Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 22 of 27
Found at i:3313734 original size:127 final size:125
Alignment explanation
Indices: 3313539--3313827 Score: 404
Period size: 127 Copynumber: 2.3 Consensus size: 125
3313529 GAAATGAGGT
3313539 GCATCCTGCTCTTTGAGGACAAAGG-AAAAAGAAA-AAAAAGTGCGTCCTACTCTTTGAGGACAA
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAAAGTGCGTCCTACTCTTTGAGGACAA
*
3313602 AAGGGAAAAGAAAAAAATGAAATATGTCCTACTCTTTAAGGACAAAAGAGAAAAGGAAAAG
66 AAGGGAAAAGAAAAAAATGAAATATGTCATACTCTTTAA-GACAAAAGAGAAAAGGAAAAG
* * * *
3313663 GCATCCTACTTTTTGAGGACAAAGGAAAAAAGAAAATAAAAAGTGTG-CCTTTCTCTTTGAGGAC
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAAAG-AAATAAAAAGTGCGTCC-TACTCTTTGAGGAC
** * *
3313727 AAAAGGGAAAAGAAGGAAATGAAATGTGTCATGCTCTTTAAGACAAAAGAGAAAAGGAAAAG
64 AAAAGGGAAAAGAAAAAAATGAAATATGTCATACTCTTTAAGACAAAAGAGAAAAGGAAAAG
* *
3313789 GCATCCTGCACTTTGAGGACTAAGGGAAAAGAAGGAAAT
1 GCATCCTGCTCTTTGAGGAC-AAAGGAAAA-AA-GAAAT
3313828 GAGGTGCACC
Statistics
Matches: 145, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
124 23 0.16
125 6 0.04
126 43 0.30
127 66 0.46
128 6 0.04
129 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (125 bp):
GCATCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAAAGTGCGTCCTACTCTTTGAGGACAA
AAGGGAAAAGAAAAAAATGAAATATGTCATACTCTTTAAGACAAAAGAGAAAAGGAAAAG
Found at i:3313846 original size:81 final size:84
Alignment explanation
Indices: 3313717--3313915 Score: 210
Period size: 81 Copynumber: 2.4 Consensus size: 84
3313707 GTGCCTTTCT
** ***
3313717 CTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAATGTGTCATGCTCTTT-AAGACAAAAGAGAAA
1 CTTTGAGGAC-AAAGGGAAAAGAAGGAAATGAGGTGCACCATGCTCTTTGAAGACAAAAGA-AAA
3313781 AGG-A-AAAG-GCATCCTGCA
64 AGGAATAAAGTGCATCCTGCA
* * * * *
3313799 CTTTGAGGACTAAGGGAAAAGAAGGAAATGAGGTGCACCTTGGTCTTTGAGGACAAAGGAAAAAG
1 CTTTGAGGACAAAGGGAAAAGAAGGAAATGAGGTGCACCATGCTCTTTGAAGACAAAAGAAAAAG
* *
3313864 GAAATAAAGTGCATCTTGCT
66 G-AATAAAGTGCATCCTGCA
* *
3313884 CTTTGAGAACAAAGGGAAAA-AAAGAAATGAGG
1 CTTTGAGGACAAAGGGAAAAGAAGGAAATGAGG
3313916 AAAATGTCCT
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
81 36 0.37
82 19 0.20
83 1 0.01
84 15 0.15
85 26 0.27
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (84 bp):
CTTTGAGGACAAAGGGAAAAGAAGGAAATGAGGTGCACCATGCTCTTTGAAGACAAAAGAAAAAG
GAATAAAGTGCATCCTGCA
Found at i:3313854 original size:126 final size:126
Alignment explanation
Indices: 3313539--3313863 Score: 383
Period size: 127 Copynumber: 2.6 Consensus size: 126
3313529 GAAATGAGGT
* * * *
3313539 GCATCCTGCTCTTTGAGGACAAAGG-AAAAAGAAAA-AAAAGTGCGTCC-TACTCTTTGAGGACA
1 GCATCCTACACTTTGAGGACAAAGGAAAAAAGAAAATAAAAGTGC-ACCTTGCTCTTTGAGGACA
*
3313601 AAAGGGAAAAGAAAAAAATGAAATATGTCCTACTCTTTAAGGACAAAAGAGAAAAGGAAAAG
65 AAAGGGAAAAGAAAAAAATGAAATATGTCATACTCTTTAAGGACAAAAGAGAAAAGGAAAAG
** ** *
3313663 GCATCCTACTTTTTGAGGACAAAGGAAAAAAGAAAATAAAAAGTGTGCCTTTCTCTTTGAGGACA
1 GCATCCTACACTTTGAGGACAAAGGAAAAAAGAAAAT-AAAAGTGCACCTTGCTCTTTGAGGACA
** * *
3313728 AAAGGGAAAAGAAGGAAATGAAATGTGTCATGCTCTTTAA-GACAAAAGAGAAAAGGAAAAG
65 AAAGGGAAAAGAAAAAAATGAAATATGTCATACTCTTTAAGGACAAAAGAGAAAAGGAAAAG
* * * * * *
3313789 GCATCCTGCACTTTGAGGACTAAGGGAAAAGAAGGAAAT-GAGGTGCACCTTGGTCTTTGAGGAC
1 GCATCCTACACTTTGAGGAC-AAAGGAAAA-AAGAAAATAAAAGTGCACCTTGCTCTTTGAGGAC
*
3313853 -AAAGGAAAAAG
64 AAAAGGGAAAAG
3313864 GAAATAAAGT
Statistics
Matches: 173, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
124 23 0.13
125 20 0.12
126 59 0.34
127 64 0.37
128 7 0.04
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (126 bp):
GCATCCTACACTTTGAGGACAAAGGAAAAAAGAAAATAAAAGTGCACCTTGCTCTTTGAGGACAA
AAGGGAAAAGAAAAAAATGAAATATGTCATACTCTTTAAGGACAAAAGAGAAAAGGAAAAG
Found at i:3313866 original size:41 final size:42
Alignment explanation
Indices: 3313674--3313915 Score: 147
Period size: 41 Copynumber: 5.7 Consensus size: 42
3313664 CATCCTACTT
* * * ** *
3313674 TTTGAGGACAAAGGAAAAAAGAAAATAAAAAGTGTGCCTTTCTC
1 TTTGAGGACAAAGGAAAAAAGGAAAT--GAGGTGCACCTTGCTC
** *** *
3313718 TTTGAGGACAAAAGGGAAAAGAAGGAAATGAAATGTGTCATGCTC
1 TTTGAGGAC-AAA-GGAAAA-AAGGAAATGAGGTGCACCTTGCTC
* * * *
3313763 TTT-AAGACAAAAGAGAAAAGGAAA--A-G-GCATCC-TGCAC
1 TTTGAGGACAAAGGAAAAAAGGAAATGAGGTGCA-CCTTGCTC
* *
3313800 TTTGAGGACTAAGGGAAAAGAAGGAAATGAGGTGCACCTTGGTC
1 TTTGAGGAC-AAAGGAAAA-AAGGAAATGAGGTGCACCTTGCTC
* * *
3313844 TTTGAGGACAAAGG-AAAAAGGAAATAAAGTGCATCTTGCTC
1 TTTGAGGACAAAGGAAAAAAGGAAATGAGGTGCACCTTGCTC
* *
3313885 TTTGAGAACAAAGGGAAAAAAAGAAATGAGG
1 TTTGAGGACAAA-GGAAAAAAGGAAATGAGG
3313916 AAAATGTCCT
Statistics
Matches: 155, Mismatches: 29, Indels: 29
0.73 0.14 0.14
Matches are distributed among these distances:
37 8 0.05
38 5 0.03
39 7 0.05
40 7 0.05
41 38 0.25
42 10 0.06
43 22 0.14
44 28 0.18
45 17 0.11
46 6 0.04
47 7 0.05
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (42 bp):
TTTGAGGACAAAGGAAAAAAGGAAATGAGGTGCACCTTGCTC
Found at i:3314010 original size:62 final size:62
Alignment explanation
Indices: 3313936--3314067 Score: 203
Period size: 62 Copynumber: 2.1 Consensus size: 62
3313926 ACTCCTTAAA
*
3313936 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAAGAAAAAGGCATCATGCTCTTTGAG
1 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAAG-AAAAGGCATCATACTCTTTGAG
* * * *
3313998 GACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAAGGCGTCCTATTCTTTGAG
1 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAAGGCATCATACTCTTTGAG
3314060 GACTAAAA
1 GACTAAAA
3314068 AGTGGCGTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 57 0.90
63 6 0.10
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (62 bp):
GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAAGGCATCATACTCTTTGAG
Found at i:3314080 original size:29 final size:29
Alignment explanation
Indices: 3314042--3314100 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3314032 AAAAAGAAAA
3314042 GGCGTCCTATTCTTTGAGGACTAAAAAGT
1 GGCGTCCTATTCTTTGAGGACTAAAAAGT
3314071 GGCGTCCTATTCTTTGAGGACTAAAAAGT
1 GGCGTCCTATTCTTTGAGGACTAAAAAGT
3314100 G
1 G
3314101 CCACCAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (29 bp):
GGCGTCCTATTCTTTGAGGACTAAAAAGT
Found at i:3314210 original size:154 final size:153
Alignment explanation
Indices: 3313936--3314221 Score: 421
Period size: 154 Copynumber: 1.9 Consensus size: 153
3313926 ACTCCTTAAA
* * * * *
3313936 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGCATCATGCTCTTTGAGGAC
1 GACTAAAAAGTGCCACCAACTCGTGTAGGCTTTAAAAAAAAAAAGACATCATGCTCTTTGAGAAC
* *
3314001 TAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAAGGCGTCCTATTCTTTGAGGACTAA
66 TAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAA
3314066 AAAGTGGCGTCCTATTCTTTGAG
131 AAAGTGGCGTCCTATTCTTTGAG
* * *
3314089 GACTAAAAAGTGCCACCAACTCGTGTAGGCTTTGAAAAAAAAAAAGACGTCCTGCTTTTTGAGAA
1 GACTAAAAAGTGCCACCAACTCGTGTAGGCTTT-AAAAAAAAAAAGACATCATGCTCTTTGAGAA
* * * *
3314154 CTAAAGGGTGCCACCAACTGGTGTAGGCTTTG-AAAAGAAAAAGGTGTCTTGCTCTTTGAGGACT
65 CTAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAAG-AAAAGGCGTCCTACTCTTTGAGGACT
3314218 AAAA
129 AAAA
3314222 GGTGCCACCA
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
153 36 0.31
154 81 0.69
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (153 bp):
GACTAAAAAGTGCCACCAACTCGTGTAGGCTTTAAAAAAAAAAAGACATCATGCTCTTTGAGAAC
TAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAA
AAAGTGGCGTCCTATTCTTTGAG
Found at i:3314226 original size:62 final size:62
Alignment explanation
Indices: 3314071--3314409 Score: 430
Period size: 62 Copynumber: 5.5 Consensus size: 62
3314061 ACTAAAAAGT
** * * *
3314071 GGCGTCCTATTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAGGCTTTGAAAAAAAAAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTG-AAAAGAAAAA
* * * * * *
3314134 GACGTCCTGCTTTTTGAGAACTAAAGGGTGCCACCAACTGGTGTAGGCTTTGAAAAGAAAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
* * *
3314196 GGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGC-TTGAAAAGAAAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
* * *
3314257 GGCATCCTACTCTTTGAGGACTAAAAGGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAA
1 GGCGTCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
* * * * * *
3314320 GGCATTCTGCT-TTGTGTGGACTAAAAGGTGCCACCAACTCATATGGGCTTTGAAAAGGAAAA
1 GGCGTCCTGCTCTT-TGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
3314382 GGCGTCCTGCTCTTTGAGGACTAAAAGG
1 GGCGTCCTGCTCTTTGAGGACTAAAAGG
3314410 GTTAAAAGGG
Statistics
Matches: 238, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
61 35 0.15
62 124 0.52
63 79 0.33
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (62 bp):
GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA
Found at i:3314395 original size:186 final size:186
Alignment explanation
Indices: 3314075--3314409 Score: 483
Period size: 186 Copynumber: 1.8 Consensus size: 186
3314065 AAAAGTGGCG
* *
3314075 TCCTATTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAGGCTTTGAAAAAAAAAAAGACGTC
1 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAGGCTTTGAAAAAAAAAAAGACATC
* * ** * * *
3314140 CTGCTTTTTGAGAACTAAAGGGTGCCACCAACTGGTGTAGGCTTTGAAAAGAAAAAGGTGTCTTG
66 CTGCTTTGTGAGAACTAAAAGGTGCCACCAACTCATATAGGCTTTGAAAAGAAAAAGGCGTCCTG
3314205 CTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTGAAAAGAAAAAGGCA
131 CTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTGAAAAGAAAAAGGCA
* * * * *
3314261 TCCTACTCTTTGAGGACTAAAAGGGTGCCACTAACTCGTGTGGGCTTTG-AAAAGAAAAAGGCAT
1 TCCTACTCTTTGAGGACTAAAA-AGTGCCACCAACTCGTGTAGGCTTTGAAAAAAAAAAAGACAT
* * * * *
3314325 TCTGCTTTGTGTGGACTAAAAGGTGCCACCAACTCATATGGGCTTTGAAAAGGAAAAGGCGTCCT
65 CCTGCTTTGTGAGAACTAAAAGGTGCCACCAACTCATATAGGCTTTGAAAAGAAAAAGGCGTCCT
3314390 GCTCTTTGAGGACTAAAAGG
130 GCTCTTTGAGGACTAAAAGG
3314410 GTTAAAAGGG
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
186 106 0.82
187 23 0.18
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (186 bp):
TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAGGCTTTGAAAAAAAAAAAGACATC
CTGCTTTGTGAGAACTAAAAGGTGCCACCAACTCATATAGGCTTTGAAAAGAAAAAGGCGTCCTG
CTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTGAAAAGAAAAAGGCA
Found at i:3315629 original size:20 final size:21
Alignment explanation
Indices: 3315601--3315640 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3315591 TCATATAGGC
*
3315601 ATCTATGTC-TTCGCTTTTTG
1 ATCTATGTCGTTCCCTTTTTG
*
3315621 ATCTTTGTCGTTCCCTTTTT
1 ATCTATGTCGTTCCCTTTTT
3315641 ATTCTTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.07, C:0.23, G:0.12, T:0.57
Consensus pattern (21 bp):
ATCTATGTCGTTCCCTTTTTG
Found at i:3315664 original size:19 final size:18
Alignment explanation
Indices: 3315636--3315676 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
3315626 TGTCGTTCCC
3315636 TTTTTATTCTTTCATTTT
1 TTTTTATTCTTTCATTTT
*
3315654 GTTTTTTTTCTTTCATTTT
1 -TTTTTATTCTTTCATTTT
3315673 TTTT
1 TTTT
3315677 GCTTTTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTATTCTTTCATTTT
Found at i:3320678 original size:79 final size:79
Alignment explanation
Indices: 3320542--3320920 Score: 365
Period size: 79 Copynumber: 4.8 Consensus size: 79
3320532 ATAAAAACGA
* * *
3320542 GGTTGGAGTATCCCCGATAGTGGAAAATCGATATTTT-GAAAATAAAACCG-GGATTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTTAG-AAATAAAATCGAAG-TTGGAGTATC
*
3320605 CTCTCAAAAATAATAG
64 CTCTCAAAAATAACAG
*** * *
3320621 GGTTGGAGTATCTTTGATTGT-GAGAAATTGATATTTTAGAAATAAAGTCGAAGTTGGAGTAT-C
1 GGTTGGAGTATCCCCGATTGTGGA-AAATCGATATTTTAGAAATAAAATCGAAGTTGGAGTATCC
** *
3320684 TCCTCGGAAATAACAA
65 T-CTCAAAAATAACAG
* * * ** * *
3320700 GATTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAAAAATAAAATCGGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTTAGAAATAAAATCGAAGTTGGAGTATCCT
*
3320765 CTCGAAAATAAC-G
66 CTCAAAAATAACAG
* * * * *
3320778 GGTTGGAGTATCCCCGATTGTGGAAAATCAAAATTTTAGAAATAAAATTGAGGTTAGAGTAT-CT
1 GGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTTAGAAATAAAATCGAAGTTGGAGTATCCT
* *
3320842 CTTCAGAAATAACGG
66 C-TCAAAAATAACAG
*** * * * *
3320857 GGTTGGAGTATTTTCGATTATGGAAAATCGATGTTTTGGAAATAAAACCGAAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTTAGAAATAAAATCGAAGTTGGAGTATCC
3320921 CCTCGATGGT
Statistics
Matches: 243, Mismatches: 48, Indels: 17
0.79 0.16 0.06
Matches are distributed among these distances:
77 2 0.01
78 68 0.28
79 168 0.69
80 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTTAGAAATAAAATCGAAGTTGGAGTATCCT
CTCAAAAATAACAG
Found at i:3320852 original size:157 final size:158
Alignment explanation
Indices: 3320544--3320926 Score: 455
Period size: 157 Copynumber: 2.4 Consensus size: 158
3320534 AAAAACGAGG
* * *
3320544 TTGGAGTATCCCCGATAGTGGAAAATCGATATTTTGAAAATAAAACCGGGATTGGAGTATCCTCT
1 TTGGAGTATCCCCGATTGTGGAAAATCGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCT
* *** ** * *
3320609 CAAAAATAATAGGGTTGGAGTATCTTTGATTGTGAGAAATTGATATTTTAGAAATAAAGTCGAAG
66 CGAAAATAATAGGGTTGGAGTATCCCCGATTGTGAGAAATCAAAATTTTAGAAATAAAATCGAAG
* *
3320674 TTGGAGTATCTCCTCGGAAATAACAAGA
131 TTAGAGTATCTCCTCAGAAATAACAAGA
* * * *
3320702 TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAAAAATAAAATCGGGGTTAGAGTATCCCCT
1 TTGGAGTATCCCCGATTGTGGAAAATCGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCT
* * *
3320767 CGAAAATAA-CGGGTTGGAGTATCCCCGATTGTG-GAAAATCAAAATTTTAGAAATAAAATTGAG
66 CGAAAATAATAGGGTTGGAGTATCCCCGATTGTGAG-AAATCAAAATTTTAGAAATAAAATCGAA
* ** *
3320830 GTTAGAGTATCTCTTCAGAAATAACGGGG
130 GTTAGAGTATCTCCTCAGAAATAACAAGA
*** * * * **
3320859 TTGGAGTATTTTCGATTATGGAAAATCGATGTTTTGGAAATAAAACCGAAGTTGGAGTATCCCCT
1 TTGGAGTATCCCCGATTGTGGAAAATCGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCT
3320924 CGA
66 CGA
3320927 TGGTGGAAAA
Statistics
Matches: 188, Mismatches: 36, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
156 1 0.01
157 121 0.64
158 66 0.35
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (158 bp):
TTGGAGTATCCCCGATTGTGGAAAATCGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCT
CGAAAATAATAGGGTTGGAGTATCCCCGATTGTGAGAAATCAAAATTTTAGAAATAAAATCGAAG
TTAGAGTATCTCCTCAGAAATAACAAGA
Found at i:3320934 original size:53 final size:53
Alignment explanation
Indices: 3320877--3320979 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 53
3320867 TTTTCGATTA
*
3320877 TGGAAAATC-GATGTTTTGGAAATAAAACCGAAGTTGGAGTATCCCCTCGATGG
1 TGGAAAATCAG-TGTTTTGGAAATAAAACAGAAGTTGGAGTATCCCCTCGATGG
**
3320930 TGGAAAATCAGTGTTTTGGAAATAAAACAGGGGTTGGAGTATCCCCTCGA
1 TGGAAAATCAGTGTTTTGGAAATAAAACAGAAGTTGGAGTATCCCCTCGA
3320980 AAATAACGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 45 0.98
54 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (53 bp):
TGGAAAATCAGTGTTTTGGAAATAAAACAGAAGTTGGAGTATCCCCTCGATGG
Found at i:3321034 original size:132 final size:130
Alignment explanation
Indices: 3320779--3321035 Score: 286
Period size: 132 Copynumber: 2.0 Consensus size: 130
3320769 AAAATAACGG
* ** * *
3320779 GTTGGAGTATCCCCGATTGTGGAAAATCAAAATTTTAGAAATAAAATTGAGGTTAGAGTATCTCT
1 GTTGGAGTATCCCCGATGGTGGAAAATCAAAATTTTAGAAATAAAACAGAGGTTAGAGTATCCCC
* *** * *
3320844 TCAGAAATAACGGGGTTGGAGTATTTTCGATTATGGAAAATCGATGTTTTGGAAATAAAACCGAA
66 TCAGAAATAACGGAGTTGGAGTATGCCCGATGATGGAAAATCGATGTTTTAGAAATAAAACCGAA
*** * * *
3320909 GTTGGAGTATCCCCTCGATGGTGGAAAATCAGTGTTTTGGAAATAAAACAGGGGTTGGAGTATCC
1 GTTGGAGTAT-CCC-CGATGGTGGAAAATCAAAATTTTAGAAATAAAACAGAGGTTAGAGTATCC
*
3320974 CCTC-GAAAATAACGGAGTTGGAGTATGCCCGATGGTGGAAAATC-A-GTATCTTAGAAATAAAA
64 CCTCAG-AAATAACGGAGTTGGAGTATGCCCGATGATGGAAAATCGATGT-T-TTAGAAATAAAA
3321036 TTAGGGCTGG
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
130 12 0.12
131 6 0.06
132 86 0.83
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (130 bp):
GTTGGAGTATCCCCGATGGTGGAAAATCAAAATTTTAGAAATAAAACAGAGGTTAGAGTATCCCC
TCAGAAATAACGGAGTTGGAGTATGCCCGATGATGGAAAATCGATGTTTTAGAAATAAAACCGAA
Found at i:3321047 original size:79 final size:78
Alignment explanation
Indices: 3320908--3321114 Score: 263
Period size: 79 Copynumber: 2.6 Consensus size: 78
3320898 ATAAAACCGA
* * *
3320908 AGTTGGAGTATCCCCTCGATGGTGGAAAATCAGTGTTTTGGAAATAAAACAGGGGTTGGAGTATC
1 AGTTGGAGTAT--CC-CGATGGTGGAAAATCAGTATTTTAGAAATAAAACAGGGGCTGGAGTATC
3320973 CCCTCGAAAATAACGG
63 CCCTCGAAAATAACGG
* * *
3320989 AGTTGGAGTATGCCCGATGGTGGAAAATCAGTATCTTAGAAATAAAATTA-GGGCTGGAGTATCT
1 AGTTGGAGTAT-CCCGATGGTGGAAAATCAGTATTTTAGAAATAAAA-CAGGGGCTGGAGTATCC
*
3321053 CCTCGGAAATAACGG
64 CCTCGAAAATAACGG
* * *
3321068 GGTTGGAGTATCTCCAATGGTGAAAAATCAGTATTTTAGAAATAAAA
1 AGTTGGAGTATC-CCGATGGTGGAAAATCAGTATTTTAGAAATAAAA
3321115 ACATGAATGA
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 97 0.87
80 3 0.03
81 11 0.10
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.26
Consensus pattern (78 bp):
AGTTGGAGTATCCCGATGGTGGAAAATCAGTATTTTAGAAATAAAACAGGGGCTGGAGTATCCCC
TCGAAAATAACGG
Found at i:3333936 original size:2 final size:2
Alignment explanation
Indices: 3333929--3333960 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3333919 TATCCTAATA
3333929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3333961 TAATTGGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3334655 original size:3 final size:3
Alignment explanation
Indices: 3334647--3334685 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
3334637 CTATCCTACC
3334647 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATGA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
3334686 TGAATATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3334691 original size:18 final size:18
Alignment explanation
Indices: 3334647--3334697 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
3334637 CTATCCTACC
3334647 ATAATAATAAT-AATAATA
1 ATAATAAT-ATGAATAATA
3334665 ATAATAATATGAATAATA
1 ATAATAATATGAATAATA
3334683 AT-ATGAATATGAATA
1 ATAAT-AATATGAATA
3334698 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAATAATATGAATAATA
Found at i:3334698 original size:12 final size:12
Alignment explanation
Indices: 3334652--3334691 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
3334642 CTACCATAAT
3334652 AATAATAATAAT-
1 AATAATAAT-ATG
3334664 AATAATAATATG
1 AATAATAATATG
3334676 AATAATAATATG
1 AATAATAATATG
3334688 AATA
1 AATA
3334692 TGAATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 2 0.07
12 25 0.93
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
AATAATAATATG
Found at i:3336047 original size:54 final size:54
Alignment explanation
Indices: 3335965--3336069 Score: 201
Period size: 54 Copynumber: 1.9 Consensus size: 54
3335955 TTTGAAATAA
3335965 GTAAAAAAAATGAGGATAACATAACATTAAACAATACAAAGAGAAAAAAAATGT
1 GTAAAAAAAATGAGGATAACATAACATTAAACAATACAAAGAGAAAAAAAATGT
*
3336019 GTAAAAAAAATGAGGATAACATAACATTAAACAATACCAAGAGAAAAAAAA
1 GTAAAAAAAATGAGGATAACATAACATTAAACAATACAAAGAGAAAAAAAA
3336070 AATGTGTGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (54 bp):
GTAAAAAAAATGAGGATAACATAACATTAAACAATACAAAGAGAAAAAAAATGT
Found at i:3338014 original size:2 final size:2
Alignment explanation
Indices: 3338007--3338039 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3337997 TCAAATTTTG
*
3338007 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3338040 GAGAGAGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3339941 original size:16 final size:16
Alignment explanation
Indices: 3339920--3339951 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3339910 GTGATATGGC
3339920 GAAATACTTTTTACAT
1 GAAATACTTTTTACAT
3339936 GAAATACTTTTTACAT
1 GAAATACTTTTTACAT
3339952 ATGTTTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
GAAATACTTTTTACAT
Found at i:3344372 original size:28 final size:27
Alignment explanation
Indices: 3344311--3344392 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
3344301 TTTTGGAGAT
*
3344311 AATAACGGGGTTGGAGTGTTCCCTCGA-A
1 AATAACGGGGTTGGAGT-ATCCC-CGATA
*
3344339 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGAT-A
* *
3344367 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
3344393 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.06
27 4 0.09
28 40 0.85
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCCCGATA
Found at i:3344436 original size:52 final size:52
Alignment explanation
Indices: 3344376--3344504 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
3344366 AAATAACGAG
* * * * *
3344376 GTTGGAGTATCCTCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGT
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGT-GTTTTGAAAATAAAATCGGA
*
3344428 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
3344479 GTTGGACTATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
3344505 TTGAGAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
51 36 0.55
52 26 0.39
53 4 0.06
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:3346867 original size:13 final size:13
Alignment explanation
Indices: 3346849--3346874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3346839 ACAAAGATCC
3346849 ATGTATCGATACA
1 ATGTATCGATACA
3346862 ATGTATCGATACA
1 ATGTATCGATACA
3346875 CAGAAAAATG
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:3346870 original size:33 final size:33
Alignment explanation
Indices: 3346828--3346894 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3346818 AAAATTTCCA
***
3346828 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3346861 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3346894 A
1 A
3346895 TTTCCTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3346938 original size:19 final size:18
Alignment explanation
Indices: 3346914--3346981 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3346904 TAGTAGCTAA
3346914 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3346933 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3346948 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3346965 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3346982 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3346954 original size:13 final size:13
Alignment explanation
Indices: 3346936--3346960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3346926 ACAATACTTA
3346936 TGTATCGATACAT
1 TGTATCGATACAT
3346949 TGTATCGATACA
1 TGTATCGATACA
3346961 AAACTTATGT
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:3346958 original size:32 final size:32
Alignment explanation
Indices: 3346917--3346979 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3346907 TAGCTAATTA
*
3346917 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3346949 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3346980 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3347061 original size:21 final size:21
Alignment explanation
Indices: 3347037--3347114 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
3347027 CATTTGTAGG
*
3347037 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCTACAA
3347058 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCTACAA
3347079 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCTACAA
3347100 ATGTATCGATACATT
1 ATGTATCGATACATT
3347115 TGGATAATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCTACAA
Found at i:3347962 original size:55 final size:55
Alignment explanation
Indices: 3347862--3348501 Score: 722
Period size: 55 Copynumber: 11.4 Consensus size: 55
3347852 ATAAAGTGTA
* * * * * * * *
3347862 TCCTACTCATTGAGGAGTAAAAAGTGCGACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
3347917 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
3347972 TCCTGCTCTTTGAGGACTGGAAA-ATGTCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
3348027 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
3348082 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * *
3348143 TCCTGCTCTTTGAGGACT-AAAGGTTCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
3348202 TTCC-GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 -TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
** * * *
3348261 TCCCACTCTTTAAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
3348315 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGCCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
3348370 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
3348425 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACTAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
3348480 TCCTGCTCTTTGGGGACTGAAA
1 TCCTGCTCTTTGAGGACTGAAA
3348502 AGCGGAAGGA
Statistics
Matches: 523, Mismatches: 43, Indels: 39
0.86 0.07 0.06
Matches are distributed among these distances:
54 30 0.06
55 333 0.64
56 12 0.02
58 3 0.01
59 92 0.18
60 29 0.06
61 18 0.03
64 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:3348049 original size:26 final size:26
Alignment explanation
Indices: 3348020--3348107 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
3348010 GTGGGCTTTA
3348020 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
3348046 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
*
3348075 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
3348101 AAAGGTG
1 AAAGGTG
3348108 CCACCAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 6 0.13
28 6 0.13
29 11 0.23
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:3348392 original size:27 final size:27
Alignment explanation
Indices: 3348362--3348447 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
3348352 TGTGGCCTTT
3348362 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
3348389 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
3348417 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
3348444 GAAA
1 GAAA
3348448 ATGCCACTAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:3349505 original size:13 final size:12
Alignment explanation
Indices: 3349491--3349546 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
3349481 TTTTTCTTTG
3349491 TTTTGTTTTTTT
1 TTTTGTTTTTTT
3349503 GTTTTGTTTTTTT
1 -TTTTGTTTTTTT
**
3349516 TTTTACTTTTTT
1 TTTTGTTTTTTT
3349528 TTTTGCTCTTTTTT
1 TTTTG-T-TTTTTT
3349542 TTTTG
1 TTTTG
3349547 AAGAGAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 14 0.38
13 12 0.32
14 11 0.30
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:3349525 original size:18 final size:17
Alignment explanation
Indices: 3349481--3349531 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
3349471 CTTTTCTCTC
3349481 TTTTTC-TTTGTTTTGTT
1 TTTTTCTTTTGTTTT-TT
*
3349498 TTTTTGTTTTGTTTTTT
1 TTTTTCTTTTGTTTTTT
3349515 TTTTTACTTTT-TTTTTT
1 TTTTT-CTTTTGTTTTTT
3349532 GCTCTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (17 bp):
TTTTTCTTTTGTTTTTT
Found at i:3359845 original size:28 final size:27
Alignment explanation
Indices: 3359784--3359865 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
3359774 TTTTGGAGAT
*
3359784 AATAACGGGGTTGGAGTGTTCCCTCGA-A
1 AATAACGGGGTTGGAGT-ATCCC-CGATA
*
3359812 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGAT-A
* *
3359840 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
3359866 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.06
27 4 0.09
28 40 0.85
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCCCGATA
Found at i:3359909 original size:52 final size:52
Alignment explanation
Indices: 3359849--3359977 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
3359839 AAATAACGAG
* * * * *
3359849 GTTGGAGTATCCTCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGT
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGT-GTTTTGAAAATAAAATCGGA
*
3359901 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
3359952 GTTGGACTATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
3359978 TTGAGAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
51 36 0.55
52 26 0.39
53 4 0.06
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:3362343 original size:13 final size:13
Alignment explanation
Indices: 3362325--3362350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3362315 ACAAAGATCC
3362325 ATGTATCGATACA
1 ATGTATCGATACA
3362338 ATGTATCGATACA
1 ATGTATCGATACA
3362351 CAGAAAAATG
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:3362346 original size:33 final size:33
Alignment explanation
Indices: 3362304--3362370 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3362294 AAAATTTTCA
***
3362304 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3362337 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3362370 A
1 A
3362371 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3362414 original size:19 final size:18
Alignment explanation
Indices: 3362390--3362457 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
3362380 CAGTAGCTAA
3362390 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3362409 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
3362424 -T-TGTATCAATACAAAAC
1 TTATGTATCGATAC-AAAC
3362441 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3362458 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3362436 original size:32 final size:32
Alignment explanation
Indices: 3362393--3362455 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3362383 TAGCTAATTA
* *
3362393 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCAATACAAAACTTATGTATCGATACAT
3362425 TGTATCAATACAAAACTTATGTATCGATACA
1 TGTATCAATACAAAACTTATGTATCGATACA
3362456 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCAATACAAAACTTATGTATCGATACAT
Found at i:3364606 original size:17 final size:15
Alignment explanation
Indices: 3364584--3364627 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3364574 AAAAGTTTGA
3364584 TAATATCTTTAAAATAG
1 TAATAT-TTTAAAA-AG
* *
3364601 TAATATATTAAAAAT
1 TAATATTTTAAAAAG
3364616 TAATATTTTAAA
1 TAATATTTTAAA
3364628 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 6 0.25
17 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATATTTTAAAAAG
Found at i:3365521 original size:14 final size:14
Alignment explanation
Indices: 3365479--3365521 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3365469 TAATGTCTAA
* *
3365479 AAATTTTAGATATT
1 AAATTTTATATTTT
3365493 AAATATTTATAATTTT
1 AAAT-TTTAT-ATTTT
3365509 AAATTTTATATTT
1 AAATTTTATATTT
3365522 GTATTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
AAATTTTATATTTT
Found at i:3365928 original size:22 final size:23
Alignment explanation
Indices: 3365894--3365937 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
3365884 TATTATTATA
3365894 ATAAATAATTATTAATAATGAAAT
1 ATAAATAATTATTAAT-ATGAAAT
*
3365918 ATAAA-AA-TATTTATATGAAA
1 ATAAATAATTATTAATATGAAA
3365938 AAATGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 2 0.11
24 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
ATAAATAATTATTAATATGAAAT
Found at i:3366752 original size:16 final size:17
Alignment explanation
Indices: 3366723--3366756 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3366713 TATTTAAAAT
3366723 ATATTTTATAATTAATA
1 ATATTTTATAATTAATA
*
3366740 ATATTTT-TTATTAATA
1 ATATTTTATAATTAATA
3366756 A
1 A
3366757 AAATAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTTATAATTAATA
Found at i:3366761 original size:19 final size:19
Alignment explanation
Indices: 3366718--3366761 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3366708 ATTAATATTT
3366718 AAAATATATTTTATAATTA
1 AAAATATATTTTATAATTA
* *
3366737 ATAATATTTTTTATTAA-TA
1 AAAATATATTTTA-TAATTA
3366756 AAAATA
1 AAAATA
3366762 ATATAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATATATTTTATAATTA
Found at i:3367219 original size:26 final size:27
Alignment explanation
Indices: 3367190--3367250 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 27
3367180 ATTTAATTAT
*
3367190 ATATATTAATATTA-AATAATTTTTTA
1 ATATATTAATATTATAATAATTATTTA
*
3367216 ATATTTTAATATTATTAATAATTATTTA
1 ATATATTAATATTA-TAATAATTATTTA
3367244 ATTATAT
1 A-TATAT
3367251 AAGTTTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 13 0.45
28 12 0.41
29 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATATTAATATTATAATAATTATTTA
Found at i:3367219 original size:28 final size:29
Alignment explanation
Indices: 3367188--3367251 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
3367178 AAATTTAATT
*
3367188 ATATATATTAATATTA-AATAATTTTTTA
1 ATATATATTAATATTATAATAATTATTTA
3367216 ATAT-T-TTAATATTATTAATAATTATTTA
1 ATATATATTAATATTA-TAATAATTATTTA
3367244 ATTATATA
1 A-TATATA
3367252 AGTTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 9 0.30
27 1 0.03
28 16 0.53
29 3 0.10
30 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATATATTAATATTATAATAATTATTTA
Found at i:3368008 original size:24 final size:24
Alignment explanation
Indices: 3367960--3368024 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
3367950 ATAATTTATG
* *
3367960 TTTATTTAAATTAATTTTTTATAT
1 TTTATTTAAATAAATTTTATATAT
* *
3367984 TTTATTTATATAAATTTTATGTAT
1 TTTATTTAAATAAATTTTATATAT
**
3368008 TAAATTTTAAATAAATT
1 TTTA-TTTAAATAAATT
3368025 AAAAATATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 22 0.67
25 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTATTTAAATAAATTTTATATAT
Found at i:3368013 original size:14 final size:15
Alignment explanation
Indices: 3367982--3368016 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3367972 AATTTTTTAT
*
3367982 ATTTTATTTATATAA
1 ATTTTATGTATATAA
3367997 ATTTTATGTAT-TAA
1 ATTTTATGTATATAA
3368011 ATTTTA
1 ATTTTA
3368017 AATAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTATGTATATAA
Found at i:3368261 original size:2 final size:2
Alignment explanation
Indices: 3368256--3368283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3368246 ACACACACAC
3368256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3368284 TGTGATTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3370506 original size:17 final size:18
Alignment explanation
Indices: 3370474--3370507 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3370464 AACCCTAATA
*
3370474 TTTTTAATAATTATTTAG
1 TTTTTAATAATAATTTAG
3370492 TTTTTAAT-ATAATTTA
1 TTTTTAATAATAATTTA
3370508 AATTTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTAATAATAATTTAG
Found at i:3370513 original size:18 final size:18
Alignment explanation
Indices: 3370473--3370514 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3370463 AAACCCTAAT
*
3370473 ATTTTTAATAATTATTTA
1 ATTTTTAATAATAATTTA
*
3370491 GTTTTTAAT-ATAATTTAA
1 ATTTTTAATAATAATTT-A
3370509 ATTTTT
1 ATTTTT
3370515 TAGTTGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTAATAATAATTTA
Found at i:3373257 original size:2 final size:2
Alignment explanation
Indices: 3373252--3373277 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3373242 TAAAAAAAAA
3373252 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3373278 GCAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3374410 original size:17 final size:17
Alignment explanation
Indices: 3374367--3374413 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
3374357 ATTAATTTTT
*
3374367 TAATATTTTTATAAATTA
1 TAATATTTTTA-AATTTA
3374385 T-A-A-TTTTAAATTTA
1 TAATATTTTTAAATTTA
3374399 TAATATTTTTAAATT
1 TAATATTTTTAAATT
3374414 ATTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 2 0.08
17 10 0.40
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATATTTTTAAATTTA
Found at i:3374419 original size:17 final size:17
Alignment explanation
Indices: 3374366--3374419 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3374356 AATTAATTTT
3374366 TTAATATTTTTATAA--A
1 TTAATATTTTTA-AATTA
*
3374382 TT-ATAATTTTAAATT-
1 TTAATATTTTTAAATTA
3374397 TATAATATTTTTAAATTA
1 T-TAATATTTTTAAATTA
3374415 TTAAT
1 TTAAT
3374420 TAAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 3 0.10
17 16 0.52
18 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAATATTTTTAAATTA
Found at i:3374463 original size:16 final size:17
Alignment explanation
Indices: 3374429--3374464 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3374419 TTAAATAAAA
3374429 AAAATTATTTAACATTT
1 AAAATTATTTAACATTT
*
3374446 AAAATTATTTTA-ATTT
1 AAAATTATTTAACATTT
3374462 AAA
1 AAA
3374465 TTAATCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTATTTAACATTT
Found at i:3375903 original size:2 final size:2
Alignment explanation
Indices: 3375896--3375945 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
3375886 TTTTCTACTT
* * * *
3375896 TA TA TA TA TA TA CA CA AA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3375938 TA TA TA TA
1 TA TA TA TA
3375946 CACACACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3376166 original size:2 final size:2
Alignment explanation
Indices: 3376159--3376190 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3376149 GCTAAATGGA
3376159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3376191 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3386571 original size:22 final size:22
Alignment explanation
Indices: 3386466--3386571 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
3386456 ACTATAGAAT
* *
3386466 TTACTATGTTATTAATTATTTA
1 TTACTATATTATTAATCATTTA
* * *
3386488 TTATTATACTATTCATCATTTA
1 TTACTATATTATTAATCATTTA
* * *
3386510 TTAATATATTATTGATAATTTA
1 TTACTATATTATTAATCATTTA
* * *
3386532 CTACTACATCATCT-ATCATTTA
1 TTACTATATTAT-TAATCATTTA
*
3386554 ATACTATATTATTAATCA
1 TTACTATATTATTAATCA
3386572 ACAACTATTA
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
21 1 0.02
22 63 0.97
23 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (22 bp):
TTACTATATTATTAATCATTTA
Found at i:3386841 original size:16 final size:18
Alignment explanation
Indices: 3386810--3386843 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3386800 GATTGCTTTA
3386810 TTAAATAAATATTAAAAT
1 TTAAATAAATATTAAAAT
3386828 TTAAA-AAA-ATTAAAAT
1 TTAAATAAATATTAAAAT
3386844 AAATATAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATATTAAAAT
Found at i:3397391 original size:28 final size:28
Alignment explanation
Indices: 3397357--3397419 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
3397347 ACAAATTTTG
* * * *
3397357 TAAAAATTTCAAATTAGTC-CTTAAATTT
1 TAAAAATTACAAA-GAGTCTCTAAAATAT
3397385 TAAAAATTACAAAGAGTCTCTAAAATAT
1 TAAAAATTACAAAGAGTCTCTAAAATAT
3397413 TAAAAAT
1 TAAAAAT
3397420 GTCTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (28 bp):
TAAAAATTACAAAGAGTCTCTAAAATAT
Found at i:3406064 original size:20 final size:20
Alignment explanation
Indices: 3406039--3406076 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3406029 TAAAATCTTT
3406039 TCAATTATTTAATA-TTTTAA
1 TCAATT-TTTAATACTTTTAA
3406059 TCAATTTTTAATACTTTT
1 TCAATTTTTAATACTTTT
3406077 CTTTCAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TCAATTTTTAATACTTTTAA
Found at i:3406311 original size:2 final size:2
Alignment explanation
Indices: 3406277--3406303 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3406267 GCATATTTAC
3406277 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3406304 ACATATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3408113 original size:15 final size:15
Alignment explanation
Indices: 3408093--3408141 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3408083 GAATTTGATC
3408093 TAAATTTAAAAAAAT
1 TAAATTTAAAAAAAT
* *
3408108 TAAATTTAAAATGATT
1 TAAATTTAAAA-AAAT
*
3408124 TAAATCT-AAAAAAT
1 TAAATTTAAAAAAAT
3408138 TAAA
1 TAAA
3408142 ACCCTAACAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 6 0.21
15 14 0.50
16 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
TAAATTTAAAAAAAT
Found at i:3408128 original size:16 final size:16
Alignment explanation
Indices: 3408088--3408134 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
3408078 AACTCGAATT
*
3408088 TGATCTAAATTTAAAA
1 TGATTTAAATTTAAAA
* *
3408104 -AAATTAAATTTAAAA
1 TGATTTAAATTTAAAA
*
3408119 TGATTTAAATCTAAAA
1 TGATTTAAATTTAAAA
3408135 AATTAAAACC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (16 bp):
TGATTTAAATTTAAAA
Found at i:3412954 original size:7 final size:7
Alignment explanation
Indices: 3412942--3412966 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3412932 AATAATTTTA
3412942 AAAATTT
1 AAAATTT
3412949 AAAATTT
1 AAAATTT
3412956 AAAATTT
1 AAAATTT
3412963 AAAA
1 AAAA
3412967 CATATAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:3413383 original size:15 final size:15
Alignment explanation
Indices: 3413363--3413396 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3413353 ATGTTTTCTG
3413363 AAAAAGCATAAATGC
1 AAAAAGCATAAATGC
3413378 AAAAAGCATAAATGC
1 AAAAAGCATAAATGC
3413393 AAAA
1 AAAA
3413397 GGTTAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAGCATAAATGC
Found at i:3419600 original size:37 final size:37
Alignment explanation
Indices: 3419540--3419922 Score: 333
Period size: 37 Copynumber: 10.4 Consensus size: 37
3419530 ATAATTGTGA
* * *
3419540 TCAAATACATCTC-CTCTTTAGCAAAAGCTTGAAATTT
1 TCAAATACATCTCAC-CTTCAGCAAAGGCTTGAAACTT
* *
3419577 TCAAATACATCCCCCCTTCAGCAAAGGCTTGAAACTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
3419614 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
* * * *
3419651 TCAAATACATCTTATCTTCAGCAAAAGCCT-AAGACTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAA-ACTT
* ** * *
3419688 TCAAATACATCTCGCCAACAACAAAGGCTTGAGACTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
* * * * * *
3419725 TCAAATAAAGCTCACTTTCAGTAAAGGCTTGAGATTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
* *
3419762 TCAAATAAATCTCACCTTCAGCAAAGGCTTGAGACTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
* ** ** * * * *
3419799 TCAATTATGTCTTGTCCATGA-CAAAAGCTTGAGACTT
1 TCAAATACATC-TCACCTTCAGCAAAGGCTTGAAACTT
* * **
3419836 TCAAATACATTTCGCCTTCAGC-AAGGACTTGAGGCTT
1 TCAAATACATCTCACCTTCAGCAAAGG-CTTGAAACTT
* * * *
3419873 TCAAATACATATCACCTTTAGCAAAAGCTTGAAATTT
1 TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
* *
3419910 TTAAATAAATCTC
1 TCAAATACATCTC
3419923 GTTGATAATA
Statistics
Matches: 279, Mismatches: 60, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
36 10 0.04
37 259 0.93
38 10 0.04
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (37 bp):
TCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
Found at i:3419903 original size:111 final size:110
Alignment explanation
Indices: 3419540--3419923 Score: 376
Period size: 111 Copynumber: 3.5 Consensus size: 110
3419530 ATAATTGTGA
* * * * * ** *
3419540 TCAAATACATCTC-CTCTTTAGCAAAAGCTTGAAATTTTCAAATACATCCCCCCTTCAGCAAAGG
1 TCAAATACATCTCAC-CTTCAGCAAAAGCTTGAGACTTTCAAATACATCTCGCCAACAACAAAGG
* *
3419604 CTTGAAACTTTCAAATACATCTCACCTTCAGCAAAGGCTTGAAACTT
65 CTTGAGACTTTCAAATACATCTCACCTTCAGC-AAGGCTTGAGACTT
* * * *
3419651 TCAAATACATCTTATCTTCAGCAAAAGCCTAAGACTTTCAAATACATCTCGCCAACAACAAAGGC
1 TCAAATACATCTCACCTTCAGCAAAAGCTTGAGACTTTCAAATACATCTCGCCAACAACAAAGGC
* * * * *
3419716 TTGAGACTTTCAAATAAAGCTCACTTTCAGTAAAGGCTTGAGATTT
66 TTGAGACTTTCAAATACATCTCACCTTCAG-CAAGGCTTGAGACTT
* * * ** * ** *
3419762 TCAAATAAATCTCACCTTCAGCAAAGGCTTGAGACTTTCAATTATGTCTTGTCC-ATGACAAAAG
1 TCAAATACATCTCACCTTCAGCAAAAGCTTGAGACTTTCAAATACATCTCG-CCAACAACAAAGG
* * *
3419826 CTTGAGACTTTCAAATACATTTCGCCTTCAGCAAGGACTTGAGGCTT
65 CTTGAGACTTTCAAATACATCTCACCTTCAGCAAGG-CTTGAGACTT
* * * * * *
3419873 TCAAATACATATCACCTTTAGCAAAAGCTTGAAATTTTTAAATAAATCTCG
1 TCAAATACATCTCACCTTCAGCAAAAGCTTGAGACTTTCAAATACATCTCG
3419924 TTGATAATAA
Statistics
Matches: 218, Mismatches: 51, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
110 4 0.02
111 212 0.97
112 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (110 bp):
TCAAATACATCTCACCTTCAGCAAAAGCTTGAGACTTTCAAATACATCTCGCCAACAACAAAGGC
TTGAGACTTTCAAATACATCTCACCTTCAGCAAGGCTTGAGACTT
Found at i:3420002 original size:37 final size:37
Alignment explanation
Indices: 3419961--3420085 Score: 98
Period size: 37 Copynumber: 3.4 Consensus size: 37
3419951 TGCCAACAAT
3419961 AAAGGCTTAAGACTTTCAAGTACATCTCA-CCTTT-GAC
1 AAAGGCTTAAGACTTTCAAGTACAT-TCAGCCTTTAG-C
* * * * *
3419998 AAAGGTTTAAGACTTCCAATTATATTTAGCCTTTAGC
1 AAAGGCTTAAGACTTTCAAGTACATTCAGCCTTTAGC
* * *
3420035 AAAGGCTTGAGACTTTCTAA-TACCTTTC-GCAC-TTAGT
1 AAAGGCTTAAGACTTTC-AAGTA-CATTCAGC-CTTTAGC
3420072 AAAGGCTTAAGACT
1 AAAGGCTTAAGACT
3420086 ATTACTATGC
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
36 2 0.03
37 62 0.89
38 6 0.09
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (37 bp):
AAAGGCTTAAGACTTTCAAGTACATTCAGCCTTTAGC
Found at i:3426353 original size:43 final size:43
Alignment explanation
Indices: 3426305--3426387 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
3426295 CCCCTTTTCA
*
3426305 AGGTCATCACACCAAACATGAACATTCAACAATAGAATAGAAT
1 AGGTCAACACACCAAACATGAACATTCAACAATAGAATAGAAT
* * * *
3426348 AGGTCAACCCATCAAACTTGAACATTCGACAATAGAATAG
1 AGGTCAACACACCAAACATGAACATTCAACAATAGAATAG
3426388 TTGAACAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.19
Consensus pattern (43 bp):
AGGTCAACACACCAAACATGAACATTCAACAATAGAATAGAAT
Found at i:3427433 original size:31 final size:30
Alignment explanation
Indices: 3427384--3427459 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 30
3427374 AGTTTTGATA
*
3427384 TTTTTAGATTTAACTAATTTT-AGATTTAAGG
1 TTTTTAGGTTTAACTAATTTTGAG-TTTAA-G
3427415 TTTTTAGGTTTATA-TAATTTTGAGTTTAAG
1 TTTTTAGGTTTA-ACTAATTTTGAGTTTAAG
3427445 TTATGTTAGGTTTAA
1 TT-T-TTAGGTTTAA
3427460 ACCAATTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 3 0.08
31 25 0.62
32 12 0.30
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (30 bp):
TTTTTAGGTTTAACTAATTTTGAGTTTAAG
Found at i:3430851 original size:20 final size:20
Alignment explanation
Indices: 3430804--3430855 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
3430794 GCCAAACACC
3430804 TGTATCGATACATTGCTAACA
1 TGTATCGATACATTGCT-ACA
* *
3430825 AGTATCGATACATTTGGT-CA
1 TGTATCGATACA-TTGCTACA
3430845 TGTATCGATAC
1 TGTATCGATAC
3430856 TCCTTTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.44
21 11 0.41
22 4 0.15
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTGCTACA
Found at i:3433197 original size:8 final size:8
Alignment explanation
Indices: 3433179--3433209 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
3433169 TTTTCAACAT
3433179 CAAACATCA
1 CAAA-ATCA
3433188 CAAAATCA
1 CAAAATCA
3433196 CAAAATCA
1 CAAAATCA
3433204 CAAAAT
1 CAAAAT
3433210 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:3437523 original size:3 final size:3
Alignment explanation
Indices: 3437515--3437545 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3437505 TCTGAGTCAC
*
3437515 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
3437546 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:3439174 original size:32 final size:32
Alignment explanation
Indices: 3439133--3439195 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3439123 TACAAGCCAA
3439133 TGTATCGATACAT-TTAGGATCTATCGATACAT
1 TGTATCGATACATCTTAGG-TCTATCGATACAT
* *
3439165 TGTATCGATACATCTTATGTGTATCGATACA
1 TGTATCGATACATCTTAGGTCTATCGATACA
3439196 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTAGGTCTATCGATACAT
Found at i:3439273 original size:20 final size:20
Alignment explanation
Indices: 3439226--3439278 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3439216 GCCAAACACC
3439226 TGTATCGATACATTGCTAACA
1 TGTATCGATACATTGCT-ACA
* *
3439247 AGTATCGATACATTTGGT-CA
1 TGTATCGATACA-TTGCTACA
3439267 TGTATCGATACA
1 TGTATCGATACA
3439279 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.46
21 11 0.39
22 4 0.14
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATTGCTACA
Found at i:3439284 original size:13 final size:13
Alignment explanation
Indices: 3439266--3439290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3439256 ACATTTGGTC
3439266 ATGTATCGATACA
1 ATGTATCGATACA
3439279 ATGTATCGATAC
1 ATGTATCGATAC
3439291 TGTGCAATAT
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):
ATGTATCGATACA
Found at i:3439324 original size:53 final size:54
Alignment explanation
Indices: 3439226--3439330 Score: 133
Period size: 53 Copynumber: 2.0 Consensus size: 54
3439216 GCCAAACACC
**
3439226 TGTATCGATACATTGCTAACAAGTATCGATACATTTGGTCATGTATCGATACAA
1 TGTATCGATACATTGCTAACAAGTATCGATACATTTGAACATGTATCGATACAA
* * **
3439280 TGTATCGATAC-TGTGC-AATATGTATCGATACATTTGAAGGTGTATCGATAC
1 TGTATCGATACAT-TGCTAACAAGTATCGATACATTTGAACATGTATCGATAC
3439331 TTTTAAGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
53 30 0.68
54 14 0.32
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (54 bp):
TGTATCGATACATTGCTAACAAGTATCGATACATTTGAACATGTATCGATACAA
Found at i:3443331 original size:81 final size:81
Alignment explanation
Indices: 3443196--3443352 Score: 305
Period size: 81 Copynumber: 1.9 Consensus size: 81
3443186 CTGAATTGGG
*
3443196 ACGTGCACATATGGCTATTTAAGCATGACTAAATAAGTTATAAAAATATCAAGTCTACTAGCAAA
1 ACGTGCACATATGGCTATTTAAGCATGACTAAATAAGTTATAAAAATATCAAGTCCACTAGCAAA
3443261 AGTTGACTTTTTTATC
66 AGTTGACTTTTTTATC
3443277 ACGTGCACATATGGCTATTTAAGCATGACTAAATAAGTTATAAAAATATCAAGTCCACTAGCAAA
1 ACGTGCACATATGGCTATTTAAGCATGACTAAATAAGTTATAAAAATATCAAGTCCACTAGCAAA
3443342 AGTTGACTTTT
66 AGTTGACTTTT
3443353 ATTAGGGTAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (81 bp):
ACGTGCACATATGGCTATTTAAGCATGACTAAATAAGTTATAAAAATATCAAGTCCACTAGCAAA
AGTTGACTTTTTTATC
Found at i:3445532 original size:786 final size:786
Alignment explanation
Indices: 3443597--3445931 Score: 2834
Period size: 786 Copynumber: 3.0 Consensus size: 786
3443587 GCAACATTGA
* ** * * * * *
3443597 ATCAAACAAAATTCGACTTATGATATATAAAGATTAGGAGTTTCGGTTAAAGTATTTACACAATT
1 ATCAAACAAAATTCGACTCAAAATATATAAAGATAAGGAGTTTAGGTTAAAATGTTTACACAATA
** * * * *
3443662 ATTTTTTTAATCTTGCAGGCAACAATCATGTGGCTTATTAAAAGATATCAAACAACCATCTTGCT
66 ATTTTTTTAATCTTGTGGGCAACAGTCATGTAGCTGATTAAAAGAAATCAAACAACCATCTTG-T
* * *
3443727 TTAAA-CCTAGGCAAAATTAATAGGCAAGTAAAAGGTGGTGAAAGATTTGGCCCAATGTTTTGGA
130 TTAAAGCCTAGGCAAAATTAGTAGGCAAGTAAAAAGTGGTGGAAGATTTGGCCCAATGTTTTGGA
* * * * * * *
3443791 TGATTTAAAGGACTGAAATCTTAATATAATTCTCAAA-TAGCTTTGACAACTAAAGTTTGAACT-
195 GGATTTGAGGGACTGAAATCCTAGTATGATTCTCAAAGT-GCTTTGA-TACTAAAGTTTGAACTA
* * * *
3443854 TGATAGTTGATGGATTGTGAGGAAAGATCAGCACATTTTGTCTAAAGTGCATTTTCATGAACTTG
258 TGATAGTTGATGGATTGTTAGGAAAGATCA-CACA-TTTATCTAAAGTGCATTTTCGTGGACTTG
*
3443919 TGAAAGGTTTTGAATC-----AAGAGGGAAGTTTACATTCTAAATTACATAATTTAATATC-ATA
321 TGAAAGGTTTTGAATCAAATAAAGAGGGAAGTTTACATTCTAGATTACATAATTTAATATCAAT-
* * * *
3443978 TTTCATATAAATTACAAACTTTAATTTTATTAAATTACATTATCAAACTTTAATTATTAACAAAT
385 TTTCATATAGATTACAAACTTTAATTTCATTAAATTACATCACCAAACTTTAATTATTAACAAAT
** * * *
3444043 TAAGTCAAATACATTAACTTCATTAAGTAATTTTAACAAAAAAGCTAATTTAGTATGCATATGTG
450 TAAGTCACTTACATTAACTTCATTAAGTAATTCTAACAAAAAAACTGATTTAGTATGCATATGTG
* *
3444108 AGGTATCTCTATCATATATTATCTTGATAAGATATAAAAAATAAGTCATATATGCATACTAAGTC
515 AGGTATCTCTATCATATATTATCTTGATAAGATGTAAAAAATAAGTCATATATGCATACTAAGTT
* *
3444173 AGATTTTATGTTAGAATTACTTAATGGAGCTAGTTTAAGTGACTTAATTTCTTAATAATAGAAGT
580 AGATTTTATATTAGAA-TACTTAATGGAGTTAGTTTAAGTGACTTAATTTCTTAATAATAGAAGT
* * * * * * * *
3444238 TTAGTGATATAATTTGATAAAATTAAAAGTTTATGTTCTACATGAAAGTTAACGCTAAGGTTAGT
644 TCAGTGATGTAATTTGATGAAATTAAAAGTTTGTG-TCTATACG-ATG-T---GCTAAGTTTAGT
* * * ** * *
3444303 AACTCAG-AATATAAATTACTTAAATAAGGACTCAAAACATGAGGTTTTTATTCCGAAAATAGAA
703 GACT-AGTAATGTAAATTACCTAAATAAGGACTTGAAACATGAGGTTCTTATTCCGAAAACAGAA
3444367 AACAAAATCAACAGCATAGT
767 AACAAAATCAACAGCATAGT
* * *
3444387 ATCAAACAAAATTCTACTCAAAATATATAAAGATAAAGAGTTTAGGTTAAAATGTTTACACGATA
1 ATCAAACAAAATTCGACTCAAAATATATAAAGATAAGGAGTTTAGGTTAAAATGTTTACACAATA
* * * * *
3444452 ATTTTTTTAATCTTGTGGGCAATAGTCATGTAGTTGATTAAAAGAGATCTAACAACCATCTTGCT
66 ATTTTTTTAATCTTGTGGGCAACAGTCATGTAGCTGATTAAAAGAAATCAAACAACCATCTTGTT
* * * * * * *
3444517 TAACGCCTAGGCAAAATTAGCAAGCAAGTAAAAAGTGATGGAAAATTTGGCCTAATGTTTTAGAG
131 TAAAGCCTAGGCAAAATTAGTAGGCAAGTAAAAAGTGGTGGAAGATTTGGCCCAATGTTTTGGAG
* *
3444582 GATTTGAGGGACT-AAGATCCTAGTATGATTCTTAAAGTGTTTTGATAGCTAAAGTTTGAACTAT
196 GATTTGAGGGACTGAA-ATCCTAGTATGATTCTCAAAGTGCTTTGATA-CTAAAGTTTGAACTA-
* * *
3444646 TTGATAGTTGATGGATT-TTCGAGAAATATCAACACATTTATCTAAAGTGCATATTCGTGGACTT
258 -TGATAGTTGATGGATTGTTAG-GAAAGATC-ACACATTTATCTAAAGTGCATTTTCGTGGACTT
* * *
3444710 GTGAAAGGTTTTGAATCAAATAATGAGGGAAGTTTACGTTCTAGATTATATAATTTAATATCAAT
320 GTGAAAGGTTTTGAATCAAATAAAGAGGGAAGTTTACATTCTAGATTACATAATTTAATATCAAT
** * *
3444775 TTTCATATAGATTACAGTCTTTTAATTTCATTAAGTTACATCACCGAACTTTAATTATTAACAAA
385 TTTCATATAGATTACAAAC-TTTAATTTCATTAAATTACATCACCAAACTTTAATTATTAACAAA
**
3444840 TTAAGTCACTTACATTAACTTCATTAAGTAATTCTAGTGAAAAAAACTGATTTAGTATGCATATG
449 TTAAGTCACTTACATTAACTTCATTAAGTAATTCTA-ACAAAAAAACTGATTTAGTATGCATATG
* * * *
3444905 TGAGGTATCTCTATTATATATTATCTTGATAAGATGTAAAATATAAGTCATATATGTATATTAAG
513 TGAGGTATCTCTATCATATATTATCTTGATAAGATGTAAAAAATAAGTCATATATGCATACTAAG
*
3444970 TTAGATTTTACT-TTAG-A-ACTTAATGGAGTTAGTTTGAGTGA-TCT-ATTTCTTAATAATAGA
578 TTAGATTTTA-TATTAGAATACTTAATGGAGTTAGTTTAAGTGACT-TAATTTCTTAATAATAGA
* * *
3445030 AGTTCAATGATGTAATTTGATGAAATTAAAGGTTTGTGTCT-TACG-TGTGCTAAGTTTACTGAC
641 AGTTCAGTGATGTAATTTGATGAAATTAAAAGTTTGTGTCTATACGATGTGCTAAGTTTAGTGAC
* * * * * *
3445093 TTGTAATGTAAATTACCTAAATAAGGACTTGAAACATAAGGTTCTTGTTTC-AAAAGCAGAAGAT
706 TAGTAATGTAAATTACCTAAATAAGGACTTGAAACATGAGGTTCTTATTCCGAAAA-CAGAAAAC
3445157 AAAATCAACAGCATAGT
770 AAAATCAACAGCATAGT
* **
3445174 ATCAGACAAAATAT-GACTCAAGGTATATAAAGATAAGGAGTTTAGGTTAAAATGTTTACACAAT
1 ATCAAACAAAAT-TCGACTCAAAATATATAAAGATAAGGAGTTTAGGTTAAAATGTTTACACAAT
* *
3445238 CATTTTTTTAATCTTGTGGGCAACAGTCATGTTGCTGATTAAAAGAAATC-AACAACCATCTTGT
65 AATTTTTTTAATCTTGTGGGCAACAGTCATGTAGCTGATTAAAAGAAATCAAACAACCATCTTGT
* * *
3445302 TTAAAGCTTAGGAAAAATTAGTAGGCAAGTAAAATGTGGTGGAAGATTTGGCCCAATGTTTTGGA
130 TTAAAGCCTAGGCAAAATTAGTAGGCAAGTAAAAAGTGGTGGAAGATTTGGCCCAATGTTTTGGA
* *
3445367 GGATTTGAGGGATTGAAATCCTAGTATGATTCTCAAAGTGCTTTGATTACTAAAGTTTAAACTAC
195 GGATTTGAGGGACTGAAATCCTAGTATGATTCTCAAAGTGCTTTGA-TACTAAAGTTTGAACTA-
* * * *
3445432 TCAATAGTTGATGGATTGTTAGGAAAGATCGACACATTTATCTAAAGTTCATTTTCGTGGATTTT
258 T-GATAGTTGATGGATTGTTAGGAAAGATC-ACACATTTATCTAAAGTGCATTTTCGTGGACTTG
* * * *
3445497 TGAAAGGTTTTGAATCAAATAAAGAAGGTAGTTTACATTCTAGATTACATCATTTAATATAAATT
321 TGAAAGGTTTTGAATCAAATAAAGAGGGAAGTTTACATTCTAGATTACATAATTTAATATCAATT
* * * *
3445562 TTTATATAGATTACAAACCTTTAATTTCATCAAATTACATCACCAAACTTTAATTACTAACATAT
386 TTCATATAGATTACAAA-CTTTAATTTCATTAAATTACATCACCAAACTTTAATTATTAACAAAT
* ** * * *
3445627 TTAGTCACTTACATTAACTTGGTTAAGTAATTCTAACAAAAAATTCTGATTCA--ATGCCTATGT
450 TAAGTCACTTACATTAACTTCATTAAGTAATTCTAACAAAAAA-ACTGATTTAGTATGCATATGT
* * * *
3445690 GACGTATCTCTATCATATATTACCTTGAAAAGATGTAAAAAATAAGTCATATATGCATACCAAGT
514 GAGGTATCTCTATCATATATTATCTTGATAAGATGTAAAAAATAAGTCATATATGCATACTAAGT
**
3445755 TAGATTTTATATTAGAATTACTTAACAGAGTTAGTTTAAAGTGACTTAATTTCTTAATAATAGAA
579 TAGATTTTATATTAGAA-TACTTAATGGAGTTAGTTT-AAGTGACTTAATTTCTTAATAATAGAA
* * * * *
3445820 GTTCAGCGATGCAA-TTGCTGAAATTAAAAGTTTGTATC-ATACATGAAAGTTAATGCTAAGTTT
642 GTTCAGTGATGTAATTTGATGAAATTAAAAGTTTGTGTCTATAC--G--A--T-GTGCTAAGTTT
* *
3445883 AGTGACCCA-TAATGTACATTACCTAAATAAGGACTTGAAACATGAGGTT
700 AGTGA-CTAGTAATGTAAATTACCTAAATAAGGACTTGAAACATGAGGTT
3445932 TCTATTTCTA
Statistics
Matches: 1321, Mismatches: 179, Indels: 84
0.83 0.11 0.05
Matches are distributed among these distances:
783 1 0.00
784 79 0.06
785 8 0.01
786 330 0.25
787 199 0.15
788 31 0.02
789 36 0.03
790 207 0.16
791 2 0.00
792 43 0.03
793 29 0.02
794 4 0.00
795 50 0.04
796 75 0.06
797 53 0.04
798 76 0.06
799 97 0.07
800 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (786 bp):
ATCAAACAAAATTCGACTCAAAATATATAAAGATAAGGAGTTTAGGTTAAAATGTTTACACAATA
ATTTTTTTAATCTTGTGGGCAACAGTCATGTAGCTGATTAAAAGAAATCAAACAACCATCTTGTT
TAAAGCCTAGGCAAAATTAGTAGGCAAGTAAAAAGTGGTGGAAGATTTGGCCCAATGTTTTGGAG
GATTTGAGGGACTGAAATCCTAGTATGATTCTCAAAGTGCTTTGATACTAAAGTTTGAACTATGA
TAGTTGATGGATTGTTAGGAAAGATCACACATTTATCTAAAGTGCATTTTCGTGGACTTGTGAAA
GGTTTTGAATCAAATAAAGAGGGAAGTTTACATTCTAGATTACATAATTTAATATCAATTTTCAT
ATAGATTACAAACTTTAATTTCATTAAATTACATCACCAAACTTTAATTATTAACAAATTAAGTC
ACTTACATTAACTTCATTAAGTAATTCTAACAAAAAAACTGATTTAGTATGCATATGTGAGGTAT
CTCTATCATATATTATCTTGATAAGATGTAAAAAATAAGTCATATATGCATACTAAGTTAGATTT
TATATTAGAATACTTAATGGAGTTAGTTTAAGTGACTTAATTTCTTAATAATAGAAGTTCAGTGA
TGTAATTTGATGAAATTAAAAGTTTGTGTCTATACGATGTGCTAAGTTTAGTGACTAGTAATGTA
AATTACCTAAATAAGGACTTGAAACATGAGGTTCTTATTCCGAAAACAGAAAACAAAATCAACAG
CATAGT
Found at i:3447004 original size:33 final size:33
Alignment explanation
Indices: 3446958--3447029 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
3446948 CACATCTAGA
* *
3446958 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCAACACATTATGCTTTGTATCGATACAT
3446991 TGTATCAACACATTATGCTTTGTATCGATACAT
1 TGTATCAACACATTATGCTTTGTATCGATACAT
3447024 TGTATC
1 TGTATC
3447030 GATACATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCAACACATTATGCTTTGTATCGATACAT
Found at i:3447028 original size:13 final size:13
Alignment explanation
Indices: 3447010--3447036 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3447000 ACATTATGCT
3447010 TTGTATCGATACA
1 TTGTATCGATACA
3447023 TTGTATCGATACA
1 TTGTATCGATACA
3447036 T
1 T
3447037 GCACAATTGT
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:3453187 original size:49 final size:49
Alignment explanation
Indices: 3453127--3453226 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
3453117 ATAAGTTTAA
3453127 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
1 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
*
3453176 TTGTTTGTGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
1 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
3453225 TT
1 TT
3453227 TGATACGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.19, C:0.04, G:0.25, T:0.52
Consensus pattern (49 bp):
TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
Found at i:3453237 original size:49 final size:49
Alignment explanation
Indices: 3453135--3453237 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
3453125 AATTGTTTAT
* **
3453135 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGTTTGT
1 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGTATAC
3453184 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTT-TGATAC
1 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGT-ATAC
3453233 GAATT
1 GAATT
3453238 AAGTAAGGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 1 0.02
49 49 0.98
ACGTcount: A:0.21, C:0.05, G:0.25, T:0.49
Consensus pattern (49 bp):
GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGTATAC
Found at i:3453486 original size:21 final size:22
Alignment explanation
Indices: 3453449--3453494 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
3453439 CAAACCCTAA
*
3453449 CAAATCATTTATCAAATTTCTT
1 CAAATCAATTATCAAATTTCTT
3453471 CAAATCAATT-TCAAATTTCTT
1 CAAATCAATTATCAAATTTCTT
3453492 CAA
1 CAA
3453495 TTTCACATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (22 bp):
CAAATCAATTATCAAATTTCTT
Found at i:3455882 original size:19 final size:20
Alignment explanation
Indices: 3455858--3455911 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3455848 ACTTTATGCT
* **
3455858 TTGTATAGATACATGTTC-A
1 TTGTATCGATACATGCACAA
3455877 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
3455897 TTGTATCGATACATG
1 TTGTATCGATACATG
3455912 AAACTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:3470032 original size:11 final size:12
Alignment explanation
Indices: 3469982--3470043 Score: 65
Period size: 11 Copynumber: 5.1 Consensus size: 12
3469972 AATATTTTAT
3469982 TTAAATATAA-A
1 TTAAATATAATA
3469993 TTAAATATTAATTA
1 TTAAATA-TAA-TA
* *
3470007 TGTAATTTTAATA
1 T-TAAATATAATA
3470020 TTAAATA-AATA
1 TTAAATATAATA
3470031 TTAAATATAATA
1 TTAAATATAATA
3470043 T
1 T
3470044 ATATTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
11 18 0.43
12 12 0.29
13 3 0.07
14 5 0.12
15 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
TTAAATATAATA
Found at i:3470316 original size:19 final size:19
Alignment explanation
Indices: 3470280--3470319 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3470270 TTTTTAGTAC
3470280 TAAAAAAATAATAAAAATA
1 TAAAAAAATAATAAAAATA
*
3470299 TAAAATAAAT-ATATAAATA
1 TAAAA-AAATAATAAAAATA
3470318 TA
1 TA
3470320 TTAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAAATAATAAAAATA
Found at i:3470325 original size:28 final size:27
Alignment explanation
Indices: 3470294--3470352 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
3470284 AAAATAATAA
3470294 AAATATAAAATAAATATATAAATATATT
1 AAATATAAAATAAATATATAAAT-TATT
* * *
3470322 AAATATGATATAAATATATAAATTTTT
1 AAATATAAAATAAATATATAAATTATT
3470349 AAAT
1 AAAT
3470353 TTTAGGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
AAATATAAAATAAATATATAAATTATT
Found at i:3470337 original size:11 final size:10
Alignment explanation
Indices: 3470307--3470341 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3470297 TATAAAATAA
3470307 ATATATAAAT
1 ATATATAAAT
3470317 ATAT-TAAAT
1 ATATATAAAT
3470326 ATGATATAAAT
1 AT-ATATAAAT
3470337 ATATA
1 ATATA
3470342 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 9 0.39
11 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
ATATATAAAT
Found at i:3470833 original size:23 final size:24
Alignment explanation
Indices: 3470793--3470839 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3470783 TATAAAATTA
*
3470793 AAAAAATAAAATATAATATTATAT
1 AAAAAATAAAATATAATATAATAT
*
3470817 AAAAAATAATATA-AATATAATAT
1 AAAAAATAAAATATAATATAATAT
3470840 TTATATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAATAAAATATAATATAATAT
Found at i:3470837 original size:28 final size:27
Alignment explanation
Indices: 3470792--3470846 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
3470782 ATATAAAATT
3470792 AAAAAAATAAAATATAATA-TTATATA
1 AAAAAAATAAAATATAATATTTATATA
3470818 AAAAATAATATAAATATAATATTTATATA
1 AAAAA-AATA-AAATATAATATTTATATA
3470847 TGATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 10 0.38
29 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAAAAATAAAATATAATATTTATATA
Found at i:3470845 original size:17 final size:16
Alignment explanation
Indices: 3470801--3470846 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
3470791 TAAAAAAATA
3470801 AAATATAATATTATAT
1 AAATATAATATTATAT
3470817 AAA-A-AATA--ATAT
1 AAATATAATATTATAT
3470829 AAATATAATATTTATAT
1 AAATATAATA-TTATAT
3470846 A
1 A
3470847 TGATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.28
13 1 0.04
14 8 0.32
15 1 0.04
16 3 0.12
17 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAATATTATAT
Found at i:3470873 original size:29 final size:28
Alignment explanation
Indices: 3470841--3470902 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3470831 ATATAATATT
* *
3470841 TATATATGATTATTTTAGAATTTATATAA
1 TATATATGATT-TATTAAAATTTATATAA
* *
3470870 TATAAATTATTTATTAAAATTTATATAA
1 TATATATGATTTATTAAAATTTATATAA
3470898 -ATATA
1 TATATA
3470903 AATTATGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 4 0.14
28 15 0.54
29 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TATATATGATTTATTAAAATTTATATAA
Found at i:3470879 original size:26 final size:28
Alignment explanation
Indices: 3470849--3470908 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
3470839 TTTATATATG
*
3470849 ATTATT-TTAGAATTTATAT-AATATAA
1 ATTATTATTAAAATTTATATAAATATAA
3470875 ATTATTTATTAAAATTTATATAAATATAA
1 ATTA-TTATTAAAATTTATATAAATATAA
3470904 ATTAT
1 ATTAT
3470909 GTTAAACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 2 0.07
28 13 0.43
29 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTATTATTAAAATTTATATAAATATAA
Found at i:3472037 original size:23 final size:23
Alignment explanation
Indices: 3471976--3472040 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
3471966 GTACATATCA
* * *
3471976 AATT-TTAAATAAATTAATATTT
1 AATTATTAAATATATAAAAATTT
* *
3471998 AATTATT-TATTTAATAAAAATTT
1 AATTATTAAATAT-ATAAAAATTT
3472021 AATTATTAAATATATAAAAA
1 AATTATTAAATATATAAAAA
3472041 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 6 0.18
23 24 0.73
24 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTATTAAATATATAAAAATTT
Found at i:3475847 original size:2 final size:2
Alignment explanation
Indices: 3475840--3475876 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
3475830 TAAAAAGTAA
*
3475840 AT AT AT AT AT AT CAA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
3475877 CCAATACGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3477002 original size:2 final size:2
Alignment explanation
Indices: 3476995--3477025 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3476985 GAACACATGA
3476995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3477026 AGAGATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3481277 original size:284 final size:282
Alignment explanation
Indices: 3480742--3481306 Score: 760
Period size: 284 Copynumber: 2.0 Consensus size: 282
3480732 TAGGCCTTAA
* *
3480742 AAAATGAAAAAAATAGGATTTATTTAATCTTTTAATTATCATTTATAATAAATTAAGTGAGTATA
1 AAAATAAAAAAAATAGGATTTATTTAATCTTTTAATCATCATTTATAATAAATTAAGTGAGTATA
* **
3480807 TTGTTAAATTTAAATTTTGATTTCCATTGTCAATGTTTCGTTGTTGATACAGCTTTCATAACAAT
66 TTGTTAAATTTAAATTTTGATCTCCATTGTCAATGTTTCACTGTTGATACAGCTTTCATAACAAT
* ** * * * *
3480872 TTGATCATTAATAATTTTGAAATTCATTACAATAAATTATTTTATCAATTTTGTTATATACTGAA
131 TTAATCACAAACAATTTTGAAATTCACTACAAGAAATTATTTTATCAACTTTGTTATATACTGAA
** * *
3480937 ATATCATAAGATAATATTCAAATAAGTATGCAAAGTTTATAAAAATAAGAAAAAAAGAATTCATT
196 ATATCATAAGATAATATTCAAATAAACATACAAAATTTATAAAAATAAGAAAAAAAGAATTCATT
**
3481002 ATTTTTTATGGAATTAAAATTG
261 ATTTTTTACAGAATTAAAATTG
*
3481024 AAAATAAAAAAAATTAGGGATTTATTTAA-CGTTTTAATCATCATTTATAATGAACTTAAGTGAG
1 AAAATAAAAAAAA-TA-GGATTTATTTAATC-TTTTAATCATCATTTATAAT-AAATTAAGTGAG
* * * *
3481088 TATATTGTTAGATTTATA-TTTGATCTCCATTGTCAGTGTTTCACTGTTGATACAGCTTTTATAA
62 TATATTGTTAAATTTAAATTTTGATCTCCATTGTCAATGTTTCACTGTTGATACAGCTTTCATAA
** * * * *
3481152 TGATTTAATTACAAACAATTTTGAAATTCACTATAAGGAATTATTTTATTAACTTTGTTATATA-
127 CAATTTAATCACAAACAATTTTGAAATTCACTACAAGAAATTATTTTATCAACTTTGTTATATAC
* * *
3481216 TTAAAGTATCATGAGATAATATTTAAATAAACATACAAAATTTATAAAAAATAAG-AAAAAAGAA
192 TGAAA-TATCATAAGATAATATTCAAATAAACATACAAAATTTAT-AAAAATAAGAAAAAAAGAA
3481280 TTCATTATTTTTTACAGAATTAAAATT
255 TTCATTATTTTTTACAGAATTAAAATT
3481307 CTTTTAATGT
Statistics
Matches: 245, Mismatches: 32, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
282 12 0.05
283 7 0.03
284 190 0.78
285 36 0.15
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (282 bp):
AAAATAAAAAAAATAGGATTTATTTAATCTTTTAATCATCATTTATAATAAATTAAGTGAGTATA
TTGTTAAATTTAAATTTTGATCTCCATTGTCAATGTTTCACTGTTGATACAGCTTTCATAACAAT
TTAATCACAAACAATTTTGAAATTCACTACAAGAAATTATTTTATCAACTTTGTTATATACTGAA
ATATCATAAGATAATATTCAAATAAACATACAAAATTTATAAAAATAAGAAAAAAAGAATTCATT
ATTTTTTACAGAATTAAAATTG
Found at i:3481520 original size:17 final size:17
Alignment explanation
Indices: 3481494--3481533 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3481484 ATTTATGTTT
*
3481494 ATTTAATTTTTTAAAAA
1 ATTTATTTTTTTAAAAA
*
3481511 TTTTATTTTTTTAAAAA
1 ATTTATTTTTTTAAAAA
3481528 ATTTAT
1 ATTTAT
3481534 AATGCCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTATTTTTTTAAAAA
Found at i:3482102 original size:67 final size:67
Alignment explanation
Indices: 3481994--3482128 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
3481984 CAGCAAAATA
* *
3481994 ATTGCAATGGAATATTATTTCCAGTCTTTTAGTTATGTATGAACACTCTGGTTAGATCATTTATG
1 ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTAGATCATTTATG
3482059 AC
66 AC
*
3482061 ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTCGATCATTTATG
1 ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTAGATCATTTATG
3482126 AC
66 AC
3482128 A
1 A
3482129 ACTCTTATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (67 bp):
ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTAGATCATTTATG
AC
Found at i:3482548 original size:34 final size:34
Alignment explanation
Indices: 3482502--3482686 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
3482492 GTAAAAACCA
*
3482502 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3482536 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3482570 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3482604 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3482638 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3482671 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3482687 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3487150 original size:34 final size:34
Alignment explanation
Indices: 3487104--3487288 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
3487094 GTAAAAACCA
*
3487104 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3487138 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3487172 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3487206 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3487240 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3487273 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3487289 TAAGATCTTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3487405 original size:16 final size:16
Alignment explanation
Indices: 3487386--3487435 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
3487376 AAAGTATTAG
*
3487386 AATTTAAAAAGATCCA
1 AATTTAAAAAGATTCA
*
3487402 AATTTAAAATA-ATTTA
1 AATTTAAAA-AGATTCA
3487418 AATTTAAAAAGATTCA
1 AATTTAAAAAGATTCA
3487434 AA
1 AA
3487436 CTCAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (16 bp):
AATTTAAAAAGATTCA
Found at i:3496204 original size:16 final size:16
Alignment explanation
Indices: 3496185--3496243 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
3496175 GATTAAAATC
3496185 TAAAAAGATCTAAACT
1 TAAAAAGATCTAAACT
* *
3496201 TAAAATA-ATTTAAATT
1 TAAAA-AGATCTAAACT
*
3496217 TAAAAAGATTTAAACT
1 TAAAAAGATCTAAACT
* *
3496233 CAAAAAAATCT
1 TAAAAAGATCT
3496244 CAAATTCGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 1 0.03
16 33 0.94
17 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (16 bp):
TAAAAAGATCTAAACT
Found at i:3497698 original size:27 final size:27
Alignment explanation
Indices: 3497655--3497730 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 27
3497645 TTTAAAAAAT
*
3497655 AAAAATTTATTTAATTTAAATAAAT-TA
1 AAAAATTTAATT-ATTTAAATAAATATA
*
3497682 AAAATATTTAATTATTT-ATTAAATATAA
1 AAAA-ATTTAATTATTTAAATAAATAT-A
3497710 AAAAATTT-ATT-TTTAAATAAA
1 AAAAATTTAATTATTTAAATAAA
3497731 AAAATAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
25 3 0.07
26 14 0.33
27 13 0.31
28 12 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAAATTTAATTATTTAAATAAATATA
Found at i:3497730 original size:26 final size:26
Alignment explanation
Indices: 3497637--3497730 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 26
3497627 CTTTTATGTT
*
3497637 AATTTATTTTTAAA-AAATA-AAAATT
1 AATTTATTTTTAAATAAATATAAAA-A
* *
3497662 TATTTA-ATTTAAATAAAT-TAAAAA
1 AATTTATTTTTAAATAAATATAAAAA
* *
3497686 TATTTAATTATTT-ATTAAATATAAAAA
1 AATTT-ATT-TTTAAATAAATATAAAAA
3497713 AATTTATTTTTAAATAAA
1 AATTTATTTTTAAATAAA
3497731 AAAATAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
24 11 0.20
25 17 0.31
26 14 0.25
27 13 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTTATTTTTAAATAAATATAAAAA
Found at i:3497734 original size:23 final size:23
Alignment explanation
Indices: 3497637--3497740 Score: 79
Period size: 22 Copynumber: 4.2 Consensus size: 23
3497627 CTTTTATGTT
*
3497637 AATTTATTT-TTAAA-AAATAAA
1 AATTTATTTATTAAATAAAAAAA
3497658 AATTTATTTAATTTAAATAAATTAAAA
1 AATTTATTT-A-TTAAATAAA--AAAA
*
3497685 ATATTTAATTATTTATTAAATATAAAAA
1 A-A--T--TTATTTATTAAATAAAAAAA
3497713 AATTTATTT-TTAAATAAAAAAA
1 AATTTATTTATTAAATAAAAAAA
3497735 TAATTT
1 -AATTT
3497741 TTGACGTGAT
Statistics
Matches: 68, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
21 9 0.13
22 12 0.18
23 11 0.16
24 5 0.07
25 4 0.06
27 5 0.07
28 6 0.09
30 9 0.13
31 1 0.01
32 6 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTATTTATTAAATAAAAAAA
Found at i:3500096 original size:87 final size:87
Alignment explanation
Indices: 3499950--3500123 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
3499940 TAATAACCCA
3499950 CACGCATTTCCAAAGCTGTGGTTTCTAGATTTATCTGATAACTTACTTAGCGGTACAACACCACA
1 CACGCATTTCCAAAGCTGTGGTTTCTAGATTTATCTGATAACTTACTTAGCGGTACAACACCACA
3500015 TTGGCTTTATACCCATCCAAGT
66 TTGGCTTTATACCCATCCAAGT
3500037 CACGCATTTCCAAAGCTGTGGTTTCTAGATTTATCTGATAACTTACTTAGCGGTACAACACCACA
1 CACGCATTTCCAAAGCTGTGGTTTCTAGATTTATCTGATAACTTACTTAGCGGTACAACACCACA
3500102 TTGGCTTTATACCCATCCAAGT
66 TTGGCTTTATACCCATCCAAGT
3500124 TTAATTTATT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (87 bp):
CACGCATTTCCAAAGCTGTGGTTTCTAGATTTATCTGATAACTTACTTAGCGGTACAACACCACA
TTGGCTTTATACCCATCCAAGT
Found at i:3503035 original size:21 final size:21
Alignment explanation
Indices: 3503009--3503050 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3502999 ATCTAATGCG
3503009 AAGTTTCTTAAGATTCTCGAT
1 AAGTTTCTTAAGATTCTCGAT
3503030 AAGTTTCTTAAGATTCTCGAT
1 AAGTTTCTTAAGATTCTCGAT
3503051 TTGTCTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
AAGTTTCTTAAGATTCTCGAT
Found at i:3503203 original size:21 final size:21
Alignment explanation
Indices: 3503177--3503218 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3503167 GCAAAAAGAA
3503177 GTGGATTGAAGAATCTTAACT
1 GTGGATTGAAGAATCTTAACT
3503198 GTGGATTGAAGAATCTTAACT
1 GTGGATTGAAGAATCTTAACT
3503219 TGAATAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
GTGGATTGAAGAATCTTAACT
Found at i:3512302 original size:27 final size:28
Alignment explanation
Indices: 3512272--3512327 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
3512262 ATTAAATTTT
* * *
3512272 TTTAATTATTTATTA-AATATAAAAAAA
1 TTTAATCATTAATTATAAAATAAAAAAA
*
3512299 TTTACTCATTAATTATAAAATAAAAAAA
1 TTTAATCATTAATTATAAAATAAAAAAA
3512327 T
1 T
3512328 ACTTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (28 bp):
TTTAATCATTAATTATAAAATAAAAAAA
Found at i:3512630 original size:11 final size:10
Alignment explanation
Indices: 3512614--3512714 Score: 50
Period size: 10 Copynumber: 9.9 Consensus size: 10
3512604 ATCGAATAAA
3512614 AATATTTGAAT
1 AATATTT-AAT
3512625 AATATTTAAT
1 AATATTTAAT
3512635 -ATAATTTAGAT
1 AAT-ATTTA-AT
* *
3512646 AATTTTTTAT
1 AATATTTAAT
*
3512656 AATTATTTGAT
1 AA-TATTTAAT
3512667 AAT-TTTAAAT
1 AATATTT-AAT
*
3512677 ATTATTTTAA-
1 AATA-TTTAAT
3512687 AAT-TTTAA-
1 AATATTTAAT
*
3512695 AAAATTTTAAT
1 AATA-TTTAAT
*
3512706 AATTTTTAA
1 AATATTTAA
3512715 CGTGATTTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
8 7 0.10
9 5 0.07
10 29 0.41
11 24 0.34
12 5 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (10 bp):
AATATTTAAT
Found at i:3512680 original size:20 final size:20
Alignment explanation
Indices: 3512616--3512695 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 20
3512606 CGAATAAAAA
3512616 TATTTGAATAATATTT-AATAT
1 TATTTG-ATAAT-TTTAAATAT
* **
3512637 AATTTAGATAATTTTTTATAAT
1 TATTT-GATAATTTTAAAT-AT
3512659 TATTTGATAATTTTAAATAT
1 TATTTGATAATTTTAAATAT
* *
3512679 TATTTTAAAATTTTAAA
1 TATTTGATAATTTTAAA
3512696 AAATTTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 20 0.41
21 22 0.45
22 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
TATTTGATAATTTTAAATAT
Found at i:3512803 original size:17 final size:19
Alignment explanation
Indices: 3512772--3512806 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3512762 ATTTTAATAA
3512772 TTTTTAACATAATTTTTAT
1 TTTTTAACATAATTTTTAT
3512791 TTTTTAA-AT-ATTTTTA
1 TTTTTAACATAATTTTTA
3512807 ATATTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTAACATAATTTTTAT
Found at i:3517222 original size:16 final size:16
Alignment explanation
Indices: 3517201--3517267 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
3517191 ATTATAGTTG
3517201 AAAATCTATGATTCTA
1 AAAATCTATGATTCTA
3517217 AAAATCTATGATTAC-A
1 AAAATCTATGATT-CTA
* *
3517233 TAAA-CATAT-ATT-TT
1 AAAATC-TATGATTCTA
3517247 AAAATCTATGATTCTTA
1 AAAATCTATGATTC-TA
3517264 AAAA
1 AAAA
3517268 AATGTGAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
14 6 0.15
15 8 0.20
16 20 0.50
17 6 0.15
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (16 bp):
AAAATCTATGATTCTA
Found at i:3517297 original size:18 final size:18
Alignment explanation
Indices: 3517276--3517338 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
3517266 AAAATGTGAG
*
3517276 TTTTAGAAAATCTAAAAT
1 TTTTAGAAAATCTAAGAT
*
3517294 TTTTAAAAAATCTAAGAT
1 TTTTAGAAAATCTAAGAT
*
3517312 TCTT--AAAATCT--GAT
1 TTTTAGAAAATCTAAGAT
3517326 TTTTAGAAAATCT
1 TTTTAGAAAATCT
3517339 GTGATTGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.15
16 14 0.36
18 19 0.49
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTTAGAAAATCTAAGAT
Done.