Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold68
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: 494511
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:144690 original size:14 final size:14
Alignment explanation
Indices: 144612--144770 Score: 55
Period size: 14 Copynumber: 11.5 Consensus size: 14
144602 GAAAGAAAAC
144612 ATGCATGAAATGTA
1 ATGCATGAAATGTA
* *
144626 ATGTATGAAATGAA
1 ATGCATGAAATGTA
* * *
144640 CATTACGTGAAATG-C
1 -A-TGCATGAAATGTA
*
144655 ATGCGTGAAATGTA
1 ATGCATGAAATGTA
* *
144669 ATGTATGAAATG-C
1 ATGCATGAAATGTA
*
144682 ATGAAATGAAAAT-T-
1 ATG-CATG-AAATGTA
*
144696 ATG--TGAAATG-C
1 ATGCATGAAATGTA
* *
144707 ATACATAAAATGTA
1 ATGCATGAAATGTA
*
144721 ATGCATGAAATGAAA
1 ATGCATGAAATG-TA
* * * *
144736 ATTACGTAAAATG-C
1 A-TGCATGAAATGTA
144750 ATGCATGAAATGTA
1 ATGCATGAAATGTA
144764 ATGCATG
1 ATGCATG
144771 CAATATTTAT
Statistics
Matches: 105, Mismatches: 26, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
10 4 0.04
11 4 0.04
13 27 0.26
14 47 0.45
15 7 0.07
16 16 0.15
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (14 bp):
ATGCATGAAATGTA
Found at i:144691 original size:52 final size:52
Alignment explanation
Indices: 144625--144732 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
144615 CATGAAATGT
* * * * * *
144625 AATGTATGAAATGAACATTACGTGAAATGCATGCGTGAAATGTAATGTATGA
1 AATGCATGAAATGAAAATTACGTGAAATGCATACATAAAATGTAATGCATGA
*
144677 AATGCATGAAATGAAAATTATGTGAAATGCATACATAAAATGTAATGCATGA
1 AATGCATGAAATGAAAATTACGTGAAATGCATACATAAAATGTAATGCATGA
144729 AATG
1 AATG
144733 AAAATTACGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (52 bp):
AATGCATGAAATGAAAATTACGTGAAATGCATACATAAAATGTAATGCATGA
Found at i:144730 original size:43 final size:43
Alignment explanation
Indices: 144677--144770 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
144667 TAATGTATGA
* *
144677 AATGCATGAAATGAAAATTATGTGAAATGCATACATAAAATGT
1 AATGCATGAAATGAAAATTACGTAAAATGCATACATAAAATGT
* *
144720 AATGCATGAAATGAAAATTACGTAAAATGCATGCATGAAATGT
1 AATGCATGAAATGAAAATTACGTAAAATGCATACATAAAATGT
144763 AATGCATG
1 AATGCATG
144771 CAATATTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.27
Consensus pattern (43 bp):
AATGCATGAAATGAAAATTACGTAAAATGCATACATAAAATGT
Found at i:144885 original size:22 final size:22
Alignment explanation
Indices: 144857--144899 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
144847 TATTTATTTA
144857 TTTTTTATAAATGTTAAATAAT
1 TTTTTTATAAATGTTAAATAAT
144879 TTTTTTATAAATGTTAAATAA
1 TTTTTTATAAATGTTAAATAA
144900 ACCAACGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTTTTATAAATGTTAAATAAT
Found at i:146817 original size:33 final size:33
Alignment explanation
Indices: 146775--146843 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
146765 GCCATTGGGC
* * * *
146775 ACAATGTATCGATACTTTTTACCATGTATTGAT
1 ACAATGTATCAATACTGTGTACCATGTATCGAT
*
146808 ACAATGTATCAATACTGTGTCCCATGTATCGAT
1 ACAATGTATCAATACTGTGTACCATGTATCGAT
146841 ACA
1 ACA
146844 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (33 bp):
ACAATGTATCAATACTGTGTACCATGTATCGAT
Found at i:146915 original size:19 final size:20
Alignment explanation
Indices: 146872--146925 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
146862 CTGCCGGTTT
*
146872 CATGTATTGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
146892 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
146911 CATGTATCGATACAA
1 CATGTATCGATACAA
146926 CCGATACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:148916 original size:51 final size:51
Alignment explanation
Indices: 148852--149016 Score: 188
Period size: 51 Copynumber: 3.2 Consensus size: 51
148842 AAAATAACAG
* * *
148852 GGTTGGAGTATCCCCGATGGTGGACAATTGGTGTTTCAGAAATAAAACCGA
1 GGTTGGAGTATCCCTGATGGTGGAAAATTGGTGTTTTAGAAATAAAACCGA
* * *
148903 GGTTGGAGTATCCCTAATGGTGGAAAATTGATGTTTTAGAAATAAAA-CTA
1 GGTTGGAGTATCCCTGATGGTGGAAAATTGGTGTTTTAGAAATAAAACCGA
* * * ** * * *
148953 GGGTTGGAGTATTCCTGGTGGTAGAAAATCAGTGTTTTGGAAATAAAACTGG
1 -GGTTGGAGTATCCCTGATGGTGGAAAATTGGTGTTTTAGAAATAAAACCGA
149005 GGTTGGAGTATC
1 GGTTGGAGTATC
149017 TCCTCGAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
50 2 0.02
51 92 0.98
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCTGATGGTGGAAAATTGGTGTTTTAGAAATAAAACCGA
Found at i:148918 original size:78 final size:77
Alignment explanation
Indices: 148746--148919 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 77
148736 ATAAAAAATG
* ** * * *
148746 GGTTGGCGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCGATTGTGGAAAATCGATGTTTTA
1 GGTTGGAGTATCCC-TAAAAAATAACAGGGTTGGAGTATCCCGATGGTGGAAAATCGATGTTTCA
*
148811 GAAATAAAATCGA
65 GAAATAAAACCGA
* * *
148824 GGTTGGAGTATCCCCTAAAAAATAACAGGGTTGGAGTATCCCCGATGGTGGACAATTGGTGTTTC
1 GGTTGGAGTAT-CCCTAAAAAATAACAGGGTTGGAGTAT-CCCGATGGTGGAAAATCGATGTTTC
148889 AGAAATAAAACCGA
64 AGAAATAAAACCGA
148903 GGTTGGAGTATCCCTAA
1 GGTTGGAGTATCCCTAA
148920 TGGTGGAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
78 37 0.44
79 47 0.56
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (77 bp):
GGTTGGAGTATCCCTAAAAAATAACAGGGTTGGAGTATCCCGATGGTGGAAAATCGATGTTTCAG
AAATAAAACCGA
Found at i:149035 original size:28 final size:28
Alignment explanation
Indices: 149002--149076 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
148992 GAAATAAAAC
*
149002 TGGGGTTGGAGTATCTCCTCGAAAATAA
1 TGGGGTTGGAGTATCCCCTCGAAAATAA
*
149030 TGGGGTTGGAGTATCCCCTCGAAAATGA
1 TGGGGTTGGAGTATCCCCTCGAAAATAA
* * *
149058 CGAGGTTAGAGTATCCCCT
1 TGGGGTTGGAGTATCCCCT
149077 GTTAGGATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (28 bp):
TGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:149476 original size:13 final size:13
Alignment explanation
Indices: 149458--149483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
149448 TACAGCAAGT
149458 ATGTATCGATACA
1 ATGTATCGATACA
149471 ATGTATCGATACA
1 ATGTATCGATACA
149484 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:149932 original size:15 final size:15
Alignment explanation
Indices: 149912--149942 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
149902 TAAAAATGTC
*
149912 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
149927 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
149942 C
1 C
149943 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:151974 original size:20 final size:20
Alignment explanation
Indices: 151948--152047 Score: 92
Period size: 20 Copynumber: 4.7 Consensus size: 20
151938 AATGTCCAAA
151948 ATGTATCGATACATATTTCT
1 ATGTATCGATACATATTTCT
* *
151968 GTGTATCGATACATGTTTCT
1 ATGTATCGATACATATTTCT
* *
151988 ATGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACA--T---ATTTCT
*
152013 ATGTATCGATACATTTTTTCT
1 ATGTATCGATACA-TATTTCT
*
152034 TTGTATCGATACAT
1 ATGTATCGATACAT
152048 TGTATCGATA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
20 31 0.48
21 15 0.23
22 1 0.02
24 1 0.02
25 16 0.25
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATATTTCT
Found at i:152052 original size:13 final size:13
Alignment explanation
Indices: 152034--152059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152024 CATTTTTTCT
152034 TTGTATCGATACA
1 TTGTATCGATACA
152047 TTGTATCGATACA
1 TTGTATCGATACA
152060 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:154631 original size:13 final size:13
Alignment explanation
Indices: 154613--154638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
154603 TACAGCAAGT
154613 ATGTATCGATACA
1 ATGTATCGATACA
154626 ATGTATCGATACA
1 ATGTATCGATACA
154639 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:155560 original size:77 final size:77
Alignment explanation
Indices: 155411--155560 Score: 191
Period size: 77 Copynumber: 1.9 Consensus size: 77
155401 GGAAAATCGG
*
155411 TGTTTTGGAAATAAAATCGAGGTTGGAGTATCCTCTCAAAAATAACGAGGTTGGAGTATCTCCAA
1 TGTTTTGGAAATAAAATAGAGGTTGGAGTATCCTCTCAAAAATAACGAGGTTGGAGTATCTCCAA
*
155476 TTGTGAAATTGA
66 TTATGAAATTGA
* *
155488 TGTTTTGGAAATAAAACTAG-GGTTGGAGTATCC-C-CATGGAAATAACGGGGTTGGAGTATC-C
1 TGTTTTGGAAATAAAA-TAGAGGTTGGAGTATCCTCTCA--AAAATAACGAGGTTGGAGTATCTC
*
155549 TCGATTATGAAA
63 -CAATTATGAAA
155561 AATCAATGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
75 2 0.03
76 2 0.03
77 58 0.91
78 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (77 bp):
TGTTTTGGAAATAAAATAGAGGTTGGAGTATCCTCTCAAAAATAACGAGGTTGGAGTATCTCCAA
TTATGAAATTGA
Found at i:157991 original size:50 final size:50
Alignment explanation
Indices: 157911--158044 Score: 137
Period size: 50 Copynumber: 2.7 Consensus size: 50
157901 AAAATGCCTA
* * * *
157911 AATGTATTGATACATTGAGAAATGTTTCGATACA-TCTAGGTAAAACCCAG
1 AATGTATCGATACAATGA-AAATATATCGATACATTCTAGGTAAAACCCAG
* *** *
157961 AATGTATCGATACAATGAATAATATATCGATACATTCTGGGTTTTACCTAG
1 AATGTATCGATACAATGAA-AATATATCGATACATTCTAGGTAAAACCCAG
*
158012 -ATGTATCGATACAATGAAGAATTTATCGATACA
1 AATGTATCGATACAATGAA-AATATATCGATACA
158045 AATTATGAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 59 0.83
51 11 0.15
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (50 bp):
AATGTATCGATACAATGAAAATATATCGATACATTCTAGGTAAAACCCAG
Found at i:158674 original size:40 final size:40
Alignment explanation
Indices: 158618--158834 Score: 135
Period size: 40 Copynumber: 5.7 Consensus size: 40
158608 AAAGGAGGTC
*
158618 GTCCTGCT-CTTCGAGGACAAAGGAAAAGAGAATGAAATGG
1 GTCCTACTCCTTCGAGGACAAAGGAAAAGAGAATGAAAT-G
* * *
158658 GTCCTGCTCCTT-GAGGACAAAGGAAAA-AGGA-GTACA--
1 GTCCTACTCCTTCGAGGACAAAGGAAAAGAGAATG-AAATG
* * * * *
158694 -TCCT-GTTCTTCGAGGATAAAGGAAAAAAGGAAATAAAATG
1 GTCCTACTCCTTCGAGGACAAAGGAAAAGA-G-AATGAAATG
* *
158734 CGTCCTACT-CTTTGAGGACAAAGGAAAATGAG--T-ACA--
1 -GTCCTACTCCTTCGAGGACAAAGGAAAA-GAGAATGAAATG
*
158770 -TCCTACT-CTTCGAGGACAAAAGAAAAGAGAATGAAATGG
1 GTCCTACTCCTTCGAGGACAAAGGAAAAGAGAATGAAAT-G
*
158809 GTCCTACTCCTT-GAAGACAAAGGAAA
1 GTCCTACTCCTTCGAGGACAAAGGAAA
158835 TAGAAGTGCA
Statistics
Matches: 138, Mismatches: 18, Indels: 42
0.70 0.09 0.21
Matches are distributed among these distances:
33 3 0.02
34 28 0.20
35 19 0.14
36 3 0.02
37 1 0.01
38 6 0.04
39 6 0.04
40 42 0.30
41 6 0.04
42 22 0.16
43 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (40 bp):
GTCCTACTCCTTCGAGGACAAAGGAAAAGAGAATGAAATG
Found at i:158704 original size:75 final size:74
Alignment explanation
Indices: 158594--158870 Score: 349
Period size: 75 Copynumber: 3.7 Consensus size: 74
158584 GCCCTGCTTT
* *
158594 TTGAAGACAAAGGAAAAGGAGGT-CGTCCTGCTCTTCGAGGACAAAGGAAAAGAGAATGAAATGG
1 TTGAAGACAAAGGAAAAGGA-GTACATCCTACTCTTCGAGGACAAAGGAAAAGAGAATGAAATGG
*
158658 GTCCTGCTCC
65 GTCCTACTCC
* ** * * *
158668 TTGAGGACAAAGGAAAAAGGAGTACATCCTGTTCTTCGAGGATAAAGGAAAAAAGGAAATAAAAT
1 TTGAAGACAAAGG-AAAAGGAGTACATCCTACTCTTCGAGGACAAAGGAAAAGA-G-AATGAAAT
* *
158733 GCGTCCTACTCT
63 GGGTCCTACTCC
* * *
158745 TTGAGGACAAAGGAAAATGAGTACATCCTACTCTTCGAGGACAAAAGAAAAGAGAATGAAATGGG
1 TTGAAGACAAAGGAAAAGGAGTACATCCTACTCTTCGAGGACAAAGGAAAAGAGAATGAAATGGG
158810 TCCTACTCC
66 TCCTACTCC
* * *
158819 TTGAAGACAAAGGAAATAGAAGTGCATCCTACTCTTCGATGACAAAGGAAAA
1 TTGAAGACAAAGGAAA-AGGAGTACATCCTACTCTTCGAGGACAAAGGAAAA
158871 AAAGGAAAAA
Statistics
Matches: 174, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
74 46 0.26
75 64 0.37
76 35 0.20
77 29 0.17
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (74 bp):
TTGAAGACAAAGGAAAAGGAGTACATCCTACTCTTCGAGGACAAAGGAAAAGAGAATGAAATGGG
TCCTACTCC
Found at i:158774 original size:34 final size:34
Alignment explanation
Indices: 158736--158870 Score: 105
Period size: 34 Copynumber: 3.8 Consensus size: 34
158726 ATAAAATGCG
*
158736 TCCTACTCTTTGAGGACAAAGGAAAATGAGTACA
1 TCCTACTCTTCGAGGACAAAGGAAAATGAGTACA
* *
158770 TCCTACTCTTCGAGGACAAAAGAAAA-GAGAATGAAA
1 TCCTACTCTTCGAGGACAAAGGAAAATGAG--T-ACA
* *
158806 TGGGTCCTACTCCTT-GAAGACAAAGG-AAATAGAAGTGCA
1 ----TCCTACT-CTTCGAGGACAAAGGAAAAT-G-AGTACA
*
158845 TCCTACTCTTCGATGACAAAGGAAAA
1 TCCTACTCTTCGAGGACAAAGGAAAA
158871 AAAGGAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 24
0.71 0.07 0.21
Matches are distributed among these distances:
33 3 0.04
34 27 0.34
35 18 0.22
36 5 0.06
39 4 0.05
40 17 0.21
41 4 0.05
42 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (34 bp):
TCCTACTCTTCGAGGACAAAGGAAAATGAGTACA
Found at i:158867 original size:151 final size:151
Alignment explanation
Indices: 158593--158898 Score: 445
Period size: 151 Copynumber: 2.0 Consensus size: 151
158583 CGCCCTGCTT
* * *
158593 TTTGAAGACAAAGGAAAAGGAGGTCGTCCTGCTCTTCGAGGACAAAGGAAAAGAGAATGAAATGG
1 TTTGAAGACAAAGGAAAAGGAGGTCATCCTACTCTTCGAGGACAAAAGAAAAGAGAATGAAATGG
* * * ** *
158658 GTCCTGCTCCTTGAGGACAAAGGAAAAAGGAGTACATCCTGTTCTTCGAGGATAAAGG-AAAAAA
66 GTCCTACTCCTTGAAGACAAAGGAAAAAGAAGTACATCCTACTCTTCGAGGACAAAGGAAAAAAA
158722 GGAAATAAAATGCGTCCTACTC
131 GGAAA-AAAATGCGTCCTACTC
* *
158744 TTTGAGGACAAAGGAAAATGA-GTACATCCTACTCTTCGAGGACAAAAGAAAAGAGAATGAAATG
1 TTTGAAGACAAAGGAAAAGGAGGT-CATCCTACTCTTCGAGGACAAAAGAAAAGAGAATGAAATG
* * *
158808 GGTCCTACTCCTTGAAGACAAAGGAAATAGAAGTGCATCCTACTCTTCGATGACAAAGGAAAAAA
65 GGTCCTACTCCTTGAAGACAAAGGAAAAAGAAGTACATCCTACTCTTCGAGGACAAAGGAAAAAA
*
158873 AGGAAAAAAATGCGTCCTGCTC
130 AGGAAAAAAATGCGTCCTACTC
158895 TTTG
1 TTTG
158899 CGGGTAAAAA
Statistics
Matches: 138, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
150 2 0.01
151 125 0.91
152 11 0.08
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (151 bp):
TTTGAAGACAAAGGAAAAGGAGGTCATCCTACTCTTCGAGGACAAAAGAAAAGAGAATGAAATGG
GTCCTACTCCTTGAAGACAAAGGAAAAAGAAGTACATCCTACTCTTCGAGGACAAAGGAAAAAAA
GGAAAAAAATGCGTCCTACTC
Found at i:159014 original size:61 final size:61
Alignment explanation
Indices: 158930--159266 Score: 319
Period size: 61 Copynumber: 5.6 Consensus size: 61
158920 AATTAAATAT
* * * * **
158930 GTCCTGCTCTTTGGGGACTAGAAGGTGCCACCAACTTGTATAGGCTTTGCAAGGAGAAAAC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAAC
* * * * *
158991 ATCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAA--AGAAAAT
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAAC
* ** * * * *
159050 GTCCTACTCTTTGAACATTGGAAAGTGCCACCAACTTATGTGGGCTTTCAAAA-GA-AAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAA-AC
* * **
159111 GTCTTGCTCTTTGAGGGCT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGT
1 GTCCTGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAA-AC
* * *
159172 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAGGA-AAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAA-AC
* ** *
159233 ATTTTGCTCTTTGAGGACTGGAAAGTGCCACCAA
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAA
159267 TAAAAGGAAA
Statistics
Matches: 236, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
59 47 0.20
60 14 0.06
61 171 0.72
62 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAAC
Found at i:159141 original size:120 final size:121
Alignment explanation
Indices: 158946--159266 Score: 384
Period size: 120 Copynumber: 2.7 Consensus size: 121
158936 CTCTTTGGGG
* * ** * * *
158946 ACTAGAAGGTGCCACCAACTTGTATAGGCTTTGCAAGGAGAAA-ACATCCTACTCTTTGAGGACT
1 ACTAGAAAGTGCCACCAACTTATATAGGCTTTAAAAGGA-AAAGGCATCTTGCTCTTTGAGGACT
159010 -AGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAA-TGTCCTACTCTTTGAAC
65 GA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGTGTCCTACTCTTTGAAC
* * * * * *
159066 ATTGGAAAGTGCCACCAACTTATGTGGGCTTTCAAAA-GAAAAGGCGTCTTGCTCTTTGAGGGCT
1 ACTAGAAAGTGCCACCAACTTATATAGGCTTT-AAAAGGAAAAGGCATCTTGCTCTTTGAGGACT
* **
159130 GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGG
65 GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GTGTCCTACTCTTTGAAC
* *
159188 ACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCATTTTGCTCTTTGAGGACTG
1 ACTAGAAAGTGCCACCAACTTATATAGGCTTTAAAAGGAAAAGGCATCTTGCTCTTTGAGGACT-
159253 GAAA-GTGCCACCAA
65 GAAAGGTGCCACCAA
159267 TAAAAGGAAA
Statistics
Matches: 169, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
119 7 0.04
120 76 0.45
121 7 0.04
122 75 0.44
123 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (121 bp):
ACTAGAAAGTGCCACCAACTTATATAGGCTTTAAAAGGAAAAGGCATCTTGCTCTTTGAGGACTG
AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGTGTCCTACTCTTTGAAC
Found at i:159323 original size:164 final size:165
Alignment explanation
Indices: 159118--159431 Score: 488
Period size: 164 Copynumber: 1.9 Consensus size: 165
159108 GGCGTCTTGC
* * * * ** *
159118 TCTTTGAGGGCTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTT
1 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAGGCATCATGCTCTT
* *
159183 TGAGGACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCAT-T-TTGCTCTTTG
66 TGAGGACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAAGAAAAGGC-TGTCCTGCTCTTTG
159246 AGGACTGGAAAGTGCCACCAATAAAAGGAAAAGGTG
130 AGGACTGGAAAGTGCCACCAATAAAAGGAAAAGGTG
*
159282 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAATGGCATCATGCTCTT
1 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAGGCATCATGCTCTT
* * *
159347 TGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCTGTCCTGCTCTTTGA
66 TGAGGACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAAGAAAAGGCTGTCCTGCTCTTTGA
159412 GGACTGGAAAGTGCCACCAA
131 GGACTGGAAAGTGCCACCAA
159432 CTTGTGTGGG
Statistics
Matches: 135, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
163 1 0.01
164 104 0.77
165 30 0.22
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (165 bp):
TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAGGCATCATGCTCTT
TGAGGACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAAGAAAAGGCTGTCCTGCTCTTTGA
GGACTGGAAAGTGCCACCAATAAAAGGAAAAGGTG
Found at i:159344 original size:103 final size:103
Alignment explanation
Indices: 159179--159369 Score: 319
Period size: 103 Copynumber: 1.9 Consensus size: 103
159169 GGTGTCCTGC
* * **
159179 TCTTTGAGGACTAGAAAGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCATTTTGCTCTT
1 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTATAGGCTTTAAAAGGAAAAGGCATCATGCTCTT
159244 TGAGGACTGGAAAGTGCCACCAATAAAAGGAAAAGGTG
66 TGAGGACTGGAAAGTGCCACCAATAAAAGGAAAAGGTG
* * *
159282 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAATGGCATCATGCTCTT
1 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTATAGGCTTTAAAAGGAAAAGGCATCATGCTCTT
159347 TGAGGACTGGAAAGTGCCACCAA
66 TGAGGACTGGAAAGTGCCACCAA
159370 CTTGTGTGGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 81 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (103 bp):
TCTTTGAGGACTAAAAAGTGCCACCAACCTGTATAGGCTTTAAAAGGAAAAGGCATCATGCTCTT
TGAGGACTGGAAAGTGCCACCAATAAAAGGAAAAGGTG
Found at i:159501 original size:123 final size:121
Alignment explanation
Indices: 159282--159543 Score: 341
Period size: 123 Copynumber: 2.1 Consensus size: 121
159272 GGAAAAGGTG
*
159282 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAATGGCATCATGCTCTT
1 TCTTTGAGGACT-GAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAATGGCATCATGCTCTT
159347 TGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCTGTCCT-GC
65 TGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC-GT-CTAGC
* * ** * * *
159405 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAA-GGTGTCCTGTTTT
1 TCTTTGAGGACT-GAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGA-AATGGCATCATGCTCT
* * *
159469 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCGTCTAGC
64 TTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCTAGC
*
159527 TATTTGAGGACTGAAAG
1 TCTTTGAGGACTGAAAG
159544 GATAAAAGGT
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
121 7 0.06
122 19 0.15
123 95 0.77
124 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (121 bp):
TCTTTGAGGACTGAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAATGGCATCATGCTCTTT
GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCTAGC
Found at i:159535 original size:287 final size:283
Alignment explanation
Indices: 158998--159543 Score: 783
Period size: 287 Copynumber: 1.9 Consensus size: 283
158988 AACATCCTAC
* * * *
158998 TCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAATGTCCTACTCTTTG
1 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAATGTCATACTCTTTG
* * * *
159063 AACATTGGAAAGTGCCACCAACTTATGTGGGCTTTCAAAAGAAAAGGCGTCTTGCTCTTTGAGGG
66 AACACTGGAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAGGCGTCCTGCTCTTTGAGGA
159128 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAG
131 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAG
* * *
159193 AAAGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCATTTTGCTCTTTGAGGACTGGAAAG
196 AAAGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCATCTAGCTATTTGAGGACT-GAAAG
159258 TGCCACCAATAAAAGGAAAAGGTG
260 TGCCACCAATAAAAGGAAAAGGTG
* *
159282 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTT-AAAAGGAAATGGCATCATGCTCT
1 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAT-G--TCATACTCT
** *
159346 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCTGTCCTGCTCTTTG
63 TTGAACACTGGAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAGGC-GTCCTGCTCTTTG
* * * *
159411 AGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGTGTCCTGTTTTTTGAGG
127 AGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGG
* * * * *
159475 ACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCGTCTAGCTATTTGAGGACT
191 ACTAGAAA-GTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCATCTAGCTATTTGAGGACT
159539 GAAAG
255 GAAAG
159544 GATAAAAGGT
Statistics
Matches: 231, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
283 9 0.04
284 39 0.17
286 62 0.27
287 117 0.51
288 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (283 bp):
TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAATGTCATACTCTTTG
AACACTGGAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAGGCGTCCTGCTCTTTGAGGA
CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAG
AAAGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAAGGCATCTAGCTATTTGAGGACTGAAAGT
GCCACCAATAAAAGGAAAAGGTG
Found at i:159544 original size:61 final size:60
Alignment explanation
Indices: 159282--159543 Score: 339
Period size: 61 Copynumber: 4.3 Consensus size: 60
159272 GGAAAAGGTG
* * * *
159282 TCTTTGAGGACTAAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGA-AATGGCATCATGC
1 TCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAA-GGCGTCCTGC
* *
159343 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCTGTCCTGC
1 TCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC-GTCCTGC
* * *
159405 TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGTGTCCTGT
1 TCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGC
* *
159466 TTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCGT-CTAGC
1 TCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT-GC
*
159527 TATTTGAGGACTGAAAG
1 TCTTTGAGGACTGAAAG
159544 GATAAAAGGT
Statistics
Matches: 182, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
60 7 0.04
61 118 0.65
62 57 0.31
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (60 bp):
TCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGC
Found at i:160551 original size:17 final size:18
Alignment explanation
Indices: 160522--160565 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
160512 AGTTCTTTTC
*
160522 TTTTCTCTTTTTTCT-TT
1 TTTTCTTTTTTTTCTGTT
*
160539 TTTTCTTTTTTTTGTGTT
1 TTTTCTTTTTTTTCTGTT
*
160557 ATTTCTTTT
1 TTTTCTTTT
160566 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTTTCTGTT
Found at i:160561 original size:26 final size:27
Alignment explanation
Indices: 160514--160565 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
160504 CTTAGGCAAG
*
160514 TTCTTTTCTTTTCTCTTTTTTCTTTTT
1 TTCTTTTCTTTTCTCTTATTTCTTTTT
* *
160541 TTCTTTT-TTTTGTGTTATTTCTTTT
1 TTCTTTTCTTTTCTCTTATTTCTTTT
160566 GGAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (27 bp):
TTCTTTTCTTTTCTCTTATTTCTTTTT
Found at i:175291 original size:52 final size:52
Alignment explanation
Indices: 175213--175340 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
175203 CGAAATATGA
*
175213 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
175265 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
*
175317 AAA-TTCCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
175341 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 20 0.27
52 48 0.66
53 5 0.07
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:175367 original size:13 final size:13
Alignment explanation
Indices: 175349--175373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175339 CAAAGATCAG
175349 TGTATCGATACAA
1 TGTATCGATACAA
175362 TGTATCGATACA
1 TGTATCGATACA
175374 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:176618 original size:77 final size:78
Alignment explanation
Indices: 176510--176675 Score: 237
Period size: 77 Copynumber: 2.1 Consensus size: 78
176500 TAAAAAATGG
* * *
176510 GGTTGGAGTATGCCCTCAGAAATAATAGGGTTGGAGTATCCCGATTGTGGAAAATTAG-TGTTTT
1 GGTTGGAGTATGCCCTCAAAAATAATAGGGTTGAAGTATCCCGATGGTGGAAAA-TAGATGTTTT
176574 AGAAATAAAACCAA
65 AGAAATAAAACCAA
* * * *
176588 GGTTGGAGTAT-TCCTCAAAAATAATGGGGTTGAAGTATCCTGATGGTGGAAAATCGATGTTTTA
1 GGTTGGAGTATGCCCTCAAAAATAATAGGGTTGAAGTATCCCGATGGTGGAAAATAGATGTTTTA
*
176652 GAAATAAAACCGA
66 GAAATAAAACCAA
176665 GGTTGGAGTAT
1 GGTTGGAGTAT
176676 CCTTGATGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
76 2 0.03
77 66 0.84
78 11 0.14
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATGCCCTCAAAAATAATAGGGTTGAAGTATCCCGATGGTGGAAAATAGATGTTTTA
GAAATAAAACCAA
Found at i:176678 original size:50 final size:51
Alignment explanation
Indices: 176615--176728 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 51
176605 AAAATAATGG
* * * * * *
176615 GGTTGAAGTATCC-TGATGGTGGAAAATCGATGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATCCTTGATGATGAAAAATCAAAGTTTTAGAAACAAAACCGA
* *
176665 GGTTGGAGTATCCTTGATGATGAAAAATCAAAGTTTTAGAAACAAAACTGG
1 GGTTGGAGTATCCTTGATGATGAAAAATCAAAGTTTTAGAAACAAAACCGA
176716 GGTTGGAGTATCC
1 GGTTGGAGTATCC
176729 CCTCAGAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 12 0.22
51 43 0.78
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (51 bp):
GGTTGGAGTATCCTTGATGATGAAAAATCAAAGTTTTAGAAACAAAACCGA
Found at i:176756 original size:79 final size:79
Alignment explanation
Indices: 176664--176837 Score: 190
Period size: 79 Copynumber: 2.2 Consensus size: 79
176654 AATAAAACCG
** * **
176664 AGGTTGGAGTATCCTTGATGATGAAAAATCAAAGTTTTAGAAACAAAA-CTGGGGTTGGAGTATC
1 AGGTTGGAGTATCCCCGATGATAAAAAATCAAAGTTTTAGAAACAAAATC-AAGGTTGGAGTATC
176728 CCCTC-AGAAATAACA
65 CCCTCGA-AAATAACA
* *** * *
176743 AGGTTGGAGTATCCCCGATGGTAAAAAATCGGTGTTTTGGAAATAAAATCAAGGTTGGAGTATCC
1 AGGTTGGAGTATCCCCGATGATAAAAAATCAAAGTTTTAGAAACAAAATCAAGGTTGGAGTATCC
**
176808 CCTCGAAAATAATG
66 CCTCGAAAATAACA
*
176822 GGGTTGGAGTATCCCC
1 AGGTTGGAGTATCCCC
176838 TCAGAAATAA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
79 77 0.97
80 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (79 bp):
AGGTTGGAGTATCCCCGATGATAAAAAATCAAAGTTTTAGAAACAAAATCAAGGTTGGAGTATCC
CCTCGAAAATAACA
Found at i:176798 original size:130 final size:128
Alignment explanation
Indices: 176569--176807 Score: 307
Period size: 130 Copynumber: 1.9 Consensus size: 128
176559 GAAAATTAGT
* * *** *
176569 GTTTTAGAAATAAAACCAAGGTTGGAGTATTCCTCAAAAATAATGGGGTTGAAGTATCCTGATGG
1 GTTTTAGAAACAAAACCAAGGTTGGAGTATCCCTCAAAAATAACAAGGTTGAAGTATCCCGATGG
** *
176634 TGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCTTGATGATGAAAAATCAAA
66 TAAAAAATCGATGTTTTAGAAATAAAACCAAGGTTGGAGTATCCTTGATGATGAAAAATCAAA
*** * *
176697 GTTTTAGAAACAAAACTGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGAT
1 GTTTTAGAAACAAAACCAAGGTTGGAGTAT-CCCTCAAAAATAACAAGGTTGAAGTAT-CCCGAT
* * *
176762 GGTAAAAAATCGGTGTTTTGGAAATAAAATCAAGGTTGGAGTATCC
64 GGTAAAAAATCGATGTTTTAGAAATAAAACCAAGGTTGGAGTATCC
176808 CCTCGAAAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
128 26 0.28
129 21 0.23
130 45 0.49
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (128 bp):
GTTTTAGAAACAAAACCAAGGTTGGAGTATCCCTCAAAAATAACAAGGTTGAAGTATCCCGATGG
TAAAAAATCGATGTTTTAGAAATAAAACCAAGGTTGGAGTATCCTTGATGATGAAAAATCAAA
Found at i:176828 original size:28 final size:28
Alignment explanation
Indices: 176795--176862 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
176785 ATAAAATCAA
*
176795 GGTTGGAGTATCCCCTC-GAAAATAATGG
1 GGTTGGAGTATCCCCTCAG-AAATAACGG
176823 GGTTGGAGTATCCCCTCAGAAATAACGG
1 GGTTGGAGTATCCCCTCAGAAATAACGG
176851 GGTTGGAGTATC
1 GGTTGGAGTATC
176863 TCCGATTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCAGAAATAACGG
Found at i:176906 original size:107 final size:107
Alignment explanation
Indices: 176713--176944 Score: 317
Period size: 107 Copynumber: 2.2 Consensus size: 107
176703 GAAACAAAAC
*
176713 TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATGGTAAAAAATCGGTGT
1 TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATGATAAAAAATCGGTGT
176778 TTTGGAAATAAAATCAAGGTTGGAGTA-TCCCCTCGAAAATAA
66 TTTGGAAATAAAATCAAGGTTGGAGTATTCCCC-CGAAAATAA
** * * * *
176820 TGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATTGGTG-
1 TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATGATAAAAAATCGGTGT
** *
176884 TTTGGAAAATAAAA-CTGGGGTTGGAGTATTCCCCCGGAAATAA
66 TTTGG-AAATAAAATC-AAGGTTGGAGTATTCCCCCGAAAATAA
*
176927 CGGGGTTGGAGTATCCCC
1 TGGGGTTGGAGTATCCCC
176945 GATTGTGAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
106 6 0.05
107 100 0.90
108 5 0.05
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (107 bp):
TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATGATAAAAAATCGGTGT
TTTGGAAATAAAATCAAGGTTGGAGTATTCCCCCGAAAATAA
Found at i:176965 original size:79 final size:79
Alignment explanation
Indices: 176820--176965 Score: 222
Period size: 79 Copynumber: 1.8 Consensus size: 79
176810 TCGAAAATAA
* ***
176820 TGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATTGGTGT
1 TGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGT
176885 TTGGAAAATAAAAC
66 TTGGAAAATAAAAC
* *
176899 TGGGGTTGGAGTATTCCCC-CGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATG
1 TGGGGTTGGAGTA-TCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATG
176963 TTT
65 TTT
176966 TAGAAATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
79 55 0.92
80 5 0.08
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (79 bp):
TGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGT
TTGGAAAATAAAAC
Found at i:179362 original size:50 final size:50
Alignment explanation
Indices: 179298--179432 Score: 182
Period size: 50 Copynumber: 2.7 Consensus size: 50
179288 AAAAATGCCT
* * * *
179298 GAATATATCGATACATTG-AGAAATGTATCGATACATTTGGGTAAAACCCA
1 GAATGTATCGATACAATGAAG-AATGTATCGATACATCTAGGTAAAACCCA
*
179348 GAATGTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAACCCA
1 GAATGTATCGATACAATGAAGAATGTATCGATACATCTAGGTAAAACCCA
* * *
179398 AAATGTATCGACACAATGAAGAAGGTATCGATACA
1 GAATGTATCGATACAATGAAGAATGTATCGATACA
179433 AATTATGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
50 74 0.99
51 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (50 bp):
GAATGTATCGATACAATGAAGAATGTATCGATACATCTAGGTAAAACCCA
Found at i:185640 original size:52 final size:52
Alignment explanation
Indices: 185562--185690 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
185552 CAAAATATGA
* *
185562 AAATTTACCTGCATGTATCGAAACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
* * *
185614 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
*
185666 AAATTTTCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
185691 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
Found at i:185703 original size:52 final size:51
Alignment explanation
Indices: 185562--185710 Score: 192
Period size: 52 Copynumber: 2.9 Consensus size: 51
185552 CAAAATATGA
*
185562 AAATTTACCTGCATGTATCGAAACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
* * * *
185614 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
* *
185666 AAATTTTCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
185711 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGC
Found at i:185717 original size:13 final size:13
Alignment explanation
Indices: 185699--185723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185689 CAAAGATCAG
185699 TGTATCGATACAA
1 TGTATCGATACAA
185712 TGTATCGATACA
1 TGTATCGATACA
185724 TTTGAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:185805 original size:13 final size:13
Alignment explanation
Indices: 185787--185811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185777 AAAAAAAAAC
185787 TGTATCGATACAT
1 TGTATCGATACAT
185800 TGTATCGATACA
1 TGTATCGATACA
185812 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:191092 original size:20 final size:20
Alignment explanation
Indices: 191067--191121 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
191057 GTTGGGCACA
* *
191067 ATGTATCGATACTTTTTAC-C
1 ATGTATCGATACATTGT-CTC
*
191087 ATGTATCGACACATTGTCTC
1 ATGTATCGATACATTGTCTC
191107 ATGTATCGATACATT
1 ATGTATCGATACATT
191122 TCACTTAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGTCTC
Found at i:191193 original size:19 final size:20
Alignment explanation
Indices: 191148--191200 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
191138 CTTCCAGTTT
* *
191148 CATGTATTGATACAATTACG
1 CATGTATCGATACAATGACG
*
191168 TATGTATCGATACAATGA-G
1 CATGTATCGATACAATGACG
*
191187 CATGTATCAATACA
1 CATGTATCGATACA
191201 TTGTATCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGACG
Found at i:191207 original size:13 final size:13
Alignment explanation
Indices: 191189--191213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
191179 ACAATGAGCA
191189 TGTATCAATACAT
1 TGTATCAATACAT
191202 TGTATCAATACA
1 TGTATCAATACA
191214 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:192137 original size:155 final size:155
Alignment explanation
Indices: 191818--192245 Score: 458
Period size: 155 Copynumber: 2.8 Consensus size: 155
191808 CTACTTCTAG
* * * *
191818 GCCAAAGGTGCACCTTTAGGATAGGTTCATCTTTTTATGATTATTTTCAAACCCTTTATA-GATA
1 GCCAAAGGTGCACCTTTAGGATAGGTTCATCTTTTTATGATCATTTTTAAATCCTTTA-AGGGTA
* * * * * * * ** * *
191882 -CTAGGTACTTCTACATTAAAGATAT-CCTCAAAGGTATTTTTGTAATTTTTGTAGAATCGAGTC
65 TCGAAGTACTTCTACATAAAAGGTATCCCTTAGAGGCATTTTCATAATTTTTCTA-AACCGAGTC
**
191945 CTAGGTTATTGCCAAGTCCTCTTTTAT
129 CTAGGTTATCACCAAGTCCTCTTTTAT
* * * * *
191972 GCCAAAGGTGCGCCTATAGGATAGGTTCATCTTTTTATGATCGTTTTTAAGTCCTTTAGGGGTAT
1 GCCAAAGGTGCACCTTTAGGATAGGTTCATCTTTTTATGATCATTTTTAAATCCTTTAAGGGTAT
* *
192037 C-AAGTACTTCTACGTCAAAGGTATCCCTTAGAGGCATTTTCATAATTTTTCTAAAGCCGAGTCC
66 CGAAGTACTTCTACATAAAAGGTATCCCTTAGAGGCATTTTCATAATTTTTCTAAA-CCGAGTCC
*
192101 TAGGTTATCACCATG-CCTGCTTTTAT
130 TAGGTTATCACCAAGTCCT-CTTTTAT
* * **
192127 GCCAAAGGTGCACCTTTAGGATAGGTTCATCTTTCTATGATCATTTTTAACTTGTTTAAGGGTAT
1 GCCAAAGGTGCACCTTTAGGATAGGTTCATCTTTTTATGATCATTTTTAAATCCTTTAAGGGTAT
* * * *
192192 CGAA-CACTTTTAAATAAAAGGTATCTCC-TAGGGGCATTTTCATAA-TTTTCTAAA
66 CGAAGTACTTCTACATAAAAGGTATC-CCTTAGAGGCATTTTCATAATTTTTCTAAA
192246 ATCTAGTACT
Statistics
Matches: 230, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
154 87 0.38
155 139 0.60
156 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (155 bp):
GCCAAAGGTGCACCTTTAGGATAGGTTCATCTTTTTATGATCATTTTTAAATCCTTTAAGGGTAT
CGAAGTACTTCTACATAAAAGGTATCCCTTAGAGGCATTTTCATAATTTTTCTAAACCGAGTCCT
AGGTTATCACCAAGTCCTCTTTTAT
Found at i:193835 original size:152 final size:156
Alignment explanation
Indices: 193513--193843 Score: 366
Period size: 158 Copynumber: 2.1 Consensus size: 156
193503 GTGCTCGATA
* * * * *
193513 CCCTAAAGGACATAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGGCGGC
1 CCCTAAAGGACTTAAAAAGGATTAGAGATGGGATGAACATATCCTAAATACCCACCAT--GCGAC
* * * * * * * * *
193578 ACAAAAGGGGACCCGGTGACAACCTGGGACTCGATTTTGGAAAATTATGAAAATGCCCCTAGGGG
64 ACAAAAGAGGACCCAGTGACAACCTAGCACTCGATTCTAGAAAATTATAAAAATACACCTAGGGG
* *
193643 ATACCTTCGAATTAGAAGTGCTTGATAC
129 ATACCTTCGAATTAGAAGTGCCTAATAC
* * *
193671 CCCTAAAAGACTTAAAACGTATTACGA-ATGGGATGAACATATCCTAAATACCCACCAT-CGACA
1 CCCTAAAGGACTTAAAAAGGATTA-GAGATGGGATGAACATATCCTAAATACCCACCATGCGACA
* * * *
193734 TAACAGAGGA-CCAGT-ACAACCTAGCACTCGGTTCTAGAAACTTATAAAAATACACCTA-GGGA
65 CAAAAGAGGACCCAGTGACAACCTAGCACTCGATTCTAGAAAATTATAAAAATACACCTAGGGGA
** *
193796 TACCTTTTACTTAGAAGTGCCTAATAC
130 TACCTTCGAATTAGAAGTGCCTAATAC
193823 CCCTAAAGGACTTAAAAAGGA
1 CCCTAAAGGACTTAAAAAGGA
193844 AAAGGGAACC
Statistics
Matches: 143, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
152 44 0.31
153 34 0.24
154 4 0.03
155 11 0.08
158 49 0.34
159 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (156 bp):
CCCTAAAGGACTTAAAAAGGATTAGAGATGGGATGAACATATCCTAAATACCCACCATGCGACAC
AAAAGAGGACCCAGTGACAACCTAGCACTCGATTCTAGAAAATTATAAAAATACACCTAGGGGAT
ACCTTCGAATTAGAAGTGCCTAATAC
Found at i:194093 original size:149 final size:149
Alignment explanation
Indices: 193823--194627 Score: 818
Period size: 149 Copynumber: 5.4 Consensus size: 149
193813 TGCCTAATAC
* * * * * * *
193823 CCCTAAAGGACTTAAAAAGGAAAAGGGAACCTATGCCTATTACATGCCCTCGGCATAGAAGC-AA
1 CCCTAAAGGACTTAAAAAAGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCGAC
* *
193887 CTCGGTGACAAATTTGGACT-AGATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTT
66 CT-AGTGACAAATTAGGACTCA-ATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTT
* * * *
193951 GTCATAAAAGTATCCCGGTTA
129 GACATGAAAGTATCCCGATAA
* * * * * * ** * *
193972 CCCT-AAGCAACTTAAAAAAGAAAAGTGAACTTATGCGTAATACGTATCCTGGGTATAAAACCGA
1 CCCTAAAG-GACTTAAAAAAGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCGA
* * * ** *
194036 CCTAGTGACAAATTAAGACTCAATTCTAGTAAAATTATGAAAATGCCTTTGTGGGTATACCTTCG
65 CCTAGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTTG
*
194101 ACATGAAAGTATCTCGATAA
130 ACATGAAAGTATCCCGATAA
*** * *
194121 CCCTAAAGGACTTAAAAAAGAAAAATAAACCTACGCCTAATACGTACCCTCGACATAGAAGCAAC
1 CCCTAAAGGACTTAAAAAAGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCGAC
** * * * * * *
194186 CCGGTGACAAATTAGGACTCAATTCTAGAAAAATTATAAAAATACCCCTATAGGCACACCTTTCA
66 CTAGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTTGA
194251 CATGAAAGTATCCC-AGTAA
131 CATGAAAGTATCCCGA-TAA
* * * *
194270 CCAT-AA-GACTTAAAAAGGAAAAGCGAACCTATGCCTAATACGTACCCTCGGCATAGAAGGGAC
1 CCCTAAAGGACTTAAAAAAGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCGAC
* * * *
194333 CTAGTGAAAAATTAGGACTCAGTTCTAAAAAAATTATGAAAATGCCCCTGTGGGTATA-CTTTCG
66 CTAGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTT-G
**
194397 ACATGAAAGTATCTTGATAA
130 ACATGAAAGTATCCCGATAA
* * * *
194417 CCCTAAAGGACATAAAAAGGAAAAGCGAACCTATGCCTAAAACGTACCCTCGACATAGGAGCGAC
1 CCCTAAAGGACTTAAAAAAGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCGAC
* * ** * * * *
194482 CTGGTGACCAATTAGGACTCGGTTCTAGAAAAATTATGAAAATACCCTTATAGGTATACCTTCGA
66 CTAGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTTGA
* **
194547 CATGAAAGTATCTCGGCAA
131 CATGAAAGTATCCCGATAA
* * ** * *
194566 CCCTTAAA-GACTT-AAAAGGAAAAAGTGAACCTACACCTAATACATACCCTCGGCATAGAAGC
1 CCC-TAAAGGACTTAAAAAAG-AAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGC
194628 AACCCAATGA
Statistics
Matches: 539, Mismatches: 105, Indels: 24
0.81 0.16 0.04
Matches are distributed among these distances:
146 4 0.01
147 115 0.21
148 15 0.03
149 391 0.73
150 14 0.03
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (149 bp):
CCCTAAAGGACTTAAAAAAGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCGAC
CTAGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTTGA
CATGAAAGTATCCCGATAA
Found at i:194418 original size:296 final size:296
Alignment explanation
Indices: 193823--194627 Score: 1013
Period size: 296 Copynumber: 2.7 Consensus size: 296
193813 TGCCTAATAC
* * * * *
193823 CCCTAAAGGACTTAAAAAGGAAAAGGGAACCTATGCCTATTACATGCCCTCGGCATAGAAGCAAC
1 CCCTAAAGGACTTAAAAAGGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCAAC
* * * * *
193888 TCGGTGACAAATTTGGACT-AGATTCTAGAAAAATTATGAAAATACCCCTGTGGGTATACCTTTG
66 CCGGTGACAAATTAGGACTCA-ATTCTAGAAAAATTATGAAAATACCCCTATAGGTATACCTTTC
* * * * * * *
193952 TCATAAAAGTATCCCGGTTACCCTAAGCAACTTAAAAAAGAAAAGTGAACTTATGCGTAATACGT
130 ACATGAAAGTATCCCGGTAACCATAAG--ACTTAAAAAGGAAAAGTGAACCTATGCCTAATACGT
* * * * * * **
194017 ATCCTGGGTATAAAACCGACCTAGTGACAAATTAAGACTCAATTCTAGTAAAATTATGAAAATGC
193 ACCCTCGGCATAGAAGCGACCTAGTGAAAAATTAAGACTCAATTCTAAAAAAATTATGAAAATGC
**
194082 CTTTGTGGGTATACCTTCGACATGAAAGTATCTCGATAA
258 CCCTGTGGGTATACCTTCGACATGAAAGTATCTCGATAA
* *** *
194121 CCCTAAAGGACTTAAAAAAGAAAAATAAACCTACGCCTAATACGTACCCTCGACATAGAAGCAAC
1 CCCTAAAGGACTTAAAAAGGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCAAC
* * *
194186 CCGGTGACAAATTAGGACTCAATTCTAGAAAAATTATAAAAATACCCCTATAGGCACACCTTTCA
66 CCGGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTATAGGTATACCTTTCA
* *
194251 CATGAAAGTATCCCAGTAACCATAAGACTTAAAAAGGAAAAGCGAACCTATGCCTAATACGTACC
131 CATGAAAGTATCCCGGTAACCATAAGACTTAAAAAGGAAAAGTGAACCTATGCCTAATACGTACC
* * *
194316 CTCGGCATAGAAGGGACCTAGTGAAAAATTAGGACTCAGTTCTAAAAAAATTATGAAAATGCCCC
196 CTCGGCATAGAAGCGACCTAGTGAAAAATTAAGACTCAATTCTAAAAAAATTATGAAAATGCCCC
* *
194381 TGTGGGTATACTTTCGACATGAAAGTATCTTGATAA
261 TGTGGGTATACCTTCGACATGAAAGTATCTCGATAA
* * * *
194417 CCCTAAAGGACATAAAAAGGAAAAGCGAACCTATGCCTAAAACGTACCCTCGACATAGGAGCGAC
1 CCCTAAAGGACTTAAAAAGGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCAAC
* * ** *
194482 CTGGTGACCAATTAGGACTCGGTTCTAGAAAAATTATGAAAATACCCTTATAGGTATACC-TTCG
66 CCGGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTATAGGTATACCTTTC-
* * * ** *
194546 ACATGAAAGTATCTCGGCAACCCTTAAAGACTT-AAAAGGAAAAAGTGAACCTACACCTAATACA
130 ACATGAAAGTATCCCGGTAA-CCAT-AAGACTTAAAAAGG-AAAAGTGAACCTATGCCTAATACG
194610 TACCCTCGGCATAGAAGC
192 TACCCTCGGCATAGAAGC
194628 AACCCAATGA
Statistics
Matches: 435, Mismatches: 67, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
295 3 0.01
296 246 0.57
297 9 0.02
298 176 0.40
299 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (296 bp):
CCCTAAAGGACTTAAAAAGGAAAAGCGAACCTATGCCTAATACGTACCCTCGACATAGAAGCAAC
CCGGTGACAAATTAGGACTCAATTCTAGAAAAATTATGAAAATACCCCTATAGGTATACCTTTCA
CATGAAAGTATCCCGGTAACCATAAGACTTAAAAAGGAAAAGTGAACCTATGCCTAATACGTACC
CTCGGCATAGAAGCGACCTAGTGAAAAATTAAGACTCAATTCTAAAAAAATTATGAAAATGCCCC
TGTGGGTATACCTTCGACATGAAAGTATCTCGATAA
Found at i:196921 original size:167 final size:164
Alignment explanation
Indices: 196659--197182 Score: 520
Period size: 167 Copynumber: 3.1 Consensus size: 164
196649 AAGGATAAGG
* * * *
196659 GAATTTCAAAG-AAAAATGAAAAACTTATGAAAATAAATGAATTTCTTGAAATTGATTTACTATG
1 GAATTTCAAAGAAAAAAAGAAAAA-TTATGAAAATAAATGAATTTTTTGAAACTGATTTAATATG
*
196723 AATTAAATGATGATATTTGATGAATTTTAAAAATTACATACAAAGAAAAATCCCCTCGAAAATAA
65 AGTTAAATGATGATATTTGATGAATTTTAAAAATTACA-ACAAAGAAAAATCCCCTCGAAAATAA
*
196788 TTACAGAGTAGAAAACTCTATATTTTGAAAACAGGA
129 TTACGGAGTAGAAAACTCTATATTTTGAAAACAGGA
* * * *
196824 GAATTTCAAAGACAAAAAAGAAAAATTAATG-AAATAAAGGTAATTTTTTGAAACTAATTTATTG
1 GAATTTCAAAGA-AAAAAAGAAAAATT-ATGAAAATAAATG-AATTTTTTGAAACTGATTTAATA
* * * * * *
196888 TGAGTTAGATGATGATATTTGATAAATTTTAAAAATTATAAACTAAGAAAAATCGCTCC-CGTAG
63 TGAGTTAAATGATGATATTTGATGAATTTTAAAAATTA-CAACAAAGAAAAATC-C-CCTCGAAA
* *** *
196952 ATATTTACGGAGTAGAAAACTCCGCATTTTGAAAACAAGA
125 ATAATTACGGAGTAGAAAACTCTATATTTTGAAAACAGGA
* * * *
196992 GAATTTTAAGGTAAAAATA-AAAAATTCATGAAAATAAATGAATTTTTTAAAACTGATTTAATAT
1 GAATTTCAAAG-AAAAAAAGAAAAATT-ATGAAAATAAATGAATTTTTTGAAACTGATTTAATAT
* * * ** ** * * *
197056 GAGTTAAATAATAATATTTGATGAATATTAAAAAATTTTGAACCGATAAAAATACACTCGAAAA-
64 GAGTTAAATGATGATATTTGATGAAT-TTTAAAAA-TTACAACAAAGAAAAATCCCCTCGAAAAT
* * *
197120 AATTTACGGAGAAGAAAATTCTATATTTTAAAAACAGGA
127 AA-TTACGGAGTAGAAAACTCTATATTTTGAAAACAGGA
* *
197159 GGAATTT-AAGGAAAAAATGAAAAA
1 -GAATTTCAAAGAAAAAAAGAAAAA
197183 CTCCTAAAAT
Statistics
Matches: 291, Mismatches: 53, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
165 11 0.04
166 17 0.06
167 174 0.60
168 84 0.29
169 5 0.02
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (164 bp):
GAATTTCAAAGAAAAAAAGAAAAATTATGAAAATAAATGAATTTTTTGAAACTGATTTAATATGA
GTTAAATGATGATATTTGATGAATTTTAAAAATTACAACAAAGAAAAATCCCCTCGAAAATAATT
ACGGAGTAGAAAACTCTATATTTTGAAAACAGGA
Found at i:199128 original size:20 final size:20
Alignment explanation
Indices: 199103--199156 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
199093 TTATCACTGT
* *
199103 TTGTATCGATACATGGGACA
1 TTGTATCGATACATAGGAAA
*
199123 TTGTATCGATACATAGTAAA
1 TTGTATCGATACATAGGAAA
*
199143 ATGTATCGATACAT
1 TTGTATCGATACAT
199157 TGTGCCCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATAGGAAA
Found at i:200261 original size:11 final size:11
Alignment explanation
Indices: 200245--200269 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
200235 ATGAACAGGA
200245 CACAAAAATGG
1 CACAAAAATGG
200256 CACAAAAATGG
1 CACAAAAATGG
200267 CAC
1 CAC
200270 GCATTGTTTT
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:0.52, C:0.24, G:0.16, T:0.08
Consensus pattern (11 bp):
CACAAAAATGG
Found at i:207013 original size:14 final size:14
Alignment explanation
Indices: 206957--207015 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
206947 GAATTGTCAC
*
206957 CAAG-AATTTTTAT
1 CAAGAAATTTTTGT
*
206970 CAA-AAATCTTTGT
1 CAAGAAATTTTTGT
**
206983 CAAGTAAAACATTTGT
1 CAAG--AAATTTTTGT
206999 CAAGAAATTTTTGT
1 CAAGAAATTTTTGT
207013 CAA
1 CAA
207016 CACCAATCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 13 0.36
14 11 0.31
16 12 0.33
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (14 bp):
CAAGAAATTTTTGT
Found at i:207096 original size:31 final size:32
Alignment explanation
Indices: 207027--207102 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
207017 ACCAATCCTT
* * *
207027 TTCATAGTCCACACGAGTTGGTGGCACTATAG
1 TTCAAAGTCCACACGAGTTGGTGACACCATAG
* *
207059 TT-AAAGTTCACACGAGTTGGTGACACCCTA-
1 TTCAAAGTCCACACGAGTTGGTGACACCATAG
207089 TTCAAAGTCCACAC
1 TTCAAAGTCCACAC
207103 TATAGACACC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.05
31 33 0.89
32 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (32 bp):
TTCAAAGTCCACACGAGTTGGTGACACCATAG
Found at i:210328 original size:155 final size:153
Alignment explanation
Indices: 209859--210343 Score: 494
Period size: 155 Copynumber: 3.1 Consensus size: 153
209849 TTTACATCCC
* * *
209859 GCACTTCTACGTCGAAGGTATCCCCTAAGGGCATTTTCATAATTTTACAAAATCGAGTCTTAGGT
1 GCACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGTAATTTTCCAAAATCGAGTCTTAGGT
* * * * *
209924 TGTCACCAGGTTTGCTTTTACGCTGAAGGTGGGTATTTAGGATAGGTTCATCCTTCTTTAAATCT
66 TGTCACCAGGTTCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCATC--TATATAT
*
209989 TTTTAA-GTCCTTTAGGGGTACTAAGA
129 TTTTAATGTCCTTTA-GGGT-CTTAGA
* * * * * * * *
210015 -TAGTTTCACGTCGAAGGTATCCCTTAAGGGCATTTTCGTAATTTTCTAAAACCAATTCTTAGGT
1 GCACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGTAATTTTCCAAAATCGAGTCTTAGGT
* * * * * *
210079 TGTCACTAGGTTCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGCTCAACCCGTTTATAATTA
66 TGTCACCAGGTTCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTC-ATCCATCTAT-A-TA
*
210144 TTTTTAAT-TCCTTTAAGGGTATTAG-
128 TTTTTAATGTCCTTT-AGGGTCTTAGA
* * * *
210169 GCACTTTTAAGTCGAAGGTATCCCCTAAAGGTATTTTTGTAATTTTCCAAAATCGAGTCTTAGGT
1 GCACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGTAATTTTCCAAAATCGAGTCTTAGGT
* * * *
210234 TGTCACC-GAGTCCGTTTTTATGCTAAAGGTGGGTATTAAGGATAGGTTCATGCCATCTATAGTA
66 TGTCACCAG-GTTCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCAT-CCATCTATA-TA
* * * *
210298 TTTTTCATGTCCTCTAGGATCTTCGA
128 TTTTTAATGTCCTTTAGGGTCTTAGA
* *
210324 GCACTTTTATGTCGATGGTA
1 GCACTTTTACGTCGAAGGTA
210344 GGTCTTAGGG
Statistics
Matches: 266, Mismatches: 53, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
154 21 0.08
155 222 0.83
156 22 0.08
157 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (153 bp):
GCACTTTTACGTCGAAGGTATCCCCTAAGGGCATTTTCGTAATTTTCCAAAATCGAGTCTTAGGT
TGTCACCAGGTTCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCATCTATATATTT
TTAATGTCCTTTAGGGTCTTAGA
Found at i:211254 original size:20 final size:20
Alignment explanation
Indices: 211226--211263 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
211216 CCATGTATCA
211226 ATACAATGTATCGATATAAT
1 ATACAATGTATCGATATAAT
*
211246 ATACCATGTATCGATATA
1 ATACAATGTATCGATATA
211264 TTTCACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
ATACAATGTATCGATATAAT
Found at i:212466 original size:37 final size:37
Alignment explanation
Indices: 212368--212449 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
212358 GCGGCACTCA
212368 AAAAGCCCACACAAGCTAGTGGCACTCAAACCTTTCC
1 AAAAGCCCACACAAGCTAGTGGCACTCAAACCTTTCC
212405 AAAAGCCCACACAAGCTAGTGGCACTCAAACCTTTCC
1 AAAAGCCCACACAAGCTAGTGGCACTCAAACCTTTCC
212442 AAAAGCCC
1 AAAAGCCC
212450 GTATGAGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (37 bp):
AAAAGCCCACACAAGCTAGTGGCACTCAAACCTTTCC
Found at i:213011 original size:160 final size:162
Alignment explanation
Indices: 212549--212996 Score: 377
Period size: 161 Copynumber: 2.8 Consensus size: 162
212539 ATTCTGCCAT
** * * * **
212549 AGTCATGCGGCATCTATCAAAAC-CTTTTTCCTCAAAGTCTAATGTTACCAACCTTGAATCAACA
1 AGTCATGCAACATCTATCAAAACTCTTTTTCC-C-AAGCCTAATATTGCTGACCTTGAATCAACA
** * * * * * * * * * * **
212613 CATTAGCATTCTGCCTATGTTAAAAAGCACATGTTAAATATTTTTTACTAAA-ACCAATGTTGCT
64 CATTAGCACCCTGCCTATGTCAAAAAGCACTTGTCATATAGTCTTAAATAAACCCCAATATCACT
** * *
212677 GGCCTTGAATCAGCAC-CTAGGCACCTTGCCTTA
129 AACCTTGAATCAGCACATTAGGCACCTTGCCCTA
* * * ***
212710 AGTCATGCAACATCTATCAAAACCTTTTTTTCTCAAGCCTAATATTGTTGACCTTGAATTGGCAC
1 AGTCATGCAACATCTATCAAAA-CTCTTTTTCCCAAGCCTAATATTGCTGACCTTGAATCAACAC
* * * ** * * * *
212775 ATTAGTACCCTGCCTATGTCAAAAGGTACTTGTCATATCTTCTTCACTAAAGCCCAATGTCACTA
65 ATTAGCACCCTGCCTATGTCAAAAAGCACTTGTCATATAGTCTTAAATAAACCCCAATATCACTA
212840 ACCTTGAATCAGCACATTA-GCACCTTGCCCTA
130 ACCTTGAATCAGCACATTAGGCACCTTGCCCTA
** * * * * *
212872 AGTCATGCTGCATCTATCTAAA-TCTTTTTCCCAAGCTTAATGTTGCTGGCCTTGAATCAATACA
1 AGTCATGCAACATCTATCAAAACTCTTTTTCCCAAGCCTAATATTGCTGACCTTGAATCAACACA
* *
212936 TTGGCACCCTGCCTATGTCAAAAAGCACTTGTCATATAGT-TTAAATCGAACCCCAATATCA
66 TTAGCACCCTGCCTATGTCAAAAAGCACTTGTCATATAGTCTTAAAT-AAACCCCAATATCA
212997 TTCGGCTTGA
Statistics
Matches: 226, Mismatches: 56, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
159 4 0.02
160 77 0.34
161 81 0.36
162 56 0.25
163 8 0.04
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (162 bp):
AGTCATGCAACATCTATCAAAACTCTTTTTCCCAAGCCTAATATTGCTGACCTTGAATCAACACA
TTAGCACCCTGCCTATGTCAAAAAGCACTTGTCATATAGTCTTAAATAAACCCCAATATCACTAA
CCTTGAATCAGCACATTAGGCACCTTGCCCTA
Found at i:213703 original size:20 final size:21
Alignment explanation
Indices: 213667--213718 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
213657 TTTTGCAATT
*
213667 TGTATCGATACCATAAGTTAA
1 TGTATCGATACCATAAGTGAA
*
213688 TGTATCGAT-GCATAAGTGAA
1 TGTATCGATACCATAAGTGAA
*
213708 TGTATCAATAC
1 TGTATCGATAC
213719 TAAGGCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (21 bp):
TGTATCGATACCATAAGTGAA
Found at i:215117 original size:13 final size:13
Alignment explanation
Indices: 215099--215123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
215089 TCACTATTCA
215099 TGTATCGATACAG
1 TGTATCGATACAG
215112 TGTATCGATACA
1 TGTATCGATACA
215124 TCATAAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:217226 original size:13 final size:13
Alignment explanation
Indices: 217208--217233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
217198 CAATTTTTTG
217208 TGTATCGATACAT
1 TGTATCGATACAT
217221 TGTATCGATACAT
1 TGTATCGATACAT
217234 ACTTGCTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:217994 original size:12 final size:12
Alignment explanation
Indices: 217977--218002 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
217967 TAATTCACAC
217977 ATATCAAAATTT
1 ATATCAAAATTT
217989 ATATCAAAATTT
1 ATATCAAAATTT
218001 AT
1 AT
218003 TTGCATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATCAAAATTT
Found at i:219808 original size:13 final size:13
Alignment explanation
Indices: 219790--219828 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
219780 ATAATCCTCT
*
219790 TGTATCGATACAG
1 TGTATCGATACAA
219803 TGTATCGATACAA
1 TGTATCGATACAA
219816 TGTATCGATACAA
1 TGTATCGATACAA
219829 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:221903 original size:15 final size:15
Alignment explanation
Indices: 221883--221913 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
221873 ATTTCGTTTG
*
221883 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
221898 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
221913 G
1 G
221914 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:223746 original size:21 final size:21
Alignment explanation
Indices: 223717--223761 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
223707 AAGTTTTCAT
*
223717 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
223737 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
223759 TTT
1 TTT
223762 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:226801 original size:83 final size:83
Alignment explanation
Indices: 226662--226829 Score: 309
Period size: 83 Copynumber: 2.0 Consensus size: 83
226652 ACAAAATGAA
* *
226662 GAGTTGTTACCAATGGTGTTGATTCTTTCGATTTTTTCTTTCGAATTATCACCAAATGTAACACA
1 GAGTTGTTACCAATGGTGCTGATTCTTTCGATTTTTTCTTTCAAATTATCACCAAATGTAACACA
226727 TCCACCTTCCTTTGATTT
66 TCCACCTTCCTTTGATTT
*
226745 GAGTTGTTACCAATGGTGCTGATTCTTTTGATTTTTTCTTTCAAATTATCACCAAATGTAACACA
1 GAGTTGTTACCAATGGTGCTGATTCTTTCGATTTTTTCTTTCAAATTATCACCAAATGTAACACA
226810 TCCACCTTCCTTTGATTT
66 TCCACCTTCCTTTGATTT
226828 GA
1 GA
226830 TTTCTGTGAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (83 bp):
GAGTTGTTACCAATGGTGCTGATTCTTTCGATTTTTTCTTTCAAATTATCACCAAATGTAACACA
TCCACCTTCCTTTGATTT
Found at i:229667 original size:13 final size:13
Alignment explanation
Indices: 229649--229674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
229639 CAATTTTTTG
229649 TGTATCGATACAT
1 TGTATCGATACAT
229662 TGTATCGATACAT
1 TGTATCGATACAT
229675 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:232210 original size:13 final size:13
Alignment explanation
Indices: 232192--232256 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
232182 ATAATCACCC
*
232192 TGTATCGATACAG
1 TGTATCGATACAA
232205 TGTATCGATACAA
1 TGTATCGATACAA
*
232218 TGTATCGATACAG
1 TGTATCGATACAA
232231 TGTATCGATACAA
1 TGTATCGATACAA
232244 TGTATCGATACAA
1 TGTATCGATACAA
232257 AGAAAAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:232221 original size:26 final size:26
Alignment explanation
Indices: 232192--232255 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
232182 ATAATCACCC
232192 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
232218 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
232244 TGTATCGATACA
1 TGTATCGATACA
232256 AAGAAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAA
Found at i:232267 original size:20 final size:20
Alignment explanation
Indices: 232242--232320 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
232232 GTATCGATAC
232242 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
232262 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
232287 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
232307 CATGTATCGATACA
1 AATGTATCGATACA
232321 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:236186 original size:21 final size:21
Alignment explanation
Indices: 236157--236201 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
236147 AAGTTTTCAT
*
236157 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
236177 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
236199 TTT
1 TTT
236202 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:238442 original size:13 final size:13
Alignment explanation
Indices: 238424--238449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238414 CAATTTTTTG
238424 TGTATCGATACAT
1 TGTATCGATACAT
238437 TGTATCGATACAT
1 TGTATCGATACAT
238450 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:238989 original size:22 final size:22
Alignment explanation
Indices: 238955--238997 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
238945 AGTTAAGTAT
238955 AAATGTTTTTCAAGTAATAAATC
1 AAATGTTTTTCAAGTAA-AAATC
238978 AAATG-TTTTCAAGTAAAAAT
1 AAATGTTTTTCAAGTAAAAAT
238998 AGTCCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATGTTTTTCAAGTAAAAATC
Found at i:239169 original size:16 final size:16
Alignment explanation
Indices: 239145--239176 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
239135 GGTATTGATA
*
239145 CACATTAAATTGTATC
1 CACACTAAATTGTATC
239161 CACACTAAATTGTATC
1 CACACTAAATTGTATC
239177 GATACATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (16 bp):
CACACTAAATTGTATC
Found at i:239240 original size:13 final size:13
Alignment explanation
Indices: 239218--239251 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
239208 CTCAGTGTCG
*
239218 ATACAGTGTATCA
1 ATACATTGTATCA
*
239231 ATACATTGTATCG
1 ATACATTGTATCA
239244 ATACATTG
1 ATACATTG
239252 AGCACAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (13 bp):
ATACATTGTATCA
Found at i:243604 original size:22 final size:23
Alignment explanation
Indices: 243579--243621 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
243569 ATGGTTAGCT
243579 GAAA-AAATAGAGAAA-AAAAAGA
1 GAAAGAAA-AGAGAAATAAAAAGA
243601 GAAAGAAAAGAGAAATAAAAA
1 GAAAGAAAAGAGAAATAAAAA
243622 ATATAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (23 bp):
GAAAGAAAAGAGAAATAAAAAGA
Found at i:244814 original size:128 final size:126
Alignment explanation
Indices: 244580--244947 Score: 420
Period size: 128 Copynumber: 2.9 Consensus size: 126
244570 TCCATTAATT
* * * * * *
244580 TAAACAAATATTATTCATTTTTAATCTTTTAAATT-CTAATGGATTTCTGTAGGGGTTTAAAAAA
1 TAAATAAATATTAATCATTTTTAAT-TTTTATATTCCT-ATGGATATCTATAGGGGTTTAAAAGA
* * * * * * * *
244644 TTTCAAAAACTCTTCGCATCTTTTTGGGTATCCATTAAGGTACAAAATGATTTTTTTCTAAACA
64 TTTCAAAAACTTTTTGTATC-TTTTAGGTTTCCATTAAGGTACGAAATGATTTTTTTCCAAAAA
* * * *
244708 TAAATTAATATTAATCATTTTTAATTTGTTATATTCCTATTGATATCCATAGGGGTGTAAAAGAT
1 TAAATAAATATTAATCATTTTTAATTT-TTATATTCCTATGGATATCTATAGGGGTTTAAAAGAT
*
244773 TTCAAAAACTTTTTGTATCTTTTCAGGTTTCCTTTAAGGTACGAAATGATTTTTTTCCAAAAA
65 TTCAAAAACTTTTTGTATCTTTT-AGGTTTCCATTAAGGTACGAAATGATTTTTTTCCAAAAA
* * * *
244836 TAAATAAATATTAATCGTTTTTAATTTTTATATTCTTATGGGTATTTATAGGGGTATTAAAAGAT
1 TAAATAAATATTAATCATTTTTAATTTTTATATTCCTATGGATATCTATAGGGGT-TTAAAAGAT
*
244901 TTC--AAA-TTCTTTGTATCTTTGTAGGTTTCCATCAAGGTACGAAATGA
65 TTCAAAAACTT-TTTGTATCTTT-TAGGTTTCCATTAAGGTACGAAATGA
244948 CACTTTTTAA
Statistics
Matches: 205, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
125 2 0.01
126 37 0.18
127 30 0.15
128 134 0.65
129 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (126 bp):
TAAATAAATATTAATCATTTTTAATTTTTATATTCCTATGGATATCTATAGGGGTTTAAAAGATT
TCAAAAACTTTTTGTATCTTTTAGGTTTCCATTAAGGTACGAAATGATTTTTTTCCAAAAA
Found at i:246687 original size:19 final size:19
Alignment explanation
Indices: 246663--246717 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
246653 ACATTATGCT
*
246663 TTGTATCGATACATGATCA
1 TTGTATCGATACATGATAA
246682 TTGTATCGATACATGCATAA
1 TTGTATCGATACATG-ATAA
*
246702 TTGTATCAATACATGA
1 TTGTATCGATACATGA
246718 AACTTGCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGATAA
Found at i:252953 original size:33 final size:33
Alignment explanation
Indices: 252909--252990 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
252899 AAAACCCAGA
*
252909 TGTATCGATACAATGTTTTTTGTATCAATATAT
1 TGTATCGATACAATGTTCTTTGTATCAATATAT
* *
252942 TGTATCAATACAATGTTCTTTGTATCGATATAT
1 TGTATCGATACAATGTTCTTTGTATCAATATAT
252975 TGTATCGATACAATGT
1 TGTATCGATACAATGT
252991 ATCGATACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACAATGTTCTTTGTATCAATATAT
Found at i:252979 original size:13 final size:13
Alignment explanation
Indices: 252961--253000 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
252951 ACAATGTTCT
*
252961 TTGTATCGATATA
1 TTGTATCGATACA
252974 TTGTATCGATACA
1 TTGTATCGATACA
*
252987 ATGTATCGATACA
1 TTGTATCGATACA
253000 T
1 T
253001 GGGTTACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:255553 original size:165 final size:165
Alignment explanation
Indices: 255242--255554 Score: 382
Period size: 165 Copynumber: 1.9 Consensus size: 165
255232 TCAAACAAAA
* * * * *
255242 AAATTAATCAAATATTATCATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTTATTTTCAT
1 AAATTAATCAAACATCATCATTTATTTCATATTAATTCAGTTTTAAAAAATTAATTCATTTTCAT
* * * * * **
255307 GAGTTTTTTATTTTTTCCTTGAAATTCTTTTTTTTCGAAATACGGTGTTTTCAATACTATAAATT
66 GAGTTTTTGAATTTTTCCTTAAAAATCTTTTTTTTCGAAAAACGAAGTTTTCAATACTATAAATT
*
255372 TTTTTTAAGAGGATTTTTCTCATTTTTCAATTTTT
131 TTTTTGAAGAGGATTTTTCTCATTTTTCAATTTTT
*
255407 AAATTCATCAAACATCATCATTTGA-TTCATATTAATTCAGTTTTAAAAAATTAATTCATTTTCA
1 AAATTAATCAAACATCATCATTT-ATTTCATATTAATTCAGTTTTAAAAAATTAATTCATTTTCA
* * * * *
255471 TGAG-TTTTGAATTTTTCTTTAAAAATCTCTTTTTTTCGAAAAAACTAAGTTTTC-TTCTCTGTA
65 TGAGTTTTTGAATTTTTCCTTAAAAATCT-TTTTTTTCG-AAAAACGAAGTTTTCAAT-ACTATA
*
255534 AATTTTTTTGGAG-GGATTTTT
127 AATTTTTTTGAAGAGGATTTTT
255555 TTCAGCTTAA
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
164 19 0.15
165 78 0.63
166 27 0.22
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (165 bp):
AAATTAATCAAACATCATCATTTATTTCATATTAATTCAGTTTTAAAAAATTAATTCATTTTCAT
GAGTTTTTGAATTTTTCCTTAAAAATCTTTTTTTTCGAAAAACGAAGTTTTCAATACTATAAATT
TTTTTGAAGAGGATTTTTCTCATTTTTCAATTTTT
Found at i:256180 original size:13 final size:12
Alignment explanation
Indices: 256132--256185 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
256122 AGGTTCAACT
256132 AAAAAAA-AGAG
1 AAAAAAAGAGAG
*
256143 AATAAAAGAGAG
1 AAAAAAAGAGAG
*
256155 AAAAAAAGGGAG
1 AAAAAAAGAGAG
256167 AAAGAAAAGAGAG
1 AAA-AAAAGAGAG
256180 AAAAAA
1 AAAAAA
256186 TAGAAACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 6 0.16
12 20 0.54
13 11 0.30
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (12 bp):
AAAAAAAGAGAG
Found at i:258001 original size:97 final size:97
Alignment explanation
Indices: 257876--258309 Score: 665
Period size: 97 Copynumber: 4.5 Consensus size: 97
257866 AATTTTATTT
* * * *
257876 ATCGGGGATACTCCAACCCTATTCCTTCGAGGGGATACTCAAACCCTGCTTTTAAACACATCAAA
1 ATCGAGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAA
*
257941 GTTTAAATCTTATTCTCACTTAAATTGCCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
*
257973 ATCGAGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCTTGCTTTTAAACACATCAAA
1 ATCGAGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAA
258038 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * * * *
258070 ATCG-GGAACGCTCCAACCTCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACACATCAA
1 ATCGAGG-ACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAA
*
258134 AGTTTAAATCTTATTCTTACTTAAATTGTCATC
65 AGTTTAAATCTTATTCTCACTTAAATTGTCATC
* * *
258167 ATCGAGGACGCTGCAACCCCATTCCTTCGAGGGGATACTCTAACCCTGCTTTTAAACACATCAAA
1 ATCGAGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAA
258232 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * **
258264 ATTGAGGACAATCCAACCCCATT-CTTCCGAGAAGATACTCCAACCC
1 ATCGAGGACACTCCAACCCCATTCCTT-CGAGGGGATACTCCAACCC
258310 CATTTTTCAA
Statistics
Matches: 307, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
96 5 0.02
97 300 0.98
98 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29
Consensus pattern (97 bp):
ATCGAGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:262751 original size:96 final size:97
Alignment explanation
Indices: 262598--262837 Score: 349
Period size: 97 Copynumber: 2.5 Consensus size: 97
262588 AATTTTATTT
* * * * *
262598 ATCGAGGATACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACACA-CAAA
1 ATCGGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACACATCAAA
*
262662 CTTTAAATCTTATTCTCACTTAAATTGTCATC
66 CTTTAAATCTTATTCTCACTTAAATTGCCATC
*
262694 ATCGGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCTGCTTTTAAACACATCAAA
1 ATCGGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACACATCAAA
* *
262759 GTTTAAATCTTATTCTCACTTAAATTGCCGTC
66 CTTTAAATCTTATTCTCACTTAAATTGCCATC
* * *
262791 ATCAGGGACACTCTAACCCCATTCCTCC-AAGGGGATTCTCCAACCCC
1 ATCGGGGACACTCCAACCCCATTCCTCCGAA-GGGATACTCCAACCCC
262838 TTTTTTTAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
96 56 0.43
97 73 0.57
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (97 bp):
ATCGGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGCTTTTAAACACATCAAA
CTTTAAATCTTATTCTCACTTAAATTGCCATC
Found at i:270950 original size:20 final size:20
Alignment explanation
Indices: 270924--270979 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
270914 CAAAAACCCA
270924 AAATGTATCGATACAATGAAT
1 AAATGTATCGATACAAT-AAT
* *
270945 -AATGTATCGATATAAATAGT
1 AAATGTATCGATA-CAATAAT
270965 AAATGTATCGATACA
1 AAATGTATCGATACA
270980 TTTATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACAATAAT
Found at i:270971 original size:21 final size:19
Alignment explanation
Indices: 270923--270977 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
270913 TCAAAAACCC
*
270923 AAAATGTATCGATACAATG
1 AAAATGTATCGATAAAATG
270942 AATAATGTATCGATATAAATAG
1 AA-AATGTATCGATA-AAAT-G
*
270964 TAAATGTATCGATA
1 AAAATGTATCGATA
270978 CATTTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATAAAATG
Found at i:274146 original size:26 final size:26
Alignment explanation
Indices: 274117--274171 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
274107 TAGAAGCAAT
* *
274117 ATATCGATACAAT-TCATCATGTATCG
1 ATATCAATACAATGT-ACCATGTATCG
274143 ATATCAATACAATGTACCATGTATCG
1 ATATCAATACAATGTACCATGTATCG
274169 ATA
1 ATA
274172 CAAACAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (26 bp):
ATATCAATACAATGTACCATGTATCG
Found at i:276763 original size:13 final size:13
Alignment explanation
Indices: 276745--276769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
276735 AGTAACCCAT
276745 GTATCGATACAAC
1 GTATCGATACAAC
276758 GTATCGATACAA
1 GTATCGATACAA
276770 GGAATATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:283081 original size:13 final size:13
Alignment explanation
Indices: 283063--283088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283053 CAATTTTTGG
283063 TGTATCGATACAT
1 TGTATCGATACAT
283076 TGTATCGATACAT
1 TGTATCGATACAT
283089 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:283100 original size:32 final size:33
Alignment explanation
Indices: 283043--283106 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
283033 TACAAGCCAA
**
283043 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
283076 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
283107 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:283113 original size:19 final size:18
Alignment explanation
Indices: 283043--283113 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
283033 TACAAGCCAA
283043 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
283063 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
283076 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
283095 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
283114 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:285614 original size:13 final size:13
Alignment explanation
Indices: 285596--285620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
285586 ATAATCACCC
285596 TGTATCGATACAT
1 TGTATCGATACAT
285609 TGTATCGATACA
1 TGTATCGATACA
285621 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:287711 original size:15 final size:15
Alignment explanation
Indices: 287691--287721 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
287681 ATTTCGTTTG
*
287691 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
287706 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
287721 G
1 G
287722 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:289554 original size:21 final size:21
Alignment explanation
Indices: 289525--289569 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
289515 AAGTTTTCAT
*
289525 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
289545 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
289567 TTT
1 TTT
289570 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:291805 original size:13 final size:13
Alignment explanation
Indices: 291787--291812 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
291777 CAATTTTTGG
291787 TGTATCGATACAT
1 TGTATCGATACAT
291800 TGTATCGATACAT
1 TGTATCGATACAT
291813 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:291824 original size:32 final size:33
Alignment explanation
Indices: 291767--291830 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
291757 TACAAGCCAA
**
291767 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
291800 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
291831 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:291837 original size:19 final size:18
Alignment explanation
Indices: 291767--291837 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
291757 TACAAGCCAA
291767 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
291787 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
291800 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
291819 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
291838 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:292885 original size:43 final size:43
Alignment explanation
Indices: 292821--292921 Score: 184
Period size: 43 Copynumber: 2.3 Consensus size: 43
292811 TACAATATAC
* *
292821 CATGTATCAATACAAATAGTGGTAGGGTAGCTACTGCCAGTTT
1 CATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGTTT
292864 CATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGTTT
1 CATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGTTT
292907 CATGTATCGATACAA
1 CATGTATCGATACAA
292922 TTGTTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
CATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGTTT
Found at i:292929 original size:21 final size:21
Alignment explanation
Indices: 292903--292962 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
292893 GCTACTGCCA
292903 GTTTCATGTATCGATACAATT
1 GTTTCATGTATCGATACAATT
*
292924 GTTTCATGTATCAATACAA-T
1 GTTTCATGTATCGATACAATT
**
292944 G-AACATGTATCGATACAAT
1 GTTTCATGTATCGATACAAT
292963 GTATAGATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.41
20 2 0.06
21 18 0.53
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (21 bp):
GTTTCATGTATCGATACAATT
Found at i:294145 original size:114 final size:112
Alignment explanation
Indices: 293833--294163 Score: 308
Period size: 105 Copynumber: 3.0 Consensus size: 112
293823 TCGATCTAAC
* *
293833 ATAATTAAATAAAATAGGTCCCAAATAAATTAATTAAATATGCATACA-G-G-CTTTATTTTATC
1 ATAATTAAAT-AAATAAGT-CCAAATAAATTAATTAAATAAG--TACATGAGAC-TTATTTTATC
* * * *
293895 TAATGTAAATCTTTTATAAGGCTTGACCTTAAATTAAATAATTTATGACCTAAT
61 T-ATATATAT-TTTTATAAGACTTGACCTTAAATTAAATAATTTATGACCCAAT
* ** * * *
293949 ACAATTAAAT-AA-AA-TGGAAATAAATAAATCAAATAAG--CATGTATGAC-TA-TTTA-ATAT
1 ATAATTAAATAAATAAGTCCAAATAAATTAATTAAATAAGTACATG-A-GACTTATTTTATCTAT
* * *
294006 TTAT-TTTTTATAAGACTTGGCCTTAAATTAAATAATTTATGACCCGAT
64 ATATATTTTTATAAGACTTGACCTTAAATTAAATAATTTATGACCCAAT
294054 ATAATTAAATGAAATAAGTCCAAATAAATTAATTAAATAAGTACATGAGACTTATTTTATCTACT
1 ATAATTAAAT-AAATAAGTCCAAATAAATTAATTAAATAAGTACATGAGACTTATTTTATCTA-T
* * * *
294119 ATATATTTTTATAAGATTTGATCTTAAACTAAATAATTTACGACC
64 ATATATTTTTATAAGACTTGACCTTAAATTAAATAATTTATGACC
294164 TTACCTTAGC
Statistics
Matches: 173, Mismatches: 26, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
105 48 0.28
106 1 0.01
107 8 0.05
108 4 0.02
109 26 0.15
110 5 0.03
111 26 0.15
112 4 0.02
113 5 0.03
114 37 0.21
116 9 0.05
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (112 bp):
ATAATTAAATAAATAAGTCCAAATAAATTAATTAAATAAGTACATGAGACTTATTTTATCTATAT
ATATTTTTATAAGACTTGACCTTAAATTAAATAATTTATGACCCAAT
Found at i:295604 original size:19 final size:18
Alignment explanation
Indices: 295580--295620 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
295570 AGAATTAGAG
*
295580 AATAAATCAAAACTAATTT
1 AATAAAACAAAACT-ATTT
*
295599 AATAAAACTAAACTATTT
1 AATAAAACAAAACTATTT
295617 AATA
1 AATA
295621 GTGGAAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAAACAAAACTATTT
Found at i:296766 original size:22 final size:22
Alignment explanation
Indices: 296693--296773 Score: 58
Period size: 22 Copynumber: 3.7 Consensus size: 22
296683 ATTTTTTTAT
*
296693 ATATTTAAAAA-ATTATATTATT
1 ATATTTAAAAATATTATA-TATA
* ** *
296715 ATATTTATATTTA-AATATATA
1 ATATTTAAAAATATTATATATA
* **
296736 TTAGATAAAAATATTATATATA
1 ATATTTAAAAATATTATATATA
*
296758 ATATTTAAAAAAATTA
1 ATATTTAAAAATATTA
296774 AAAAGCACAA
Statistics
Matches: 41, Mismatches: 16, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
21 10 0.24
22 30 0.73
23 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (22 bp):
ATATTTAAAAATATTATATATA
Found at i:297231 original size:18 final size:18
Alignment explanation
Indices: 297204--297245 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
297194 ATATATATGT
297204 AAAT-AAATTT-GAAATAA
1 AAATAAAATTTAGAAAT-A
*
297221 AAATAAAATTTATAAATA
1 AAATAAAATTTAGAAATA
297239 AAATAAA
1 AAATAAA
297246 TCTAAGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAAAATTTAGAAATA
Found at i:298905 original size:2 final size:2
Alignment explanation
Indices: 298898--298938 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
298888 ACACGAAATT
*
298898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
298939 GGTGTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:299084 original size:19 final size:20
Alignment explanation
Indices: 299057--299096 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
299047 ATATTTAAAA
*
299057 ATATCATTTT-ATATTTATT
1 ATATCATTTTAAAATTTATT
*
299076 ATATTATTTTAAAATTTATT
1 ATATCATTTTAAAATTTATT
299096 A
1 A
299097 AATGTGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATCATTTTAAAATTTATT
Found at i:299778 original size:15 final size:15
Alignment explanation
Indices: 299754--299785 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
299744 ATTATCACGT
*
299754 ATAAATATATATTTA
1 ATAAAAATATATTTA
299769 ATAAAAATATATTTA
1 ATAAAAATATATTTA
299784 AT
1 AT
299786 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAAATATATTTA
Found at i:299812 original size:20 final size:21
Alignment explanation
Indices: 299759--299815 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 21
299749 CACGTATAAA
299759 TATATATTTAATAAAAATATATT
1 TATATATTT-AT-AAAATATATT
*
299782 TA-AT-TTT-TAAAAT-TTTT
1 TATATATTTATAAAATATATT
299799 TATATATTTATAAAATA
1 TATATATTTATAAAATA
299816 ATGTCTCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 4 0.14
20 6 0.21
21 3 0.10
22 2 0.07
23 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATATTTATAAAATATATT
Found at i:305228 original size:13 final size:13
Alignment explanation
Indices: 305210--305236 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
305200 ACATATTGCT
305210 TTGTATCGATACA
1 TTGTATCGATACA
305223 TTGTATCGATACA
1 TTGTATCGATACA
305236 T
1 T
305237 GTTCTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:305249 original size:19 final size:19
Alignment explanation
Indices: 305225--305273 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
305215 TCGATACATT
305225 GTATCGATACATGTTCTTG
1 GTATCGATACATGTTCTTG
305244 GTATCGATACATGTTCTTG
1 GTATCGATACATGTTCTTG
*
305263 GTATTGATACA
1 GTATCGATACA
305274 CACTGAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (19 bp):
GTATCGATACATGTTCTTG
Found at i:305253 original size:32 final size:33
Alignment explanation
Indices: 305191--305255 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
305181 CACACCCAGA
*
305191 TGTATCAATACATATTGCTTTGTATCGATACAT
1 TGTATCAATACATATTGCTTGGTATCGATACAT
* *
305224 TGTATCGATACATGTT-CTTGGTATCGATACAT
1 TGTATCAATACATATTGCTTGGTATCGATACAT
305256 GTTCTTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCAATACATATTGCTTGGTATCGATACAT
Found at i:305627 original size:13 final size:13
Alignment explanation
Indices: 305609--305634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
305599 TCAAAGAGCT
305609 TTGTTATTCTTTG
1 TTGTTATTCTTTG
305622 TTGTTATTCTTTG
1 TTGTTATTCTTTG
305635 AAAGCTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (13 bp):
TTGTTATTCTTTG
Found at i:306942 original size:12 final size:12
Alignment explanation
Indices: 306927--306952 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
306917 GCAACCATCA
306927 AAGATGATGATG
1 AAGATGATGATG
306939 AAGATGATGATG
1 AAGATGATGATG
306951 AA
1 AA
306953 AAATTGACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (12 bp):
AAGATGATGATG
Found at i:313355 original size:34 final size:32
Alignment explanation
Indices: 313288--313355 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
313278 AGGGAAAGAA
*
313288 ATATTTTGAAAATAAATTTGAAAATGGGGGAG
1 ATATTTTGAAAATAAATTTGAAAATGGGAGAG
*
313320 ATATTTTGAGAAATAAAATTTTATAAA-GGGAGAG
1 ATATTTTGA-AAAT-AAATTTGA-AAATGGGAGAG
313354 AT
1 AT
313356 TTTGTGGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.29
33 4 0.13
34 15 0.48
35 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (32 bp):
ATATTTTGAAAATAAATTTGAAAATGGGAGAG
Found at i:316258 original size:20 final size:20
Alignment explanation
Indices: 316220--316259 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
316210 TAGCCTTTAA
*
316220 TCATGCATTTTCACTATGTT
1 TCATGCATTTTAACTATGTT
316240 TCATGCATTTTTAAC-ATGTT
1 TCATGCA-TTTTAACTATGTT
316260 CGGCATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (20 bp):
TCATGCATTTTAACTATGTT
Found at i:317141 original size:61 final size:59
Alignment explanation
Indices: 316868--317611 Score: 901
Period size: 59 Copynumber: 12.4 Consensus size: 59
316858 AATTAAAGCA
* * * *
316868 CGTCCTACTCTTTTG-GGACTAGAAGGTACCACTAACTTGTATGGGCTTTGAAAGG-AAAG
1 CGTCCTGCTC-TTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
*
316927 CGTCTTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-
1 CGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* * *
316986 CATCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAA-
1 CGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
*
317045 CGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTGAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-G
* *
317106 CGTCTTGCTCTTTGAGGACTGACAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAG
1 CGTCCTGCTCTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* *
317165 CATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAA-
1 CGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* * *
317224 TGTCCTGCTCTTGGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 CGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* * * * * * *
317284 ACGTCCTGCTTTTTAAGGCCTGAAAGGTGCCACCAACTTTTATGGGCTTTAAAAGGAGAAGG
1 -CGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AAAG
* * *
317346 TGTCCTGCTCTGTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-
1 CGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
* * ** * *
317405 CATCTTGCTCTTTGAGGACTGGAAGGTGCCATTAACTTATGTGGGCTTTGAAAAGAAAAGG
1 CGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-G
* *
317466 CATCCTTCTCTTTGAGGACTGACAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGAAAA-G
* *
317527 CGTCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAATGG
1 CGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAA-AG
**
317589 CGTTTTGCTCTTTGAGGACTGAA
1 CGTCCTGCTCTTTGAGGACTGAA
317612 ATGATAAAAG
Statistics
Matches: 601, Mismatches: 62, Indels: 42
0.85 0.09 0.06
Matches are distributed among these distances:
58 5 0.01
59 304 0.51
60 19 0.03
61 239 0.40
62 32 0.05
63 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (59 bp):
CGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
Found at i:317171 original size:120 final size:120
Alignment explanation
Indices: 316868--317609 Score: 951
Period size: 120 Copynumber: 6.2 Consensus size: 120
316858 AATTAAAGCA
* * * * * * *
316868 CGTCCTACTCTTTTG-GGACTAGAAGGTACCACTAACTTGTATGGGCTTTGAAAGGAAAGCGTCT
1 CGTCCTGCTC-TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCGTCC
316932 TGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA--
65 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
* * * * *
316986 CATCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAACGTCCT
1 CGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCGTCCT
*
317051 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTGAAAGGAAAAGG
66 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
* *
317106 CGTCTTGCTCTTTGAGGACT-GACAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCATCC
1 CGTCCTGCTCTTTGAGGACTGGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCGTCC
*
317170 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAA--
65 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
* *
317224 TGTCCTGCTCTTGGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTC
1 CGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAG-CGTC
* * * * * * *
317289 CTGCTTTTTAAGGCCTGAAAGGTGCCACCAACTTTTATGGGCTTTAAAAGGAGAAGG
64 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
* * * * * * *
317346 TGTCCTGCTCTGTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACATCTT
1 CGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCGTCCT
* ** * *
317411 GCTCTTTGAGGACTGGAAGGTGCCATTAACTTATGTGGGCTTTGAAAAGAAAAGG
66 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
* * *
317466 CATCCTTCTCTTTGAGGACT-GACAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGAAAAGGCGT
1 CGTCCTGCTCTTTGAGGACTGGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAA-GCGT
* *
317530 CTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAATGG
63 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAAGG
**
317589 CGTTTTGCTCTTTGAGGACTG
1 CGTCCTGCTCTTTGAGGACTG
317610 AAATGATAAA
Statistics
Matches: 542, Mismatches: 67, Indels: 24
0.86 0.11 0.04
Matches are distributed among these distances:
117 4 0.01
118 151 0.28
119 11 0.02
120 249 0.46
121 6 0.01
122 96 0.18
123 25 0.05
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (120 bp):
CGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGCGTCCT
GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
Found at i:318605 original size:9 final size:9
Alignment explanation
Indices: 318583--318620 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
318573 CTTAAGCAAG
318583 TTCTTTTCTT
1 TTCTTTT-TT
318593 TTCTTTTTT
1 TTCTTTTTT
318602 TTCTTTTTT
1 TTCTTTTTT
*
318611 CTCTTTTTT
1 TTCTTTTTT
318620 T
1 T
318621 GTTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:318617 original size:23 final size:23
Alignment explanation
Indices: 318589--318643 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
318579 CAAGTTCTTT
318589 TCTTTTCTTT-TT-TTTCTTTTTTC
1 TCTTTT-TTTGTTGTTT-TTTTTTC
*
318612 TCTTTTTTTGTTGTTTTTTTTTG
1 TCTTTTTTTGTTGTTTTTTTTTC
*
318635 TTTTTTTTT
1 TCTTTTTTT
318644 AATTTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 22 0.79
24 3 0.11
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.85
Consensus pattern (23 bp):
TCTTTTTTTGTTGTTTTTTTTTC
Found at i:318628 original size:10 final size:10
Alignment explanation
Indices: 318615--318667 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
318605 TTTTTTCTCT
318615 TTTTTTGTTG
1 TTTTTTGTTG
*
318625 TTTTTTTTTG
1 TTTTTTGTTG
* *
318635 TTTTTTTTTA
1 TTTTTTGTTG
*
318645 ATTTTTGTTG
1 TTTTTTGTTG
318655 TTTTCTT-TTG
1 TTTT-TTGTTG
318665 TTT
1 TTT
318668 AGAAAAAGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 34 0.94
11 2 0.06
ACGTcount: A:0.04, C:0.02, G:0.11, T:0.83
Consensus pattern (10 bp):
TTTTTTGTTG
Done.