Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 2 of 153
Found at i:401876 original size:3 final size:3
Alignment explanation
Indices: 401870--401899 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
401860 TTCATGTTCG
401870 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
401900 TGAATCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:405338 original size:18 final size:18
Alignment explanation
Indices: 405315--405350 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
405305 GGGTTTGGGG
* *
405315 TTTAAATTTTTTTAAAAT
1 TTTAAAATTTTATAAAAT
405333 TTTAAAATTTTATAAAAT
1 TTTAAAATTTTATAAAAT
405351 ACTAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAAATTTTATAAAAT
Found at i:408630 original size:39 final size:40
Alignment explanation
Indices: 408535--408796 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
408525 TTGAATGATG
*
408535 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
408573 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
408614 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
408653 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
408692 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
408731 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
408770 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
408797 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:424693 original size:66 final size:68
Alignment explanation
Indices: 424613--424751 Score: 194
Period size: 66 Copynumber: 2.1 Consensus size: 68
424603 CTGAAACTCG
*
424613 CACCCTTTAATTTTTTTCCTAATT-TTTTTACATTATTAGAAAAAAAAATA-TCATACATGCTCA
1 CACCCTTTAATTTTTTTCCT-ATTCTTTTTACAATATTAGAAAAAAAAATATTCATACATGCTCA
424676 AAAA
65 AAAA
* * * * *
424680 CACCC-TTCATTTTTTTCCTATTCTTTTTACAATATTAGATAAAAAAATATTCATGCATGCTTAG
1 CACCCTTTAATTTTTTTCCTATTCTTTTTACAATATTAGAAAAAAAAATATTCATACATGCTCAA
424744 AAA
66 AAA
424747 CACCC
1 CACCC
424752 AAAAATCCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
65 3 0.05
66 37 0.58
67 24 0.38
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (68 bp):
CACCCTTTAATTTTTTTCCTATTCTTTTTACAATATTAGAAAAAAAAATATTCATACATGCTCAA
AAA
Found at i:438302 original size:52 final size:52
Alignment explanation
Indices: 438160--438295 Score: 202
Period size: 52 Copynumber: 2.6 Consensus size: 52
438150 GGCTACTATA
* * * *
438160 GAATGTATATGCGAGTTGTCATTGTATCGAATGCATGAATTATTTTGTGATG
1 GAATGTATATGCGACTTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
438212 GAATGTATATGCGAAC-TGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
1 GAATGTATATGCG-ACTTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
* *
438264 GAATATATATGCGACTTATCATTGCATCGAAT
1 GAATGTATATGCGACTTGTCATTGCATCGAAT
438296 ATATGAAATG
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 2 0.03
52 73 0.96
53 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (52 bp):
GAATGTATATGCGACTTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
Found at i:438427 original size:16 final size:15
Alignment explanation
Indices: 438400--438438 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
438390 TGCGTGAGAT
438400 GTAATATG-CGAGCC
1 GTAATATGTCGAGCC
*
438414 GTAATATGTACGAGCT
1 GTAATATGT-CGAGCC
438430 GTAATATGT
1 GTAATATGT
438439 GAGTTCTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (15 bp):
GTAATATGTCGAGCC
Found at i:438763 original size:17 final size:17
Alignment explanation
Indices: 438737--438783 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
438727 TCCATGCCAA
* *
438737 ATGTGCGAGTTGTGCCC
1 ATGTGTGAGTTGTGACC
*
438754 ATGTGTGAGTTGTGATC
1 ATGTGTGAGTTGTGACC
*
438771 ATGTGTAAGTTGT
1 ATGTGTGAGTTGT
438784 AACAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.34, T:0.38
Consensus pattern (17 bp):
ATGTGTGAGTTGTGACC
Found at i:439008 original size:16 final size:16
Alignment explanation
Indices: 438983--439029 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
438973 CATCCATAGT
*
438983 ATGTGCGAGTTGTTTA
1 ATGTGTGAGTTGTTTA
*
438999 ATGTGTGAGTTGTGGTA
1 ATGTGTGAGTTGT-TTA
*
439016 AAGTGTGAGTTGTT
1 ATGTGTGAGTTGTT
439030 GCAATATGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.43
Consensus pattern (16 bp):
ATGTGTGAGTTGTTTA
Found at i:455454 original size:22 final size:22
Alignment explanation
Indices: 455382--455507 Score: 107
Period size: 22 Copynumber: 5.8 Consensus size: 22
455372 CGACATACAT
**
455382 AATATGCCACAAAGGCTAGTAG
1 AATATGCCACAAAGGCTAACAG
* * *
455404 -A-ATGCCACAAAGACTAAAAA
1 AATATGCCACAAAGGCTAACAG
*
455424 AATGTGCCACAAAGGCTAACAG
1 AATATGCCACAAAGGCTAACAG
* *
455446 AATACGCCAAAAAGGCTAACA-
1 AATATGCCACAAAGGCTAACAG
* *
455467 AA-ATGCATTACAAAGGCTAATAG
1 AATATGC--CACAAAGGCTAACAG
*
455490 AATATGCCATAAAGGCTA
1 AATATGCCACAAAGGCTA
455508 TCGGAATGCC
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
20 18 0.22
21 4 0.05
22 53 0.65
23 2 0.02
24 4 0.05
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (22 bp):
AATATGCCACAAAGGCTAACAG
Found at i:458133 original size:12 final size:12
Alignment explanation
Indices: 458118--458192 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
458108 TTTTATTTTT
458118 TATTTTTAAAAA
1 TATTTTTAAAAA
*
458130 TATTTTTAAAATGC
1 TATTTTTAAAA--A
* * *
458144 TTTTTTTATAAG
1 TATTTTTAAAAA
*
458156 CA-TTTTAAAAA
1 TATTTTTAAAAA
458167 TATTTTTAAAATA
1 TATTTTTAAAA-A
*
458180 CTTTTTTTAAAAA
1 -TATTTTTAAAAA
458193 AAAATTGGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
11 8 0.17
12 19 0.40
13 2 0.04
14 19 0.40
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (12 bp):
TATTTTTAAAAA
Found at i:461188 original size:51 final size:50
Alignment explanation
Indices: 461058--461188 Score: 163
Period size: 51 Copynumber: 2.6 Consensus size: 50
461048 ATACACGCAG
* * * * * *
461058 TAGCCTTCACATAGTACTACACACGTGATCACGCTTTTCGGTTCACGTAG
1 TAGCCTACACATAGTACTACACACGTGACCACGCCTTCCGGTTCACATAA
* *
461108 TAGCCTACACATAGTACTACACACATGACCAAGGCCTTCCGGTTCACATAA
1 TAGCCTACACATAGTACTACACACGTGACC-ACGCCTTCCGGTTCACATAA
* *
461159 TAGCCTACACTTAGTACTACACATGTGACC
1 TAGCCTACACATAGTACTACACACGTGACC
461189 GTTATTTATC
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 27 0.39
51 42 0.61
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (50 bp):
TAGCCTACACATAGTACTACACACGTGACCACGCCTTCCGGTTCACATAA
Found at i:466872 original size:41 final size:41
Alignment explanation
Indices: 466815--466916 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
466805 GCATAGCGCT
*
466815 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
466856 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
466897 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
466917 TACTGAATCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.05
41 54 0.95
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:478574 original size:25 final size:25
Alignment explanation
Indices: 478524--478588 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
478514 ATAATTTTAG
* * *
478524 TAAAATATATATTTTTTATTTCTTA
1 TAAAATATATATTTTTAAGTTATTA
478549 TAAAATATCA-ATTTTTAAGTTATTA
1 TAAAATAT-ATATTTTTAAGTTATTA
478574 TTCAAAAATATATAT
1 -T--AAAATATATAT
478589 AAAATGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 20 0.62
26 2 0.06
27 1 0.03
28 9 0.28
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (25 bp):
TAAAATATATATTTTTAAGTTATTA
Found at i:478676 original size:15 final size:16
Alignment explanation
Indices: 478656--478685 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
478646 TATTTTAAAA
478656 AATAT-ATAAAAATAC
1 AATATAATAAAAATAC
478671 AATATAATAAAAATA
1 AATATAATAAAAATA
478686 ATTAAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AATATAATAAAAATAC
Found at i:478824 original size:9 final size:9
Alignment explanation
Indices: 478810--478856 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
478800 ATGTAAATTT
478810 TTTTATATA
1 TTTTATATA
478819 TTTTAT-TA
1 TTTTATATA
* *
478827 ATTTATACA
1 TTTTATATA
*
478836 TTTTA-AAA
1 TTTTATATA
478844 TTTTATATA
1 TTTTATATA
478853 TTTT
1 TTTT
478857 TAATTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 14 0.45
9 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTATATA
Found at i:478833 original size:17 final size:17
Alignment explanation
Indices: 478810--478856 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
478800 ATGTAAATTT
*
478810 TTTTATATATTTTATTAA
1 TTTTATATATTTTA-AAA
*
478828 -TTTATACATTTTAAAA
1 TTTTATATATTTTAAAA
478844 TTTTATATATTTT
1 TTTTATATATTTT
478857 TAATTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATATATTTTAAAA
Found at i:478855 original size:25 final size:24
Alignment explanation
Indices: 478818--478868 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
478808 TTTTTTATAT
*
478818 ATTTTATTAATTTATACATTTTAAA
1 ATTTTATTAATTTATA-ATTTCAAA
*
478843 ATTTTA-TATATTTTTAATTTCAAA
1 ATTTTATTA-ATTTATAATTTCAAA
478867 AT
1 AT
478869 AATAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTATTAATTTATAATTTCAAA
Found at i:480239 original size:22 final size:23
Alignment explanation
Indices: 480214--480257 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
480204 ATATATATAT
480214 GAAAATATTC-ATTTAAAAAAAG
1 GAAAATATTCGATTTAAAAAAAG
*
480236 GAAAATATTCGTTTTAAAAAAA
1 GAAAATATTCGATTTAAAAAAA
480258 TATATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
GAAAATATTCGATTTAAAAAAAG
Found at i:480920 original size:19 final size:19
Alignment explanation
Indices: 480896--481008 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
480886 AATCATATAT
480896 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
480915 TCTAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
*
480934 TCTAAGATTGCATATCGTA
1 TCTAAGATTGCATATCATA
*
480953 TCTAATATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
480974 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
480993 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
481009 CTCAAAAATT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 63 0.81
21 15 0.19
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:480983 original size:40 final size:40
Alignment explanation
Indices: 480896--481007 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
480886 AATCATATAT
*
480896 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATC
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
* *
480934 TCTAAGATTGCATATCGTATCTAATATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
480974 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
481008 CCTCAAAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 26 0.40
40 39 0.60
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:481310 original size:22 final size:21
Alignment explanation
Indices: 481248--481306 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
481238 AAATTAAAAT
481248 AAAAATATTTTTTAAAATTTA
1 AAAAATATTTTTTAAAATTTA
481269 AAAAATATTTTTTAAAATTTA
1 AAAAATATTTTTTAAAATTTA
481290 AAAAATATTTTTTAAAA
1 AAAAATATTTTTTAAAA
481307 ATTTTCATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAAATATTTTTTAAAATTTA
Found at i:485604 original size:59 final size:58
Alignment explanation
Indices: 485513--485636 Score: 212
Period size: 59 Copynumber: 2.1 Consensus size: 58
485503 CATTGTAAAC
485513 AAATTATATTTTTTGTACCAATCAAAACATTTTGTAAAAATGCAAGAGTTTGTTAGTA
1 AAATTATATTTTTTGTACCAATCAAAACATTTTGTAAAAATGCAAGAGTTTGTTAGTA
* * *
485571 AAATTATATTTTTTTGTACCAATCGAAACATTTTGTAAAAATGCTATAGTTTGTTAGTA
1 AAATTATA-TTTTTTGTACCAATCAAAACATTTTGTAAAAATGCAAGAGTTTGTTAGTA
485630 AAATTAT
1 AAATTAT
485637 TAATTGTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 8 0.13
59 54 0.87
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (58 bp):
AAATTATATTTTTTGTACCAATCAAAACATTTTGTAAAAATGCAAGAGTTTGTTAGTA
Found at i:485759 original size:43 final size:43
Alignment explanation
Indices: 485710--485818 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
485700 AGGGTTAGGG
485710 TTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
1 TTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
**** *
485753 TTTTAAGTTGTTTGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
1 TTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
485796 TTTTAAGTTAAAGTGTTAGGGTT
1 TTTTAAGTTAAAG-GTTAGGGTT
485819 AGGGTTAGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
43 47 0.84
44 9 0.16
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (43 bp):
TTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGT
Found at i:485814 original size:22 final size:21
Alignment explanation
Indices: 485700--485818 Score: 141
Period size: 22 Copynumber: 5.6 Consensus size: 21
485690 GGCTAGGTTT
485700 AGGGTTAGGG-TTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
485720 AAGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
* *
485741 AGGGTTTAAGGTTTTTAAGTTG
1 AGGG-TTAGGGTTTTTAAGTTA
***
485763 TTTGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
485784 AGGGTTTAGGGTTTTTAAGTTAA
1 AGGG-TTAGGGTTTTTAAGTT-A
*
485807 AGTGTTAGGGTT
1 AGGGTTAGGGTT
485819 AGGGTTAGGG
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.11
21 29 0.35
22 40 0.49
23 4 0.05
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:485916 original size:21 final size:21
Alignment explanation
Indices: 485892--485937 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
485882 ATAAATTAGT
*
485892 TTAGGGTTTTTAAATTAAGGG
1 TTAGGGTTTTTAAATTAAAGG
*
485913 TTAGGGTTTTTAAGTTAAAGG
1 TTAGGGTTTTTAAATTAAAGG
485934 TTAG
1 TTAG
485938 AGTTAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.43
Consensus pattern (21 bp):
TTAGGGTTTTTAAATTAAAGG
Found at i:485985 original size:127 final size:125
Alignment explanation
Indices: 485767--486031 Score: 401
Period size: 127 Copynumber: 2.1 Consensus size: 125
485757 AAGTTGTTTG
* *
485767 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAGTGTTAGGGTTAGGGTTAGGGTTT
1 TTAGGGTTTTTAAATTAAGGGTTTAGGGTTTTTAAGTTAAAGTGTTAGAGTTAGGGTTAGGGTTT
* * *
485832 GTCAATTAATATCAAAATTTAATTATAAATTATAAATTTATAATTTTTTAATAAATTAGT
66 GTCAATCAAAATCAAAATTTAATTATAAATTATAAATTTATAAATTTTTAATAAATTAGT
485892 TTAGGGTTTTTAAATTAAGGG-TTAGGGTTTTTAAGTTAAAG-GTTAGAGTTAGGGTTTTTTAGG
1 TTAGGGTTTTTAAATTAAGGGTTTAGGGTTTTTAAGTTAAAGTGTTAGAGTTAGGG----TTAGG
* *
485955 GTTTGTCAA-CAAAATTATAAATTTAATTATAAATTATAAATTTATAAATTTTTAATAAATTATT
62 GTTTGTCAATCAAAATCA-AAATTTAATTATAAATTATAAATTTATAAATTTTTAATAAATTAGT
486019 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
486032 GTAATACCTC
Statistics
Matches: 128, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
123 12 0.09
124 20 0.16
125 20 0.16
126 5 0.04
127 71 0.55
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (125 bp):
TTAGGGTTTTTAAATTAAGGGTTTAGGGTTTTTAAGTTAAAGTGTTAGAGTTAGGGTTAGGGTTT
GTCAATCAAAATCAAAATTTAATTATAAATTATAAATTTATAAATTTTTAATAAATTAGT
Found at i:485989 original size:7 final size:7
Alignment explanation
Indices: 485966--486004 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
485956 TTTGTCAACA
485966 AAATTAT
1 AAATTAT
485973 AAATT-T
1 AAATTAT
485979 -AATTAT
1 AAATTAT
485985 AAATTAT
1 AAATTAT
485992 AAATTTAT
1 AAA-TTAT
486000 AAATT
1 AAATT
486005 TTTAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.14
6 2 0.07
7 16 0.55
8 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AAATTAT
Found at i:486519 original size:17 final size:19
Alignment explanation
Indices: 486487--486529 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
486477 GACTCGAAAA
* *
486487 AGGAAACATATAA-GGGTT
1 AGGATACATATAAGGGGCT
486505 AGGATACAT-TAAGGGGCT
1 AGGATACATATAAGGGGCT
486523 AGGATAC
1 AGGATAC
486530 GCACCTGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (19 bp):
AGGATACATATAAGGGGCT
Found at i:487181 original size:7 final size:7
Alignment explanation
Indices: 487171--487196 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
487161 TTATATACAT
487171 AATACTA
1 AATACTA
487178 AATACTA
1 AATACTA
487185 AATACTA
1 AATACTA
487192 AATAC
1 AATAC
487197 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:488423 original size:11 final size:11
Alignment explanation
Indices: 488407--488437 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
488397 ATTTGGAAGG
488407 AAATTGAGAGC
1 AAATTGAGAGC
488418 AAATTGAGAGC
1 AAATTGAGAGC
488429 AAATTGAGA
1 AAATTGAGA
488438 AAATAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:496410 original size:16 final size:16
Alignment explanation
Indices: 496389--496424 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
496379 TTTGGTTCGC
496389 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
496405 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
496421 TGTA
1 TGTA
496425 ATAGCAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:496677 original size:16 final size:16
Alignment explanation
Indices: 496640--496681 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
496630 TTAATCATAT
*
496640 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
496656 TT-AAATATATTATAA
1 TTAAAATATATTATAA
496671 TTAAAATATAT
1 TTAAAATATAT
496682 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:496688 original size:14 final size:15
Alignment explanation
Indices: 496649--496690 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
496639 TTTAAACATA
*
496649 ATTATTATTAAATAT
1 ATTATAATTAAATAT
496664 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
496678 A-TATAATTTAATA
1 ATTATAATTAAATA
496691 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:496740 original size:61 final size:61
Alignment explanation
Indices: 496675--496862 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
496665 TTATAATTAA
*
496675 AATATATAATTTAATAAAATTTTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
496736 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTATTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
496795 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
496856 AATATAT
1 AATATAT
496863 GATACTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 24 0.25
61 37 0.38
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:496788 original size:120 final size:120
Alignment explanation
Indices: 496643--496872 Score: 451
Period size: 120 Copynumber: 1.9 Consensus size: 120
496633 ATCATATTTA
*
496643 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
496708 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
496763 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
496828 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
496873 TTTACTCAAA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:496808 original size:14 final size:15
Alignment explanation
Indices: 496759--496810 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
496749 ATAAAATATA
496759 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
496774 TATTAAATATATTAT
1 AATTAAATATATTAT
496789 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
496802 AATTTAATA
1 AATTAAATA
496811 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:496861 original size:59 final size:59
Alignment explanation
Indices: 496678--496861 Score: 166
Period size: 59 Copynumber: 3.1 Consensus size: 59
496668 TAATTAAAAT
*
496678 ATATAATTTAATAAAATTTTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
* * * * * *
496737 ATAT-ATGATACTATAAAA-TATAAATTAA-CATAATTATTATTAAAT-ATATTATAATTAAA--
1 ATATAAT-TTA--ATAAAATTATTAA-TAATC--AA-TATTCTTATATGA-ATT-TACTCAAATC
496796 AT-
57 ATA
*
496798 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
496857 ATATA
1 ATATA
496862 TGATACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 6 0.06
57 12 0.13
58 7 0.07
59 20 0.21
60 10 0.11
61 15 0.16
62 7 0.07
63 12 0.13
64 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
Found at i:503626 original size:41 final size:40
Alignment explanation
Indices: 503579--503727 Score: 176
Period size: 41 Copynumber: 3.6 Consensus size: 40
503569 AAATTGTTCA
*
503579 GACTATACGTCTAGCAGGCTAAGTGCCGATGAATTGAATCG
1 GACTATACGTCCAGCAGGCTAAGTGCCG-TGAATTGAATCG
503620 GACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCCAGCAGGCTAAGTGCC-GTGAATTGAATCG
* * * * *
503661 GATTATATGTCCAGTAGGCTAAGTGCCTGTGAACTGAATCAT
1 GACTATACGTCCAGCAGGCTAAGTGCC-GTGAATTGAATC-G
*
503703 G-CTATA-GGCCTAGCAGGCTAAGTGC
1 GACTATACGTCC-AGCAGGCTAAGTGC
503728 TGGTGAACGG
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 3 0.03
41 90 0.95
42 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (40 bp):
GACTATACGTCCAGCAGGCTAAGTGCCGTGAATTGAATCG
Found at i:503749 original size:41 final size:41
Alignment explanation
Indices: 503576--503775 Score: 149
Period size: 41 Copynumber: 4.9 Consensus size: 41
503566 GTGAAATTGT
* * * * *
503576 TCAGACTATACGTCTAGCAGGCTAAGTGCCGATGAATTGAA
1 TCAGACTATAGGCCTAGCAGGCTAAGTGCTGGTGAACTGAA
* * * *
503617 TCGGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATA-GGCCTAGCAGGCTAAGTGCTGGTGAACTGAA
* * * *
503658 TCGGATTATATGTCC-AGTAGGCTAAGTGCCT-GTGAACTGAA
1 TCAGACTATA-GGCCTAGCAGGCTAAGTG-CTGGTGAACTGAA
*
503699 TCATG-CTATAGGCCTAGCAGGCTAAGTGCTGGTGAACGGAA
1 TCA-GACTATAGGCCTAGCAGGCTAAGTGCTGGTGAACTGAA
* * * * *
503740 TTAGACTATAAGTCTATCAGG-TGAAGTGCTAGTGAA
1 TCAGACTATAGGCCTAGCAGGCT-AAGTGCTGGTGAA
503776 TCTGTTTAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
40 7 0.05
41 122 0.92
42 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (41 bp):
TCAGACTATAGGCCTAGCAGGCTAAGTGCTGGTGAACTGAA
Found at i:504005 original size:37 final size:37
Alignment explanation
Indices: 503961--504037 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
503951 TTTAAATGTG
* *
503961 TATATGTACGCATTCGTCATAGCTGGATATAAGTGTA
1 TATATGTACGCATTCGGCATAGCTGGATATAAGTGAA
* * *
503998 TATATGTATGCATTCGGCATAGGTGGGTATAAGTGAA
1 TATATGTACGCATTCGGCATAGCTGGATATAAGTGAA
504035 TAT
1 TAT
504038 GTGCATTCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (37 bp):
TATATGTACGCATTCGGCATAGCTGGATATAAGTGAA
Found at i:514360 original size:27 final size:27
Alignment explanation
Indices: 514338--514564 Score: 258
Period size: 27 Copynumber: 8.4 Consensus size: 27
514328 AAGGGTATAA
*
514338 CAGTCATTGTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* ** *
514365 CGGTCATCCTACCCTATTGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
514392 TAGTCATTTTACCCTATGAGAGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
514419 TAATCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
** **
514446 TGGTCATTTTACCCTATAAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
514473 AAATCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
514500 C-GATCATTTTACCCTATAGTGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
*
514527 TAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
514554 CAGTCATTTTA
1 CAGTCATTTTA
514565 TTGACCTCTC
Statistics
Matches: 167, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
27 166 0.99
28 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:514451 original size:81 final size:81
Alignment explanation
Indices: 514341--514564 Score: 304
Period size: 81 Copynumber: 2.8 Consensus size: 81
514331 GGTATAACAG
* * ** * *
514341 TCATTGTACCCTATGGGGGTATTTCGGTCATCCTACCCTATTGGGGTATTTTAGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTAAGTCATTTTACCC
*
514406 TATGAGAGTATTTTAA
66 TATGAGAGTATTTCAA
* *
514422 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTAAATCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTAAGTCATTTTACCC
* *
514487 TATGAGGGTATTTCGA
66 TATGAGAGTATTTCAA
* * * * *
514503 TCATTTTACCCTATAGTGGTATTTTAGTCATTTTACCCTATGGGGGTATTTCAGTCATTTTA
1 TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTAAGTCATTTTA
514565 TTGACCTCTC
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 125 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTAAGTCATTTTACCC
TATGAGAGTATTTCAA
Found at i:540986 original size:26 final size:25
Alignment explanation
Indices: 540955--541004 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
540945 AGAGCAAAAA
540955 GAAAAGATGGAAAAACAAAAGGAAAG
1 GAAAAG-TGGAAAAACAAAAGGAAAG
540981 GAAAAGTGGAAAAACAAAAGGAAA
1 GAAAAGTGGAAAAACAAAAGGAAA
541005 ACAAGAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (25 bp):
GAAAAGTGGAAAAACAAAAGGAAAG
Found at i:543737 original size:18 final size:18
Alignment explanation
Indices: 543714--543750 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
543704 CTTATATAGC
*
543714 TGAAAAGAAAAATGAAAA
1 TGAAAAAAAAAATGAAAA
*
543732 TGAAAAAAAAAATTAAAA
1 TGAAAAAAAAAATGAAAA
543750 T
1 T
543751 CCCTCTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
TGAAAAAAAAAATGAAAA
Found at i:545970 original size:27 final size:27
Alignment explanation
Indices: 545939--546116 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
545929 TAAATTGTAC
545939 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
545966 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
545992 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
546020 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
546048 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
546075 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
546102 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
546117 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:546053 original size:82 final size:81
Alignment explanation
Indices: 545940--546095 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
545930 AAATTGTACA
* *
545940 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
546004 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
546021 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
546086 TGCGAGTTGA
65 TGCGAATTGA
546096 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:546107 original size:82 final size:81
Alignment explanation
Indices: 545936--546116 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
545926 GATTAAATTG
* *
545936 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
546001 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
546017 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
546081 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
546099 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
546117 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:554447 original size:27 final size:27
Alignment explanation
Indices: 554416--554593 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
554406 TAAATTGTAC
554416 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
554443 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
554469 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
554497 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
554525 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
554552 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
554579 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
554594 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:554530 original size:82 final size:81
Alignment explanation
Indices: 554417--554572 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
554407 AAATTGTACA
* *
554417 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
554481 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
554498 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
554563 TGCGAGTTGA
65 TGCGAATTGA
554573 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:554584 original size:82 final size:81
Alignment explanation
Indices: 554413--554593 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
554403 GATTAAATTG
* *
554413 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
554478 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
554494 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
554558 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
554576 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
554594 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:556976 original size:51 final size:51
Alignment explanation
Indices: 556896--556997 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
556886 GAGATTTAGT
* * *
556896 GTGATGCCTCAGGTATAGGTATTGGGGCTGTGCTGACTCAAGATGGGCATC
1 GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAAATAGGCATC
556947 GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAAATAGGCATC
1 GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAAATAGGCATC
556998 CTATAGCCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (51 bp):
GTGATGCCTCAGGTATAGGTATTGAGGCTGTGCTGACTCAAAATAGGCATC
Found at i:564757 original size:13 final size:13
Alignment explanation
Indices: 564739--564763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
564729 TTGTCGTGTT
564739 ATTTAGTTAATTA
1 ATTTAGTTAATTA
564752 ATTTAGTTAATT
1 ATTTAGTTAATT
564764 TTAGTTTTAA
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:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTAGTTAATTA
Found at i:575225 original size:21 final size:22
Alignment explanation
Indices: 575200--575242 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
575190 ATTTTATTTA
575200 AAAAAATCAATCAAAAA-AAAAG
1 AAAAAA-CAATCAAAAAGAAAAG
*
575222 AAAAAAGAATCAAAAAGAAAA
1 AAAAAACAATCAAAAAGAAAA
575243 AATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAAAACAATCAAAAAGAAAAG
Found at i:575254 original size:18 final size:17
Alignment explanation
Indices: 575215--575255 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
575205 ATCAATCAAA
575215 AAAAAAGAAAAAAGAAT
1 AAAAAAGAAAAAAGAAT
* *
575232 CAAAAAGAAAAAATATAT
1 AAAAAAGAAAAAAGA-AT
575250 AAAAAA
1 AAAAAA
575256 ATTATTTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.10
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAT
Found at i:580725 original size:40 final size:40
Alignment explanation
Indices: 580670--580865 Score: 225
Period size: 40 Copynumber: 4.9 Consensus size: 40
580660 GAATTTAGGA
* * * *
580670 GTATCGTAGTACAAATAGGGGCACGTATGTGCATTCAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
* ** * *
580710 GTATCGAAGTACAAATAAAAGCATTTAAGTGCATTCAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
** * *
580750 GTGCCGAAGTACAAACATGGGCACTTATGTGCATTTAGGG
1 GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
*
580790 GTATCAAAGTACAAAC-AGTGGCACTTATGTGCATTCAGGG
1 GTATCGAAGTACAAACAAG-GGCACTTATGTGCATTCAGGG
*
580830 GTA-CAGAAGTACAAACAATGGCACTTATGTGCATTC
1 GTATC-GAAGTACAAACAAGGGCACTTATGTGCATTC
580866 CTATATATAC
Statistics
Matches: 130, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 127 0.98
41 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (40 bp):
GTATCGAAGTACAAACAAGGGCACTTATGTGCATTCAGGG
Found at i:584858 original size:20 final size:21
Alignment explanation
Indices: 584830--584868 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
584820 AATTGGGAAC
584830 CAAAATGATAAAAA-AATAGT
1 CAAAATGATAAAAATAATAGT
*
584850 CAAAGTGATAAAAATAATA
1 CAAAATGATAAAAATAATA
584869 AATGATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (21 bp):
CAAAATGATAAAAATAATAGT
Found at i:584902 original size:14 final size:14
Alignment explanation
Indices: 584885--584915 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
584875 AATGGATAAA
584885 TTTACTCCGTGAAG
1 TTTACTCCGTGAAG
584899 TTTACTCCGTGAAG
1 TTTACTCCGTGAAG
584913 TTT
1 TTT
584916 GGTGTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (14 bp):
TTTACTCCGTGAAG
Found at i:585483 original size:11 final size:11
Alignment explanation
Indices: 585464--585500 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
585454 TTACTATGTA
*
585464 TTTACTATTTAT
1 TTTA-TATTAAT
585476 TTTATATTAAT
1 TTTATATTAAT
585487 TTTATATTAAT
1 TTTATATTAAT
585498 TTT
1 TTT
585501 CTTCCATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTAAT
Found at i:586209 original size:21 final size:21
Alignment explanation
Indices: 586183--586224 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
586173 TAAAAAATCA
*
586183 AAATTTACATTAA-ATAATTTT
1 AAATTTAAATTAATAT-ATTTT
586204 AAATTTAAATTAATATATTTT
1 AAATTTAAATTAATATATTTT
586225 CATTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTTAAATTAATATATTTT
Found at i:588215 original size:30 final size:30
Alignment explanation
Indices: 588179--588258 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
588169 TAACTTCGAA
* *
588179 ATAATGTCAGCTTATGTGAGCAATAC-AATT
1 ATAATGTCAGCTTGTGTGAGCAACACTAA-T
* *
588209 ATAATGTTAGCTTGTGTGAGCAACCCTAAT
1 ATAATGTCAGCTTGTGTGAGCAACACTAAT
*
588239 ATATTGTCAGCTTGTGTGAG
1 ATAATGTCAGCTTGTGTGAG
588259 TAATTTATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 41 0.95
31 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (30 bp):
ATAATGTCAGCTTGTGTGAGCAACACTAAT
Found at i:590840 original size:6 final size:6
Alignment explanation
Indices: 590829--590877 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
590819 ATTAAATTAG
* * * * *
590829 TTATTT TTATTT TTATTA TAATTT TTGTTT TTAGTT TAATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
590877 T
1 T
590878 CTAATGTCTC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:590852 original size:18 final size:18
Alignment explanation
Indices: 590831--590877 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
590821 TAAATTAGTT
590831 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
*
590849 ATTTTTGTTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
590867 ATTTTTATTTT
1 ATTTTTATTTT
590878 CTAATGTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:594132 original size:30 final size:30
Alignment explanation
Indices: 594076--594133 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
594066 CTAGGCATTT
** *
594076 CCACACAGGCTAGCCACAGGCTCATGTGAG
1 CCACACAGGCTAGCCACACACCCATGTGAG
*
594106 CCACACGGGCTAGCCACACACCCATGTG
1 CCACACAGGCTAGCCACACACCCATGTG
594134 CCAGCCCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.38, G:0.24, T:0.12
Consensus pattern (30 bp):
CCACACAGGCTAGCCACACACCCATGTGAG
Found at i:595624 original size:19 final size:18
Alignment explanation
Indices: 595600--595643 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
595590 TAACATCTTA
595600 GAAAATTAATCAATATACT
1 GAAAATTAATCAAT-TACT
* *
595619 GAAAATTTATTAATTACT
1 GAAAATTAATCAATTACT
*
595637 TAAAATT
1 GAAAATT
595644 TATGTGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (18 bp):
GAAAATTAATCAATTACT
Found at i:595641 original size:18 final size:19
Alignment explanation
Indices: 595600--595646 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
595590 TAACATCTTA
*
595600 GAAAATTAATCAATATACT
1 GAAAATTTATCAATATACT
*
595619 GAAAATTTATTAAT-TACT
1 GAAAATTTATCAATATACT
*
595637 TAAAATTTAT
1 GAAAATTTAT
595647 GTGATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (19 bp):
GAAAATTTATCAATATACT
Found at i:595804 original size:3 final size:3
Alignment explanation
Indices: 595798--595822 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
595788 ATTATTATTA
595798 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
595823 AATACCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:601482 original size:14 final size:15
Alignment explanation
Indices: 601456--601488 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
601446 TCCCAAGCTG
601456 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
601471 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
601485 GGAA
1 GGAA
601489 AAGCGTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:601580 original size:7 final size:7
Alignment explanation
Indices: 601568--601609 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
601558 ATATTTCAAA
601568 AAAAAAC
1 AAAAAAC
601575 AAAAAAC
1 AAAAAAC
601582 AAAAAAAC
1 -AAAAAAC
*
601590 AAAAAAA
1 AAAAAAC
601597 AACAAAAC
1 AA-AAAAC
601605 AAAAA
1 AAAAA
601610 TGAAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:601585 original size:15 final size:15
Alignment explanation
Indices: 601565--601628 Score: 87
Period size: 15 Copynumber: 4.3 Consensus size: 15
601555 GAAATATTTC
601565 AAAAA-AAAACAAAA
1 AAAAACAAAACAAAA
601579 AACAAA-AAAACAAAA
1 AA-AAACAAAACAAAA
601594 AAAAACAAAACAAAA
1 AAAAACAAAACAAAA
*
601609 ATGAAACAAAACAAAA
1 A-AAAACAAAACAAAA
601625 AAAA
1 AAAA
601629 GGGAAAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
14 5 0.11
15 26 0.58
16 14 0.31
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (15 bp):
AAAAACAAAACAAAA
Found at i:602982 original size:88 final size:88
Alignment explanation
Indices: 602824--603191 Score: 508
Period size: 88 Copynumber: 4.2 Consensus size: 88
602814 AGCAGATCAA
* *
602824 TAAAAA-AGTAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGTCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
602888 CCCTGGGTTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * *
602911 TAAAAATAGCAGATCTTGCCTTCCTGCGA-CGACAGCAAAGCAGATCAAAGACATCAGCCTTGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGC-ACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCC
602975 TCCCTGGGTTGCAGTGGAGCAGGT
65 TCCCTGGGTTGCAGTGGAGCAGGT
* *
602999 TAAAAATAGCAGATATTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
*
603064 TCCTGGGTTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
** * * * * *
603087 TAAAAATAGCAGATCTTGCCTTCCTATACCGACAGCGAAGCAGATCGAAGTCCCCAGCCTTGTCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
* * ** *
603152 CTCTGAGAAGCAGTGGAGTAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
*
603175 TGAAAATTA-CAGATCTT
1 T-AAAAATAGCAGATCTT
603192 ATCTCCCTAA
Statistics
Matches: 252, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
87 7 0.03
88 238 0.94
89 7 0.03
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGTGGAGCAGGT
Found at i:603108 original size:44 final size:44
Alignment explanation
Indices: 602889--603111 Score: 162
Period size: 44 Copynumber: 5.1 Consensus size: 44
602879 GCCTTGTCTC
602889 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
1 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
* ** *** * * * * * * *
602933 CCTGCGACGACAGCAAAGCAGATCAAAGACATCAG-CCTTGCCTC
1 CCTGGGTTG-CAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
*
602977 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATATTGCCTT
1 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
**** ** * * ** * * * *
603021 CCTGCACCGACAACGAAGCAGATCGAAGACACCAG-CCTTGCCTT
1 CCTGGGTTG-CAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
603065 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
1 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
603109 CCT
1 CCT
603112 ATACCGACAG
Statistics
Matches: 119, Mismatches: 56, Indels: 8
0.65 0.31 0.04
Matches are distributed among these distances:
43 33 0.28
44 53 0.45
45 33 0.28
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (44 bp):
CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
Found at i:603245 original size:87 final size:87
Alignment explanation
Indices: 603125--603655 Score: 875
Period size: 87 Copynumber: 6.1 Consensus size: 87
603115 CCGACAGCGA
* *
603125 AGCAGATCGAAGTCCCCAGCCTTGTCTCTCTGAGAAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
603190 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* **
603212 AGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTCAAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
*
603277 TTATCTCCCTAAGCAGTAGTGT
66 TTATCTCCCTAAGCAGTAGTGG
* * * **
603299 AGCAGATCAAAGTCCTCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTATGTCAAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
*
603364 TTATCTTCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* * *
603386 AGCAGATCGAAGTCCCCAACTTTGTCTCCCTGAGCAGCAGTAGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
603451 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
603473 AGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
*
603538 TTATCTCCCTAAGCGGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
603560 AGCAGATCGAAATCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACCGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
603625 TTATCTCCCTAA-CAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
603646 AGCAGATCGA
1 AGCAGATCGA
603656 GGATGTGGAG
Statistics
Matches: 412, Mismatches: 32, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
86 18 0.04
87 394 0.96
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (87 bp):
AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
TTATCTCCCTAAGCAGTAGTGG
Found at i:606486 original size:3 final size:3
Alignment explanation
Indices: 606478--606515 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
606468 GGTTTCGACA
606478 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
606516 CACCGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:607410 original size:21 final size:22
Alignment explanation
Indices: 607353--607411 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 22
607343 ATTTAAAATT
* *
607353 AAAAAAATGTATTAGAATTCTTA
1 AAAAAAAT-TATTAAAATTCGTA
607376 AAAAAGAA-TA--AAAATT-GTA
1 AAAAA-AATTATTAAAATTCGTA
607395 AAAAAAATTATTAAAAT
1 AAAAAAATTATTAAAAT
607412 ATATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 2 0.07
19 9 0.30
20 5 0.17
21 5 0.17
22 2 0.07
23 5 0.17
24 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.29
Consensus pattern (22 bp):
AAAAAAATTATTAAAATTCGTA
Found at i:607719 original size:3 final size:3
Alignment explanation
Indices: 607706--607740 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
607696 AGTTCAATTA
*
607706 AAT AA- AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
607741 TGATTCAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:607948 original size:22 final size:22
Alignment explanation
Indices: 607918--607961 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
607908 TTTATAATTT
*
607918 TATGGTTTTTATAGAATTTTAA
1 TATGGTTTTTATAAAATTTTAA
*
607940 TATGTTTTTTATAAAATTTTAA
1 TATGGTTTTTATAAAATTTTAA
607962 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (22 bp):
TATGGTTTTTATAAAATTTTAA
Found at i:608003 original size:18 final size:18
Alignment explanation
Indices: 607982--608042 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
607972 AATGTTTTGT
607982 TAATTTTATATATTTTTA
1 TAATTTTATATATTTTTA
*
608000 TAA-TTTATTAGAATTTTTA
1 TAATTTTA-TA-TATTTTTA
*
608019 T-ATTTT-TATGATTTTTT
1 TAATTTTATAT-ATTTTTA
608036 TAATTTT
1 TAATTTT
608043 TTTAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 13 0.37
18 11 0.31
19 11 0.31
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TAATTTTATATATTTTTA
Found at i:608015 original size:19 final size:18
Alignment explanation
Indices: 607985--608133 Score: 85
Period size: 18 Copynumber: 8.2 Consensus size: 18
607975 GTTTTGTTAA
*
607985 TTTTATATATTTTTATAAT
1 TTTTATA-ATTTTTATGAT
*
608004 TTATTAGAATTTTTAT-AT
1 TT-TTATAATTTTTATGAT
* * *
608022 TTTTATGATTTTTTTAAT
1 TTTTATAATTTTTATGAT
* *
608040 TTTTTTAATTTTTAAG-T
1 TTTTATAATTTTTATGAT
* *
608057 TTATATCAATTTTCAT-A-
1 TTTTAT-AATTTTTATGAT
* *
608074 TTTTCTAATATTTAAT-AT
1 TTTTATAAT-TTTTATGAT
*
608092 TTTT-TATATTTTTCTGAT
1 TTTTATA-ATTTTTATGAT
608110 TTTTGATAATTTATTATGAT
1 TTTT-ATAATTT-TTATGAT
608130 TTTT
1 TTTT
608134 TAAACATTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
16 3 0.03
17 31 0.31
18 36 0.36
19 14 0.14
20 16 0.16
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTATAATTTTTATGAT
Found at i:608043 original size:18 final size:18
Alignment explanation
Indices: 607976--608043 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
607966 TTTAAAAATG
*
607976 TTTTGTTAATTTTATAT-A
1 TTTTTTTAATTTT-TATGA
*
607994 TTTTTATAATTTATTA-GA
1 TTTTTTTAATTT-TTATGA
*
608012 -ATTTTTATATTTTTATGA
1 TTTTTTTA-ATTTTTATGA
608030 TTTTTTTAATTTTT
1 TTTTTTTAATTTTT
608044 TTAATTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 8 0.20
18 25 0.62
19 7 0.17
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTTTTAATTTTTATGA
Found at i:608043 original size:27 final size:26
Alignment explanation
Indices: 607976--608104 Score: 88
Period size: 27 Copynumber: 4.9 Consensus size: 26
607966 TTTAAAAATG
* *
607976 TTTTGTTAATTTTATATATTTTTATA
1 TTTTATTAATTTTTTATATTTTTATA
* *
608002 ATTTATTAGAATTTTTATATTTTTATGA
1 TTTTATTA-ATTTTTTATATTTTTAT-A
*
608030 TTTTTTTAATTTTTT-TAATTTTTA-A
1 TTTTATTAATTTTTTAT-ATTTTTATA
* *
608055 GTTTATATCAA-TTTTCATATTTTCTA-A
1 -TTT-TATTAATTTTTTATATTTT-TATA
*
608082 TATTTAAT-ATTTTTTATATTTTT
1 T-TTTATTAATTTTTTATATTTTT
608105 CTGATTTTTG
Statistics
Matches: 81, Mismatches: 13, Indels: 19
0.72 0.12 0.17
Matches are distributed among these distances:
25 3 0.04
26 33 0.41
27 38 0.47
28 7 0.09
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTATTAATTTTTTATATTTTTATA
Found at i:608097 original size:10 final size:9
Alignment explanation
Indices: 607985--608135 Score: 62
Period size: 9 Copynumber: 16.6 Consensus size: 9
607975 GTTTTGTTAA
607985 TTTTATATAT
1 TTTTATAT-T
607995 TTTTATAATT
1 TTTTAT-ATT
* * *
608005 TATTAGAAT
1 TTTTATATT
608014 TTTTATA-T
1 TTTTATATT
608022 TTTTATGATT
1 TTTTAT-ATT
608032 TTTT-TAATT
1 TTTTAT-ATT
*
608041 TTTT-TAAT
1 TTTTATATT
*
608049 TTTTA-AGT
1 TTTTATATT
* *
608057 TTATATCAAT
1 TTTTAT-ATT
*
608067 TTTCATATT
1 TTTTATATT
* *
608076 TTCTA-ATA
1 TTTTATATT
*
608084 TTTAATATT
1 TTTTATATT
608093 TTTTATATT
1 TTTTATATT
*
608102 TTTCT-GATT
1 TTT-TATATT
*
608111 TTTGATAATT
1 TTTTAT-ATT
*
608121 TATTATGATT
1 TTTTAT-ATT
608131 TTTTA
1 TTTTA
608136 AACATTTTAA
Statistics
Matches: 104, Mismatches: 27, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
8 24 0.23
9 41 0.39
10 37 0.36
11 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:609887 original size:20 final size:20
Alignment explanation
Indices: 609864--609911 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
609854 TTTAGCTCGG
* *
609864 TTCAGCTCATATGAGTTTAA
1 TTCAGCTCACATGAGCTTAA
*
609884 TTCAGCTTACATGAGCTTAA
1 TTCAGCTCACATGAGCTTAA
*
609904 TTTAGCTC
1 TTCAGCTC
609912 GTTTGAGCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (20 bp):
TTCAGCTCACATGAGCTTAA
Found at i:611527 original size:70 final size:70
Alignment explanation
Indices: 611420--611742 Score: 268
Period size: 70 Copynumber: 4.7 Consensus size: 70
611410 AAGCTCCTAG
* * *** * *
611420 CTGTACTCTTAAGGCTCACTGATTTAATATCATGGCCTCCAAAATAGTTAGTGTGAGCTTAAGCT
1 CTGTACTCTTAAGGCTCGCTGATTCAATATTGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCT
611485 CTCAA
66 CTCAA
* *
611490 CTGTACTCTTAAGGCTCACTGATTCAATATTGCGGCCTCCAAAATTGTTAGC---A---CAAG--
1 CTGTACTCTTAAGGCTCGCTGATTCAATATTGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCT
611547 CTCAA
66 CTCAA
* * ** * ***
611552 GCTGTACTCTTAAGGCTTGCTAATTCAATATTGCGGCCTTTAAAATTGTTAGCACAAGCTCAAGC
1 -CTGTACTCTTAAGGCTCGCTGATTCAATATTGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGC
*
611617 TCCCAA
65 TCTCAA
* ** * * * * *
611623 CTGTACTCTTAAGGCTCGTTGATTCAATACCGCAGCCCCCAAAACAGTTAGCGGGAGCTTAAGCT
1 CTGTACTCTTAAGGCTCGCTGATTCAATATTGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCT
*
611688 GC-CAG
66 -CTCAA
* * * * * *
611693 CTATATTCTTAAGGCTTGCTAATTCAATATTACGACCTCCAAAATAGTTA
1 CTGTACTCTTAAGGCTCGCTGATTCAATATTGCGGCCTCCAAAATAGTTA
611743 ACCAGCAGTA
Statistics
Matches: 202, Mismatches: 41, Indels: 20
0.77 0.16 0.08
Matches are distributed among these distances:
62 5 0.02
63 47 0.23
64 3 0.01
66 1 0.00
67 1 0.00
69 4 0.02
70 136 0.67
71 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (70 bp):
CTGTACTCTTAAGGCTCGCTGATTCAATATTGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCT
CTCAA
Found at i:611589 original size:63 final size:63
Alignment explanation
Indices: 611485--611617 Score: 214
Period size: 63 Copynumber: 2.1 Consensus size: 63
611475 AGCTTAAGCT
*
611485 CTCAA-CTGTACTCTTAAGGCTCACTGATTCAATATTGCGGCCTCCAAAATTGTTAGCACAAG
1 CTCAAGCTGTACTCTTAAGGCTCACTAATTCAATATTGCGGCCTCCAAAATTGTTAGCACAAG
** **
611547 CTCAAGCTGTACTCTTAAGGCTTGCTAATTCAATATTGCGGCCTTTAAAATTGTTAGCACAAG
1 CTCAAGCTGTACTCTTAAGGCTCACTAATTCAATATTGCGGCCTCCAAAATTGTTAGCACAAG
611610 CTCAAGCT
1 CTCAAGCT
611618 CCCAACTGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
62 5 0.08
63 60 0.92
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (63 bp):
CTCAAGCTGTACTCTTAAGGCTCACTAATTCAATATTGCGGCCTCCAAAATTGTTAGCACAAG
Found at i:611665 original size:133 final size:137
Alignment explanation
Indices: 611475--611723 Score: 326
Period size: 133 Copynumber: 1.8 Consensus size: 137
611465 AGTTAGTGTG
* * ** * * **
611475 AGCTTAAGCTCTCAACTGTACTCTTAAGGCTCACTGATTCAATATTGCGGCCTCCAAAATTGTTA
1 AGCTCAAGCTCCCAACTGTACTCTTAAGGCTCACTGATTCAATACCGCAGCCCCCAAAACAGTTA
*
611540 GC-A-C-AAGCT-CAAGCTGTACTCTTAAGGCTTGCTAATTCAATATTGCGGCCTTTAAAATTGT
66 GCGAGCTAAGCTGCAAGCTATACTCTTAAGGCTTGCTAATTCAATATTGCGGCCTTTAAAATTGT
611601 TAGCACA
131 TAGCACA
**
611608 AGCTCAAGCTCCCAACTGTACTCTTAAGGCTCGTTGATTCAATACCGCAGCCCCCAAAACAGTTA
1 AGCTCAAGCTCCCAACTGTACTCTTAAGGCTCACTGATTCAATACCGCAGCCCCCAAAACAGTTA
* *
611673 GCGGGAGCTTAAGCTGCCAGCTATATTCTTAAGGCTTGCTAATTCAATATT
66 GC--GAGC-TAAGCTGCAAGCTATACTCTTAAGGCTTGCTAATTCAATATT
611724 ACGACCTCCA
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
133 57 0.59
136 1 0.01
137 1 0.01
139 5 0.05
140 32 0.33
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (137 bp):
AGCTCAAGCTCCCAACTGTACTCTTAAGGCTCACTGATTCAATACCGCAGCCCCCAAAACAGTTA
GCGAGCTAAGCTGCAAGCTATACTCTTAAGGCTTGCTAATTCAATATTGCGGCCTTTAAAATTGT
TAGCACA
Found at i:615195 original size:21 final size:21
Alignment explanation
Indices: 615157--615197 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
615147 ATTCACAATT
*
615157 TTAGGTAGGTTTTTTTTAAAG
1 TTAGGTAGGTTTTATTTAAAG
615178 TTAGGTA-GTTGTTATTTAAA
1 TTAGGTAGGTT-TTATTTAAA
615198 CACTAATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (21 bp):
TTAGGTAGGTTTTATTTAAAG
Found at i:622032 original size:16 final size:17
Alignment explanation
Indices: 622011--622043 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
622001 GGGTGCGCTT
622011 GTAAATA-TGATTCGCA
1 GTAAATAGTGATTCGCA
*
622027 GTAAATAGTGGTTCGCA
1 GTAAATAGTGATTCGCA
622044 TGTGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (17 bp):
GTAAATAGTGATTCGCA
Found at i:622627 original size:37 final size:37
Alignment explanation
Indices: 622586--622656 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
622576 ACAGTGTTAA
622586 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
1 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
*
622623 AAAGAATGTTTATTAATCCTTTCTTTAAAAACTT
1 AAAGAATGCTTATTAATCCTTTCTTTAAAAACTT
622657 TCTTTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (37 bp):
AAAGAATGCTTATTAATCCTTTCTTTAAAAACTTGCT
Found at i:622665 original size:12 final size:13
Alignment explanation
Indices: 622641--622666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
622631 TTTATTAATC
622641 CTTTCTTTAAAAA
1 CTTTCTTTAAAAA
622654 CTTTCTTTAAAAA
1 CTTTCTTTAAAAA
622667 GGCTCGCTTT
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:0.00, T:0.46
Consensus pattern (13 bp):
CTTTCTTTAAAAA
Found at i:624893 original size:7 final size:7
Alignment explanation
Indices: 624881--624912 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
624871 GATGCCTCTT
624881 CCCCTTC
1 CCCCTTC
624888 CCCCTTC
1 CCCCTTC
624895 CCCCTTC
1 CCCCTTC
624902 CCCCTTC
1 CCCCTTC
624909 CCCC
1 CCCC
624913 ATCCTTGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (7 bp):
CCCCTTC
Found at i:627347 original size:13 final size:14
Alignment explanation
Indices: 627312--627346 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
627302 GAAAAGTAAG
627312 TCATTTTTCAGAAA
1 TCATTTTTCAGAAA
*
627326 TCATTTTTCGGAAA
1 TCATTTTTCAGAAA
*
627340 TTATTTT
1 TCATTTT
627347 CAGTCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (14 bp):
TCATTTTTCAGAAA
Found at i:627896 original size:25 final size:25
Alignment explanation
Indices: 627844--627897 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
627834 TTGACCGGCA
* * *
627844 AACCCAGTTTGCAACTCAATTGGTG
1 AACCCAGTTCGCAACTCAACTGGCG
* *
627869 AACCCAGTTCGCAACTTACCTGGCG
1 AACCCAGTTCGCAACTCAACTGGCG
627894 AACC
1 AACC
627898 TAATTCACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (25 bp):
AACCCAGTTCGCAACTCAACTGGCG
Found at i:646912 original size:85 final size:85
Alignment explanation
Indices: 646790--647069 Score: 375
Period size: 85 Copynumber: 3.3 Consensus size: 85
646780 AAAGGTTTGT
* *
646790 TCTATAGCGGCTTTTGT-GAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
1 TCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
*
646854 AGCGCCGCTAAAGGTCTA-GA
66 AGCGCCGCTAAAGGTC-ACGG
* * * * *
646874 TCTATAGTGGCATTTGTGGAAAAAGCGTCGCTAAAGGTCTTGGTCTATAGCAGCGTTTGTGGTAA
1 TCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGG-AA
*
646939 AAGTGCCGCTAAAGGTCACGG
65 AAGCGCCGCTAAAGGTCACGG
* * * * *
646960 TCTATAGCGGCGTTTGGGGGAAAAGTGCCGTTAAAGGTCTTGATCTGTAGCGGCGTTTGTGGAAA
1 TCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* *
647025 AGCGCCGCTAAAAGTCATGG
66 AGCGCCGCTAAAGGTCACGG
647045 TCTATAGCGGCGTTTGTGGGAAAAA
1 TCTATAGCGGCGTTTGT-GGAAAAA
647070 CACCGCAAAA
Statistics
Matches: 169, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
84 15 0.09
85 78 0.46
86 76 0.45
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (85 bp):
TCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
AGCGCCGCTAAAGGTCACGG
Found at i:647081 original size:42 final size:43
Alignment explanation
Indices: 646770--647068 Score: 363
Period size: 43 Copynumber: 7.0 Consensus size: 43
646760 TTTTAGCGAG
* * * *
646770 AAGCGTCGCTAAAGGT-TTGTTCTATAGCGGCTTTTGT-GAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
646811 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGG-A
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * *
646853 AAGCGCCGCTAAAGGTCTAGATCTATAGTGGCATTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * *
646896 AAGCGTCGCTAAAGGTCTTGGTCTATAGCAGCGTTTGTGGTAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* ** * *
646939 AAGTGCCGCTAAAGGTCACGGTCTATAGCGGCGTTTGGGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * *
646982 AAGTGCCGTTAAAGGTCTTGATCTGTAGCGGCGTTTGT-GGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * *
647024 AAGCGCCGCTAAAAGTCATGGTCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
647067 AA
1 AA
647069 ACACCGCAAA
Statistics
Matches: 220, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
41 15 0.07
42 93 0.42
43 112 0.51
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
Found at i:647225 original size:19 final size:19
Alignment explanation
Indices: 647196--647280 Score: 91
Period size: 19 Copynumber: 4.5 Consensus size: 19
647186 GTATGTGCAT
*
647196 CAGGGGTACTGAAGTACAA
1 CAGGGGCACTGAAGTACAA
*
647215 TAGGGGCACTGAAGTACAA
1 CAGGGGCACTGAAGTACAA
* * *
647234 CAGGGGCAC-GCATGTGCAT
1 CAGGGGCACTG-AAGTACAA
* *
647253 CAGGGGTACCGAAGTACAA
1 CAGGGGCACTGAAGTACAA
647272 CAGGGGCAC
1 CAGGGGCAC
647281 GTATGTGCAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.02
19 51 0.96
20 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.34, T:0.13
Consensus pattern (19 bp):
CAGGGGCACTGAAGTACAA
Found at i:647258 original size:38 final size:38
Alignment explanation
Indices: 647216--647291 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
647206 GAAGTACAAT
*
647216 AGGGGCACTGAAGTACAACAGGGGCACGCATGTGCATC
1 AGGGGCACCGAAGTACAACAGGGGCACGCATGTGCATC
* *
647254 AGGGGTACCGAAGTACAACAGGGGCACGTATGTGCATC
1 AGGGGCACCGAAGTACAACAGGGGCACGCATGTGCATC
647292 GGGTATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.14
Consensus pattern (38 bp):
AGGGGCACCGAAGTACAACAGGGGCACGCATGTGCATC
Found at i:650081 original size:13 final size:13
Alignment explanation
Indices: 650063--650087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
650053 ACTTTCATGA
650063 TTGCTTACTTTCC
1 TTGCTTACTTTCC
650076 TTGCTTACTTTC
1 TTGCTTACTTTC
650088 TCTTCCATTT
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:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (13 bp):
TTGCTTACTTTCC
Found at i:650552 original size:18 final size:18
Alignment explanation
Indices: 650507--650541 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
650497 ATGAGTTTAC
650507 AAATATTTTAAATTATTG
1 AAATATTTTAAATTATTG
650525 AAATATTTTAAATTATT
1 AAATATTTTAAATTATT
650542 TATGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATATTTTAAATTATTG
Found at i:654337 original size:19 final size:21
Alignment explanation
Indices: 654315--654362 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
654305 AGCTAATAAC
654315 GAGCTGAA-TTGAG-TCGAA-T
1 GAGCTGAACTTGAGCTC-AAGT
654334 GAGCT-AACTTGAGCTCAAGT
1 GAGCTGAACTTGAGCTCAAGT
654354 GAGCTGAAC
1 GAGCTGAAC
654363 CACATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 12 0.48
20 8 0.32
21 3 0.12
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (21 bp):
GAGCTGAACTTGAGCTCAAGT
Found at i:660733 original size:24 final size:22
Alignment explanation
Indices: 660706--660763 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
660696 AAATATATAA
*
660706 TTTTTTTATTTTACAAATTTTAAT
1 TTTTTTTATTTTAC-AA-GTTAAT
*
660730 TTTTTGTT-TTTTTCAAGTTAAT
1 TTTTT-TTATTTTACAAGTTAAT
*
660752 ATTTTTTATTTT
1 TTTTTTTATTTT
660764 TGCAACCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.07
22 13 0.45
23 2 0.07
24 10 0.34
25 2 0.07
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTTTTATTTTACAAGTTAAT
Found at i:662361 original size:41 final size:41
Alignment explanation
Indices: 662304--662385 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
662294 TCAGATTCAG
662304 CTCCTAGTGTTCTTTGCGGTGCTGCCAGTATCATGTGGAAT
1 CTCCTAGTGTTCTTTGCGGTGCTGCCAGTATCATGTGGAAT
662345 CTCCTAGTGTTCTTTGCGGTGCTGCCAGTATCATGTGGAAT
1 CTCCTAGTGTTCTTTGCGGTGCTGCCAGTATCATGTGGAAT
662386 TGGAATGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.37
Consensus pattern (41 bp):
CTCCTAGTGTTCTTTGCGGTGCTGCCAGTATCATGTGGAAT
Found at i:666208 original size:33 final size:35
Alignment explanation
Indices: 666166--666230 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
666156 TTTTTTGCCC
666166 GTTAGGGTTTTGG-GTTATT-GGTTTAGGGTTAGG
1 GTTAGGGTTTTGGTGTTATTAGGTTTAGGGTTAGG
*
666199 GTTAGGGTTTTGGTGTTTTTAGGTTTAGGGTT
1 GTTAGGGTTTTGGTGTTATTAGGTTTAGGGTT
666231 TTAGAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 13 0.45
34 5 0.17
35 11 0.38
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.49
Consensus pattern (35 bp):
GTTAGGGTTTTGGTGTTATTAGGTTTAGGGTTAGG
Found at i:666431 original size:95 final size:96
Alignment explanation
Indices: 666282--666549 Score: 319
Period size: 95 Copynumber: 2.8 Consensus size: 96
666272 ATTTGTTAAT
* * * * * * *
666282 TAAATTAATTATAAAATTTT-CAAAATTGGATTA-GGTTTCGTGTTTATTGTTTTTTAAGAAAAA
1 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGAGTTTA-GGGTTTTTAAGAAAAA
* * *
666345 ATCAATTAAATTAAGATTTAGGGTTACTTGAG
65 ATCAAATAAATTAAGATTCAGGGTTACTTGAA
* *
666377 TAATTTAATTA-AAATTTTTTAAAAAATTAGATTAGGGTTTAGAG-TTAGGGTTTTTAAGGAAAA
1 TAAATTAATTATAAA-TTTTTAAAAAATTAGATTAGGGTTTAGAGTTTAGGGTTTTTAAGAAAAA
* *
666440 ATCAAATAAATTAGGGTTCAGGGTTACTTGAA
65 ATCAAATAAATTAAGATTCAGGGTTACTTGAA
* *
666472 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTGTTTTTAAGTAAAAA
1 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGAGTTTAGGGTTTTTAAG-AAAAA
* *
666537 CTTAAATAAATTA
65 ATCAAATAAATTA
666550 GGGTTTGGGG
Statistics
Matches: 147, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
94 3 0.02
95 92 0.63
96 30 0.20
97 22 0.15
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.41
Consensus pattern (96 bp):
TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGAGTTTAGGGTTTTTAAGAAAAAA
TCAAATAAATTAAGATTCAGGGTTACTTGAA
Found at i:666579 original size:96 final size:93
Alignment explanation
Indices: 666284--666579 Score: 257
Period size: 95 Copynumber: 3.1 Consensus size: 93
666274 TTGTTAATTA
* * * * *
666284 AATTAATTATAAAATTTT-CAAAATTGGATTA-GGTTTCGTGTTTATTGTTTTTTAAGAAAAAAT
1 AATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTG-TTTTTAAG-AAAAAT
* * * * *
666347 CAATTAAATTAAGATTTAGGG-TTACTTGAG-T
64 CAAATAAATTAGGGTTTGGGGTTTA--AG-GTT
* *
666378 AATTTAATTA-AAATTTTTTAAAAAATTAGATTAGGGTTTAGAG-TTAGGGTTTTTAAGGAAAAA
1 AA-TTAATTATAAA-TTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTGTTTTTAA-GAAAAA
* * *
666441 TCAAATAAATTAGGGTTCAGGGTTACTTGAA--TA
63 TCAAATAAATTAGGGTT-TGGGGT--TT-AAGGTT
666474 AATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTGTTTTTAAGTAAAAACT
1 AATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTGTTTTTAAG-AAAAA-T
*
666539 TAAATAAATTAGGGTTTGGGGTTTAAGGTT
64 CAAATAAATTAGGGTTTGGGGTTTAAGGTT
666569 AATTAAATTAT
1 AATT-AATTAT
666580 TTGTTAATTT
Statistics
Matches: 163, Mismatches: 21, Indels: 34
0.75 0.10 0.16
Matches are distributed among these distances:
93 2 0.01
94 7 0.04
95 78 0.48
96 50 0.31
97 23 0.14
99 2 0.01
100 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.42
Consensus pattern (93 bp):
AATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGTGTTTAGTGTTTTTAAGAAAAATCA
AATAAATTAGGGTTTGGGGTTTAAGGTT
Found at i:666820 original size:127 final size:127
Alignment explanation
Indices: 666594--667007 Score: 636
Period size: 126 Copynumber: 3.3 Consensus size: 127
666584 TAATTTAAAA
* * * * **
666594 AAGCTCTCACGTGGACGTGCTTTTGCTACAGTAGCTCCT-AAAAATATAATTTCGAGTTGATATT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAATAATTTCGAGTAGACGTT
*
666658 TCTGAGTAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTACTGAAAG
66 TCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTACTGAAAG
* * * *
666720 AAGCTCTCACGTGGACGCGCTTTTACTACAGTAGTTCCTGAAAAAAATAATTTCGTGTAGACGTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAATAATTTCGAGTAGACGTT
* *
666785 TCTGAGCAAATAGTGTCAAAAACGCTTTAAACAAGATGCTTTGTCAGCAATAGTACTGAAAA
66 TCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTACTGAAAG
666847 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG-AAAAAATAATTTCGAGTAGACGTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAATAATTTCGAGTAGACGTT
* * *
666911 TTTGAGCAAATAGTGTCAAAAACCCTTTAAGCAGGATGCTTTGTCAGCAGA-AGTACTGAAAG
66 TCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCA-ATAGTACTGAAAG
* *
666973 AAGCTCCCATGTGGACACGCTTTTGCTACAGTAGC
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
667008 GCATGTTTGG
Statistics
Matches: 264, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
126 147 0.56
127 117 0.44
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (127 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAATAATTTCGAGTAGACGTT
TCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAATAGTACTGAAAG
Found at i:670460 original size:21 final size:21
Alignment explanation
Indices: 670422--670461 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
670412 TTGTGGTTGC
670422 TCCGGCAGGGATTCTAGTTCT
1 TCCGGCAGGGATTCTAGTTCT
*
670443 TCCGGTAGAGGATT-TAGTT
1 TCCGGCAG-GGATTCTAGTT
670462 GTCGGTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (21 bp):
TCCGGCAGGGATTCTAGTTCT
Found at i:670729 original size:18 final size:18
Alignment explanation
Indices: 670703--670745 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
670693 GACTAAAAAA
* * *
670703 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
670721 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
670739 AGGATAC
1 AGGATAC
670746 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:671399 original size:7 final size:7
Alignment explanation
Indices: 671387--671411 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
671377 TATTAGTTAT
671387 ATACATA
1 ATACATA
671394 ATACATA
1 ATACATA
671401 ATACATA
1 ATACATA
671408 ATAC
1 ATAC
671412 TAAATACTAA
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:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:671417 original size:7 final size:7
Alignment explanation
Indices: 671407--671446 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
671397 CATAATACAT
671407 AATACTA
1 AATACTA
671414 AATACTA
1 AATACTA
671421 AATACTA
1 AATACTA
671428 AATACTA
1 AATACTA
671435 AATACTA
1 AATACTA
671442 AATAC
1 AATAC
671447 CGATCGACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:674154 original size:15 final size:16
Alignment explanation
Indices: 674134--674163 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
674124 CATATCAACA
674134 AAAAATTAA-AAAAAT
1 AAAAATTAATAAAAAT
674149 AAAAATTAATAAAAA
1 AAAAATTAATAAAAA
674164 ATATATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATTAATAAAAAT
Found at i:675254 original size:17 final size:17
Alignment explanation
Indices: 675232--675268 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
675222 TAATTTAACT
675232 TTAATTAATTAGTTAAA
1 TTAATTAATTAGTTAAA
**
675249 TTAATTAATTTTTTAAA
1 TTAATTAATTAGTTAAA
675266 TTA
1 TTA
675269 TAAATAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAATTAATTAGTTAAA
Found at i:682227 original size:13 final size:13
Alignment explanation
Indices: 682209--682235 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
682199 ATTTTTCAAG
682209 TCATTTTCATTTT
1 TCATTTTCATTTT
682222 TCATTTTCATTTT
1 TCATTTTCATTTT
682235 T
1 T
682236 GAGAAAACCA
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:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:687806 original size:13 final size:13
Alignment explanation
Indices: 687788--687814 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
687778 ATTTTTCAAG
687788 TCATTTTCATTTT
1 TCATTTTCATTTT
687801 TCATTTTCATTTT
1 TCATTTTCATTTT
687814 T
1 T
687815 GAGAAAACCA
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:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:693279 original size:16 final size:17
Alignment explanation
Indices: 693258--693295 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
693248 ATTCGCTTGC
693258 TATGTAAACCACATT-A
1 TATGTAAACCACATTAA
693274 TATGTAAACCACATTAA
1 TATGTAAACCACATTAA
693291 TATGT
1 TATGT
693296 TGTTACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
TATGTAAACCACATTAA
Found at i:706320 original size:18 final size:19
Alignment explanation
Indices: 706299--706334 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
706289 ATTATTTTTG
*
706299 TAATTCTTTTCA-AAAAAA
1 TAATTATTTTCATAAAAAA
706317 TAATTATTTTCATAAAAA
1 TAATTATTTTCATAAAAA
706335 GTATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTATTTTCATAAAAAA
Found at i:710088 original size:66 final size:66
Alignment explanation
Indices: 709971--710104 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
709961 AATCTGAAGC
* * ** * * *
709971 TGTAGCTAGAGTTCGTCATATTTTCTTGTTGCCTCTGTTTCCCTCGCTGCTGCTTTCGCTTTAAG
1 TGTAGCTAGAGTTCATCATATTTTCTTGTAGCCTCTACTTCCCTCGATGCTGCCTCCGCTTTAAG
710036 T
66 T
* * *
710037 TGTAGCTGGAGTTCATCATATTTTCTT-TGAGCCTCTACTTCTCTTGATGCTGCCTCCGCTTTAA
1 TGTAGCTAGAGTTCATCATATTTTCTTGT-AGCCTCTACTTCCCTCGATGCTGCCTCCGCTTTAA
710101 GT
65 GT
710103 TG
1 TG
710105 AGCAATTTGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (66 bp):
TGTAGCTAGAGTTCATCATATTTTCTTGTAGCCTCTACTTCCCTCGATGCTGCCTCCGCTTTAAG
T
Found at i:714325 original size:50 final size:50
Alignment explanation
Indices: 714205--714488 Score: 232
Period size: 50 Copynumber: 5.6 Consensus size: 50
714195 GAAGATGAGA
* * *
714205 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-TA--AGAGG
*
714261 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
* * * * * *
714311 TCACATGTAAGACCATGTTTGGGACATGGCGTTGGCATCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
** * * * * **
714361 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
* * * * * * * *
714411 TCTCATGTAAGACCATATTTAGGATATGGCATTGGCAGTACAAGA-AACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGAGATAAGAGG
*
714460 TCCCATGTAAGACTATGTCTGGGACATGG
1 TCCCATGTAAGACCATGTCTGGGACATGG
714489 ATCTTGAAGA
Statistics
Matches: 187, Mismatches: 39, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
49 23 0.12
50 117 0.63
51 2 0.01
52 5 0.03
53 4 0.02
55 1 0.01
56 35 0.19
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
Found at i:714398 original size:100 final size:102
Alignment explanation
Indices: 714208--714488 Score: 297
Period size: 100 Copynumber: 2.8 Consensus size: 102
714198 GATGAGATCC
*
714208 CATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGATCCCATGTAAGA
1 CATGTAAGACCATGTTTGGGACATGGCATTGGCATCA-T-AG--TATGAGAGATCCCACGTAAGA
* * **
714273 CCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGGTCA
62 CCATGTCTGGGACATGGCATGGGCACCGAGATAAGAACTCA
* * *
714314 CATGTAAGACCATGTTTGGGACATGGCGTTGGCATCA-AG-ATGAGAGGTCCCCCGTAAGACCAT
1 CATGTAAGACCATGTTTGGGACATGGCATTGGCATCATAGTATGAGAGATCCCACGTAAGACCAT
* * * *
714377 GTCTGGGACATGGCATGGGCACCTATATGAGAACTCT
66 GTCTGGGACATGGCATGGGCACCGAGATAAGAACTCA
* * * * * *
714414 CATGTAAGACCATATTTAGGATATGGCATTGGCAGTACA-AG-A--A-ACATCCCATGTAAGACT
1 CATGTAAGACCATGTTTGGGACATGGCATTGGCA-T-CATAGTATGAGAGATCCCACGTAAGACC
714474 ATGTCTGGGACATGG
64 ATGTCTGGGACATGG
714489 ATCTTGAAGA
Statistics
Matches: 152, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
99 27 0.18
100 81 0.53
101 1 0.01
102 5 0.03
103 2 0.01
106 36 0.24
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (102 bp):
CATGTAAGACCATGTTTGGGACATGGCATTGGCATCATAGTATGAGAGATCCCACGTAAGACCAT
GTCTGGGACATGGCATGGGCACCGAGATAAGAACTCA
Found at i:720206 original size:50 final size:50
Alignment explanation
Indices: 720141--720334 Score: 203
Period size: 50 Copynumber: 3.9 Consensus size: 50
720131 GCATTAAGAG
* * *
720141 GATGAGA--TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCAT
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
* *
720189 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
** * * *
720239 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACACGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
* ** * * * * * *
720289 TATGAGAACTCTCATGTAAAACCATATCTAGGATATGACATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
720335 GTACAAGAAA
Statistics
Matches: 119, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
48 6 0.05
50 113 0.95
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
Found at i:720333 original size:100 final size:100
Alignment explanation
Indices: 720154--720334 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 100
720144 GAGATCCCAT
* * * * ** * * *
720154 GTAAGACCATGTTTGGGACATGGCATTGGCATCATTATGAGAGGTCCCATGTAAGACCATGTCTG
1 GTAAGACCATGTCTGGGACACGGCATGGGCACCATTATGAGAACTCCCATGTAAAACCATATCTA
* *
720219 GGACATGGCGTTGGCACCAAGATGAGAGGTCCCCC
66 GGACATGACATTGGCACCAAGATGAGAGGTCCCCC
*
720254 GTAAGACCATGTCTGGGACACGGCATGGGCACC-TATATGAGAACTCTCATGTAAAACCATATCT
1 GTAAGACCATGTCTGGGACACGGCATGGGCACCAT-TATGAGAACTCCCATGTAAAACCATATCT
*
720318 AGGATATGACATTGGCA
65 AGGACATGACATTGGCA
720335 GTACAAGAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
99 1 0.01
100 66 0.99
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (100 bp):
GTAAGACCATGTCTGGGACACGGCATGGGCACCATTATGAGAACTCCCATGTAAAACCATATCTA
GGACATGACATTGGCACCAAGATGAGAGGTCCCCC
Done.