGGAAAAACAGGGA
1 AAAATAAATAGAAAAAAAGGGA
40363238 GAAGAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (23 bp):
AAAATAAATAGAAAAAAAGGGAA
Found at i:40376300 original size:17 final size:17
Alignment explanation
Indices: 40376278--40376312 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40376268 ATTACAAAAT
*
40376278 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
40376295 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
40376312 C
1 C
40376313 TTTCCCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:40379134 original size:52 final size:52
Alignment explanation
Indices: 40379051--40379153 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
40379041 ATTTTAGGCC
* *
40379051 TAGTTAGAATAGTGCTTTTAGAACCACTCACCCGAGGTCAGAGAAAATATTA
1 TAGTCAGAATAGTGCTTTCAGAACCACTCACCCGAGGTCAGAGAAAATATTA
*
40379103 TAGTCAGAATAGTGGTTTCAGAACCACTCACCCGAGGTCAGAGAAAATATT
1 TAGTCAGAATAGTGCTTTCAGAACCACTCACCCGAGGTCAGAGAAAATATT
40379154 TTTGATATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (52 bp):
TAGTCAGAATAGTGCTTTCAGAACCACTCACCCGAGGTCAGAGAAAATATTA
Found at i:40380053 original size:30 final size:30
Alignment explanation
Indices: 40380017--40380084 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
40380007 AACACGGGTA
*
40380017 GACACACGAGCGTGTGTCTAGGCCGTGTGT
1 GACACACGAGCGTGTATCTAGGCCGTGTGT
40380047 GACACACGAGCGTGTATCTAGGCCGTGTGT
1 GACACACGAGCGTGTATCTAGGCCGTGTGT
40380077 GACACACG
1 GACACACG
40380085 GCCAGCCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.21
Consensus pattern (30 bp):
GACACACGAGCGTGTATCTAGGCCGTGTGT
Found at i:40390794 original size:16 final size:18
Alignment explanation
Indices: 40390773--40390805 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40390763 CATACTAGCT
40390773 CCAAAAT-ATAG-TAGTA
1 CCAAAATGATAGATAGTA
40390789 CCAAAATGATAGATAGT
1 CCAAAATGATAGATAGT
40390806 GCGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (18 bp):
CCAAAATGATAGATAGTA
Found at i:40391358 original size:41 final size:42
Alignment explanation
Indices: 40391283--40391384 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 42
40391273 AAAACACTGG
* *
40391283 CATTTAGCCTGCTAGGTTTTAAACCCGAGTTCA-TTCACCGA
1 CATTTAGCCTGCTAGGCTTGAAACCCGAGTTCATTTCACCGA
* * *
40391324 CATTTCGCCTGCTAGGCTTGAAACTCGA-TATCATTTCACCGG
1 CATTTAGCCTGCTAGGCTTGAAACCCGAGT-TCATTTCACCGA
40391366 CATTATAGCCTGCTAGGCT
1 CATT-TAGCCTGCTAGGCT
40391385 CGAAGGCCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 27 0.52
42 11 0.21
43 13 0.25
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (42 bp):
CATTTAGCCTGCTAGGCTTGAAACCCGAGTTCATTTCACCGA
Found at i:40397035 original size:23 final size:24
Alignment explanation
Indices: 40397003--40397061 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
40396993 AATTAAACTT
* *
40397003 AAATTTTAAAATT-TTAAAATTACA
1 AAATATTAAAATTCTTAAAAATA-A
40397027 AAA-ATT-AAATTCTTAAAAATAA
1 AAATATTAAAATTCTTAAAAATAA
*
40397049 AAATATAAAAATT
1 AAATATTAAAATT
40397062 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 9 0.31
23 12 0.41
24 8 0.28
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATATTAAAATTCTTAAAAATAA
Found at i:40397059 original size:29 final size:29
Alignment explanation
Indices: 40396975--40397086 Score: 95
Period size: 30 Copynumber: 3.8 Consensus size: 29
40396965 TTATCAATAT
* *
40396975 AATTTT-AATAATAGAAACA-ATTAAACTTA
1 AATTTTAAATAATA-AAA-ATATAAAAATTA
** * *
40397004 AATTTTAAAATTTTAAAATTACAAAAATTA
1 AATTTT-AAATAATAAAAATATAAAAATTA
40397034 AATTCTTAAA-AATAAAAATATAAAAATTA
1 AATT-TTAAATAATAAAAATATAAAAATTA
*
40397063 AATTTTAAATTAAAAAAAATATAA
1 AATTTTAAA-TAATAAAAATATAA
40397087 TTAACCCTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
28 5 0.08
29 25 0.38
30 29 0.44
31 7 0.11
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (29 bp):
AATTTTAAATAATAAAAATATAAAAATTA
Found at i:40397529 original size:67 final size:67
Alignment explanation
Indices: 40397451--40397626 Score: 271
Period size: 67 Copynumber: 2.6 Consensus size: 67
40397441 TAAGTTAAAT
* * *
40397451 TACTTACTAAAACATTTATTCTGAAATGCATATACTTAATTTAATAAAACTTTTCATTGTTTCAA
1 TACTTACTAAAACATTTATTCTGAAATGCATAAACTTAATTTAATAAAACATCTCATTGTTTCAA
40397516 AC
66 AC
* *
40397518 TACTTACTAAAAGATTTATTCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTTCAA
1 TACTTACTAAAACATTTATTCTGAAATGCATAAACTTAATTTAATAAAACATCTCATTGTTTCAA
40397583 AC
66 AC
** *
40397585 TACTTACTAAAACATTTATTCAAAAAATGTATAAACTTAATT
1 TACTTACTAAAACATTTATTC-TGAAATGCATAAACTTAATT
40397627 GTTTTTGTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 82 0.82
68 18 0.18
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (67 bp):
TACTTACTAAAACATTTATTCTGAAATGCATAAACTTAATTTAATAAAACATCTCATTGTTTCAA
AC
Found at i:40398104 original size:67 final size:67
Alignment explanation
Indices: 40397991--40398259 Score: 373
Period size: 67 Copynumber: 4.0 Consensus size: 67
40397981 GATCCCGAAG
* *
40397991 TCAAACTACTTACTAAAACCCTTAGTT-GGAAATGTATAAA-TCTAATTTAATAAAACATCTCAT
1 TCAAACTACTTACTAAAACCTTTA-TTCTGAAATGTATAAACT-TAATTTAATAAAACATCTCAT
40398054 TGTT
64 TGTT
* * * *
40398058 CCAAACTACTTACTAAAACCTTTATTCTGAAATGTATAAACTTAATTTAATAAATCATCTTATTA
1 TCAAACTACTTACTAAAACCTTTATTCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40398123 TT
66 TT
* *
40398125 TTAAACTACTTACTAAAACATTTA-TCTTGAAATGTATAAACTTAATTTAATAAAACATCTCATT
1 TCAAACTACTTACTAAAACCTTTATTC-TGAAATGTATAAACTTAATTTAATAAAACATCTCATT
40398189 GTT
65 GTT
* * * * *
40398192 TAAAACTACTTACTAAAATCTTTATTCAGAAATGTATAAATTTAATTTAATAACACATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATTCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40398257 TT
66 TT
40398259 T
1 T
40398260 TTGTTTCTGT
Statistics
Matches: 180, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
66 4 0.02
67 173 0.96
68 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (67 bp):
TCAAACTACTTACTAAAACCTTTATTCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
TT
Found at i:40398732 original size:67 final size:66
Alignment explanation
Indices: 40398648--40398990 Score: 499
Period size: 67 Copynumber: 5.1 Consensus size: 66
40398638 GATCTCAAAG
** * * *
40398648 TCAAACTACTTACTAAAACCCATATTTGGAAATATATAAATTTAATTTAATAAAATATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATTT-GAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40398713 TT
65 TT
* * *
40398715 TCAAACTATTTAGTAAAACCTTTATTCTAAAATGTATAAACTTAATTTAATAAAACATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATT-TGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40398780 TT
65 TT
40398782 TCAAACTACTTACTAAAACCTTTATTCTGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
1 TCAAACTACTTACTAAAACCTTTATT-TGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40398847 TT
65 TT
* * *
40398849 TCAAACTACTTACTAAAACCCTTATTCAT-AATTGTATAAATTTAATTTAATAAAACATCTCATT
1 TCAAACTACTTACTAAAACCTTTATT--TGAAATGTATAAACTTAATTTAATAAAACATCTCATT
40398913 GTT
64 GTT
* * *
40398916 TCAAACTACTTACTAAAACCTTTATTCCGAAATGTATAAACTTAATTTAAAAAAACATATCATTG
1 TCAAACTACTTACTAAAACCTTTATT-TGAAATGTATAAACTTAATTTAATAAAACATCTCATTG
40398981 TT
65 TT
40398983 TCAAACTA
1 TCAAACTA
40398991 TTGATGTGGA
Statistics
Matches: 251, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
67 249 0.99
68 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (66 bp):
TCAAACTACTTACTAAAACCTTTATTTGAAATGTATAAACTTAATTTAATAAAACATCTCATTGT
T
Found at i:40404178 original size:67 final size:67
Alignment explanation
Indices: 40404070--40404201 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
40404060 GGTGTATAAC
*
40404070 AACTACTTACTAAAACCTTTATTCCAAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTT
1 AACTACTTACTAAAACATTTATTCCAAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTT
40404135 CA
66 CA
*
40404137 AACTACTTACTAAAACATTTATTCGAAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTT
1 AACTACTTACTAAAACATTTATTCCAAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTT
40404202 TTTTTTTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (67 bp):
AACTACTTACTAAAACATTTATTCCAAAATGTATAAACTTAATTTAATAAAACATCTCATTGTTT
CA
Found at i:40404288 original size:21 final size:21
Alignment explanation
Indices: 40404262--40404304 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40404252 CACATTGCAC
40404262 TCAATTTCTCTGTTTCAGACA
1 TCAATTTCTCTGTTTCAGACA
40404283 TCAATTTCTCTGTTTCAGACA
1 TCAATTTCTCTGTTTCAGACA
40404304 T
1 T
40404305 TGGTTGGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (21 bp):
TCAATTTCTCTGTTTCAGACA
Found at i:40415328 original size:30 final size:30
Alignment explanation
Indices: 40415292--40415351 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40415282 TTCCCGAGCC
40415292 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
40415322 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
40415352 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:40421725 original size:17 final size:17
Alignment explanation
Indices: 40421703--40421738 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40421693 AAGATCCATG
40421703 ATGTGTTCCACGTATCT
1 ATGTGTTCCACGTATCT
40421720 ATGTGTTCCACGTATCT
1 ATGTGTTCCACGTATCT
40421737 AT
1 AT
40421739 ATTACGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (17 bp):
ATGTGTTCCACGTATCT
Found at i:40423350 original size:47 final size:47
Alignment explanation
Indices: 40423299--40423475 Score: 202
Period size: 47 Copynumber: 3.8 Consensus size: 47
40423289 TGGTTGAACA
*
40423299 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
40423346 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
*
40423393 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * * *
40423439 CCCGAGCTCGTTGAGTTGATTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40423476 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 1 0.01
46 36 0.33
47 58 0.53
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:40427650 original size:30 final size:31
Alignment explanation
Indices: 40427608--40427681 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 31
40427598 AAATTACATC
* *
40427608 AAAAATCACTCAATTTTGATCTTAATGACAA
1 AAAAATCACTCAAATTTGATCTCAATGACAA
40427639 AAAAATC-CTCAAATTTGATCTCAATGACAA
1 AAAAATCACTCAAATTTGATCTCAATGACAA
*
40427669 AACAATCACTCAA
1 AAAAATCACTCAA
40427682 CTTTCAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 27 0.69
31 12 0.31
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAAATCACTCAAATTTGATCTCAATGACAA
Found at i:40428552 original size:29 final size:29
Alignment explanation
Indices: 40428495--40428553 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
40428485 AAGTATAAGG
*
40428495 ATATTGGGTCATTTATGTAAAAAGTAAAA
1 ATATTGGGTCATTTATGTAAAAAGCAAAA
40428524 ATATTGGGTCATTTAT-TAAAAAGACAAAA
1 ATATTGGGTCATTTATGTAAAAAG-CAAAA
40428553 A
1 A
40428554 AGGAAGGACG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.32
Consensus pattern (29 bp):
ATATTGGGTCATTTATGTAAAAAGCAAAA
Found at i:40428875 original size:175 final size:174
Alignment explanation
Indices: 40428571--40428907 Score: 428
Period size: 175 Copynumber: 1.9 Consensus size: 174
40428561 ACGAAAAAAA
* * * * * *
40428571 TTTGTCTCGTCTAACGTGGTAAGTTAACTAGCCACATTAGCTAGTTCACTGGCCACGTCACCTAT
1 TTTGTCTCGTCCAACATGGTAAGTTAACTAGCCACATCAGCTAGTTAACTAGCCACATCACCTAT
*
40428636 CCCGTTAGACCTGTAACAGAAAATGTTAATGAGTGACTGATTTGTAATTTTTCGATAACGTTAGT
66 CCCGTTAGACCTATAACAGAAAATGTTAATGAGTGACTGATTTGTAATTTTTCGATAACGTTAGT
40428701 GACTAATTTGTTATTTTTTGAAAGTTGAGTGAATAAATTGCAAC
131 GACTAATTTGTTATTTTTTGAAAGTTGAGTGAATAAATTGCAAC
* * **
40428745 TTTGTCTCGTCCAACATGGTAAGTTAAATTGGCCA-AGTCAGCTAGTTAACTAGCCACATCATTT
1 TTTGTCTCGTCCAACATGGTAAGTT-AACTAGCCACA-TCAGCTAGTTAACTAGCCACATCACCT
* * * * ** * *
40428809 GTTCCGTTAGGCCTATAAC-GAAAAATGTTCATGAGTGGTTGATTTGTCACTTTTT-GATAGCGT
64 ATCCCGTTAGACCTATAACAG-AAAATGTTAATGAGTGACTGATTTGT-AATTTTTCGATAACGT
* *
40428872 TAGTGATTGATTTGTTATTTTTTGAAAGTTGAGTGA
127 TAGTGACTAATTTGTTATTTTTTGAAAGTTGAGTGA
40428908 CTGAATTGAA
Statistics
Matches: 138, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
174 25 0.18
175 107 0.78
176 6 0.04
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (174 bp):
TTTGTCTCGTCCAACATGGTAAGTTAACTAGCCACATCAGCTAGTTAACTAGCCACATCACCTAT
CCCGTTAGACCTATAACAGAAAATGTTAATGAGTGACTGATTTGTAATTTTTCGATAACGTTAGT
GACTAATTTGTTATTTTTTGAAAGTTGAGTGAATAAATTGCAAC
Found at i:40428907 original size:30 final size:32
Alignment explanation
Indices: 40428840--40428907 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
40428830 AAAATGTTCA
* *
40428840 TGAGTGGTTGATTTGTCACTTTTTGATAGCGT
1 TGAGTGATTGATTTGTCACTTTTTGATAGAGT
* *
40428872 T-AGTGATTGATTTGTTATTTTTTGA-A-AGT
1 TGAGTGATTGATTTGTCACTTTTTGATAGAGT
40428901 TGAGTGA
1 TGAGTGA
40428908 CTGAATTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 3 0.10
30 6 0.19
31 21 0.68
32 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (32 bp):
TGAGTGATTGATTTGTCACTTTTTGATAGAGT
Found at i:40433632 original size:21 final size:21
Alignment explanation
Indices: 40433606--40433686 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 21
40433596 AACGGAAGCA
* *
40433606 CATAAGTGCTAAACAGAAACC
1 CATAAGGGTTAAACAGAAACC
* * *
40433627 CATAAGGGTTGAACGGAAACT
1 CATAAGGGTTAAACAGAAACC
* * *
40433648 CATAAGTGTTGAACGGAAACC
1 CATAAGGGTTAAACAGAAACC
40433669 CATAAGGGTTAAACAGAA
1 CATAAGGGTTAAACAGAA
40433687 CCTCAAAAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
CATAAGGGTTAAACAGAAACC
Found at i:40433641 original size:42 final size:42
Alignment explanation
Indices: 40433594--40433678 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
40433584 GCTCGAAGGC
*
40433594 TGAACGGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TGAACGGAAACACATAAGTGCTAAACAGAAACCCATAAGGGT
* * * *
40433636 TGAACGGAAACTCATAAGTGTTGAACGGAAACCCATAAGGGT
1 TGAACGGAAACACATAAGTGCTAAACAGAAACCCATAAGGGT
40433678 T
1 T
40433679 AAACAGAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (42 bp):
TGAACGGAAACACATAAGTGCTAAACAGAAACCCATAAGGGT
Found at i:40433703 original size:42 final size:42
Alignment explanation
Indices: 40433621--40433723 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
40433611 GTGCTAAACA
* * * * *
40433621 GAAACCCATAAGGGTTGAACGGAAACTCATAAGTGTTGAACG
1 GAAACCCATAAGGGTTAAACAGAAACTCAAAAGAGCTGAACG
*
40433663 GAAACCCATAAGGGTTAAACAGAACCTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAACTCAAAAGAGCTGAACG
* * *
40433705 GAAACTCATATGAGTTAAA
1 GAAACCCATAAGGGTTAAA
40433724 TAAAAGCTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACAGAAACTCAAAAGAGCTGAACG
Found at i:40433703 original size:63 final size:63
Alignment explanation
Indices: 40433594--40433714 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
40433584 GCTCGAAGGC
* * * * *
40433594 TGAACGGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGGAAACTCATAAGTGT
1 TGAACGGAAACACATAAGGGCTAAACAGAAACCCAAAAGAGCTGAACGGAAACTCATAAGTGT
* *
40433657 TGAACGGAAACCCATAAGGGTTAAACAG-AACCTCAAAAGAGCTGAACGGAAACTCATA
1 TGAACGGAAACACATAAGGGCTAAACAGAAACC-CAAAAGAGCTGAACGGAAACTCATA
40433715 TGAGTTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 4 0.08
63 46 0.92
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (63 bp):
TGAACGGAAACACATAAGGGCTAAACAGAAACCCAAAAGAGCTGAACGGAAACTCATAAGTGT
Found at i:40439178 original size:30 final size:30
Alignment explanation
Indices: 40439143--40439225 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
40439133 TCCAGTGGCT
** * *
40439143 GGCTGCTGCTGCTGCTGAGGCTG-GGATTGT
1 GGCTGCTGCTGAGGCTGAGACTGTGG-CTGT
40439173 GGCTGCTGCTGAGGCTGAGACTGTGGCTGT
1 GGCTGCTGCTGAGGCTGAGACTGTGGCTGT
*
40439203 GGCTGCTGC-GAAGACTGAGACTG
1 GGCTGCTGCTG-AGGCTGAGACTG
40439226 AGACTGAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.02
30 43 0.93
31 2 0.04
ACGTcount: A:0.12, C:0.20, G:0.42, T:0.25
Consensus pattern (30 bp):
GGCTGCTGCTGAGGCTGAGACTGTGGCTGT
Found at i:40439207 original size:24 final size:24
Alignment explanation
Indices: 40439150--40439201 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
40439140 GCTGGCTGCT
* *
40439150 GCTGCTGCTGAGGCTGGGATTGTG
1 GCTGCTGCTGAGGCTGAGACTGTG
40439174 GCTGCTGCTGAGGCTGAGACTGTG
1 GCTGCTGCTGAGGCTGAGACTGTG
40439198 GCTG
1 GCTG
40439202 TGGCTGCTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.10, C:0.19, G:0.44, T:0.27
Consensus pattern (24 bp):
GCTGCTGCTGAGGCTGAGACTGTG
Found at i:40442356 original size:29 final size:29
Alignment explanation
Indices: 40442299--40442362 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
40442289 ATAAAATATG
* * *
40442299 GAACTCGTCGAAGGAAGCTCCTAAACTTA
1 GAACTCGTCAAAGGAAGCACCGAAACTTA
* *
40442328 GAACTCGTCAAAGGGAGCACCGAATCTTA
1 GAACTCGTCAAAGGAAGCACCGAAACTTA
40442357 G-ACTCG
1 GAACTCG
40442363 AAAGAAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (29 bp):
GAACTCGTCAAAGGAAGCACCGAAACTTA
Found at i:40448646 original size:80 final size:80
Alignment explanation
Indices: 40448511--40448669 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 80
40448501 CAACACAGTT
40448511 GATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACCACCACAATACCTAGGTAGGCAAAA
1 GATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACCACCACAATACCTAGGTAGGCAAAA
*
40448576 CTTCCATAGTTCTCA
66 CTTCCACAGTTCTCA
*
40448591 GATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACCACCACAATATCTAGGTAGGCAAAA
1 GATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACCACCACAATACCTAGGTAGGCAAAA
40448656 CTTCCACAGTTCTC
66 CTTCCACAGTTCTC
40448670 CCATTGATAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.21
Consensus pattern (80 bp):
GATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACCACCACAATACCTAGGTAGGCAAAA
CTTCCACAGTTCTCA
Found at i:40448767 original size:195 final size:197
Alignment explanation
Indices: 40448427--40448783 Score: 549
Period size: 195 Copynumber: 1.8 Consensus size: 197
40448417 ACTTCCAGCA
* * * * * *
40448427 CTAACCACCACAATACCAAAGTAGGGAAAATTTCGACTGTTCTTCCATTGAATATTTTAATGTGT
1 CTAACCACCACAATACCAAAGTAGGCAAAACTTCCACAGTTCTCCCATTGAATATCTTAATGTGT
* *
40448492 CCCAACTCCCAACACAGTTGATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACCACCAC
66 CCCAACT--CAACACAATTGATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACAACCAC
40448557 AATACCTAGGTAGGCAAAACTTCCATAGTTCTCAGATTTTCAGAAACACAATACACCAAGACTCC
129 AATACCTAGGTAGGCAAAACTTCCATAGTTCTCAGATTTTCAGAAACACAATACACCAAGACTCC
40448622 AGTC
194 AGTC
* * *
40448626 CTAACCACCACAATATCTAGGTAGGCAAAACTTCCACAGTTCTCCCATTG-ATATCTTAATGTGT
1 CTAACCACCACAATACCAAAGTAGGCAAAACTTCCACAGTTCTCCCATTGAATATCTTAATGTGT
*
40448690 CCCAACT-AACACAATTGATTTTCCGAAACACAATACACCAAGACTCCAGTCCTAACAACCACAA
66 CCCAACTCAACACAATTGATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACAACCACAA
*
40448754 TACCTCA-GTAGGCAAAACTTCCATATTTCT
131 TACCT-AGGTAGGCAAAACTTCCATAGTTCT
40448784 TCCATTGAAT
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
195 81 0.56
196 1 0.01
198 20 0.14
199 42 0.29
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.25
Consensus pattern (197 bp):
CTAACCACCACAATACCAAAGTAGGCAAAACTTCCACAGTTCTCCCATTGAATATCTTAATGTGT
CCCAACTCAACACAATTGATTTTCAGAAACACAATACACCAAGACTCCAGTCCTAACAACCACAA
TACCTAGGTAGGCAAAACTTCCATAGTTCTCAGATTTTCAGAAACACAATACACCAAGACTCCAG
TC
Found at i:40449401 original size:21 final size:21
Alignment explanation
Indices: 40449377--40449416 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
40449367 TTCAATTCCA
40449377 CTTCTACTTATTTTCTTAGAG
1 CTTCTACTTATTTTCTTAGAG
40449398 CTTCTACTTATTTTCTTAG
1 CTTCTACTTATTTTCTTAG
40449417 CAGCCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.55
Consensus pattern (21 bp):
CTTCTACTTATTTTCTTAGAG
Found at i:40449813 original size:19 final size:18
Alignment explanation
Indices: 40449761--40449822 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
40449751 TGACTCTAAT
*
40449761 ATTTAATTTGATATTTAAA
1 ATTTAATTTAATATTT-AA
40449780 ATTTTTTAATTTAATATTTAA
1 A---TTTAATTTAATATTTAA
*
40449801 ATTTAATTTTAATGTTTAA
1 ATTTAA-TTTAATATTTAA
40449820 ATT
1 ATT
40449823 AGAATCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.14
19 15 0.41
21 3 0.08
22 14 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTAATTTAATATTTAA
Found at i:40449819 original size:13 final size:13
Alignment explanation
Indices: 40449757--40449812 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 13
40449747 AGTTTGACTC
40449757 TAATATTT-AATT
1 TAATATTTAAATT
* *
40449769 TGATATTTAAAAT
1 TAATATTTAAATT
40449782 T--T-TTT-AATT
1 TAATATTTAAATT
40449791 TAATATTTAAATT
1 TAATATTTAAATT
40449804 TAAT-TTTAA
1 TAATATTTAA
40449813 TGTTTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
9 4 0.11
10 3 0.08
11 2 0.06
12 15 0.42
13 12 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TAATATTTAAATT
Found at i:40450303 original size:18 final size:19
Alignment explanation
Indices: 40450266--40450303 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
40450256 TTTTTTTAAA
* *
40450266 TATGTTTGTTAAAAAGTTT
1 TATGTTTGTAAAAAAATTT
40450285 TATGTTT-TAAAAAAATTT
1 TATGTTTGTAAAAAAATTT
40450303 T
1 T
40450304 GTTAGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (19 bp):
TATGTTTGTAAAAAAATTT
Found at i:40451607 original size:19 final size:19
Alignment explanation
Indices: 40451544--40451607 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
40451534 CTTATGCGCC
*
40451544 AGGATGCACTTTGTACGTC
1 AGGATGCACTTTGTACGTT
* * ** *
40451563 AAGATGCACTTTATGTGCT
1 AGGATGCACTTTGTACGTT
*
40451582 AGTATGCACTTTGTACGTT
1 AGGATGCACTTTGTACGTT
40451601 AGGATGC
1 AGGATGC
40451608 GTTTCGAGCA
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (19 bp):
AGGATGCACTTTGTACGTT
Found at i:40453920 original size:3 final size:3
Alignment explanation
Indices: 40453882--40453967 Score: 65
Period size: 3 Copynumber: 29.7 Consensus size: 3
40453872 AAATTATATA
* * *
40453882 TAT TA- TAT TA- TAT TA- TAT AAT TGAT TAT TAT AAT TAT TAAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT
** *
40453926 TAT GGT T-T TA- TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40453968 AATAAATTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
2 10 0.15
3 49 0.75
4 6 0.09
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:40454457 original size:6 final size:5
Alignment explanation
Indices: 40454428--40454492 Score: 53
Period size: 5 Copynumber: 12.4 Consensus size: 5
40454418 TTTATTAATT
*
40454428 AAATA TAATA TAAATA AAATA AAATA AAA-A GAAATA AAGCATA AAAT-
1 AAATA AAATA -AAATA AAATA AAATA AAATA -AAATA AA--ATA AAATA
*
40454475 AAATA GAAACA AAATA AA
1 AAATA -AAATA AAATA AA
40454493 CAGAAAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
4 5 0.10
5 30 0.61
6 9 0.18
7 5 0.10
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:40454474 original size:22 final size:20
Alignment explanation
Indices: 40454439--40454492 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
40454429 AATATAATAT
40454439 AAATAAAATAAAATAAAAAG
1 AAATAAAATAAAATAAAAAG
*
40454459 AAATAAAGCATAAAATAAATAG
1 AAATAAA--ATAAAATAAAAAG
*
40454481 AAACAAAATAAA
1 AAATAAAATAAA
40454493 CAGAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.15
Consensus pattern (20 bp):
AAATAAAATAAAATAAAAAG
Found at i:40454566 original size:16 final size:17
Alignment explanation
Indices: 40454539--40454574 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40454529 AAAAAGAGAA
40454539 AGAAAAAGGGAAAAAAT
1 AGAAAAAGGGAAAAAAT
*
40454556 AGAAAAA-GGAAAAACT
1 AGAAAAAGGGAAAAAAT
40454572 AGA
1 AGA
40454575 GATTTAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.06
Consensus pattern (17 bp):
AGAAAAAGGGAAAAAAT
Found at i:40455574 original size:12 final size:12
Alignment explanation
Indices: 40455557--40455581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40455547 GCCGACTACT
40455557 GTTACTGTTACC
1 GTTACTGTTACC
40455569 GTTACTGTTACC
1 GTTACTGTTACC
40455581 G
1 G
40455582 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:40455611 original size:45 final size:45
Alignment explanation
Indices: 40455559--40455671 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
40455549 CGACTACTGT
*
40455559 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* ** *
40455604 TTCTGTTACCACTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
40455649 TACTGTTACTGTTACTGCTACAG
1 TACTGTTACCGTTACTGTTACAG
40455672 CTACCGTTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 56 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:40459690 original size:2 final size:2
Alignment explanation
Indices: 40459683--40459717 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40459673 ACATATGCTT
40459683 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40459718 TTTCACGAGC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40462050 original size:17 final size:17
Alignment explanation
Indices: 40462028--40462066 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40462018 TCTTGATCGT
40462028 GGTGCAT-GCAAGGCAAG
1 GGTGCATGGCAA-GCAAG
*
40462045 GGTGCATGGCTAGCAAG
1 GGTGCATGGCAAGCAAG
40462062 GGTGC
1 GGTGC
40462067 GCACGGGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.23, C:0.18, G:0.44, T:0.15
Consensus pattern (17 bp):
GGTGCATGGCAAGCAAG
Found at i:40469745 original size:25 final size:25
Alignment explanation
Indices: 40469699--40469756 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
40469689 TAGCTTGTGA
* * *
40469699 GAGCATACCGATCCATATCTCGAGT
1 GAGCATACCGATCCACAACTCGACT
* *
40469724 GAGCATACCGATTCACAACTCGTCT
1 GAGCATACCGATCCACAACTCGACT
40469749 GAGCATAC
1 GAGCATAC
40469757 ATGTACATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (25 bp):
GAGCATACCGATCCACAACTCGACT
Done.