Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 61 of 226
Found at i:19744282 original size:73 final size:73
Alignment explanation
Indices: 19744200--19744458 Score: 473
Period size: 73 Copynumber: 3.5 Consensus size: 73
19744190 ACAACTTGAC
*
19744200 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCATCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
19744265 CACTAACA
66 CACTAACA
* *
19744273 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCATTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
19744338 CACTAACA
66 CACTAACA
*
19744346 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
19744411 CACTAACA
66 CACTAACA
*
19744419 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
19744459 AATAATAATA
Statistics
Matches: 180, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 180 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:19748788 original size:73 final size:73
Alignment explanation
Indices: 19748701--19748886 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
19748691 ACAACTTGAC
19748701 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
19748766 CACTAACA
66 CACTAACA
*
19748774 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
19748839 CACTAACA
66 CACTAACA
*
19748847 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
19748887 AATAACAATA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:19764761 original size:27 final size:27
Alignment explanation
Indices: 19764723--19764793 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
19764713 AACAAATGTG
*
19764723 GGTGCCGCCTCTGGCAGTGGCACCATT
1 GGTGCCGCCTCTGGCAGAGGCACCATT
* *
19764750 GGTGCCGCCTCTGCCACAGGCACCATT
1 GGTGCCGCCTCTGGCAGAGGCACCATT
19764777 GGTGCCGCCTCTGGCAG
1 GGTGCCGCCTCTGGCAG
19764794 GCCCTCCATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.11, C:0.37, G:0.32, T:0.20
Consensus pattern (27 bp):
GGTGCCGCCTCTGGCAGAGGCACCATT
Found at i:19768850 original size:7 final size:6
Alignment explanation
Indices: 19768819--19768849 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
19768809 AAAAAAAAAG
19768819 AAATGA AAATGA AAATGA AAATGA TAAATGA
1 AAATGA AAATGA AAATGA AAATGA -AAATGA
19768850 TCCATTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (6 bp):
AAATGA
Found at i:19784952 original size:25 final size:24
Alignment explanation
Indices: 19784924--19784982 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
19784914 CGAGAAATGC
*
19784924 AACGGGAAGCTCACAAAGAGC-CTAT
1 AACGGGAAGCTC-CAAAGAGCAAT-T
* *
19784949 AACGGGTAGCTCCGAAGAGCAATT
1 AACGGGAAGCTCCAAAGAGCAATT
19784973 AACGGGAAGC
1 AACGGGAAGC
19784983 ACCGAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.12
Consensus pattern (24 bp):
AACGGGAAGCTCCAAAGAGCAATT
Found at i:19785002 original size:25 final size:25
Alignment explanation
Indices: 19784946--19785006 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
19784936 ACAAAGAGCC
* * *
19784946 TATAACGGGTAGCTCCGAAGAGCAA
1 TATAACGGGAAGCACCGAAGAACAA
* *
19784971 T-TAACGGGAAGCACCGAATAATAA
1 TATAACGGGAAGCACCGAAGAACAA
19784995 TATAACGGGAAG
1 TATAACGGGAAG
19785007 TTCAAGCGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.16
Consensus pattern (25 bp):
TATAACGGGAAGCACCGAAGAACAA
Found at i:19785549 original size:11 final size:11
Alignment explanation
Indices: 19785533--19785598 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
19785523 TATACGAGTA
19785533 AATTTAACATC
1 AATTTAACATC
*
19785544 AATTTAATA-C
1 AATTTAACATC
19785554 AATTT-ACAT-
1 AATTTAACATC
*
19785563 AATTTAACATA
1 AATTTAACATC
*
19785574 AATTTAATA-C
1 AATTTAACATC
19785584 AATTT-ACATTC
1 AATTTAACA-TC
19785595 AATT
1 AATT
19785599 CAATCCAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
9 9 0.20
10 15 0.33
11 21 0.47
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTTAACATC
Found at i:19785569 original size:30 final size:30
Alignment explanation
Indices: 19785533--19785592 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
19785523 TATACGAGTA
*
19785533 AATTTAACATCAATTTAATACAATTTACAT
1 AATTTAACATAAATTTAATACAATTTACAT
19785563 AATTTAACATAAATTTAATACAATTTACAT
1 AATTTAACATAAATTTAATACAATTTACAT
19785593 TCAATTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (30 bp):
AATTTAACATAAATTTAATACAATTTACAT
Found at i:19786152 original size:10 final size:10
Alignment explanation
Indices: 19786139--19786166 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
19786129 ATCATTTATC
19786139 ATCTTTTAAT
1 ATCTTTTAAT
19786149 ATCTTTTAAT
1 ATCTTTTAAT
19786159 ATCTTTTA
1 ATCTTTTA
19786167 TTTCCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (10 bp):
ATCTTTTAAT
Found at i:19789867 original size:63 final size:63
Alignment explanation
Indices: 19789765--19789887 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 63
19789755 ACACTCCATG
** * *
19789765 TTGTGGCCAAGCCACTGTATATTGCAGTCAAGCTACACGTTATGGTCAAACCACTAAATAACA
1 TTGTGGCCAAGCCACTCAATATTACAGACAAGCTACACGTTATGGTCAAACCACTAAATAACA
* * * *
19789828 TTGTGGCCAAGCCACTCAATATTACAGACAAGCTGCACGTTCTGGTCAAGCCACTCAATA
1 TTGTGGCCAAGCCACTCAATATTACAGACAAGCTACACGTTATGGTCAAACCACTAAATA
19789888 TTGTAGTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (63 bp):
TTGTGGCCAAGCCACTCAATATTACAGACAAGCTACACGTTATGGTCAAACCACTAAATAACA
Found at i:19790072 original size:40 final size:41
Alignment explanation
Indices: 19789977--19790078 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 41
19789967 TTTCAGTGGG
* * *
19789977 CATGCTTAACATACGAATCAGATTTATAGTCAATACATTCAA
1 CATGCTTAACATGCGAATCAGATTTATA-TCAATACAATAAA
*
19790019 CATGCTTAACATGCGAATCAGATTTGAT-T-AGTACAATAAA
1 CATGCTTAACATGCGAATCAGATTT-ATATCAATACAATAAA
* *
19790059 TATGCTTAACATGCAAATCA
1 CATGCTTAACATGCGAATCA
19790079 TATATCAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 26 0.49
41 1 0.02
42 24 0.45
43 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (41 bp):
CATGCTTAACATGCGAATCAGATTTATATCAATACAATAAA
Found at i:19795414 original size:27 final size:27
Alignment explanation
Indices: 19795384--19795435 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
19795374 TGTGAATAGG
* *
19795384 CCCATTTTCATAGCTTGTATGAGCAAA
1 CCCATTTTCACAGCTCGTATGAGCAAA
*
19795411 CCCATTTTCACAGCTCGTGTGAGCA
1 CCCATTTTCACAGCTCGTATGAGCA
19795436 TTTTGATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (27 bp):
CCCATTTTCACAGCTCGTATGAGCAAA
Found at i:19795452 original size:25 final size:25
Alignment explanation
Indices: 19795420--19795484 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
19795410 ACCCATTTTC
*
19795420 ACAGCTCGTGTGAGCATTTTGATTA
1 ACAGCTCGTGTGAGCATTCTGATTA
*
19795445 ACAGCTCGTGTGAGCATTCTGATTT
1 ACAGCTCGTGTGAGCATTCTGATTA
19795470 ACAGCTCGTGTGAGC
1 ACAGCTCGTGTGAGC
19795485 GTGCATGCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCATTCTGATTA
Found at i:19798843 original size:43 final size:42
Alignment explanation
Indices: 19798760--19798952 Score: 244
Period size: 43 Copynumber: 4.5 Consensus size: 42
19798750 ACTTCCGAGG
*
19798760 TGAGATTTCATGTAAGACCATAGCTGGCTATTGGCATCGATT
1 TGAGATTTCGTGTAAGACCATAGCTGGCTATTGGCATCGATT
** *
19798802 TG-GTATTTTTTGTAAGACCATAGCTAGGCTATTAGCATCGATT
1 TGAG-ATTTCGTGTAAGACCATAGCT-GGCTATTGGCATCGATT
19798845 TGAGATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGATT
1 TGAGATTTCGTGTAAGACCATAGCTG-GCTATTGGCATCGATT
* * * *
19798888 TGAGATTTCGTGTAAGACAATAGTTGGGCTATTGGAATCGATA
1 TGAGATTTCGTGTAAGACCATAGCT-GGCTATTGGCATCGATT
* *
19798931 CGAGATTTCCTTGTAAGACCAT
1 TGAGATTT-CGTGTAAGACCAT
19798953 GTCTAAGACA
Statistics
Matches: 132, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
41 1 0.01
42 22 0.17
43 96 0.73
44 13 0.10
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATAGCTGGCTATTGGCATCGATT
Found at i:19807320 original size:23 final size:23
Alignment explanation
Indices: 19807244--19807323 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 23
19807234 GAAGATCATA
*
19807244 AGAGCCATATTC-AGGAAGCTTCGG
1 AGAGCCATA-TCGA-GAAGCTCCGG
* **
19807268 ATAGCCATATATCGAGAAGCTCAAG
1 AGAGCC--ATATCGAGAAGCTCCGG
*
19807293 CGAGCCATATCGAGAAGCTCCGG
1 AGAGCCATATCGAGAAGCTCCGG
19807316 AGAGCCAT
1 AGAGCCAT
19807324 TAATCAGGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
23 22 0.50
24 5 0.11
25 13 0.30
26 4 0.09
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (23 bp):
AGAGCCATATCGAGAAGCTCCGG
Found at i:19809823 original size:18 final size:22
Alignment explanation
Indices: 19809800--19809844 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 22
19809790 AAAATAATAA
19809800 AAATAAA-A-AATTTTA-AT-T
1 AAATAAATATAATTTTATATAT
19809818 AAATAAATATAATTTTATATAT
1 AAATAAATATAATTTTATATAT
19809840 AAATA
1 AAATA
19809845 TGATTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 7 0.30
21 2 0.09
22 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAAATATAATTTTATATAT
Found at i:19810846 original size:28 final size:28
Alignment explanation
Indices: 19810793--19810848 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
19810783 AAAATATTAT
* *
19810793 TAATTAATAAAATTATAAATCTATAAAA
1 TAATTAATAAAATTAAAAATCAATAAAA
*
19810821 TAATTGAATAAATTTAAAAAT-AATAAAA
1 TAATT-AATAAAATTAAAAATCAATAAAA
19810849 ATCCAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
TAATTAATAAAATTAAAAATCAATAAAA
Found at i:19817335 original size:9 final size:9
Alignment explanation
Indices: 19817321--19817388 Score: 75
Period size: 9 Copynumber: 7.4 Consensus size: 9
19817311 TTTGGTTAAA
*
19817321 AATTACCTG
1 AATTACCCG
19817330 AATTACCCG
1 AATTACCCG
19817339 AATTACCCG
1 AATTACCCG
*
19817348 AATTAACCG
1 AATTACCCG
*
19817357 AATTA-TCG
1 AATTACCCG
*
19817365 AAAAATACCCG
1 --AATTACCCG
19817376 AATTACCCG
1 AATTACCCG
19817385 AATT
1 AATT
19817389 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
8 2 0.04
9 42 0.84
10 4 0.08
11 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:19819902 original size:30 final size:30
Alignment explanation
Indices: 19819868--19819928 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
19819858 ATACACCTTG
19819868 GCATGATAAATTAATTTACCAGTTTAACTA
1 GCATGATAAATTAATTTACCAGTTTAACTA
* *
19819898 GCATGATAAATTGATTTTCCAGTTTAACTA
1 GCATGATAAATTAATTTACCAGTTTAACTA
19819928 G
1 G
19819929 AGTACAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (30 bp):
GCATGATAAATTAATTTACCAGTTTAACTA
Found at i:19820967 original size:5 final size:5
Alignment explanation
Indices: 19820957--19820992 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
19820947 ATATAATGTG
19820957 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
19820993 ATGTTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:19821757 original size:3 final size:3
Alignment explanation
Indices: 19821749--19821780 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19821739 AATACCCTTA
19821749 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19821781 AGGGGGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19825683 original size:29 final size:31
Alignment explanation
Indices: 19825629--19825707 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
19825619 ATCTTAAAAT
* *
19825629 TATACATGAATTTTGATTTAATGTGCAATTA
1 TATACATGAACTTTAATTTAATGTGCAATTA
19825660 TATACATGAACTTTAATTT-A-GTGCAATTA
1 TATACATGAACTTTAATTTAATGTGCAATTA
*
19825689 TACACATGAAACTTTAATT
1 TATACATG-AACTTTAATT
19825708 GTGGTCCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.36
30 11 0.25
31 17 0.39
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (31 bp):
TATACATGAACTTTAATTTAATGTGCAATTA
Found at i:19825704 original size:30 final size:29
Alignment explanation
Indices: 19825632--19825707 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 29
19825622 TTAAAATTAT
* * *
19825632 ACATGAATTTTGATTTAATGTGCAATTATAT
1 ACATGAACTTTAATTT-A-GTGCAATTATAC
19825663 ACATGAACTTTAATTTAGTGCAATTATAC
1 ACATGAACTTTAATTTAGTGCAATTATAC
19825692 ACATGAAACTTTAATT
1 ACATG-AACTTTAATT
19825708 GTGGTCCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.39
30 11 0.27
31 14 0.34
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (29 bp):
ACATGAACTTTAATTTAGTGCAATTATAC
Found at i:19831507 original size:28 final size:28
Alignment explanation
Indices: 19831456--19831523 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
19831446 AAGATAAAAT
* *
19831456 ATGCCTTGAAGGTTAAATAAAACAAAGC
1 ATGCCTTGAAGGCTAAACAAAACAAAGC
* *
19831484 ATGCCTTGAAGGCTATACACAACAAAGC
1 ATGCCTTGAAGGCTAAACAAAACAAAGC
*
19831512 GTGCCTTGAAGG
1 ATGCCTTGAAGG
19831524 ACAAACTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (28 bp):
ATGCCTTGAAGGCTAAACAAAACAAAGC
Found at i:19834700 original size:13 final size:13
Alignment explanation
Indices: 19834682--19834745 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
19834672 AGTTCTTTAT
*
19834682 TGCTTTTGCGAAG
1 TGCTTTTGAGAAG
19834695 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
19834708 TGCTTTTGAAAAG
1 TGCTTTTGAGAAG
* *
19834721 TACTTTTCAGAAG
1 TGCTTTTGAGAAG
19834734 TGCTTTTGAGAA
1 TGCTTTTGAGAA
19834746 ATTTGAGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:19835359 original size:22 final size:21
Alignment explanation
Indices: 19835334--19835377 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
19835324 AAGCATATGA
*
19835334 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
19835356 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
19835377 A
1 A
19835378 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:19839783 original size:17 final size:17
Alignment explanation
Indices: 19839741--19839788 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
19839731 TTCAGTACAC
*
19839741 ATTTCATTTC-ATATCA
1 ATTTCATTTCAATAGCA
* *
19839757 CTTGCTATTTCAATAGCA
1 ATTTC-ATTTCAATAGCA
19839775 ATTTCATTTCAATA
1 ATTTCATTTCAATA
19839789 AAACTTGTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.12
17 14 0.56
18 8 0.32
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (17 bp):
ATTTCATTTCAATAGCA
Found at i:19847486 original size:14 final size:14
Alignment explanation
Indices: 19847466--19847499 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19847456 TATAGTTAGG
*
19847466 ATTAAAATTTAAAA
1 ATTAAAATATAAAA
*
19847480 TTTAAAATATAAAA
1 ATTAAAATATAAAA
19847494 ATTAAA
1 ATTAAA
19847500 TCTGCAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAAAATATAAAA
Found at i:19848768 original size:28 final size:28
Alignment explanation
Indices: 19848731--19848826 Score: 149
Period size: 28 Copynumber: 3.4 Consensus size: 28
19848721 AAAAATAAAA
*
19848731 ATTTATCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
*
19848759 ATTTACCAAAATATTGCAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
19848787 ATTTACCAAAATATATA-AACTTTTTTATT
1 ATTTACCAAAATAT-TACAACTTTTTT-TT
19848816 ATTTACCAAAA
1 ATTTACCAAAA
19848827 AATATAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 49 0.78
29 14 0.22
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:19848937 original size:27 final size:27
Alignment explanation
Indices: 19848898--19849000 Score: 161
Period size: 27 Copynumber: 3.8 Consensus size: 27
19848888 TATTGGTCAC
** *
19848898 GCCAATAGTATTGGCGGCACCAAAGGT
1 GCCAATACCATTGGCGGCACCAATGGT
*
19848925 GCCAAAACCATTGGCGGCACCAATGGT
1 GCCAATACCATTGGCGGCACCAATGGT
19848952 GCCAATACCATTGGCGGCACCAATGGT
1 GCCAATACCATTGGCGGCACCAATGGT
*
19848979 GCCAATGCCATTGGCGGCACCA
1 GCCAATACCATTGGCGGCACCA
19849001 CTCGTATTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (27 bp):
GCCAATACCATTGGCGGCACCAATGGT
Found at i:19849077 original size:28 final size:26
Alignment explanation
Indices: 19849030--19849081 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
19849020 CTCTACCCAG
19849030 CTGAAGAGAGAAAAATAAAAAAAAAA
1 CTGAAGAGAGAAAAATAAAAAAAAAA
* *
19849056 CTGAAGAGAGAAAATTCAAAAAAAAA
1 CTGAAGAGAGAAAAATAAAAAAAAAA
19849082 GAAGAAGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.69, C:0.06, G:0.15, T:0.10
Consensus pattern (26 bp):
CTGAAGAGAGAAAAATAAAAAAAAAA
Found at i:19849181 original size:19 final size:21
Alignment explanation
Indices: 19849143--19849181 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19849133 AATAATTGAT
*
19849143 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
19849164 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
19849182 TGTTGTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:19849234 original size:3 final size:3
Alignment explanation
Indices: 19849226--19849259 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19849216 AAAATAAAAG
19849226 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19849260 GTTGTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:19849264 original size:3 final size:3
Alignment explanation
Indices: 19849258--19849304 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
19849248 ATTATTATTA
19849258 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
19849305 AGTATGAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:19849508 original size:26 final size:26
Alignment explanation
Indices: 19849479--19849542 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
19849469 TTTTAGTGTG
*
19849479 TATTATTT-TGAGTATAAAATTATTAA
1 TATTATTTGT-AGTATAAAATTAATAA
*
19849505 TATTATTCGTAGTATAAAATTAATAA
1 TATTATTTGTAGTATAAAATTAATAA
*
19849531 TTTTAGTTTGTA
1 TATTA-TTTGTA
19849543 TTATTTTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (26 bp):
TATTATTTGTAGTATAAAATTAATAA
Found at i:19850161 original size:18 final size:18
Alignment explanation
Indices: 19850118--19850162 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
19850108 TTGACATGGT
* *
19850118 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
19850136 T-GTCGGCGAAGAAGAAGG
1 TGGT-GGCGAAGAAGAAGG
19850154 TGGTGGCGA
1 TGGTGGCGA
19850163 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.29, C:0.07, G:0.47, T:0.18
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:19855761 original size:19 final size:19
Alignment explanation
Indices: 19855726--19855763 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19855716 TTTAAACACA
19855726 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
19855745 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
19855764 ACATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:19855840 original size:32 final size:33
Alignment explanation
Indices: 19855777--19855889 Score: 128
Period size: 32 Copynumber: 3.5 Consensus size: 33
19855767 TTTTTTTCCC
19855777 TTTTTTTTC-CTT-T-C-TTCCCTCTTCTTCTTCT
1 TTTTTTTTCTCTTCTCCTTTCCCTCTTC-T-TTCT
19855808 TTTTTTTTCTCTTCTCCTTTCCCT-TTCTTTCT
1 TTTTTTTTCTCTTCTCCTTTCCCTCTTCTTTCT
* * *
19855840 TTTTTCTTCTCTTCTCCTTTTCTTCTTCTTTCT
1 TTTTTTTTCTCTTCTCCTTTCCCTCTTCTTTCT
19855873 TTCCTTTTTTCTCTTCT
1 TT--TTTTTTCTCTTCT
19855890 GCCCCCACCA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
31 9 0.13
32 28 0.39
33 12 0.17
34 4 0.06
35 18 0.25
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (33 bp):
TTTTTTTTCTCTTCTCCTTTCCCTCTTCTTTCT
Found at i:19855850 original size:27 final size:27
Alignment explanation
Indices: 19855804--19855879 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
19855794 CCTCTTCTTC
*
19855804 TTCTTTTTTTTTCTCTTCTCCTTTCCCT
1 TTCTTTCTTTTT-TCTTCTCCTTTCCCT
*
19855832 TTCTTTCTTTTTTCTTCT-CTTCTCCTT
1 TTCTTTCTTTTTTCTTCTCCTT-TCCCT
*
19855859 TTC-TTCTTCTTTCTT-TCCTTT
1 TTCTTTCTTTTTTCTTCTCCTTT
19855880 TTTCTCTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
26 17 0.40
27 13 0.30
28 11 0.26
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (27 bp):
TTCTTTCTTTTTTCTTCTCCTTTCCCT
Found at i:19855871 original size:26 final size:27
Alignment explanation
Indices: 19855771--19855879 Score: 79
Period size: 26 Copynumber: 4.1 Consensus size: 27
19855761 ATTACATTTT
19855771 TTTCCCTTT-TTT-TTCCTTTCTTC-CC
1 TTTCCCTTTCTTTCTT-CTTTCTTCTCC
* * *
19855796 TCTT-CTTCTTCTTTTTTTTTCTCTTCTCC
1 T-TTCCCT-TTCTTTCTTCTT-TCTTCTCC
*
19855825 TTTCCCTTTCTTTCTTTTTTCTTCT-C
1 TTTCCCTTTCTTTCTTCTTTCTTCTCC
*
19855851 TTCTCCTTTTC-TTCTTCTTTCTT-TCC
1 TT-TCCCTTTCTTTCTTCTTTCTTCTCC
19855877 TTT
1 TTT
19855880 TTTCTCTTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
25 5 0.07
26 21 0.30
27 18 0.26
28 20 0.29
29 5 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTCCCTTTCTTTCTTCTTTCTTCTCC
Found at i:19855997 original size:27 final size:27
Alignment explanation
Indices: 19855922--19855988 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
19855912 TAAAACCAAC
19855922 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* *
19855949 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
19855976 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
19855989 ACCATTGGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:19856148 original size:28 final size:28
Alignment explanation
Indices: 19856074--19856171 Score: 137
Period size: 28 Copynumber: 3.5 Consensus size: 28
19856064 TTTTTTTTAT
* *
19856074 ATATGTTGGTAAATAATAAAAAA-TTTTA
1 ATATTTTGGTAAATAA-AAAAAAGTTGTA
19856102 TATATTTTGGTAAAT-AAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
19856130 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
19856158 ATATTTTGATAAAT
1 ATATTTTGGTAAAT
19856172 TTTTATTTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.31
28 31 0.48
29 13 0.20
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:19863006 original size:21 final size:21
Alignment explanation
Indices: 19862977--19863020 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19862967 ACACCAAAAC
*
19862977 AGGCTTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
19862998 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
19863019 AG
1 AG
19863021 CGCCGCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.30, T:0.39
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGCTTTTT
Found at i:19863218 original size:43 final size:43
Alignment explanation
Indices: 19863144--19863326 Score: 169
Period size: 43 Copynumber: 4.3 Consensus size: 43
19863134 AGACTAAGAC
* *
19863144 CTTTAGTGGCGTTTGTGGTCGAAGCGTCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTAAAGATCAGGGT
* * * *
19863187 CTTTTA-TGGCGTTTGTGG-GGAAAACGCCGCTAAAGATTAGGTT
1 C-TTTAGTGGCGTTTGTGGTCG-AAGCGCCGCTAAAGATCAGGGT
* * *
19863230 CTTTAGTGGTGTTTGTGGTCGAAGCGCCGCTATAGATCAGGCT
1 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTAAAGATCAGGGT
* * *
19863273 CTTTAGCGGCGTTT-T--TACGGAAAGCGCTGCTAAAGATTAGGGT
1 CTTTAGTGGCGTTTGTGGT-C-G-AAGCGCCGCTAAAGATCAGGGT
*
19863316 CTTTAATGGCG
1 CTTTAGTGGCG
19863327 CTTCTCCCTA
Statistics
Matches: 113, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 7 0.06
43 99 0.88
44 5 0.04
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (43 bp):
CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTAAAGATCAGGGT
Found at i:19863284 original size:86 final size:86
Alignment explanation
Indices: 19863144--19863326 Score: 251
Period size: 86 Copynumber: 2.1 Consensus size: 86
19863134 AGACTAAGAC
* * * **
19863144 CTTTAGTGGCGTTTGTGGTCGAAGCGTCGCTATAGATCAGGGTCTTTTATGGCGTTTGTGGGGAA
1 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGCTCTTTTACGGCGTTTGTACGGAA
*
19863209 AACGCCGCTAAAGATTAGGTT
66 AACGCCGCTAAAGATTAGGGT
* *
19863230 CTTTAGTGGTGTTTGTGGTCGAAGCGCCGCTATAGATCAGGCTC-TTTAGCGGCGTTTTTACGGA
1 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGCTCTTTTA-CGGCGTTTGTACGGA
* *
19863294 AAGCGCTGCTAAAGATTAGGGT
65 AAACGCCGCTAAAGATTAGGGT
*
19863316 CTTTAATGGCG
1 CTTTAGTGGCG
19863327 CTTCTCCCTA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 4 0.05
86 80 0.95
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (86 bp):
CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGCTCTTTTACGGCGTTTGTACGGAA
AACGCCGCTAAAGATTAGGGT
Found at i:19863371 original size:43 final size:42
Alignment explanation
Indices: 19863323--19863459 Score: 143
Period size: 43 Copynumber: 3.2 Consensus size: 42
19863313 GGTCTTTAAT
*
19863323 GGCGCTTCTCCCTA-AAACGCCGCAAAAGACCTTGATCTATAGC
1 GGCGCTT-TCCC-ACAAACGCCGCAAAAGACCTTGATCTTTAGC
* * * * *
19863366 GGCGCTTTCCCCATAAACGCCGCGAAAGACCATGATATTTAGG
1 GGCGCTTT-CCCACAAACGCCGCAAAAGACCTTGATCTTTAGC
* *
19863409 GGCGCTTTTTCCACAAACGCCGCTAAAGAACCTT-ATCTTTAGC
1 GGCGC-TTTCCCACAAACGCCGCAAAAG-ACCTTGATCTTTAGC
19863452 GGCGCTTT
1 GGCGCTTT
19863460 TACCATAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
42 5 0.06
43 67 0.85
44 7 0.09
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (42 bp):
GGCGCTTTCCCACAAACGCCGCAAAAGACCTTGATCTTTAGC
Found at i:19863460 original size:43 final size:42
Alignment explanation
Indices: 19863337--19863479 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 42
19863327 CTTCTCCCTA
* * **
19863337 AAACGCCGCAAAAGACCTTGATCTATAGCGGCGCTTTCCCCAT
1 AAACGCCGCTAAAGACCTT-ATCTTTAGCGGCGCTTTTACCAT
* * * * * *
19863380 AAACGCCGCGAAAGACCATGATATTTAGGGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACC-TTATCTTTAGCGGCGCTTTTACCAT
19863423 AAACGCCGCTAAAGAACCTTATCTTTAGCGGCGCTTTTACCAT
1 AAACGCCGCTAAAG-ACCTTATCTTTAGCGGCGCTTTTACCAT
* *
19863466 AAATGCCACTAAAG
1 AAACGCCGCTAAAG
19863480 GCCAACACCT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 78 0.95
44 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCTTATCTTTAGCGGCGCTTTTACCAT
Found at i:19863493 original size:86 final size:86
Alignment explanation
Indices: 19863337--19863504 Score: 194
Period size: 86 Copynumber: 2.0 Consensus size: 86
19863327 CTTCTCCCTA
* * ** *
19863337 AAACGCCGCAAAAGACCTTGATCTATAGCGGCGCTTTCCCCATAAACGCCGCGAAAGACCATGAT
1 AAACGCCGCAAAAGACCTTGATCTATAGCGGCGCTTTCACCATAAACGCCACGAAAGACCAACAC
19863402 ATTTAGGGGCGCTTTTTCCAC
66 ATTTAGGGGCGCTTTTTCCAC
* * * * * *
19863423 AAACGCCGCTAAAGAACCTT-ATCTTTAGCGGCGCTTTTACCATAAATGCCACTAAAGGCCAACA
1 AAACGCCGCAAAAG-ACCTTGATCTATAGCGGCGCTTTCACCATAAACGCCACGAAAGACCAACA
* * *
19863487 CCTTTAGTGGCGTTTTTT
65 CATTTAGGGGCGCTTTTT
19863505 TTTTAAAAAC
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
86 62 0.93
87 5 0.07
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (86 bp):
AAACGCCGCAAAAGACCTTGATCTATAGCGGCGCTTTCACCATAAACGCCACGAAAGACCAACAC
ATTTAGGGGCGCTTTTTCCAC
Found at i:19863857 original size:21 final size:21
Alignment explanation
Indices: 19863831--19863889 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
19863821 TTTGATGCTG
19863831 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGTAGC
*
19863852 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGTAGC
*
19863873 CTCTGCTTCTCTCGCTG
1 CTCTGCTTCCCTCGCTG
19863890 CAACCTGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.03, C:0.42, G:0.17, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGTAGC
Found at i:19864076 original size:66 final size:66
Alignment explanation
Indices: 19863953--19864083 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
19863943 TTAAGCTGCT
* * *
19863953 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGAATCTGCTTTCAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGAATCCGCTTTAAGTTGT
19864018 A
66 A
* * **
19864019 GCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGCTGAATCCGCTTTAAGTTG
19864083 T
65 T
19864084 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGAATCCGCTTTAAGTTGT
A
Found at i:19868968 original size:9 final size:9
Alignment explanation
Indices: 19868954--19869218 Score: 72
Period size: 9 Copynumber: 28.8 Consensus size: 9
19868944 TCTCATTAAG
19868954 TTATGTAAT
1 TTATGTAAT
19868963 TTATGTATAAT
1 TTATG--TAAT
*
19868974 ATTAATGTAAG
1 -TT-ATGTAAT
19868985 TTATGTAA-
1 TTATGTAAT
* *
19868993 GT-TGTAAG
1 TTATGTAAT
*
19869001 TTATGTAAG
1 TTATGTAAT
19869010 TTATGT-AT
1 TTATGTAAT
*
19869018 AATAT-TAA-
1 -TTATGTAAT
** *
19869026 TTAACTAAG
1 TTATGTAAT
19869035 TTATGTAAT
1 TTATGTAAT
19869044 TTATGTATAAT
1 TTATG--TAAT
*
19869055 ATTAATGTAAG
1 -TT-ATGTAAT
19869066 TTATGT-AT
1 TTATGTAAT
*
19869074 AATAT-TAAT
1 -TTATGTAAT
* *
19869083 TCAT-TAAG
1 TTATGTAAT
19869091 TTATGTAAT
1 TTATGTAAT
19869100 TTATGTATAAT
1 TTATG--TAAT
*
19869111 ATTAATGTAAG
1 -TT-ATGTAAT
19869122 TTATGT-AT
1 TTATGTAAT
*
19869130 AATAT-TAAT
1 -TTATGTAAT
* *
19869139 TAAT-TAAG
1 TTATGTAAT
19869147 TTATGTAAT
1 TTATGTAAT
19869156 TTATGTATAAT
1 TTATG--TAAT
*
19869167 ATTAATGTAAG
1 -TT-ATGTAAT
19869178 TTATGT-AT
1 TTATGTAAT
*
19869186 AATAT-TAA-
1 -TTATGTAAT
* *
19869194 TTATTTAAG
1 TTATGTAAT
19869203 TTATGTAAT
1 TTATGTAAT
19869212 TTATGTA
1 TTATGTA
19869219 TAATACTAAT
Statistics
Matches: 192, Mismatches: 32, Indels: 64
0.67 0.11 0.22
Matches are distributed among these distances:
7 10 0.05
8 32 0.17
9 94 0.49
10 8 0.04
11 28 0.15
12 8 0.04
13 12 0.06
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (9 bp):
TTATGTAAT
Found at i:19869000 original size:16 final size:16
Alignment explanation
Indices: 19868979--19869011 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19868969 ATAATATTAA
19868979 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
19868995 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
19869011 T
1 T
19869012 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:19869063 original size:56 final size:56
Alignment explanation
Indices: 19869003--19869228 Score: 416
Period size: 56 Copynumber: 4.0 Consensus size: 56
19868993 GTTGTAAGTT
*
19869003 ATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
*
19869059 ATGTAAGTTATGTATAATATTAATTCATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
19869115 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* *
19869171 ATGTAAGTTATGTATAATATTAATTATTTAAGTTATGTAATTTATGTATAATACTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
19869227 AT
1 AT
19869229 TTATGTATAA
Statistics
Matches: 165, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 165 1.00
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (56 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
Found at i:19869069 original size:22 final size:22
Alignment explanation
Indices: 19869037--19869082 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
19869027 TAACTAAGTT
*
19869037 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
19869059 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
19869081 AT
1 AT
19869083 TCATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:19869097 original size:34 final size:33
Alignment explanation
Indices: 19868948--19869229 Score: 125
Period size: 34 Copynumber: 9.0 Consensus size: 33
19868938 CGTTCATCTC
*
19868948 ATTAAGTTATGTAATTTATGTATAATATTAATGT
1 ATTAAGTTATGTAAGTTATGTATAATATTAAT-T
* * * *
19868982 AAGTTATGTAAGTTGTAAGTTATGTA-AGTTATGTATAAT
1 -A-TTAAGTTA--TGTAAGTTATGTATA-ATAT-TA-ATT
**
19869021 ATTAA-TTAACTAAGTTATG--TAAT-TT-ATGT
1 ATTAAGTTATGTAAGTTATGTATAATATTAAT-T
* * *
19869050 ATAATATTAATGTAAGTTATGTATAATATTAATT
1 ATTA-AGTTATGTAAGTTATGTATAATATTAATT
*
19869084 CATTAAGTTATGTAA--T-T-TAT-GTA-TAA-T
1 -ATTAAGTTATGTAAGTTATGTATAATATTAATT
19869111 ATT-A---ATGTAAGTTATGTATAATATTAATT
1 ATTAAGTTATGTAAGTTATGTATAATATTAATT
*
19869140 AATTAAGTTATGTAA--T-T-TAT-GTA-TAA-T
1 -ATTAAGTTATGTAAGTTATGTATAATATTAATT
19869167 ATT-A---ATGTAAGTTATGTATAATATTAATT
1 ATTAAGTTATGTAAGTTATGTATAATATTAATT
* *
19869196 ATTTAAGTTATGTAATTTATGTATAATACTAATT
1 A-TTAAGTTATGTAAGTTATGTATAATATTAATT
19869230 TATGTATAAT
Statistics
Matches: 184, Mismatches: 24, Indels: 79
0.64 0.08 0.28
Matches are distributed among these distances:
22 12 0.07
24 2 0.01
25 4 0.02
26 12 0.07
27 6 0.03
28 13 0.07
29 11 0.06
30 13 0.07
31 16 0.09
32 3 0.02
33 5 0.03
34 49 0.27
35 6 0.03
36 8 0.04
37 4 0.02
38 16 0.09
39 3 0.02
40 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (33 bp):
ATTAAGTTATGTAAGTTATGTATAATATTAATT
Found at i:19869118 original size:22 final size:22
Alignment explanation
Indices: 19869093--19869143 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
19869083 TCATTAAGTT
19869093 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
19869115 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
19869137 AT-TAATT
1 ATGTAATT
19869144 AAGTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:19869174 original size:22 final size:22
Alignment explanation
Indices: 19869149--19869194 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
19869139 TAATTAAGTT
*
19869149 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
19869171 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
19869193 AT
1 AT
19869195 TATTTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:19870031 original size:24 final size:26
Alignment explanation
Indices: 19869977--19870032 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
19869967 AATCCTGGAA
*
19869977 AAAAAAGACAGAAATACATTAATCCC
1 AAAAAAGACAGAAATACATTAAACCC
* * *
19870003 GAAAAA-ACAGAAGTA-ATTAAAGCC
1 AAAAAAGACAGAAATACATTAAACCC
19870027 AAAAAA
1 AAAAAA
19870033 CTAAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 12 0.48
25 8 0.32
26 5 0.20
ACGTcount: A:0.62, C:0.14, G:0.11, T:0.12
Consensus pattern (26 bp):
AAAAAAGACAGAAATACATTAAACCC
Found at i:19870544 original size:15 final size:15
Alignment explanation
Indices: 19870524--19870557 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
19870514 CATCAATTGC
19870524 AAGACAGCTAGAAAA
1 AAGACAGCTAGAAAA
19870539 AAGACAGCTAGAAAA
1 AAGACAGCTAGAAAA
19870554 AAGA
1 AAGA
19870558 GGTATATATG
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:0.62, C:0.12, G:0.21, T:0.06
Consensus pattern (15 bp):
AAGACAGCTAGAAAA
Found at i:19870794 original size:11 final size:11
Alignment explanation
Indices: 19870780--19870816 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
19870770 TTGATACTAC
*
19870780 ATTATAATGAA
1 ATTATAATAAA
*
19870791 ATTATAATCAA
1 ATTATAATAAA
19870802 ATTATAATAAA
1 ATTATAATAAA
19870813 ATTA
1 ATTA
19870817 GAAAAGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
ATTATAATAAA
Found at i:19872147 original size:8 final size:10
Alignment explanation
Indices: 19872124--19872160 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
19872114 TAATAACTAT
19872124 ATATATATCC
1 ATATATATCC
*
19872134 ATATATATTC
1 ATATATATCC
19872144 ATATATATCC
1 ATATATATCC
19872154 ATATATA
1 ATATATA
19872161 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:19872842 original size:8 final size:10
Alignment explanation
Indices: 19872819--19872855 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
19872809 TAATAACTAT
19872819 ATATATATCC
1 ATATATATCC
*
19872829 ATATATATTC
1 ATATATATCC
19872839 ATATATATCC
1 ATATATATCC
19872849 ATATATA
1 ATATATA
19872856 AGTAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:19873725 original size:40 final size:40
Alignment explanation
Indices: 19873668--19873747 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
19873658 ATGACCTTTA
*
19873668 AAGAAATGGCGCTGTTTAAATTAATTTTAAGTCACATTTG
1 AAGAAATGGCGCCGTTTAAATTAATTTTAAGTCACATTTG
19873708 AAGAAATGGCGCCGTTTAAATTAATTTTAAGTCACATTTG
1 AAGAAATGGCGCCGTTTAAATTAATTTTAAGTCACATTTG
19873748 CGGCGTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (40 bp):
AAGAAATGGCGCCGTTTAAATTAATTTTAAGTCACATTTG
Found at i:19875392 original size:83 final size:81
Alignment explanation
Indices: 19875295--19875515 Score: 250
Period size: 82 Copynumber: 2.7 Consensus size: 81
19875285 GCGCTTCGGC
* * * * *
19875295 AAAAAAGCCGCTAAAGGTA-AATGCATTCGCGGCGCTTACCTATAAAACGCCGCTAAAAGCCAGA
1 AAAAACGCCGCTAAAGATACAA--CATTAGCGGCGCTTA-CAAAAAAACGCCGCTAAAAGCCAGA
*
19875359 GCATTAGTGGCGCTCAGAT
63 GCATTAGTGGCGCTCAAAT
* * *
19875378 AAAAACGCCACTAAAGATACTAACATTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGGCCAGAGC
1 AAAAACGCCGCTAAAGATAC-AACATTAGCGGCGCTTACAAAAAAACGCCGCTAAAAGCCAGAGC
*
19875443 ATTAGTGGCTCTCAAAT
65 ATTAGTGGCGCTCAAAT
* *
19875460 AAAAACGCCGCTAAAGAT-CGGACCATTAGCGGCGC-TAAAATAAAAACGCCGCTAAA
1 AAAAACGCCGCTAAAGATAC--AACATTAGCGGCGCTTACAA-AAAAACGCCGCTAAA
19875516 GGTTTAAAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
81 5 0.04
82 83 0.69
83 30 0.25
85 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGATACAACATTAGCGGCGCTTACAAAAAAACGCCGCTAAAAGCCAGAGCA
TTAGTGGCGCTCAAAT
Found at i:19875405 original size:41 final size:40
Alignment explanation
Indices: 19875338--19875516 Score: 166
Period size: 41 Copynumber: 4.4 Consensus size: 40
19875328 GCTTACCTAT
* * *
19875338 AAAACGCCGCTAAA-AGCCAGAGCATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGATCCA-A-CATTAGCGGCGCTCAAATA
* * *
19875379 AAAACGCCACTAAAGATACTAACATTAGCGGCGCTTAGAA-A
1 AAAACGCCGCTAAAGAT-CCAACATTAGCGGCGCTCA-AATA
* * *
19875420 AAAACGCCGCTAAAG-GCCAGAGCATTAGTGGCTCTCAAATA
1 AAAACGCCGCTAAAGATCCA-A-CATTAGCGGCGCTCAAATA
* * *
19875461 AAAACGCCGCTAAAGATCGGACCATTAGCGGCGCTAAAATA
1 AAAACGCCGCTAAAGATC-CAACATTAGCGGCGCTCAAATA
19875502 AAAACGCCGCTAAAG
1 AAAACGCCGCTAAAG
19875517 GTTTAAAAAT
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 100 0.89
42 4 0.04
43 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCCAACATTAGCGGCGCTCAAATA
Found at i:19875445 original size:82 final size:82
Alignment explanation
Indices: 19875338--19875517 Score: 265
Period size: 82 Copynumber: 2.2 Consensus size: 82
19875328 GCTTACCTAT
* * *
19875338 AAAACGCCGCTAAAAGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATAC-TAAC
1 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAAATAAAAACGCCACTAAAGAT-CGGAAC
*
19875402 ATTAGCGGCGCTTAGAA-A
65 ATTAGCGGCGC-TAAAATA
* * *
19875420 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCTCTCAAATAAAAACGCCGCTAAAGATCGGACCA
1 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAAATAAAAACGCCACTAAAGATCGGAACA
19875485 TTAGCGGCGCTAAAATA
66 TTAGCGGCGCTAAAATA
19875502 AAAACGCCGCTAAAGG
1 AAAACGCCGCTAAAGG
19875518 TTTAAAAATC
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
81 5 0.06
82 84 0.94
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (82 bp):
AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAAATAAAAACGCCACTAAAGATCGGAACA
TTAGCGGCGCTAAAATA
Found at i:19887195 original size:4 final size:4
Alignment explanation
Indices: 19887179--19887210 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
19887169 ATCAGATCAA
*
19887179 AAAT AAAT GAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
19887211 CGAAGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:19897166 original size:44 final size:44
Alignment explanation
Indices: 19897093--19897202 Score: 105
Period size: 44 Copynumber: 2.5 Consensus size: 44
19897083 GCTTATCGTC
* * * * * *
19897093 TTGCGCTTTAGTGCTCACTGTTTCACACTTTGGTGCTTA-TCGTT
1 TTGCACTTTGGTGCTTACTGTTTCACACTTCGATGCTTAGT-GAT
* * **
19897137 TTGTAGTTTGGTGCTTACTGTTTTGCACTTCGATGCTTAGTGAT
1 TTGCACTTTGGTGCTTACTGTTTCACACTTCGATGCTTAGTGAT
*
19897181 TTGCACTTTGGTGCCTACTGTT
1 TTGCACTTTGGTGCTTACTGTT
19897203 CTTTTAGTGC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
44 51 0.98
45 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (44 bp):
TTGCACTTTGGTGCTTACTGTTTCACACTTCGATGCTTAGTGAT
Found at i:19897173 original size:22 final size:22
Alignment explanation
Indices: 19897148--19897202 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
19897138 TGTAGTTTGG
19897148 TGCTTACTGTTTTGCACTTCGA
1 TGCTTACTGTTTTGCACTTCGA
* * * *
19897170 TGCTTAGTGATTTGCACTTTGG
1 TGCTTACTGTTTTGCACTTCGA
*
19897192 TGCCTACTGTT
1 TGCTTACTGTT
19897203 CTTTTAGTGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (22 bp):
TGCTTACTGTTTTGCACTTCGA
Found at i:19902961 original size:72 final size:74
Alignment explanation
Indices: 19902872--19903049 Score: 175
Period size: 72 Copynumber: 2.4 Consensus size: 74
19902862 CTGTATAACG
* * ** *
19902872 GGAAGCTCA-TAAGAGCCAT-AATCGGGAAGCTCATGTGAGTCAATAACAGGTAGCTCTGAAGAG
1 GGAAGCTCACAAAGAGCCATAAATCGGGAAGCTCAAGCAAG-CAATAACAGGAAGCTCTGAAGAG
19902935 CCATTA-ACA
65 CCATTACACA
* * * * * * * *
19902944 GGAAGCTC-CAGATAGCCATAAATCGGAAAGTTCAAGCAAGCCATATCAGGAAGCTTTGGAGAGC
1 GGAAGCTCACAAAGAGCCATAAATCGGGAAGCTCAAGCAAGCAATAACAGGAAGCTCTGAAGAGC
*
19903008 CATTACTCA
66 CATTACACA
* *
19903017 GGAAGCTCACAAAGAGCCTTCAATCGGGAAGCT
1 GGAAGCTCACAAAGAGCCATAAATCGGGAAGCT
19903050 AACGAAGAGC
Statistics
Matches: 82, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
72 39 0.48
73 25 0.30
74 18 0.22
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (74 bp):
GGAAGCTCACAAAGAGCCATAAATCGGGAAGCTCAAGCAAGCAATAACAGGAAGCTCTGAAGAGC
CATTACACA
Found at i:19904097 original size:5 final size:5
Alignment explanation
Indices: 19904089--19904140 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
19904079 TATTATACAT
19904089 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
19904139 TA
1 TA
19904141 CTTAAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:19905095 original size:45 final size:45
Alignment explanation
Indices: 19905028--19905117 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
19905018 ATAAACCCTC
*
19905028 GATTTGGATCCTCATTCTTAGACCCTCGAAATCGCTTAAGGTGTT
1 GATTTGGATCCTCATTCATAGACCCTCGAAATCGCTTAAGGTGTT
*
19905073 GATTTGGATCCTTATTCATAGACCCTCGAAATCGCTTAAGGTGTT
1 GATTTGGATCCTCATTCATAGACCCTCGAAATCGCTTAAGGTGTT
19905118 CATAGACCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (45 bp):
GATTTGGATCCTCATTCATAGACCCTCGAAATCGCTTAAGGTGTT
Found at i:19905129 original size:29 final size:29
Alignment explanation
Indices: 19905087--19905146 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
19905077 TGGATCCTTA
19905087 TTCATAGACCCTCGAAATCGCTTAAGGTG
1 TTCATAGACCCTCGAAATCGCTTAAGGTG
*
19905116 TTCATAGACCCTCGAAATTGCTTAAGGTG
1 TTCATAGACCCTCGAAATCGCTTAAGGTG
19905145 TT
1 TT
19905147 TATTAGGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (29 bp):
TTCATAGACCCTCGAAATCGCTTAAGGTG
Found at i:19906901 original size:20 final size:21
Alignment explanation
Indices: 19906871--19906910 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19906861 TCTTCCTTAG
19906871 AAGGTGGATATCGCGATACCC
1 AAGGTGGATATCGCGATACCC
*
19906892 AAGG-GGATATCGTGATACC
1 AAGGTGGATATCGCGATACC
19906911 ACTGAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
AAGGTGGATATCGCGATACCC
Found at i:19914686 original size:31 final size:31
Alignment explanation
Indices: 19914626--19914685 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
19914616 AAAAATTTTT
**
19914626 AGAATTATTTTTAATAATTTTTTAAAAAATC
1 AGAATTATTTTTAATAATAATTTAAAAAATC
*
19914657 AGAATTATGTTTTAATTATAATTTAAAAA
1 AGAATTAT-TTTTAATAATAATTTAAAAA
19914686 TTAAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (31 bp):
AGAATTATTTTTAATAATAATTTAAAAAATC
Found at i:19915215 original size:17 final size:16
Alignment explanation
Indices: 19915172--19915215 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
19915162 GACTCTATTA
19915172 AATAAATAATAAAAAAT
1 AATAAA-AATAAAAAAT
*
19915189 AATAAGAATACAAAAAT
1 AATAAAAATA-AAAAAT
*
19915206 ATTAAAAATA
1 AATAAAAATA
19915216 TGGTTCAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AATAAAAATAAAAAAT
Found at i:19920031 original size:20 final size:20
Alignment explanation
Indices: 19920001--19920043 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
19919991 TTGGATTGTT
19920001 ATTTAATTATTTT-TTATTA
1 ATTTAATTATTTTATTATTA
*
19920020 ATTTACATTATTTTATTGTTA
1 ATTTA-ATTATTTTATTATTA
19920041 ATT
1 ATT
19920044 ATGGATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTAATTATTTTATTATTA
Found at i:19923320 original size:20 final size:19
Alignment explanation
Indices: 19923273--19923325 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
19923263 TTAAAGGGGT
** *
19923273 AATTAAATCAATTTGATTA
1 AATTAAATCAAAATGAATA
19923292 AATTCAAATCAAAATGAATA
1 AATT-AAATCAAAATGAATA
19923312 GAATTAAAT-AAAAT
1 -AATTAAATCAAAAT
19923326 CAAGATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 9 0.31
20 16 0.55
21 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.32
Consensus pattern (19 bp):
AATTAAATCAAAATGAATA
Found at i:19924945 original size:21 final size:21
Alignment explanation
Indices: 19924912--19924951 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19924902 GGGGAAAAGT
*
19924912 GGAAAGAGTAAAAGTTTTGAA
1 GGAAAGAGTAAAAGGTTTGAA
19924933 GGAAA-AGTAAAAAGGTTTG
1 GGAAAGAGT-AAAAGGTTTG
19924952 GGAGTTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (21 bp):
GGAAAGAGTAAAAGGTTTGAA
Found at i:19924946 original size:29 final size:29
Alignment explanation
Indices: 19924891--19924946 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19924881 GGGAGGGGAT
** **
19924891 TAAAAGTTTTGGGGGAAAAGTGGAAAGAG
1 TAAAAGTTTTGAAGGAAAAGTAAAAAGAG
19924920 TAAAAGTTTTGAAGGAAAAGTAAAAAG
1 TAAAAGTTTTGAAGGAAAAGTAAAAAG
19924947 GTTTGGGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (29 bp):
TAAAAGTTTTGAAGGAAAAGTAAAAAGAG
Found at i:19925003 original size:9 final size:9
Alignment explanation
Indices: 19924989--19925016 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19924979 TATAGTTTGA
19924989 TATTCGAAT
1 TATTCGAAT
19924998 TATTCGAAT
1 TATTCGAAT
19925007 TATTCGAAT
1 TATTCGAAT
19925016 T
1 T
19925017 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19938972 original size:41 final size:43
Alignment explanation
Indices: 19938870--19939026 Score: 151
Period size: 44 Copynumber: 3.7 Consensus size: 43
19938860 CATGGCAGAT
* * *
19938870 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGTC-CAAAC
* * * *
19938914 ATTATCTCTCTGAAGTTGCAGTAGAGCAGATCACA-T-CAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGTCCAAAC
** *
19938955 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CTATTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGTCCA--AA-C
*
19939000 C-TATCTCCCTGAAGTTACAGTGGAGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA
19939027 AATTAAAACG
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 33 0.35
42 1 0.01
43 1 0.01
44 56 0.60
45 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGTCCAAAC
Found at i:19939013 original size:85 final size:85
Alignment explanation
Indices: 19938870--19939026 Score: 210
Period size: 85 Copynumber: 1.8 Consensus size: 85
19938860 CATGGCAGAT
* * * *
19938870 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCGCAAATATTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGCAAATACTATCTCCCTGAAGTTACAG
19938935 TAGAGCAGATCACATCAAAC
66 TAGAGCAGATCACATCAAAC
* * *
19938955 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-C-TATTAATCCTATCTCCCTGAAGTTAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGCA--AATACTATCTCCCTGAAGTTAC
*
19939018 AGTGGAGCA
64 AGTAGAGCA
19939027 AATTAAAACG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.02
84 1 0.02
85 60 0.97
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (85 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGCAAATACTATCTCCCTGAAGTTACAG
TAGAGCAGATCACATCAAAC
Found at i:19939059 original size:44 final size:44
Alignment explanation
Indices: 19938957--19939047 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
19938947 CATCAAACCT
* * * * * *
19938957 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAATCC
1 TATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACGATGAATCC
19939001 TATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACGATGAATCC
1 TATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACGATGAATCC
19939045 TAT
1 TAT
19939048 ACCTCTGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACGATGAATCC
Found at i:19939390 original size:42 final size:42
Alignment explanation
Indices: 19939328--19939407 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
19939318 GTGAGATCGG
* *
19939328 GTGAGGGTCTTCTTCATTCAGCCTTTGGGCCCAGAAGGAGGC
1 GTGAGGGTCTTATTCATTCAGCCTTTAGGCCCAGAAGGAGGC
** *
19939370 GTGAGGGTCTTATTTTTTCAGTCTTTAGGCCCAGAAGG
1 GTGAGGGTCTTATTCATTCAGCCTTTAGGCCCAGAAGG
19939408 CTCGACCTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.31
Consensus pattern (42 bp):
GTGAGGGTCTTATTCATTCAGCCTTTAGGCCCAGAAGGAGGC
Found at i:19946247 original size:27 final size:27
Alignment explanation
Indices: 19946216--19946271 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
19946206 AAAGAATGAT
* *
19946216 AATTATCTTTTATTGAAAGCTTGGAGG
1 AATTATCATTTATTCAAAGCTTGGAGG
19946243 AATTATCATTTATTCAAAGCTTGGAGG
1 AATTATCATTTATTCAAAGCTTGGAGG
19946270 AA
1 AA
19946272 ATTTCTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
AATTATCATTTATTCAAAGCTTGGAGG
Found at i:19956449 original size:46 final size:46
Alignment explanation
Indices: 19956373--19956557 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
19956363 CATGGAAAAG
*
19956373 TGTGAAACGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
* ** *
19956419 TGTGAAAAGTAGGTATGGTGTTTCTGTGAAGAAAACCATACTAAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
* *
19956465 TGTGAGAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
* *
19956511 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
19956557 T
1 T
19956558 ATAGCATTGT
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
Found at i:19964458 original size:42 final size:42
Alignment explanation
Indices: 19964387--19964499 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
19964377 TTTAGCTCTC
* * *
19964387 ACGAGCTTCTGTTTAACTCATATGAGTTTCCATTCAGCTATT
1 ACGAGCTTCTGTTTAACCCTTATGGGTTTCCATTCAGCTATT
** ** *
19964429 TTGAGCTTCTGTTTAACCCTTATGGGTTTCTGTTCAGCTCTT
1 ACGAGCTTCTGTTTAACCCTTATGGGTTTCCATTCAGCTATT
** *
19964471 ACGAGCTTCCATTCAACCCTTATGGGTTT
1 ACGAGCTTCTGTTTAACCCTTATGGGTTT
19964500 TTGTTTATCT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (42 bp):
ACGAGCTTCTGTTTAACCCTTATGGGTTTCCATTCAGCTATT
Found at i:19964519 original size:42 final size:41
Alignment explanation
Indices: 19964441--19964542 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
19964431 GAGCTTCTGT
* *
19964441 TTAACCCTTATGGGTTTCTGTTCAGCTCTTACGAGCTTCCA
1 TTAACCCTTATGGGTTTTTGTTCAGCTCTCACGAGCTTCCA
* * * *
19964482 TTCAACCCTTATGGGTTTTTGTTTATCTCTCATGAGCTTCTA
1 TT-AACCCTTATGGGTTTTTGTTCAGCTCTCACGAGCTTCCA
* *
19964524 TTAAGCCTT-TGGGCTTTTG
1 TTAACCCTTATGGGTTTTTG
19964543 AAAACGATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
40 9 0.17
41 8 0.15
42 35 0.67
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (41 bp):
TTAACCCTTATGGGTTTTTGTTCAGCTCTCACGAGCTTCCA
Found at i:19972236 original size:66 final size:66
Alignment explanation
Indices: 19972130--19972272 Score: 277
Period size: 66 Copynumber: 2.2 Consensus size: 66
19972120 CACGGATCTC
19972130 CAACACACCAATTGACTCATAGAGTCGAACATATCTCAAAAAGTTAAGCATAAAGCTAACACTCT
1 CAACACACCAATTGACTCATAGAGTCGAACATATCTCAAAAAGTTAAGCATAAAGCTAACACTCT
19972195 T
66 T
*
19972196 CAACACACCAATTGACTCATAGAGTCGAACATATCTCAAAAAGTTAAGTATAAAGCTAACACTCT
1 CAACACACCAATTGACTCATAGAGTCGAACATATCTCAAAAAGTTAAGCATAAAGCTAACACTCT
19972261 T
66 T
19972262 CAACACACCAA
1 CAACACACCAA
19972273 ACATGTCCCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22
Consensus pattern (66 bp):
CAACACACCAATTGACTCATAGAGTCGAACATATCTCAAAAAGTTAAGCATAAAGCTAACACTCT
T
Found at i:19976730 original size:51 final size:50
Alignment explanation
Indices: 19976617--19976895 Score: 258
Period size: 51 Copynumber: 5.5 Consensus size: 50
19976607 TGGTCACGTT
* * * * * * * *
19976617 TGTAGTATTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGGTCGCATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA-GTTCGATCACATG
* *
19976667 TGTAGTACTATGTGCAGGCTACTATGCGTATCAGATAGCTTCGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAG-TTCGATCACATG
* * * * * * *
19976718 TGTAGTACTATGTGTAGGCTACTACGTGTACCAGGAT-GATAGGTCGCATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACCA-GATAGTTCGATCACATG
* *
19976768 TGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAG-TTCGATCACATG
* * * * *
19976819 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGT--TCGATCACATG
*
19976870 TGTAGTACTATGTGCATGCTACTATG
1 TGTAGTACTATGTGCAGGCTACTATG
19976896 TGAATCCGCA
Statistics
Matches: 187, Mismatches: 35, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
49 3 0.02
50 69 0.37
51 111 0.59
52 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (50 bp):
TGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTTCGATCACATG
Found at i:19976730 original size:101 final size:101
Alignment explanation
Indices: 19976610--19976895 Score: 457
Period size: 101 Copynumber: 2.8 Consensus size: 101
19976600 AAAGTGATGG
* *
19976610 TCACGTTTGTAGTATTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
*
19976675 TATGTGCAGGCTACTATGCGTATCAGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
*
19976711 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGGATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
*
19976776 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
* * * *
19976812 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
*
19976876 ACTATGTGCATGCTACTATG
64 ACTATGTGCAGGCTACTATG
19976896 TGAATCCGCA
Statistics
Matches: 172, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 134 0.78
102 34 0.20
103 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
Found at i:19976897 original size:26 final size:26
Alignment explanation
Indices: 19976817--19976897 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
19976807 TTCGATCACG
*
19976817 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
19976843 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
19976868 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
19976894 TGTG
1 TGTG
19976898 AATCCGCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:19977044 original size:85 final size:85
Alignment explanation
Indices: 19976901--19977116 Score: 353
Period size: 85 Copynumber: 2.6 Consensus size: 85
19976891 CTATGTGAAT
* *
19976901 CCGCATCATTGAATATAAATGTGGTTGCTAAGTGCTGGTTCCACCGTATCCTTAACTGTGAAAGG
1 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAACTGTGAAAGG
19976966 GGTTGCTATGTGCTGATTCC
66 GGTTGCTATGTGCTGATTCC
*
19976986 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGACTGTGAAAGG
1 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAACTGTGAAAGG
19977051 GGTTGCTATGTGCTGATTCC
66 GGTTGCTATGTGCTGATTCC
** * * *
19977071 CCATATCATTTATTAT-AAGGTGGTTGCTAAGTGTTGATTCCACCGT
1 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
19977117 GTAACGGTTA
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 29 0.24
85 94 0.76
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (85 bp):
CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAACTGTGAAAGG
GGTTGCTATGTGCTGATTCC
Found at i:19977064 original size:43 final size:43
Alignment explanation
Indices: 19976905--19977116 Score: 220
Period size: 43 Copynumber: 5.0 Consensus size: 43
19976895 GTGAATCCGC
* * * *
19976905 ATCATTGAATATAAATGTGGTTGCTAAGTGCTGGTTCCACCGT
1 ATCATTGACTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* * * *
19976948 ATCCTTAACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-CCGC
1 ATCATTGACTGT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* *
19976990 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGACTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* * *
19977033 ATCCTTGACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-CCAT
1 ATCATTGACTGT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* *
19977075 ATCATTTA-T-TATAAGGTGGTTGCTAAGTGTTGATTCCACCGT
1 ATCATTGACTGTA-AAGGTGGTTGCTAAGTGCTGATTCCACCGT
19977117 GTAACGGTTA
Statistics
Matches: 138, Mismatches: 24, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
39 1 0.01
40 5 0.04
41 24 0.17
42 42 0.30
43 57 0.41
44 9 0.07
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
ATCATTGACTGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
Found at i:19978612 original size:25 final size:25
Alignment explanation
Indices: 19978577--19978630 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
19978567 ACACACCACA
*
19978577 GCTCTCTTGAGCTTCCCGATACTTG
1 GCTCTCATGAGCTTCCCGATACTTG
*
19978602 GCTCTCATGAGCTTCCCGATATTTG
1 GCTCTCATGAGCTTCCCGATACTTG
19978627 GCTC
1 GCTC
19978631 CTAAGAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.35
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATACTTG
Found at i:19978638 original size:25 final size:25
Alignment explanation
Indices: 19978585--19978641 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
19978575 CAGCTCTCTT
*
19978585 GAGCTTCCCGATACTTGGCTCTCAT
1 GAGCTTCCCGATACTTGGCTCTCAA
*
19978610 GAGCTTCCCGATATTTGGCTC-CTAA
1 GAGCTTCCCGATACTTGGCTCTC-AA
19978635 GAGCTTC
1 GAGCTTC
19978642 TCAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGATACTTGGCTCTCAA
Found at i:19978679 original size:50 final size:49
Alignment explanation
Indices: 19978602--19978714 Score: 118
Period size: 50 Copynumber: 2.3 Consensus size: 49
19978592 CCGATACTTG
* * * *
19978602 GCTCTCATGAGCTTCCCGATATTTGGCTCCTAAGAGCTTCTCAATATATA
1 GCTCACATGAGCTTCCCGATATATGGCTCCGAAGAGCTTCTC-ATATACA
** * ** *
19978652 GCTCACATGAGCTTCTTGTTATATGGCTTGGAAGAGCTTCTCATTTACA
1 GCTCACATGAGCTTCCCGATATATGGCTCCGAAGAGCTTCTCATATACA
*
19978701 GCTCATATGAGCTT
1 GCTCACATGAGCTT
19978715 ACATGCATAT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
49 18 0.35
50 34 0.65
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (49 bp):
GCTCACATGAGCTTCCCGATATATGGCTCCGAAGAGCTTCTCATATACA
Found at i:19984347 original size:335 final size:334
Alignment explanation
Indices: 19983738--19984391 Score: 1130
Period size: 335 Copynumber: 2.0 Consensus size: 334
19983728 CCATAACCGT
19983738 CCACTAGCATCAGACTTTTACTAACACACAAACACTTACACGGCATCAAGCAAAAATATATCCCC
1 CCACTAGCATCAGACTTTTACTAACACACAAACACTTACACGGCATCAAGCAAAAATATATCCCC
* * *
19983803 CTTGCTAACGCAAGGACTTGAGCTCCAGTCCTCCTACATGCCAACTCATGCTTTAGCCACCAGAC
66 CTTGCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGATTTAGCCACCAGAC
* *
19983868 CAGCAGTCCCATTCTGACATATTTTATCAACATTTATTTATAAGCCTATTGATTAGAGATAAGGG
131 CAGCAGACCCATTCTGACATATTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGGG
* * *
19983933 TTTATTCATTTAAAAGCAAAAAAAATTTCCCAAGCTAAGGTTTAAACTCAAGACTTCTCAAACAC
196 TTTATTCATTTAAAAACAAAAAAAAATTCCCAAGCTAAGGTTTAAACTCAAGACCTCTCAAACAC
19983998 TCCCAAAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATACACAGAAACAGATAAA
261 TCCCAAAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATACACAGAAACAGATAAA
19984063 CACACTTAA
326 CACACTTAA
19984072 CCACTAGCATCAGACTTTTACTAACACACAAACACTTACACGGCATCAAG-ATAAAATATATCCC
1 CCACTAGCATCAGACTTTTACTAACACACAAACACTTACACGGCATCAAGCA-AAAATATATCCC
* *
19984136 CCATTGCTAACGCAGGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGATTTAGCTACCAG
65 CC-TTGCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGATTTAGCCACCAG
19984201 ACCAGCAGACCCATTCTGACATATTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAG
129 ACCAGCAGACCCATTCTGACATATTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAG
* * *
19984266 GGTTTATTCATTTAAAAACAAAAAAAAATTCCCAAGCTAAGGTTTGAACTCAGGACCTCTCAGAC
194 GGTTTATTCATTTAAAAACAAAAAAAAATTCCCAAGCTAAGGTTTAAACTCAAGACCTCTCAAAC
* * * *
19984331 ACTCCCAGAACACTTAACCACTGAAGTAGATACATAATTATGTCATAAATACATAGAAACA
259 ACTCCCAAAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATACACAGAAACA
19984392 AATATACAAA
Statistics
Matches: 301, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
333 1 0.00
334 64 0.21
335 236 0.78
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (334 bp):
CCACTAGCATCAGACTTTTACTAACACACAAACACTTACACGGCATCAAGCAAAAATATATCCCC
CTTGCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGATTTAGCCACCAGAC
CAGCAGACCCATTCTGACATATTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGGG
TTTATTCATTTAAAAACAAAAAAAAATTCCCAAGCTAAGGTTTAAACTCAAGACCTCTCAAACAC
TCCCAAAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATACACAGAAACAGATAAA
CACACTTAA
Found at i:19989828 original size:41 final size:41
Alignment explanation
Indices: 19989783--19989894 Score: 161
Period size: 41 Copynumber: 2.7 Consensus size: 41
19989773 AATTTATATT
* **
19989783 AATGTATCAGGCTTTATGCCTAGCAGGCTTTATGTCGGTGA
1 AATGTATCAGGCTTTATGCCTAGCAGGCTTCATACCGGTGA
*
19989824 AATGTATCAGGCTTTATGCCTAGCAGGCTTCATACCGGTGT
1 AATGTATCAGGCTTTATGCCTAGCAGGCTTCATACCGGTGA
***
19989865 ACCCTATCAGGCTTTATGCCTAGCAGGCTT
1 AATGTATCAGGCTTTATGCCTAGCAGGCTT
19989895 GGTGCCATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.32
Consensus pattern (41 bp):
AATGTATCAGGCTTTATGCCTAGCAGGCTTCATACCGGTGA
Found at i:19992881 original size:16 final size:16
Alignment explanation
Indices: 19992860--19992890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19992850 CTATGTATGC
*
19992860 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
19992876 AAAATACAAAAGACA
1 AAAATACAAAAGACA
19992891 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:20003456 original size:14 final size:14
Alignment explanation
Indices: 20003439--20003472 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20003429 GTTGCAGTTA
20003439 AAAAGTTGTTTTAG
1 AAAAGTTGTTTTAG
* *
20003453 AAAAATTGTTTTTG
1 AAAAGTTGTTTTAG
20003467 AAAAGT
1 AAAAGT
20003473 ATGGTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (14 bp):
AAAAGTTGTTTTAG
Found at i:20004046 original size:23 final size:23
Alignment explanation
Indices: 20004027--20004068 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20004017 AAATAATATA
20004027 AATAAAT-T-ATTATTTTTAATT
1 AATAAATGTAATTATTTTTAATT
*
20004048 AATAATTGTAATTATTTTTAA
1 AATAAATGTAATTATTTTTAA
20004069 ATACGTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATAAATGTAATTATTTTTAATT
Found at i:20015475 original size:34 final size:34
Alignment explanation
Indices: 20015432--20015501 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
20015422 TATAATGCTA
20015432 TCTAGAAAGGAACTTTCTTTTTTGTCCTGTTCAT
1 TCTAGAAAGGAACTTTCTTTTTTGTCCTGTTCAT
20015466 TCTAGAAAGGAACTTTCTTTTTTGTCCTGTTCAT
1 TCTAGAAAGGAACTTTCTTTTTTGTCCTGTTCAT
20015500 TC
1 TC
20015502 AATCAACTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (34 bp):
TCTAGAAAGGAACTTTCTTTTTTGTCCTGTTCAT
Found at i:20021346 original size:3 final size:3
Alignment explanation
Indices: 20021340--20021366 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20021330 GTTGTTAACA
20021340 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
20021367 GTATGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20025041 original size:2 final size:2
Alignment explanation
Indices: 20025034--20025058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20025024 CAATATCCAA
20025034 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 A
20025059 AAGAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20028924 original size:14 final size:15
Alignment explanation
Indices: 20028906--20028940 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
20028896 TTTTTTAAAT
*
20028906 TATATTATTAATTTA
1 TATATTAATAATTTA
20028921 -ATATTAATAATTTA
1 TATATTAATAATTTA
20028935 TATATT
1 TATATT
20028941 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTAATAATTTA
Found at i:20032947 original size:22 final size:22
Alignment explanation
Indices: 20032914--20032969 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
20032904 ATTTCCTCTC
20032914 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
20032937 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
20032959 AATTCTCTCAA
1 AATTCTCTCAA
20032970 ATCCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:20034845 original size:18 final size:18
Alignment explanation
Indices: 20034819--20034853 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20034809 AGGTGCGTTT
*
20034819 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
20034837 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
20034854 TCATTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:20035366 original size:25 final size:25
Alignment explanation
Indices: 20035328--20035490 Score: 185
Period size: 25 Copynumber: 6.7 Consensus size: 25
20035318 TATTTTGATA
20035328 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
* * *
20035353 TTATTTGATTTAATAAAATTGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
*
20035378 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
20035403 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
** * *
20035428 TT-TTTCGA-GT--T-ATTTTGATA-
1 TTATTT-GATGTAATAAAATAGAAAT
*
20035448 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
*
20035473 TTATTTGATATAATAAAA
1 TTATTTGATGTAATAAAA
20035491 ACCCTAACCT
Statistics
Matches: 115, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
20 4 0.03
21 10 0.09
22 1 0.01
23 1 0.01
24 9 0.08
25 90 0.78
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAAT
Found at i:20035474 original size:70 final size:72
Alignment explanation
Indices: 20035328--20035490 Score: 226
Period size: 70 Copynumber: 2.2 Consensus size: 72
20035318 TATTTTGATA
*
20035328 TTATTTGATGTAATAAAATAGAAATTTATTTGATTTAATAAAATTGAAGTTTATTTGATGTAATA
1 TTATTTGATGTAATAAAATAGAAATTTATTTGAGTTAAT--AATTGAAG-TTATTTGATGTAATA
20035393 AAATAGAAGT
63 AAATAGAAGT
*
20035403 TTATTTGATGTAATAAAATAGAAATTT-TTTCGAGTT-AT-TTTGATA-TTATTTGATGTAATAA
1 TTATTTGATGTAATAAAATAGAAATTTATTT-GAGTTAATAATTGA-AGTTATTTGATGTAATAA
20035464 AATAGAAGT
64 AATAGAAGT
*
20035473 TTATTTGATATAATAAAA
1 TTATTTGATGTAATAAAA
20035491 ACCCTAACCT
Statistics
Matches: 83, Mismatches: 3, Indels: 9
0.87 0.03 0.09
Matches are distributed among these distances:
70 42 0.51
71 4 0.05
72 1 0.01
74 5 0.06
75 31 0.37
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (72 bp):
TTATTTGATGTAATAAAATAGAAATTTATTTGAGTTAATAATTGAAGTTATTTGATGTAATAAAA
TAGAAGT
Found at i:20035538 original size:23 final size:23
Alignment explanation
Indices: 20035486--20035776 Score: 140
Period size: 23 Copynumber: 12.0 Consensus size: 23
20035476 TTTGATATAA
20035486 TAAAAACCCTAACCTAATTTAACCT
1 TAAAAACCCTAACCTAATTTAA--T
20035511 T--AAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
20035532 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
* *
20035561 TAAAATCCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
20035583 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
20035606 TAAAAACCCTAAACC----TTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
* *
20035627 TAAAAACCTTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
*
20035649 TAAAAACCCTAACCTAATTTGA-
1 TAAAAACCCTAACCTAATTTAAT
**
20035671 TACAAAACCCTAACCTAAACCCTAAT
1 TA-AAAACCCTAACCT-AA-TTTAAT
20035697 TAAAAACCTTAACTCTAACCTAATTTAAT
1 TAAAAA-C----C-CTAACCTAATTTAAT
*
20035726 TAAAGACCCTAATCCTAACCTAATTTAAT
1 T-AA-A----AACCCTAACCTAATTTAAT
* *
20035755 TAAAAACCCTAAACTAAGTTAA
1 TAAAAACCCTAACCTAATTTAA
20035777 CAATGTTACA
Statistics
Matches: 211, Mismatches: 17, Indels: 78
0.69 0.06 0.25
Matches are distributed among these distances:
20 10 0.05
21 27 0.13
22 22 0.10
23 63 0.30
24 11 0.05
25 12 0.06
26 3 0.01
27 4 0.02
28 2 0.01
29 41 0.19
30 6 0.03
31 8 0.04
35 2 0.01
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.29
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:20035546 original size:29 final size:29
Alignment explanation
Indices: 20035513--20035766 Score: 127
Period size: 29 Copynumber: 9.1 Consensus size: 29
20035503 TTTAACCTTA
20035513 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
20035542 AACCCTAACCTAATTTAATTAAAATCCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
20035571 AAACCT----TAA-CT--TTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
20035593 -A-----ACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* * * **
20035616 AAACCTTAACTTAA--AAACCTTAAACCTTAACTTT
1 -AACCCTAACCTAATTTAA--TTAAA----AACCCT
*
20035650 AAAAACCCTAACCTAATTTGA-TACAAAACCCT
1 ---AACCCTAACCTAATTTAATTA-AAAACCCT
* *
20035682 AA-CCTAAACC----CTAATTAAAAACCTT
1 AACCCT-AACCTAATTTAATTAAAAACCCT
* *
20035707 AACTCTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
20035736 AATCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
20035765 AA
1 AA
20035767 ACTAAGTTAA
Statistics
Matches: 169, Mismatches: 25, Indels: 62
0.66 0.10 0.24
Matches are distributed among these distances:
20 3 0.02
21 2 0.01
22 10 0.06
23 11 0.07
24 1 0.01
25 19 0.11
26 4 0.02
28 5 0.03
29 79 0.47
30 10 0.06
32 4 0.02
34 4 0.02
35 2 0.01
36 14 0.08
38 1 0.01
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:20035640 original size:66 final size:65
Alignment explanation
Indices: 20035556--20035683 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 65
20035546 CTAACCTAAT
*
20035556 TTAATTAAAATCCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATTA-AAAACCCTAAAC
1 TTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAA-TACAAAACCCTAAAC
20035620 C
65 C
* *
20035621 TTAACTTAAAAACCTTAAACCTTAACTTTAAAAACCCTAACCTAATTTGATACAAAACCCTAA
1 TTAA-TTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAACCCTAA
20035684 CCTAAACCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
65 6 0.10
66 52 0.90
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (65 bp):
TTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAACCCTAAACC
Found at i:20035642 original size:45 final size:45
Alignment explanation
Indices: 20035542--20035688 Score: 171
Period size: 45 Copynumber: 3.3 Consensus size: 45
20035532 TAAAAACCCT
*
20035542 AACCCTAACCTAATTTAATTAAAATCCCTAAACCTTAACTTTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTTAAA
20035587 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAAC-TTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTTAAA
* * *
20035631 AACCTTAAACCTTAA-CT--TTAAAAACCCT-AACC-TAATTTGATACAA
1 AACCCT-AACC-TAATTTAATTAAAAACCCTAAACCTTAACTT--TA-AA
20035676 AACCCTAACCTAA
1 AACCCTAACCTAA
20035689 ACCCTAATTA
Statistics
Matches: 91, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
41 3 0.03
42 5 0.05
43 14 0.15
44 16 0.18
45 50 0.55
46 3 0.03
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.28
Consensus pattern (45 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTTAAA
Found at i:20035663 original size:21 final size:22
Alignment explanation
Indices: 20035560--20035660 Score: 127
Period size: 21 Copynumber: 4.6 Consensus size: 22
20035550 CCTAATTTAA
*
20035560 TTAAAATCCCTAAACCTTAACT
1 TTAAAAACCCTAAACCTTAACT
*
20035582 TTAAAAACCCT-AACC-TAATTT
1 TTAAAAACCCTAAACCTTAA-CT
20035603 AATTAAAAACCCTAAACCTTAAC-
1 --TTAAAAACCCTAAACCTTAACT
*
20035626 TTAAAAACCTTAAACCTTAACT
1 TTAAAAACCCTAAACCTTAACT
20035648 TTAAAAACCCTAA
1 TTAAAAACCCTAA
20035661 CCTAATTTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.04
21 25 0.37
22 22 0.32
23 11 0.16
24 4 0.06
25 3 0.04
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAAAAACCCTAAACCTTAACT
Found at i:20035709 original size:25 final size:24
Alignment explanation
Indices: 20035648--20035721 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 24
20035638 AACCTTAACT
** *
20035648 TTAAAAACCCTAAC-CTAATTTGA
1 TTAAAAACCCTAACTCTAACCTAA
20035671 -TACAAAACCCTAAC-CTAAACCCTAA
1 TTA-AAAACCCTAACTCT-AA-CCTAA
*
20035696 TTAAAAACCTTAACTCTAACCTAA
1 TTAAAAACCCTAACTCTAACCTAA
20035720 TT
1 TT
20035722 TAATTAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
22 2 0.05
23 13 0.31
24 9 0.21
25 14 0.33
26 4 0.10
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (24 bp):
TTAAAAACCCTAACTCTAACCTAA
Found at i:20035913 original size:116 final size:116
Alignment explanation
Indices: 20035773--20036126 Score: 618
Period size: 116 Copynumber: 3.1 Consensus size: 116
20035763 CTAAACTAAG
* * *
20035773 TTAACAATGTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
20035838 TAATTTTACATAATTTGATAATTTTGCTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
*
20035889 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
20035954 TAATTTTACATAATTTGATAATTTTACTAATCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* **
20036005 TTAATAATTTTACATTCACATAATGCTAGATTTGGAAAAATGTTTCAACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
20036070 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
20036121 TTAATA
1 TTAATA
20036127 CAATTTATCA
Statistics
Matches: 226, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 226 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (116 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:20036143 original size:17 final size:18
Alignment explanation
Indices: 20036102--20036143 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
20036092 TTTACTAACC
* *
20036102 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
20036120 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
20036137 ATTAATA
1 ATTAATA
20036144 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:20039449 original size:126 final size:126
Alignment explanation
Indices: 20039159--20039507 Score: 585
Period size: 126 Copynumber: 2.8 Consensus size: 126
20039149 AACATGCTAC
*
20039159 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCGAATAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
*
20039224 AGCAATTTTATACTATTTGCTCAGAAACGT-AAAAAAAAATTTATTTCTTACATGACCTAT
66 AGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTTATTTCTTACATGACCTAT
* *
20039284 TGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTTTTCTCAAATAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
* * * *
20039349 AGCGATTTTATACTATTTGCTCAGAAACGTCGAAAAAATAA-TTATTTCTTCCGTGATCTAT
66 AGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAAATTTATTTCTTACATGACCTAT
20039410 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
**
20039475 AGCGATTTTATACTATTTTATCAGAAACGTCAA
66 AGCGATTTTATACTATTTGCTCAGAAACGTCAA
20039508 CTCAAAATTA
Statistics
Matches: 210, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
125 93 0.44
126 109 0.52
127 8 0.04
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (126 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
AGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTTATTTCTTACATGACCTAT
Done.