Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold164
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: 2248410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 11 of 15
Found at i:1589654 original size:14 final size:14
Alignment explanation
Indices: 1589635--1589666 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1589625 AATTGATTAA
1589635 ATTTGATTAAATCG
1 ATTTGATTAAATCG
*
1589649 ATTTGATTAATTCG
1 ATTTGATTAAATCG
1589663 ATTT
1 ATTT
1589667 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (14 bp):
ATTTGATTAAATCG
Found at i:1590259 original size:21 final size:21
Alignment explanation
Indices: 1590225--1590264 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1590215 TATTTTTATT
1590225 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1590246 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
1590265 AGTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1595163 original size:507 final size:507
Alignment explanation
Indices: 1594210--1595221 Score: 1787
Period size: 507 Copynumber: 2.0 Consensus size: 507
1594200 TACAACATCG
*
1594210 TACTTTATATCTATTTGCTTGTTATGACTCTCACTTTTATCATTCTTAGATATCTGTCAAGAATT
1 TACTTTATATATATTTGCTTGTTATGACTCTCACTTTTATCATTCTTAGATATCTGTCAAGAATT
*
1594275 TCTAACTATAAACTTTATATCAAGTTTCATATAAAATTGATCATACAAATAAGGTTACCAATACT
66 TCTAACTATAAACTTTATATCAAGTTTAATATAAAATTGATCATACAAATAAGGTTACCAATACT
* *
1594340 AGACAATATGGAATACTTTTCATATACTTTTTTCCAAATTATTTGGAGATATTAGCTGAAACTGA
131 AGAAAATATGGAATACTTTTCATATACTTTTTTCCAAATCATTTGGAGATATTAGCTGAAACTGA
* * *
1594405 AATGATATCTTTTACAATTGATGCGTTGTATGTAAATATCTTTGTATCCTAAAAATCTTTCCAAA
196 AATAATATATTTTACAATTGATGCATTGTATGTAAATATCTTTGTATCCTAAAAATCTTTCCAAA
1594470 ACTCTTTTAATATTGGCCTCTTGAGATAGATTTAATATATTTTCAGACCTATCTCTATAAATCTT
261 ACTCTTTTAATATTGGCCTCTTGAGATAGATTTAATATATTTTCAGACCTATCTCTATAAATCTT
*
1594535 TATGCCTATAACATATAAGGCTTCACCTAAATCCTTTATATCAAAGTTTTGATAAAAAGATGATT
326 TATGCCTATAACATATAAGGCTTCACCTAAATCCTTTATATCAAAGTTTTGATAAAAAAATGATT
1594600 TCAATCAGGTAACAAAGCCAATCACTATTTACAAAGAAAATATCACCAACATATAGGACTAAAAT
391 TCAATCAGGTAACAAAGCCAATCACTATTTACAAAGAAAATATCACCAACATATAGGACTAAAAT
*
1594665 TTTAAACTTACTCCTACTAACTTCGAAGTATATATAATAATAAATAACATGA
456 TTTAAACTTACTCCTACTAACTTCAAAGTATATATAATAATAAATAACATGA
*
1594717 TACTTTATATATATTTGCTTGTTATGACTCTCACTTTTATCATTCTTAGATATCTGTCAAGCATT
1 TACTTTATATATATTTGCTTGTTATGACTCTCACTTTTATCATTCTTAGATATCTGTCAAGAATT
*
1594782 TCTAACTATAAACTTTATATCAAGTTTAATATAAAATTGATCATAC-AATAAGGTTACTAATACT
66 TCTAACTATAAACTTTATATCAAGTTTAATATAAAATTGATCATACAAATAAGGTTACCAATACT
* *
1594846 AGAAAATATGGAATACTTTTTATATACTCTTTTTCCAAATCATTTGGAGATATTAGCTTAAAC-G
131 AGAAAATATGGAATACTTTTCATATACT-TTTTTCCAAATCATTTGGAGATATTAGCTGAAACTG
1594910 AAAATAATATATTTTACAATTGATGCATTGTATGTAAATATCTTTGTATCCTAAAAATCTTTCCA
195 -AAATAATATATTTTACAATTGATGCATTGTATGTAAATATCTTTGTATCCTAAAAATCTTTCCA
* * *
1594975 AAATTCTTTTAATATTGGCTTCTTGAGATAGATTTAATATATTTTTAGACCTATCTCTATAAATC
259 AAACTCTTTTAATATTGGCCTCTTGAGATAGATTTAATATATTTTCAGACCTATCTCTATAAATC
1595040 TTTATGCCTATAACATATACA-GCTTCACCTAAATCCTTTATATCAAAGTTTTGATAAAAAAATG
324 TTTATGCCTATAACATATA-AGGCTTCACCTAAATCCTTTATATCAAAGTTTTGATAAAAAAATG
* *
1595104 ATTTCAATCATGTAACAAAGCCAATCACTATTTACAAAGAGAATATCACCAACATATAGGACTAA
388 ATTTCAATCAGGTAACAAAGCCAATCACTATTTACAAAGAAAATATCACCAACATATAGGACTAA
* * *
1595169 AATTTTGAACTTAGTCCTACTAACTTTAAAGTATATATAATAATAAATAACAT
453 AATTTTAAACTTACTCCTACTAACTTCAAAGTATATATAATAATAAATAACAT
1595222 ATTTAATAAA
Statistics
Matches: 481, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
506 44 0.09
507 436 0.91
508 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (507 bp):
TACTTTATATATATTTGCTTGTTATGACTCTCACTTTTATCATTCTTAGATATCTGTCAAGAATT
TCTAACTATAAACTTTATATCAAGTTTAATATAAAATTGATCATACAAATAAGGTTACCAATACT
AGAAAATATGGAATACTTTTCATATACTTTTTTCCAAATCATTTGGAGATATTAGCTGAAACTGA
AATAATATATTTTACAATTGATGCATTGTATGTAAATATCTTTGTATCCTAAAAATCTTTCCAAA
ACTCTTTTAATATTGGCCTCTTGAGATAGATTTAATATATTTTCAGACCTATCTCTATAAATCTT
TATGCCTATAACATATAAGGCTTCACCTAAATCCTTTATATCAAAGTTTTGATAAAAAAATGATT
TCAATCAGGTAACAAAGCCAATCACTATTTACAAAGAAAATATCACCAACATATAGGACTAAAAT
TTTAAACTTACTCCTACTAACTTCAAAGTATATATAATAATAAATAACATGA
Found at i:1598203 original size:140 final size:141
Alignment explanation
Indices: 1597878--1598202 Score: 465
Period size: 141 Copynumber: 2.3 Consensus size: 141
1597868 AACCAAAAAG
* * * *
1597878 ATACCCTTATGGAGAGCCATAAGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTT
1 ATACCCCTATGGAAAACCATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTT
* **
1597943 AATTTTTAATTTTCAAAAAATTCATTTCGTACCTTAATGGAGAACTAAAAAGACATGAAAAGTTT
66 AATTTTTAATTTTCAAAAAATTCATTTCATACCTTAAAAGAGAACTAAAAAGACATGAAAAGTTT
1598008 TGAAGATTTTT
131 TGAAGATTTTT
* * * *
1598019 ATACCCCTACGAAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATCATTTTTATTT
1 ATACCCCTATGGAAAACCATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTT
* * *
1598084 AATTTTTAATATTT-AAAAAATT-ATTTCATACTTTAAAAGAGAACTGAAAAGATATGAAAAGTT
66 AATTTTTAAT-TTTCAAAAAATTCATTTCATACCTTAAAAGAGAACTAAAAAGACATGAAAAGTT
1598147 TTGAAGATTTTT
130 TTGAAGATTTTT
* * *
1598159 ATACCCCTATGGATAACCATAGGAATAATAGAAATATATAAAAA
1 ATACCCCTATGGAAAACCATAGGAATATTAGAAATCT-TAAAAA
1598203 TGATTAATTT
Statistics
Matches: 162, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
140 79 0.49
141 80 0.49
142 3 0.02
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.35
Consensus pattern (141 bp):
ATACCCCTATGGAAAACCATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTT
AATTTTTAATTTTCAAAAAATTCATTTCATACCTTAAAAGAGAACTAAAAAGACATGAAAAGTTT
TGAAGATTTTT
Found at i:1598218 original size:140 final size:140
Alignment explanation
Indices: 1597894--1598203 Score: 419
Period size: 140 Copynumber: 2.2 Consensus size: 140
1597884 TTATGGAGAG
* * * * *
1597894 CCATAAGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTTAATTTTTAATTTTCAA
1 CCATAGGAATAATAGAAATATTGAAAAATT-AGATAATCATTTTTATTTAATTTTTAATTTTCAA
* **
1597959 AAAATTCATTTCGTACCTTAATGGAGAACTAAAAAGACATGAAAAGTTTTGAAGATTTTTATACC
65 AAAATTCATTTCATACCTTAAAAGAGAACTAAAAAGACATGAAAAGTTTTGAAGATTTTTATACC
1598024 CCTACGAAAAA
130 CCTACGAAAAA
* *
1598035 CCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATCATTTTTATTTAATTTTTAATATTT-A
1 CCATAGGAATAATAGAAATATTGAAAAATT-AGATAATCATTTTTATTTAATTTTTAAT-TTTCA
* * *
1598099 AAAAATT-ATTTCATACTTTAAAAGAGAACTGAAAAGATATGAAAAGTTTTGAAGATTTTTATAC
64 AAAAATTCATTTCATACCTTAAAAGAGAACTAAAAAGACATGAAAAGTTTTGAAGATTTTTATAC
* * *
1598163 CCCTATGGATAA
129 CCCTACGAAAAA
1598175 CCATAGGAATAATAGAAATATAT-AAAAAT
1 CCATAGGAATAATAGAAATAT-TGAAAAAT
1598204 GATTAATTTT
Statistics
Matches: 153, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
140 85 0.56
141 65 0.42
142 3 0.02
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (140 bp):
CCATAGGAATAATAGAAATATTGAAAAATTAGATAATCATTTTTATTTAATTTTTAATTTTCAAA
AAATTCATTTCATACCTTAAAAGAGAACTAAAAAGACATGAAAAGTTTTGAAGATTTTTATACCC
CTACGAAAAA
Found at i:1599096 original size:13 final size:13
Alignment explanation
Indices: 1599077--1599112 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1599067 ATTTGGCATA
*
1599077 ATTTTTTTCTCTT
1 ATTTTTTTCTCTC
*
1599090 TTTTTTTTCTCTC
1 ATTTTTTTCTCTC
1599103 ATTTTTTTCT
1 ATTTTTTTCT
1599113 ACTTGCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTTTTCTCTC
Found at i:1599102 original size:15 final size:15
Alignment explanation
Indices: 1599078--1599110 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1599068 TTTGGCATAA
1599078 TTTTTTTCTC-TTTT
1 TTTTTTTCTCATTTT
1599092 TTTTTTCTCTCATTTT
1 TTTTTT-TCTCATTTT
1599108 TTT
1 TTT
1599111 CTACTTGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCTCATTTT
Found at i:1600384 original size:15 final size:16
Alignment explanation
Indices: 1600366--1600407 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1600356 TTTAACAAAA
1600366 ATAAAATTCGTG-ACT
1 ATAAAATTCGTGAACT
*
1600381 ATAATATTCGTGATACT
1 ATAAAATTCGTGA-ACT
1600398 ATGAAAATTC
1 AT-AAAATTC
1600408 TTAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
17 5 0.23
18 6 0.27
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
ATAAAATTCGTGAACT
Found at i:1601199 original size:45 final size:45
Alignment explanation
Indices: 1601135--1601228 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
1601125 AGATGTACCA
* * *
1601135 AGTTTGACCAAGGCTAAACCTTTATGTCAAACAAATATAAAAAAG
1 AGTTTGACCAAGGCTAAACCATCATGTCAAACAAAGATAAAAAAG
* * *
1601180 AGTTTGACCAGGGCTAAACCATCATGTTAAACAAAGATAAAAAGG
1 AGTTTGACCAAGGCTAAACCATCATGTCAAACAAAGATAAAAAAG
1601225 AGTT
1 AGTT
1601229 CGATTGGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (45 bp):
AGTTTGACCAAGGCTAAACCATCATGTCAAACAAAGATAAAAAAG
Found at i:1601243 original size:45 final size:45
Alignment explanation
Indices: 1601135--1601256 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 45
1601125 AGATGTACCA
* * * * *
1601135 AGTTTGACCAAGGCTAAACCTTTATGTCAAACAAATATAAAAAAG
1 AGTTCGACCAGGGCTAAACCATCATGTCAAACAAAGATAAAAAAG
* * *
1601180 AGTTTGACCAGGGCTAAACCATCATGTTAAACAAAGATAAAAAGG
1 AGTTCGACCAGGGCTAAACCATCATGTCAAACAAAGATAAAAAAG
*** * *
1601225 AGTTCGATTGGGGTTAAACCATCACGTCAAAC
1 AGTTCGACCAGGGCTAAACCATCATGTCAAAC
1601257 GAGATGTGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
AGTTCGACCAGGGCTAAACCATCATGTCAAACAAAGATAAAAAAG
Found at i:1601386 original size:47 final size:47
Alignment explanation
Indices: 1601335--1601921 Score: 221
Period size: 47 Copynumber: 12.8 Consensus size: 47
1601325 AGGACTAATT
* *
1601335 GCCAATACAGTCAAA-GAAGGGTAAGAGAAGTTTGACCAGGTCTTAAC
1 GCCAATACAGTCAAACGAAGGGTAA-AGAAGTTTGACTAGGTCCTAAC
* * * * * * *
1601382 GCCAATAAAGTCGAAC-AAGGATAAAAAGAGTTTGACCAAGTCTTAAC
1 GCCAATACAGTCAAACGAAGGGTAAAGA-AGTTTGACTAGGTCCTAAC
* * * * * * * *
1601429 ACTAATACAATTAAATG-AGGGTAAAAAGAGTTTAACTAGG-ACTAAC
1 GCCAATACAGTCAAACGAAGGGTAAAGA-AGTTTGACTAGGTCCTAAC
** * * *
1601475 GCCAATACAACCAAGCGAA-GG--AAGACAGTTTGACTAAGTCCTAAT
1 GCCAATACAGTCAAACGAAGGGTAAAGA-AGTTTGACTAGGTCCTAAC
* * * *
1601520 GCCAATATAGTCAAACG-AGGGTGAAA-AGAGTTTTACTAGG-ACTAAT
1 GCCAATACAGTCAAACGAAGGGT-AAAGA-AGTTTGACTAGGTCCTAAC
** * * *
1601566 GCCAATACAACCAAATGAA-GG--AAGACTA-TTTGACTAGGTTCTAAT
1 GCCAATACAGTCAAACGAAGGGTAAAGA--AGTTTGACTAGGTCCTAAC
* * * * *
1601611 GCTAATATAGTTAAA-TAAGGGTGGAAA-AAGTTTGACTAGG-ACTAAC
1 GCCAATACAGTCAAACGAAGGGT--AAAGAAGTTTGACTAGGTCCTAAC
* * * * *
1601657 G-CAATACAGCCAAATGAA---AAAAGATAATTTGAAC-AGGTCTTAAC
1 GCCAATACAGTCAAACGAAGGGTAAAGA-AGTTTG-ACTAGGTCCTAAC
** * * **
1601701 ATCAATACAGTCAAACG-AGGGTAAAAATAATTTGACTAGG-AGTAAC
1 GCCAATACAGTCAAACGAAGGGTAAAGA-AGTTTGACTAGGTCCTAAC
* * * * *
1601747 GCCAATATAGCCAAACAAAGGG---AGACAGTTTGACCAAGTCCTAAC
1 GCCAATACAGTCAAACGAAGGGTAAAGA-AGTTTGACTAGGTCCTAAC
* * *
1601792 GCCAATACAGTTAAACG-AGGGTGAAA-AGAGTTTGACCAGGTCCTAAT
1 GCCAATACAGTCAAACGAAGGGT-AAAGA-AGTTTGACTAGGTCCTAAC
* * * *
1601839 GCTAGTACCACT-AAACGAAGGTGAAAAG-AGTTTGACTAGGTCCTAAC
1 GCCAATA-CAGTCAAACGAAGG-GTAAAGAAGTTTGACTAGGTCCTAAC
* * *
1601886 GTCAATACAGTCAAGC-AAGGGTGAAAGGAGTTTGAC
1 GCCAATACAGTCAAACGAAGGGT-AAAGAAGTTTGAC
1601922 CAATACTAAT
Statistics
Matches: 398, Mismatches: 100, Indels: 84
0.68 0.17 0.14
Matches are distributed among these distances:
41 3 0.01
42 1 0.00
43 10 0.03
44 48 0.12
45 77 0.19
46 76 0.19
47 167 0.42
48 13 0.03
49 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (47 bp):
GCCAATACAGTCAAACGAAGGGTAAAGAAGTTTGACTAGGTCCTAAC
Found at i:1601526 original size:45 final size:45
Alignment explanation
Indices: 1601469--1601617 Score: 122
Period size: 45 Copynumber: 3.3 Consensus size: 45
1601459 TTTAACTAGG
* *
1601469 ACTAACGCCAATACAACCAAGCGAAGGAAGACAGTTTGACTAAGT
1 ACTAATGCCAATACAACCAAACGAAGGAAGACAGTTTGACTAAGT
* * ** * * * * *
1601514 CCTAATGCCAATATAGTCAAACGAGGGTGAAAAGAGTTTTACT-AGG
1 ACTAATGCCAATACAACCAAACGA-AG-GAAGACAGTTTGACTAAGT
* *
1601560 ACTAATGCCAATACAACCAAATGAAGGAAGACTA-TTTGACTAGGT
1 ACTAATGCCAATACAACCAAACGAAGGAAGAC-AGTTTGACTAAGT
* *
1601605 TCTAATGCTAATA
1 ACTAATGCCAATA
1601618 TAGTTAAATA
Statistics
Matches: 76, Mismatches: 24, Indels: 8
0.70 0.22 0.07
Matches are distributed among these distances:
44 10 0.13
45 32 0.42
46 22 0.29
47 12 0.16
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
ACTAATGCCAATACAACCAAACGAAGGAAGACAGTTTGACTAAGT
Found at i:1601540 original size:91 final size:91
Alignment explanation
Indices: 1601410--1601940 Score: 431
Period size: 91 Copynumber: 5.8 Consensus size: 91
1601400 GGATAAAAAG
* * * * * * * * *
1601410 AGTTTGACCAAGTCTTAACACTAATACAATTAAATGAGGGTAAAAAGAGTTTAACTAGGACTAAC
1 AGTTTGACTAAGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACTAGGACTAAC
*
1601475 GCCAATACAACCAAGCGAAGGAAGAC
66 GCCAATACAACCAAACGAAGGAAGAC
* * * *
1601501 AGTTTGACTAAGTCCTAATGCCAATATAGTCAAACGAGGGTGAAAAGAGTTTTACTAGGACTAAT
1 AGTTTGACTAAGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACTAGGACTAAC
*
1601566 GCCAATACAACCAAATGAAGGAAGAC
66 GCCAATACAACCAAACGAAGGAAGAC
* * * * * * **
1601592 TA-TTTGACTAGGTTCTAATGCTAATATAGTTAAATAAGGGTGGAAAA-AGTTTGACTAGGACTA
1 -AGTTTGACTAAGTCCTAACGCCAATACAGTCAAACGAGGGT-GAAAAGAGTTTGACTAGGACTA
* * ** *
1601655 ACG-CAATACAGCCAAATGAAAAAAGAT
64 ACGCCAATACAACCAAACGAAGGAAGAC
* * * ** * * * *
1601682 AATTTGAAC-AGGTCTTAACATCAATACAGTCAAACGAGGGTAAAAATAATTTGACTAGGAGTAA
1 AGTTTG-ACTAAGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACTAGGACTAA
* * * *
1601746 CGCCAATATAGCCAAACAAAGGGAGAC
65 CGCCAATACAACCAAACGAAGGAAGAC
* * * *
1601773 AGTTTGACCAAGTCCTAACGCCAATACAGTTAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAA
1 AGTTTGACTAAGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACTAGG-ACTAA
* * * * * * *
1601838 TGCTAGTACCACTAAACGAAGGTGAAAAG
65 CGCCAATACAACCAAACGAA-G-GAAGAC
* * * * * * ** *
1601867 AGTTTGACTAGGTCCTAACGTCAATACAGTCAAGCAAGGGTGAAAGGAGTTTGACCAATACTAAT
1 AGTTTGACTAAGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACTAGGACTAAC
1601932 GCCAATACA
66 GCCAATACA
1601941 GTTAAATAAA
Statistics
Matches: 348, Mismatches: 82, Indels: 18
0.78 0.18 0.04
Matches are distributed among these distances:
89 5 0.01
90 65 0.19
91 192 0.55
92 21 0.06
93 12 0.03
94 53 0.15
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.22
Consensus pattern (91 bp):
AGTTTGACTAAGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACTAGGACTAAC
GCCAATACAACCAAACGAAGGAAGAC
Found at i:1601806 original size:181 final size:183
Alignment explanation
Indices: 1601410--1601827 Score: 450
Period size: 181 Copynumber: 2.3 Consensus size: 183
1601400 GGATAAAAAG
* * * * *
1601410 AGTTTGACCAAGTCTTAACACTAATACAATTAAATGAGGGTAAAAAGAGTTTAACTAGGACTAAC
1 AGTTTGACCAAGTCCTAACGCTAATACAGTTAAATGAGGGTGAAAAGAGTTTGACTAGGACTAAC
* ** * ** *
1601475 GCCAATACAACCAAGCGAAGGAAGACAGTTTGACTAAGTCCTAATGCCAATATAGTCAAACGAGG
66 GCCAATACAACCAAACGAAAAAAGACAATTTGACTAAGTCCTAACACCAATACAGTCAAACGAGG
* * * * **
1601540 GTGAAAAGAGTTTTACTAGGACTAATGCCAATACAACCAAATGAAGGAAGACT
131 GTAAAAAGAATTTGACTAGGACTAACGCCAATACAACCAAACAAAGGAAGACT
* * * * * *
1601593 A-TTTGACTAGGTTCTAATGCTAATATAGTTAAATAAGGGTGGAAAA-AGTTTGACTAGGACTAA
1 AGTTTGACCAAGTCCTAACGCTAATACAGTTAAATGAGGGT-GAAAAGAGTTTGACTAGGACTAA
* * * * * *
1601656 CG-CAATACAGCCAAATGAAAAAAGATAATTTGAAC-AGGTCTTAACATCAATACAGTCAAACGA
65 CGCCAATACAACCAAACGAAAAAAGACAATTTG-ACTAAGTCCTAACACCAATACAGTCAAACGA
* * * * *
1601719 GGGTAAAAATAATTTGACTAGGAGTAACGCCAATATAGCCAAACAAAGGGAGAC-
129 GGGTAAAAAGAATTTGACTAGGACTAACGCCAATACAACCAAACAAAGGAAGACT
* *
1601773 AGTTTGACCAAGTCCTAACGCCAATACAGTTAAACGAGGGTGAAAAGAGTTTGAC
1 AGTTTGACCAAGTCCTAACGCTAATACAGTTAAATGAGGGTGAAAAGAGTTTGAC
1601828 CAGGTCCTAA
Statistics
Matches: 188, Mismatches: 43, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
180 6 0.03
181 127 0.68
182 50 0.27
183 5 0.03
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (183 bp):
AGTTTGACCAAGTCCTAACGCTAATACAGTTAAATGAGGGTGAAAAGAGTTTGACTAGGACTAAC
GCCAATACAACCAAACGAAAAAAGACAATTTGACTAAGTCCTAACACCAATACAGTCAAACGAGG
GTAAAAAGAATTTGACTAGGACTAACGCCAATACAACCAAACAAAGGAAGACT
Found at i:1601963 original size:46 final size:47
Alignment explanation
Indices: 1601743--1601963 Score: 173
Period size: 47 Copynumber: 4.8 Consensus size: 47
1601733 TGACTAGGAG
* ** * *
1601743 TAACGCCAATATAGCCAAACAAAGG-G-AGACAGTTTGACCA-AGTCC
1 TAACGCCAATACAGTTAAACAAAGGTGAAAAGAGTTTGACCAGA-TCC
* * *
1601788 TAACGCCAATACAGTTAAACGAGGGTGAAAAGAGTTTGACCAGGTCC
1 TAACGCCAATACAGTTAAACAAAGGTGAAAAGAGTTTGACCAGATCC
* * * * * * *
1601835 TAATGCTAGTACCA-CTAAACGAAGGTGAAAAGAGTTTGACTAGGTCC
1 TAACGCCAATA-CAGTTAAACAAAGGTGAAAAGAGTTTGACCAGATCC
* * * * * *
1601882 TAACGTCAATACAGTCAAGCAAGGGTGAAAGGAGTTTGACCA-ATAC
1 TAACGCCAATACAGTTAAACAAAGGTGAAAAGAGTTTGACCAGATCC
* * *
1601928 TAATGCCAATACAGTTAAATAAAGGTAAAAAGAGTT
1 TAACGCCAATACAGTTAAACAAAGGTGAAAAGAGTT
1601964 CAATTAAGGC
Statistics
Matches: 136, Mismatches: 35, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
45 20 0.15
46 33 0.24
47 81 0.60
48 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (47 bp):
TAACGCCAATACAGTTAAACAAAGGTGAAAAGAGTTTGACCAGATCC
Found at i:1612379 original size:52 final size:52
Alignment explanation
Indices: 1612323--1612886 Score: 306
Period size: 52 Copynumber: 10.9 Consensus size: 52
1612313 AAAGATATTA
* * *
1612323 GACTTAAAGATGACAAGGATGCCAATGTGCTGATGT-AAAGCTAGCGGCATTG
1 GACTTAAAGATGACAAGGATGCCAATGTGCTGAT-TCAAGGCCAGCGACATTG
* * * * * *
1612375 GACTTAAAGATGACCAGAATGCTATTGTGCTGATTCAAGGCTAGCGACATTA
1 GACTTAAAGATGACAAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * * *
1612427 GATTTAAAGGTGATAA-GAGTGCCAATGTGATGATTCAAGGCCAGCAACATTG
1 GACTTAAAGATGACAAGGA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * * * *
1612479 GATTTAAATATGATGAAAG-TGCCAATATGCTGATTCAAGGCCAGCGATATTG
1 GACTTAAAGATGA-CAAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * *
1612531 GACTTAAAGATGACAA-AAGTGCTAATGTGCCGATTCAAGGCCAACGACATTG
1 GACTTAAAGATGACAAGGA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * * * ** * *
1612583 GATTTAAAGGTAATAAAGG-TGCCAATGTGTTGATTCAAGGCCAATGATATCG
1 GACTTAAAGATGA-CAAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * ** * * * * * * *
1612635 GATTTAACGATGATAAAAAGTGTCAATATGTTGATTCAAGGCCAACAATATTA
1 GACTTAAAGATGACAAGGA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * * ** *
1612688 GATTTAAAGAT---AAGAATGCCAATGTGCTGACTT-AAAGCTAATGAAATTG
1 GACTTAAAGATGACAAGGATGCCAATGTGCTGA-TTCAAGGCCAGCGACATTG
* * ** * * * *
1612737 GACTTAAAGGTGATAAAAATGCTAATATGCTGATTCAAGGCCAGCGATATCG
1 GACTTAAAGATGACAAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * * * * * *
1612789 AACTTAAAGAT-A-AGAGGAATGCTAATATGCTAATTCAAGGCTAACGACATTA
1 GACTTAAAGATGACA-AGG-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* ** * * *
1612841 GACTTAAAGATGA-AAAGATGTAAATATTCTAATTCAAGGCCAGCGA
1 GACTTAAAGATGACAAGGATGCCAATGTGCTGATTCAAGGCCAGCGA
1612887 TATTTGACAT
Statistics
Matches: 398, Mismatches: 96, Indels: 37
0.75 0.18 0.07
Matches are distributed among these distances:
49 30 0.08
50 7 0.02
51 34 0.09
52 283 0.71
53 43 0.11
54 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (52 bp):
GACTTAAAGATGACAAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
Found at i:1612540 original size:156 final size:155
Alignment explanation
Indices: 1612371--1612853 Score: 472
Period size: 156 Copynumber: 3.1 Consensus size: 155
1612361 AGCTAGCGGC
* * *
1612371 ATTGGACTTAAAGATGACCAGAATGCTATTGTGCTGATTCAAGGCTAGCGACATTAGATTTAAAG
1 ATTGGACTTAAAGATGA-CAGAATGCTAATGTGCTGATTCAAGGCTAACGACATTGGATTTAAAG
* * *
1612436 GTGATAAGAGTGCCAATGTGATGATTCAAGGCCAGCAACATTGGATTTAAATATGAT-GAAAGTG
65 GTGATAA-AGTGCCAATGTGATGATTCAAGGCCAGCAACATCGGATTTAAAGATGATAAAAAGTG
* *
1612500 CCAATATGCTGATTCAAGGCCAGCGAT
129 CCAATATGCTGATTCAAGGCCAACAAT
* * *
1612527 ATTGGACTTAAAGATGACAAAAGTGCTAATGTGCCGATTCAAGGCCAACGACATTGGATTTAAAG
1 ATTGGACTTAAAGATGACAGAA-TGCTAATGTGCTGATTCAAGGCTAACGACATTGGATTTAAAG
* * *** * *
1612592 GTAATAAAGGTGCCAATGTGTTGATTCAAGGCCAATGATATCGGATTTAACGATGATAAAAAGTG
65 GTGATAAA-GTGCCAATGTGATGATTCAAGGCCAGCAACATCGGATTTAAAGATGATAAAAAGTG
* *
1612657 TCAATATGTTGATTCAAGGCCAACAAT
129 CCAATATGCTGATTCAAGGCCAACAAT
* * * * * * *
1612684 ATTAGATTTAAAGAT-A-AGAATGCCAATGTGCTGACTT-AAAGCTAATGAAATTGGACTTAAAG
1 ATTGGACTTAAAGATGACAGAATGCTAATGTGCTGA-TTCAAGGCTAACGACATTGGATTTAAAG
* * * * * * * * * * **
1612746 GTGATAAAAATGCTAATATGCTGATTCAAGGCCAGCGATATCGAACTTAAAGATAAGAGGAA-TG
65 GTGAT-AAAGTGCCAATGTGATGATTCAAGGCCAGCAACATCGGATTTAAAGATGATAAAAAGTG
* * * * *
1612810 CTAATATGCTAATTCAAGGCTAACGAC
129 CCAATATGCTGATTCAAGGCCAACAAT
*
1612837 ATTAGACTTAAAGATGA
1 ATTGGACTTAAAGATGA
1612854 AAAGATGTAA
Statistics
Matches: 269, Mismatches: 52, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
153 36 0.13
154 77 0.29
155 13 0.05
156 101 0.38
157 42 0.16
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (155 bp):
ATTGGACTTAAAGATGACAGAATGCTAATGTGCTGATTCAAGGCTAACGACATTGGATTTAAAGG
TGATAAAGTGCCAATGTGATGATTCAAGGCCAGCAACATCGGATTTAAAGATGATAAAAAGTGCC
AATATGCTGATTCAAGGCCAACAAT
Found at i:1612632 original size:104 final size:103
Alignment explanation
Indices: 1612400--1612779 Score: 372
Period size: 104 Copynumber: 3.7 Consensus size: 103
1612390 AGAATGCTAT
* ** * * * * * * * *
1612400 TGTGCTGATTCAAGGCTAGCGACATTAGATTTAAAGGTGATAAGAGTGCCAATGTGATGATTCAA
1 TGTGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGATAAAAGTGCTAATATGCTGATTCAA
* * *
1612465 GGCCAGCAACATTGGATTTAAATATGATGAAAGTGCCAA
66 GGCCAACAACATTGGATTTAAAGATAAT-AAAGTGCCAA
* ** * * *
1612504 TATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAAGTGCTAATGTGCCGATTCAA
1 TGTGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGATAAAAGTGCTAATATGCTGATTCAA
* *
1612569 GGCCAACGACATTGGATTTAAAGGTAATAAAGGTGCCAA
66 GGCCAACAACATTGGATTTAAAGATAATAAA-GTGCCAA
* * * * *
1612608 TGTGTTGATTCAAGGCCAATGATATCGGATTTAACGATGATAAAAAGTG-TCAATATGTTGATTC
1 TGTGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAT-AAAAGTGCT-AATATGCTGATTC
* * *
1612672 AAGGCCAACAATATTAGATTTAAAGATAA-GAA-TGCCAA
64 AAGGCCAACAACATTGGATTTAAAGATAATAAAGTGCCAA
* * * * *
1612710 TGTGCTGACTT-AAAGCTAATGAAATTGGACTTAAAGGTGATAAAAATGCTAATATGCTGATTCA
1 TGTGCTGA-TTCAAGGCCAATGATATTGGACTTAAAGATGATAAAAGTGCTAATATGCTGATTCA
1612774 AGGCCA
65 AGGCCA
1612780 GCGATATCGA
Statistics
Matches: 229, Mismatches: 42, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
101 25 0.11
102 37 0.16
103 5 0.02
104 120 0.52
105 42 0.18
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (103 bp):
TGTGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGATAAAAGTGCTAATATGCTGATTCAA
GGCCAACAACATTGGATTTAAAGATAATAAAGTGCCAA
Found at i:1612958 original size:32 final size:32
Alignment explanation
Indices: 1612922--1613164 Score: 136
Period size: 32 Copynumber: 7.4 Consensus size: 32
1612912 CGATTTATAC
1612922 AGGCTTTTGAAAGGGTTGCCACTAACTTGTGT
1 AGGCTTTTGAAAGGGTTGCCACTAACTTGTGT
* * * *
1612954 AGGCTTTAGAAAAAAGGTTGCCATTAACTTATGT
1 AGGCTTTTG--AAAGGGTTGCCACTAACTTGTGT
* * *
1612988 -GAGC-TTTGAAAAAGGTTACCACTGACTTGTGT
1 AG-GCTTTTG-AAAGGGTTGCCACTAACTTGTGT
* * * *
1613020 TGGCTTTTTAAAAGGGTTACCACTAACTTGTAT
1 AGGC-TTTTGAAAGGGTTGCCACTAACTTGTGT
* * ** * *
1613053 GGGC-TTCGAAAAAGGGATTATCATTGACTTGTGT
1 AGGCTTTTG--AAAGGG-TTGCCACTAACTTGTGT
* *
1613087 AGGCTTTTTAAAAAGGTTGCCACTAACTTGTGT
1 AGGC-TTTTGAAAGGGTTGCCACTAACTTGTGT
** *
1613120 -GATTTTTAAAAAGGGTTGCCA-TCAACTTGTGT
1 AGGCTTTT-GAAAGGGTTGCCACT-AACTTGTGT
* *
1613152 GGGCTTTGGAAAG
1 AGGCTTTTGAAAG
1613165 AGGGCCACAG
Statistics
Matches: 162, Mismatches: 35, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
31 7 0.04
32 56 0.35
33 51 0.31
34 46 0.28
36 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34
Consensus pattern (32 bp):
AGGCTTTTGAAAGGGTTGCCACTAACTTGTGT
Found at i:1613092 original size:67 final size:65
Alignment explanation
Indices: 1612935--1613117 Score: 213
Period size: 67 Copynumber: 2.8 Consensus size: 65
1612925 CTTTTGAAAG
* * ** * * * *
1612935 GGTTGCCACTAACTTGTGTAGGCTTTAGAAAAAAGGTTGCCATTAACTTATGTGAGCTTTGAAAA
1 GGTTACCACTGACTTGTGTAGGCTTT-TTAAAAAGGTTGCCACTAACTTGTATGAGCTTCGAAAA
1613000 A
65 A
* * * *
1613001 GGTTACCACTGACTTGTGTTGGCTTTTTAAAAGGGTTACCACTAACTTGTATGGGCTTCGAAAAA
1 GGTTACCACTGACTTGTGTAGGCTTTTTAAAAAGGTTGCCACTAACTTGTATGAGCTTCGAAAAA
* *
1613066 GGGATTATCATTGACTTGTGTAGGCTTTTTAAAAAGGTTGCCACTAACTTGT
1 -GG-TTACCACTGACTTGTGTAGGCTTTTTAAAAAGGTTGCCACTAACTTGT
1613118 GTGATTTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
65 30 0.31
66 25 0.26
67 43 0.44
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (65 bp):
GGTTACCACTGACTTGTGTAGGCTTTTTAAAAAGGTTGCCACTAACTTGTATGAGCTTCGAAAAA
Found at i:1613093 original size:99 final size:97
Alignment explanation
Indices: 1612926--1613157 Score: 254
Period size: 99 Copynumber: 2.4 Consensus size: 97
1612916 TTATACAGGC
* * *
1612926 TTTTGAAAGGGTTGCCACTAACTTGTGTAGGCTTTAGAAAAAAGGTTGCCATTAACTTATGTGAG
1 TTTTAAAAGGGTTGCCACTAACTTGTGTGGGC-TTAGAAAAAAGGTTACCATTAACTTATGTGAG
* *
1612991 C-TTTGAAAAAGGTTACCACTGACTTGTGTTGGCT
65 CTTTTGAAAAAGGTTACCACTAACTTGTG-T-GAT
* * * * * * *
1613025 TTTTAAAAGGGTTACCACTAACTTGTATGGGCTTCGAAAAAGGGATTATCATTGACTTGTGT-AG
1 TTTTAAAAGGGTTGCCACTAACTTGTGTGGGCTTAGAAAAAAGG-TTACCATTAACTTATGTGA-
* *
1613089 GCTTTTTAAAAAGGTTGCCACTAACTTGTGTGAT
64 GCTTTTGAAAAAGGTTACCACTAACTTGTGTGAT
1613123 TTTTAAAAAGGGTTGCCA-TCAACTTGTGTGGGCTT
1 TTTT-AAAAGGGTTGCCACT-AACTTGTGTGGGCTT
1613158 TGGAAAGAGG
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
98 18 0.16
99 70 0.62
100 24 0.21
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (97 bp):
TTTTAAAAGGGTTGCCACTAACTTGTGTGGGCTTAGAAAAAAGGTTACCATTAACTTATGTGAGC
TTTTGAAAAAGGTTACCACTAACTTGTGTGAT
Found at i:1613298 original size:61 final size:60
Alignment explanation
Indices: 1613161--1613438 Score: 209
Period size: 59 Copynumber: 4.7 Consensus size: 60
1613151 TGGGCTTTGG
*
1613161 AAAGAGGGCCACAGAGTTGTGGAC-TTTAAAAAAGGGTGCCACAAAATGTGGACTTTAGA
1 AAAGAGTGCCACAGAGTTGTGGACTTTTAAAAAAGGGTGCCACAAAATGTGGACTTTAGA
* * * * * * *
1613220 AAATG-GTGCTACGGAGTTATGGACTTTTGAAAATGGGTGCGACAATATTGTGGACTTTA-A
1 AAA-GAGTGCCACAGAGTTGTGGACTTTTAAAAAAGGGTGCCACAA-AATGTGGACTTTAGA
* * * ** *
1613280 AAGAGAGTGCCATAGAGTTGTAGAC-TTT--AAGAGGGATGCCATTAAGTCGTGGACTTTA-A
1 AA-AGAGTGCCACAGAGTTGTGGACTTTTAAAAAAGGG-TGCCACAAAAT-GTGGACTTTAGA
* * * **
1613339 GAAGAGTGCCA-ATGAGTCGTGGAC--TTAAAAAAAGGTGCCACGAAGTTGTGGACTTTAGA
1 AAAGAGTGCCACA-GAGTTGTGGACTTTTAAAAAAGGGTGCCAC-AAAATGTGGACTTTAGA
* * * *
1613398 AAATAGTGCCACAAAGTTATGGAC-TTTAAAAAAAGGTGCCA
1 AAAGAGTGCCACAGAGTTGTGGACTTTTAAAAAAGGGTGCCA
1613439 TGGAGTTATG
Statistics
Matches: 172, Mismatches: 33, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
57 3 0.02
58 40 0.23
59 60 0.35
60 42 0.24
61 27 0.16
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.25
Consensus pattern (60 bp):
AAAGAGTGCCACAGAGTTGTGGACTTTTAAAAAAGGGTGCCACAAAATGTGGACTTTAGA
Found at i:1613308 original size:30 final size:30
Alignment explanation
Indices: 1613267--1613538 Score: 169
Period size: 29 Copynumber: 9.4 Consensus size: 30
1613257 TGCGACAATA
1613267 TTGTGGACTTTAAAAGAGAGTGCCATAGAG
1 TTGTGGACTTTAAAAGAGAGTGCCATAGAG
* * *
1613297 TTGTAGACTTTAAGAGGGA-TGCCATTA-AG
1 TTGTGGACTTTAAAAGAGAGTGCCA-TAGAG
* *
1613326 TCGTGGACTTTAAGA-AGAGTGCCA-ATGAG
1 TTGTGGACTTTAAAAGAGAGTGCCATA-GAG
* * * *
1613355 TCGTGGACTTAAAAAAAG-GTGCCA-CGAAG
1 TTGTGGACTTTAAAAGAGAGTGCCATAG-AG
* * *
1613384 TTGTGGACTTTAGAAA-ATAGTGCCACAAAG
1 TTGTGGACTTTA-AAAGAGAGTGCCATAGAG
* * *
1613414 TTATGGACTTTAAAA-AAAGGTGCCATGGAG
1 TTGTGGACTTTAAAAGAGA-GTGCCATAGAG
* * *
1613444 TTATGGACTTTAAAAG-G-GTACCACAGAG
1 TTGTGGACTTTAAAAGAGAGTGCCATAGAG
* *
1613472 TCGTGGACTTT-AAA-AGCGTGCC-TCAGAG
1 TTGTGGACTTTAAAAGAGAGTGCCAT-AGAG
** *
1613500 TCATGGACTTTAAAAG-G-GTGCCATGGAG
1 TTGTGGACTTTAAAAGAGAGTGCCATAGAG
*
1613528 TTATGGACTTT
1 TTGTGGACTTT
1613539 TCAAAAAAGG
Statistics
Matches: 195, Mismatches: 30, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
27 5 0.03
28 56 0.29
29 69 0.35
30 65 0.33
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (30 bp):
TTGTGGACTTTAAAAGAGAGTGCCATAGAG
Found at i:1613472 original size:28 final size:28
Alignment explanation
Indices: 1613168--1613538 Score: 194
Period size: 30 Copynumber: 12.7 Consensus size: 28
1613158 TGGAAAGAGG
*
1613168 GCCACAGAGTTGTGGACTTTAAAAAAGGGT
1 GCCACAGAGTTATGGACTTT--AAAAGGGT
** * *
1613198 GCCACA-AAATGTGGACTTTAGAAAATGGT
1 GCCACAGAGTTATGGACTTT--AAAAGGGT
* *
1613227 GCTACGGAGTTATGGACTTTTGAAAATGGGT
1 GCCACAGAGTTATGGAC-TTT-AAAA-GGGT
* * *
1613258 GCGACA-ATATTGTGGACTTTAAAAGAGAGT
1 GCCACAGA-GTTATGGACTTTAAAAG-G-GT
* * * *
1613288 GCCATAGAGTTGTAGACTTTAAGAGGGAT
1 GCCACAGAGTTATGGACTTTAAAAGGG-T
* ** *
1613317 GCCATTA-AGTCGTGGACTTTAAGAAGAGT
1 GCCA-CAGAGTTATGGACTTTAA-AAGGGT
** * *
1613346 GCCA-ATGAGTCGTGGACTTAAAAAAAGGT
1 GCCACA-GAGTTATGGACTT-TAAAAGGGT
* **
1613375 GCCAC-GAAGTTGTGGACTTTAGAAAATAGT
1 GCCACAG-AGTTATGGACTTT--AAAAGGGT
* *
1613405 GCCACAAAGTTATGGACTTTAAAAAAAGGT
1 GCCACAGAGTTATGGACTTT--AAAAGGGT
**
1613435 GCCATGGAGTTATGGACTTTAAAAGGGT
1 GCCACAGAGTTATGGACTTTAAAAGGGT
* ** *
1613463 ACCACAGAGTCGTGGACTTTAAAAGCGT
1 GCCACAGAGTTATGGACTTTAAAAGGGT
* *
1613491 GCCTCAGAGTCATGGACTTTAAAAGGGT
1 GCCACAGAGTTATGGACTTTAAAAGGGT
**
1613519 GCCATGGAGTTATGGACTTT
1 GCCACAGAGTTATGGACTTT
1613539 TCAAAAAAGG
Statistics
Matches: 270, Mismatches: 53, Indels: 38
0.75 0.15 0.11
Matches are distributed among these distances:
27 1 0.00
28 72 0.27
29 83 0.31
30 96 0.36
31 18 0.07
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (28 bp):
GCCACAGAGTTATGGACTTTAAAAGGGT
Found at i:1613616 original size:30 final size:30
Alignment explanation
Indices: 1613149--1613737 Score: 137
Period size: 30 Copynumber: 19.8 Consensus size: 30
1613139 CATCAACTTG
* * * *
1613149 TGTGGGCTTTGGAAAGAGG-GCCACAGAGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
* * **
1613178 TGTGGACTTTA-AAAAAGGGTGCCAC-AAAA
1 TGTGGACTTTAGAAAGA-GGTGCCACGGATT
* *
1613207 TGTGGACTTTAGAAA-ATGGTGCTACGGAGT
1 TGTGGACTTTAGAAAGA-GGTGCCACGGATT
* * * *
1613237 TATGGACTTTTGAAA-ATGGGTGCGAC-AATAT
1 TGTGGACTTTAGAAAGA--GGTGCCACGGAT-T
** *
1613268 TGTGGACTTTA-AAAGAGAGTGCCATAGAGT
1 TGTGGACTTTAGAAAGAG-GTGCCACGGATT
* * *** *
1613298 TGTAGACTTTA-AGAG-GGATGCCATTAAGT
1 TGTGGACTTTAGAAAGAGG-TGCCACGGATT
* ** *
1613327 CGTGGACTTTA-AGAAGA-GTGCCAATGAGT
1 TGTGGACTTTAGA-AAGAGGTGCCACGGATT
* * * * *
1613356 CGTGGAC-TTAAAAAAAGGTGCCACGAAGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
* ** *
1613385 TGTGGACTTTAGAAA-ATAGTGCCACAAAGT
1 TGTGGACTTTAGAAAGA-GGTGCCACGGATT
* * * * *
1613415 TATGGACTTTAAAAAAAGGTGCCATGGAGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
* * * *
1613445 TATGGACTTTA-AAAG-GGTACCACAGAGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
* * * * *
1613473 CGTGGACTTTA-AAAG-CGTGCCTCAGAGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
** * *
1613501 CATGGACTTTA-AAAG-GGTGCCATGGAGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
* * *** * *
1613529 TATGGACTTTTCA-AAAAAGGGTATAATGGAGT
1 TGTGGAC-TTT-AGAAAGA-GGTGCCACGGATT
* ***
1613561 TGTGGACTTTGGAAA-AGAACACCACGGATT
1 TGTGGACTTTAGAAAGAG-GTGCCACGGATT
* **
1613591 TGTGGACTTTAGAAAGGGGTGCCACGGGGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
*
1613621 TGT-GAGCTTT-GAAAAGAAGGTGCCACAG-TT
1 TGTGGA-CTTTAG-AAAG-AGGTGCCACGGATT
* * **
1613651 TGTAGACTTTAGAAAAAGGTGCCACGGGGT
1 TGTGGACTTTAGAAAGAGGTGCCACGGATT
* * *
1613681 TGTGGACTTTAAAAAAGGGGTGCCATGGATT
1 TGTGGACTTT-AGAAAGAGGTGCCACGGATT
* * *
1613712 TGTGAACTTTGAAAAAAAGGTGCCAC
1 TGTGGACTTT-AGAAAGAGGTGCCAC
1613738 AAAATTATGG
Statistics
Matches: 431, Mismatches: 98, Indels: 60
0.73 0.17 0.10
Matches are distributed among these distances:
28 73 0.17
29 105 0.24
30 163 0.38
31 74 0.17
32 16 0.04
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (30 bp):
TGTGGACTTTAGAAAGAGGTGCCACGGATT
Found at i:1613623 original size:60 final size:59
Alignment explanation
Indices: 1613559--1613695 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
1613549 GTATAATGGA
* * **
1613559 GTTGTGGACTTTGGAAAAGAA-CACCACGGATTTGTGGACTTTAGAAAGGGGTGCCACGGG
1 GTTGTGGACTTT-GAAAAGAAGCACCACAG-TTTGTAGACTTTAGAAAAAGGTGCCACGGG
**
1613619 GTTGT-GAGCTTTGAAAAGAAGGTGCCACAGTTTGTAGACTTTAGAAAAAGGTGCCACGGG
1 GTTGTGGA-CTTTGAAAAGAA-GCACCACAGTTTGTAGACTTTAGAAAAAGGTGCCACGGG
*
1613679 GTTGTGGACTTTAAAAA
1 GTTGTGGACTTTGAAAA
1613696 AGGGGTGCCA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
59 10 0.15
60 49 0.74
61 7 0.11
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (59 bp):
GTTGTGGACTTTGAAAAGAAGCACCACAGTTTGTAGACTTTAGAAAAAGGTGCCACGGG
Found at i:1613703 original size:60 final size:60
Alignment explanation
Indices: 1613582--1613737 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 60
1613572 GAAAAGAACA
* **
1613582 CCACGGATTTGTGGACTTTAGAAAGGGGTGCCACGGGGTTGTGAGCTTTGAAAAGAAGGTG
1 CCACAGATTTGT-GACTTTAGAAAAAGGTGCCACGGGGTTGTGAGCTTTGAAAAGAAGGTG
1613643 CCACAG-TTTGTAGACTTTAGAAAAAGGTGCCACGGGGTTGTG-GACTTT-AAAA-AAGGGGTG
1 CCACAGATTTGT-GACTTTAGAAAAAGGTGCCACGGGGTTGTGAG-CTTTGAAAAGAA--GGTG
** *
1613703 CCATGGATTTGTGAACTTTGAAAAAAAGGTGCCAC
1 CCACAGATTTGTG-ACTTT-AGAAAAAGGTGCCAC
1613738 AAAATTATGG
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
58 2 0.02
59 5 0.06
60 46 0.56
61 15 0.18
62 14 0.17
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (60 bp):
CCACAGATTTGTGACTTTAGAAAAAGGTGCCACGGGGTTGTGAGCTTTGAAAAGAAGGTG
Found at i:1613785 original size:64 final size:65
Alignment explanation
Indices: 1613691--1613816 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 65
1613681 TGTGGACTTT
* * * *
1613691 AAAAAAGGGGTGCCATGGATTTGTGAACTTTG-AAAAAAAGGTGCCACAAAATTATGGACTTAAG
1 AAAAAAAGGGTGCCACGGAGTTGTGAACTTTGAAAAAAAAGGTGCCACAAAATTATGCACTTAAG
* * * * *
1613755 AAAAAAAGGGTGTCACGGAGTTGTGGACTTTGAAAAAAAATGTGCCACTAAGTTATGCACTT
1 AAAAAAAGGGTGCCACGGAGTTGTGAACTTTGAAAAAAAAGGTGCCACAAAATTATGCACTT
1613817 TAAAAAAGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
64 27 0.52
65 25 0.48
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.25
Consensus pattern (65 bp):
AAAAAAAGGGTGCCACGGAGTTGTGAACTTTGAAAAAAAAGGTGCCACAAAATTATGCACTTAAG
Found at i:1613817 original size:32 final size:32
Alignment explanation
Indices: 1613717--1613823 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 32
1613707 GGATTTGTGA
*
1613717 ACTTTG-AAAAAAAGGTGCCACAAAATTATGG
1 ACTTTGAAAAAAAAGGTGCCACAAAGTTATGG
* * * ** *
1613748 ACTTAAGAAAAAAAGGGTGTCACGGAGTTGTGG
1 ACTT-TGAAAAAAAAGGTGCCACAAAGTTATGG
* * *
1613781 ACTTTGAAAAAAAATGTGCCACTAAGTTATGC
1 ACTTTGAAAAAAAAGGTGCCACAAAGTTATGG
1613813 ACTTT-AAAAAA
1 ACTTTGAAAAAA
1613824 GGATGTTATG
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
31 10 0.17
32 26 0.44
33 23 0.39
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (32 bp):
ACTTTGAAAAAAAAGGTGCCACAAAGTTATGG
Found at i:1623590 original size:20 final size:22
Alignment explanation
Indices: 1623550--1623597 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1623540 TGGCCTTTGA
*
1623550 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1623572 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
1623591 CCA-GCAT
1 CCATGCAT
1623598 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1626001 original size:52 final size:52
Alignment explanation
Indices: 1625945--1626043 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
1625935 TAGTTGGGTG
* * *
1625945 AAAAA-CTCAAAATGTATCGATACGATGAAGAATGTATCGATACATTTATGTC
1 AAAAACCT-AAAATGCATCGATACAATGAAAAATGTATCGATACATTTATGTC
* *
1625997 AAAAACCTAGAATGCATCTATACAATGAAAAATGTATCGATACATTT
1 AAAAACCTAAAATGCATCGATACAATGAAAAATGTATCGATACATTT
1626044 TCTTTCCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
52 39 0.95
53 2 0.05
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.28
Consensus pattern (52 bp):
AAAAACCTAAAATGCATCGATACAATGAAAAATGTATCGATACATTTATGTC
Found at i:1629298 original size:132 final size:132
Alignment explanation
Indices: 1629061--1629321 Score: 441
Period size: 132 Copynumber: 2.0 Consensus size: 132
1629051 AGTTAAAAGG
*
1629061 TTAATATTGCATCATAAAATAAATTAAGACGTTTCATGTCTTCCAATTTCATGCTTATATTTATT
1 TTAATATTGCATCATAAAATAAATTAAGAAGTTTCATGTCTTCCAATTTCATGCTTATATTTATT
* * * *
1629126 AAAACAAATCTTCGCTTTAGTTTATAATAGCACAATTAATAAAATCTTACAACCAACAAATCTTT
66 AAAACAAATCCTCACTTTAGTTTACAATAGCACAATTAATAAAATATTACAACCAACAAATCTTT
1629191 TA
131 TA
* *
1629193 TTAATATTGCGTCATAAAATAGATTAAGAAGTTTCATGTCTTCCAATTTCATGCTTATATTTATT
1 TTAATATTGCATCATAAAATAAATTAAGAAGTTTCATGTCTTCCAATTTCATGCTTATATTTATT
* *
1629258 AAAACAAATCCTCACTTTAGTTTGCCATAGCACAATTAATAAAATATTACAACCAACAAATCTT
66 AAAACAAATCCTCACTTTAGTTTACAATAGCACAATTAATAAAATATTACAACCAACAAATCTT
1629322 GTGTTGGTGA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (132 bp):
TTAATATTGCATCATAAAATAAATTAAGAAGTTTCATGTCTTCCAATTTCATGCTTATATTTATT
AAAACAAATCCTCACTTTAGTTTACAATAGCACAATTAATAAAATATTACAACCAACAAATCTTT
TA
Found at i:1629731 original size:21 final size:20
Alignment explanation
Indices: 1629704--1629743 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1629694 AAATATAAAA
1629704 TTAT-TTTTAT-ATTAATATT
1 TTATATTTTATAATTAA-ATT
1629723 TTATATTTTATAATTAAATT
1 TTATATTTTATAATTAAATT
1629743 T
1 T
1629744 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTTTATAATTAAATT
Found at i:1631483 original size:2 final size:2
Alignment explanation
Indices: 1631476--1631506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1631466 ATCTAAATCC
1631476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1631507 AACATGCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1635629 original size:129 final size:129
Alignment explanation
Indices: 1635465--1635723 Score: 464
Period size: 129 Copynumber: 2.0 Consensus size: 129
1635455 GTTCAATTTT
1635465 TTCAATTTCTTCCTTTATAACAACTAATCATTTTCTCCCCCTTACTAAAATATCTCCCCATTTCT
1 TTCAATTTCTTCCTTTATAACAACTAATCATTTTCTCCCCCTTACTAAAATATCTCCCCATTTCT
* * *
1635530 ATTAGGCTAAAACTATTCTTCCCCTTTTGTTATTCTTGTAACTAATACCAGGAGTTTATGCATG
66 ATTAGGCCAAAACTATTCTTCCCCTTTTGTTATTCTTGTAACTAATAACAAGAGTTTATGCATG
* *
1635594 TTCAATTTCTTTCTTTATAACAACTAATCATTTTCTCCCCCTTACTAAAATATCTCCCCCTTTCT
1 TTCAATTTCTTCCTTTATAACAACTAATCATTTTCTCCCCCTTACTAAAATATCTCCCCATTTCT
*
1635659 ATTAGGCCAAAACTATTCTTCCCTTTTTGTTATTCTTGTAACTAATAACAAGAGTTTATGCATG
66 ATTAGGCCAAAACTATTCTTCCCCTTTTGTTATTCTTGTAACTAATAACAAGAGTTTATGCATG
1635723 T
1 T
1635724 CTAGACGCCA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (129 bp):
TTCAATTTCTTCCTTTATAACAACTAATCATTTTCTCCCCCTTACTAAAATATCTCCCCATTTCT
ATTAGGCCAAAACTATTCTTCCCCTTTTGTTATTCTTGTAACTAATAACAAGAGTTTATGCATG
Found at i:1636475 original size:20 final size:20
Alignment explanation
Indices: 1636450--1636503 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1636440 TACCCAGATC
*
1636450 TATCGATACATTTTTCAATG
1 TATCGATACATTCTTCAATG
1636470 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
*
1636490 TATTGATACATTCT
1 TATCGATACATTCT
1636504 ATCTTTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:1637451 original size:20 final size:22
Alignment explanation
Indices: 1637411--1637451 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1637401 TAGCCTTTGA
*
1637411 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1637433 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
1637452 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1641221 original size:23 final size:24
Alignment explanation
Indices: 1641176--1641222 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1641166 CAAAAGATTG
*
1641176 AACACAAATTCAATTAAGTACAAA
1 AACACAAATTCAATTAAGAACAAA
1641200 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
1641223 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.17, G:0.04, T:0.17
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1641926 original size:21 final size:22
Alignment explanation
Indices: 1641877--1641928 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1641867 AGTTAACTCA
*
1641877 TCATTTTCATTTTGCAACTCATT
1 TCATTTTC-TTTTCCAACTCATT
*
1641900 TC-TTTTCTTTTCCAACTTA-T
1 TCATTTTCTTTTCCAACTCATT
1641920 TCATTTTCT
1 TCATTTTCT
1641929 CTTTTAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 5 0.19
23 2 0.08
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (22 bp):
TCATTTTCTTTTCCAACTCATT
Found at i:1643574 original size:35 final size:36
Alignment explanation
Indices: 1643528--1643595 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
1643518 AGATAGAAAC
* ** *
1643528 CTCCTTATC-TTTTCACGGGCTAGGATAGAACCTTT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTTT
1643563 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACC
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACC
1643596 ACACAATCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 8 0.29
36 20 0.71
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTTT
Found at i:1644111 original size:24 final size:24
Alignment explanation
Indices: 1644079--1644148 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
1644069 ACAATGTATC
* *
1644079 GATACATGAACAGTGATGAATAGT
1 GATACATGAACAGTGATGAACAAT
1644103 GATACATGAACAGTGATGAACAAT
1 GATACATGAACAGTGATGAACAAT
1644127 GATACATGAACAGTGATGAACA
1 GATACATGAACAGTGATGAACA
1644149 GTAATAAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (24 bp):
GATACATGAACAGTGATGAACAAT
Found at i:1644117 original size:14 final size:14
Alignment explanation
Indices: 1644079--1644143 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 14
1644069 ACAATGTATC
1644079 GATACATGAACAGT
1 GATACATGAACAGT
*
1644093 G----ATGAATAGT
1 GATACATGAACAGT
1644103 GATACATGAACAGT
1 GATACATGAACAGT
*
1644117 G----ATGAACAAT
1 GATACATGAACAGT
1644127 GATACATGAACAGT
1 GATACATGAACAGT
1644141 GAT
1 GAT
1644144 GAACAGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
10 18 0.46
14 21 0.54
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (14 bp):
GATACATGAACAGT
Found at i:1647848 original size:19 final size:19
Alignment explanation
Indices: 1647803--1647855 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1647793 CTGCCAATTT
**
1647803 TATGTATCGATACAATTCA
1 TATGTATCGATACAATGAA
*
1647822 TGATGTATCGATATAATGAA
1 T-ATGTATCGATACAATGAA
1647842 TATGTATCGATACA
1 TATGTATCGATACA
1647856 TTGTATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
TATGTATCGATACAATGAA
Found at i:1648226 original size:23 final size:25
Alignment explanation
Indices: 1648194--1648247 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
1648184 CCCATGTGCT
* *
1648194 TATTTAATTTATTTAT-TTGGG-CA
1 TATTTTATTTAATTATATTGGGCCA
1648217 TATTTTATTTAATTATATTGGGCCA
1 TATTTTATTTAATTATATTGGGCCA
1648242 -ATTTTA
1 TATTTTA
1648248 GAAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 14 0.52
24 11 0.41
25 2 0.07
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (25 bp):
TATTTTATTTAATTATATTGGGCCA
Found at i:1651996 original size:16 final size:16
Alignment explanation
Indices: 1651975--1652008 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1651965 TGCATTCTTG
1651975 CAATTTACGTTTATTA
1 CAATTTACGTTTATTA
**
1651991 CAATTTATTTTTATTA
1 CAATTTACGTTTATTA
1652007 CA
1 CA
1652009 TTGTACATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (16 bp):
CAATTTACGTTTATTA
Found at i:1653428 original size:79 final size:77
Alignment explanation
Indices: 1653283--1653535 Score: 278
Period size: 79 Copynumber: 3.3 Consensus size: 77
1653273 ATTTAAAAAG
* * * * * * **
1653283 AAACAGGGTTAGAGTATCCTCTCTAAATACGGGGTTGG-GTATCCCGAGAA-AAAAAATTTAGCA
1 AAACGGGGTTAGAGTATCCCCTCAAAATATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAATA
1653346 TTTTGGAAATAA
66 TTTTGGAAATAA
* * *
1653358 CAGCGGGGTTATAGTATCCCCTCAAAATTGATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAA
1 AAACGGGGTTAGAGTATCCCCTCAAAA-T-ATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAA
1653423 TATTTTGGAAATAA
64 TATTTTGGAAATAA
* * * * *
1653437 AAACGGGGTTCA-AGTATTCCCTCGAAAATAATGAGGTTGGAGTATCCCCGAGATAAAAATTTTA
1 AAACGGGGTT-AGAGTATCCCCTC-AAAAT-ATGGGGTTGGAGTATCCCCAAAATAAAAAATTTA
*
1653501 ATATTTTAGAAATAA
63 ATATTTTGGAAATAA
*
1653516 AAACGGGGTTGGAGTATCCC
1 AAACGGGGTTAGAGTATCCC
1653536 TGAGATGAAA
Statistics
Matches: 149, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
75 21 0.14
76 1 0.01
77 9 0.06
78 10 0.07
79 103 0.69
80 5 0.03
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (77 bp):
AAACGGGGTTAGAGTATCCCCTCAAAATATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAATA
TTTTGGAAATAA
Found at i:1653529 original size:51 final size:51
Alignment explanation
Indices: 1653471--1653568 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
1653461 AAAATAATGA
1653471 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTT-AGAAATAAAAACGG
1 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTGA-AAATAAAAACGG
* *
1653522 GGTTGGAGTATCCCTGAGATGAAAATTTTAATATTTTGAAAATAAAA
1 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTGAAAATAAAA
1653569 GCAGGGTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTGAAAATAAAAACGG
Found at i:1653565 original size:130 final size:130
Alignment explanation
Indices: 1653390--1653666 Score: 378
Period size: 130 Copynumber: 2.1 Consensus size: 130
1653380 CAAAATTGAT
* * *
1653390 GGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGGAAATAAAAACGGGGTTCAAGTATT
1 GGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGAAAATAAAAACAGGGTTAAAGTA-T
*
1653455 CC-CT-CGAAAATAATGAGGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTAGAAATAAAA
65 CCTCTCCG-AAATAATGAGGTTGGAGTATCCCCAAGATAAAAATTTTAATATTTTAGAAATAAAA
1653518 AC
129 AC
** * * * *
1653520 GGGGTTGGAGTATCCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAGCAGGGTTAAAGTATC
1 GGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGAAAATAAAAACAGGGTTAAAGTATC
* * * * * *
1653585 CTCTCCGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAGATAAAAAC
66 CTCTCCGAAATAATGAGGTTGGAGTATCCCCAAGATAAAAATTTTAATATTTTAGAAATAAAAAC
1653650 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
1653667 TCAGAAATAA
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
129 3 0.02
130 123 0.96
131 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (130 bp):
GGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGAAAATAAAAACAGGGTTAAAGTATC
CTCTCCGAAATAATGAGGTTGGAGTATCCCCAAGATAAAAATTTTAATATTTTAGAAATAAAAAC
Found at i:1653576 original size:51 final size:51
Alignment explanation
Indices: 1653471--1653585 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
1653461 AAAATAATGA
*
1653471 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTAGAAATAAAAACGG
1 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTAGAAATAAAAACAG
* * *
1653522 GGTTGGAGTATCCCTGAGATGAAAATTTTAATATTTT-GAAAATAAAAGCAG
1 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTAG-AAATAAAAACAG
**
1653573 GGTTAAAGTATCC
1 GGTTGGAGTATCC
1653586 TCTCCGAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 1 0.02
51 56 0.98
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTAGAAATAAAAACAG
Found at i:1653687 original size:209 final size:207
Alignment explanation
Indices: 1653306--1653741 Score: 592
Period size: 209 Copynumber: 2.1 Consensus size: 207
1653296 GTATCCTCTC
* * * * * *
1653306 TAAATACGGGGTTGG-GTATCCCGAGAAAAAAAATTTAGCATTTTGGAAATAACAGCGGGGTTAT
1 TAAAAACGGGGTTGGAGTATCCCGAGAAAAAAAATTTAACATTTTGAAAATAAAAGCAGGGTTAA
1653370 AGTATCCCCTCAAAATTGATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGGAAAT
66 AGTATCCCCTCAAAATTGATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGGAAAT
*
1653435 AAAAACGGGGTTCAAGTATTCCCTCGAAAATAATGAGGTTGGAGTATCCCCGAGATAAAAATTTT
131 AAAAACGGGGTTCAAGTATCCCCTCGAAAATAATGAGGTTGGAGTATCCCCGAGAT-AAAATTTT
1653500 AATATTTT-AGAAA
195 AATATTTTGA-AAA
** * *
1653513 TAAAAACGGGGTTGGAGTATCCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAGCAGGGTTA
1 TAAAAACGGGGTTGGAGTATCCC-GAGAAAAAAAATTTAACATTTTGAAAATAAAAGCAGGGTTA
* ** * * * *
1653578 AAGTATCCTCTCCGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAGA
65 AAGTATCCCCTCAAAATTGATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGGAAA
** * *
1653643 TAAAAACGGGGTTGGAGTATCCCCTC-AGAAATAAT-AGAGTTGGAGTATTCCCGAGATGAAATT
130 TAAAAACGGGGTTCAAGTATCCCCTCGA-AAATAATGAG-GTTGGAGTATCCCCGAGATAAAATT
1653706 TTAATATTTTGAAAA
193 TTAATATTTTGAAAA
*
1653721 TAAAAACAGGGTTGGAGTATC
1 TAAAAACGGGGTTGGAGTATC
1653742 TCCTCGAAAA
Statistics
Matches: 201, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
207 14 0.07
208 48 0.24
209 139 0.69
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (207 bp):
TAAAAACGGGGTTGGAGTATCCCGAGAAAAAAAATTTAACATTTTGAAAATAAAAGCAGGGTTAA
AGTATCCCCTCAAAATTGATGGGGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTGGAAAT
AAAAACGGGGTTCAAGTATCCCCTCGAAAATAATGAGGTTGGAGTATCCCCGAGATAAAATTTTA
ATATTTTGAAAA
Found at i:1653734 original size:78 final size:78
Alignment explanation
Indices: 1653523--1653750 Score: 289
Period size: 79 Copynumber: 2.9 Consensus size: 78
1653513 TAAAAACGGG
* ** *
1653523 GTTGGAGTA-TCCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAGCAGGGTTAAAGTATCCT
1 GTTGGAGTATTCCC-GAGATGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCC
* * * *
1653587 CTCCGAATTGATGGG
65 CT-CGAAATAATAGA
* * * * *
1653602 GTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAGATAAAAACGGGGTTGGAGTATCCCC
1 GTTGGAGTATTCCCGAGATGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCC
1653667 TCAGAAATAATAGA
66 TC-GAAATAATAGA
*
1653681 GTTGGAGTATTCCCGAGATG-AAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCTCC
1 GTTGGAGTATTCCCGAGATGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCC
1653745 TCGAAA
66 TCGAAA
1653751 ATAACGGGGT
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
77 4 0.03
78 43 0.34
79 78 0.61
80 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (78 bp):
GTTGGAGTATTCCCGAGATGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCC
TCGAAATAATAGA
Found at i:1653793 original size:78 final size:77
Alignment explanation
Indices: 1653520--1653781 Score: 285
Period size: 79 Copynumber: 3.3 Consensus size: 77
1653510 AAATAAAAAC
** * **
1653520 GGGGTTGGAGTATCCCTGAGATGAAAATTTTAATATTTTGAAAATAAAAGCAGGGTTAAAGTATC
1 GGGGTTGGAGTATCCCCAAGAT-AAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATC
* *
1653585 CTCTCCG-AATTGAT
65 C-CT-CGAAAATAAT
* * *
1653599 GGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAGATAAAAACGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAAGAT-AAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTAT-
1653664 CCCTC-AGAAATAAT
64 CCCTCGA-AAATAAT
* * * * *
1653678 AGAGTTGGAGTATTCCCGAGATGAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCT
1 GGGGTTGGAGTATCCCCAAGATAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATC-
*
1653743 CCTCGAAAATAAC
65 CCTCGAAAATAAT
* *
1653756 GGGGTTAGAATATCCCCAAGATAAAA
1 GGGGTTGGAGTATCCCCAAGATAAAA
1653782 AATCAATATT
Statistics
Matches: 152, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
77 1 0.01
78 67 0.44
79 82 0.54
80 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (77 bp):
GGGGTTGGAGTATCCCCAAGATAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCC
CTCGAAAATAAT
Found at i:1660268 original size:21 final size:20
Alignment explanation
Indices: 1660201--1660274 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
1660191 AAGGTGATAT
*
1660201 TGTATCGATACATTTCGA-GCA
1 TGTATCGATACA-TTC-ACTCA
*
1660222 TGCATCGATACATTCACTCA
1 TGTATCGATACATTCACTCA
*
1660242 TGTATCGATACATTTACT-A
1 TGTATCGATACATTCACTCA
1660261 TTTGTATCGATACA
1 --TGTATCGATACA
1660275 ATTTGTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.04
20 21 0.46
21 23 0.50
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTCACTCA
Found at i:1663964 original size:16 final size:16
Alignment explanation
Indices: 1663939--1664006 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
1663929 TTCGAGTTAT
* *
1663939 TTTCGGGTTCGGGTCA
1 TTTCGAGTTCAGGTCA
*
1663955 TTTCGAGTTCAGGTTA
1 TTTCGAGTTCAGGTCA
**
1663971 TTTCGAGTTTGGGTCA
1 TTTCGAGTTCAGGTCA
1663987 TTTCGAGTTCAGGTCA
1 TTTCGAGTTCAGGTCA
1664003 TTTC
1 TTTC
1664007 AGATTTGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.13, C:0.16, G:0.28, T:0.43
Consensus pattern (16 bp):
TTTCGAGTTCAGGTCA
Found at i:1663985 original size:32 final size:32
Alignment explanation
Indices: 1663934--1664016 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
1663924 AAACTTTCGA
* *
1663934 GTTATTTTCGGGTTCGGGTCATTTCGAGTTCAG
1 GTTA-TTTCGAGTTTGGGTCATTTCGAGTTCAG
1663967 GTTATTTCGAGTTTGGGTCATTTCGAGTTCAG
1 GTTATTTCGAGTTTGGGTCATTTCGAGTTCAG
*
1663999 GTCATTTC-AGATTTGGGT
1 GTTATTTCGAG-TTTGGGT
1664017 TAATCGGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.04
32 40 0.87
33 4 0.09
ACGTcount: A:0.14, C:0.13, G:0.29, T:0.43
Consensus pattern (32 bp):
GTTATTTCGAGTTTGGGTCATTTCGAGTTCAG
Found at i:1664056 original size:53 final size:55
Alignment explanation
Indices: 1663993--1664112 Score: 156
Period size: 53 Copynumber: 2.2 Consensus size: 55
1663983 GTCATTTCGA
** * *
1663993 GTTCAGGTCATTTC-AGATTTGGGTTAATCGGGTTTAACACTTGGGTT-AATCGG
1 GTTCAGGTCATTTCTAGATTTGGGCCAATCAGGTTTAACACTTGAGTTAAATCGG
* *
1664046 GTTCAGGTCA-TTCTAGATTTGGGCCAATTAGGTTTAACATTTGAGTTAAATCGG
1 GTTCAGGTCATTTCTAGATTTGGGCCAATCAGGTTTAACACTTGAGTTAAATCGG
*
1664100 GTTCAAGTCATTT
1 GTTCAGGTCATTT
1664113 TAGGTTTAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
52 3 0.05
53 37 0.65
54 15 0.26
55 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (55 bp):
GTTCAGGTCATTTCTAGATTTGGGCCAATCAGGTTTAACACTTGAGTTAAATCGG
Found at i:1664851 original size:16 final size:16
Alignment explanation
Indices: 1664830--1664862 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1664820 ATTATCCAGG
*
1664830 TCATTTCGGGTTCGGA
1 TCATTTCGAGTTCGGA
1664846 TCATTTCGAGTTCGGA
1 TCATTTCGAGTTCGGA
1664862 T
1 T
1664863 TCTTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.39
Consensus pattern (16 bp):
TCATTTCGAGTTCGGA
Found at i:1666113 original size:17 final size:18
Alignment explanation
Indices: 1666091--1666124 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1666081 TAAATATTAA
1666091 ATATAAATATA-TAATTG
1 ATATAAATATATTAATTG
1666108 ATATAAATATATTAATT
1 ATATAAATATATTAATT
1666125 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATAAATATATTAATTG
Found at i:1673214 original size:29 final size:29
Alignment explanation
Indices: 1673166--1673233 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1673156 TTCAGTATAT
* *
1673166 TATATTT-AAATAAATTTTATTTTAAA-A
1 TATATTTAAAATAAATATTATATTAAATA
* *
1673193 TATAATTTAAAATATATATTATATTAACTA
1 TAT-ATTTAAAATAAATATTATATTAAATA
1673223 TATATTTAAAA
1 TATATTTAAAA
1673234 ATAATAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 3 0.09
28 4 0.12
29 23 0.68
30 4 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTAAAATAAATATTATATTAAATA
Found at i:1673297 original size:12 final size:12
Alignment explanation
Indices: 1673183--1673301 Score: 54
Period size: 12 Copynumber: 9.7 Consensus size: 12
1673173 AAATAAATTT
*
1673183 TATTTTAAAATA
1 TATTTAAAAATA
1673195 TAATTTAAAATATA
1 T-ATTTAAAA-ATA
*
1673209 TATTATATTAACTATA
1 TATT-TA--AA-AATA
1673225 TATTTAAAAATAA
1 TATTTAAAAAT-A
*
1673238 TAATT-AAAATCA
1 TATTTAAAAAT-A
1673250 TATTTAAGAAAT-
1 TATTTAA-AAATA
**
1673262 TATTGCAAAATAA
1 TATTTAAAAAT-A
1673275 TATTT-----TA
1 TATTTAAAAATA
1673282 TATTTAAAAATA
1 TATTTAAAAATA
1673294 TATTTAAA
1 TATTTAAA
1673302 TTTGATATTT
Statistics
Matches: 82, Mismatches: 9, Indels: 32
0.67 0.07 0.26
Matches are distributed among these distances:
7 6 0.07
8 1 0.01
11 4 0.05
12 28 0.34
13 22 0.27
14 10 0.12
15 2 0.02
16 9 0.11
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (12 bp):
TATTTAAAAATA
Found at i:1673514 original size:5 final size:5
Alignment explanation
Indices: 1673504--1673573 Score: 68
Period size: 5 Copynumber: 13.2 Consensus size: 5
1673494 TATTAAATAA
* * *
1673504 TTATT TTATT TTATT TTATTT TTATT TTATTT TTATT TTATA TAATAA
1 TTATT TTATT TTATT TTA-TT TTATT TTA-TT TTATT TTATT TTAT-T
*
1673552 TTATT TAATT TTAGTT TTATT T
1 TTATT TTATT TTA-TT TTATT T
1673574 CATTCAACGA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
5 36 0.65
6 19 0.35
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:1673526 original size:11 final size:11
Alignment explanation
Indices: 1673504--1673544 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
1673494 TATTAAATAA
1673504 TTATTTTA-TT
1 TTATTTTATTT
1673514 TTATTTTATTT
1 TTATTTTATTT
1673525 TTATTTTATTT
1 TTATTTTATTT
1673536 TTATTTTAT
1 TTATTTTAT
1673545 ATAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 8 0.27
11 22 0.73
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:1673526 original size:16 final size:16
Alignment explanation
Indices: 1673504--1673573 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
1673494 TATTAAATAA
1673504 TTATTTTATTTTA-TT
1 TTATTTTATTTTATTT
1673519 TTATTTTTATTTTATTT
1 TTA-TTTTATTTTATTT
* * **
1673536 TTATTTTATATAATAA
1 TTATTTTATTTTATTT
* *
1673552 TTATTTAATTTTAGTT
1 TTATTTTATTTTATTT
1673568 TTATTT
1 TTATTT
1673574 CATTCAACGA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 3 0.07
16 35 0.81
17 5 0.12
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:1673555 original size:27 final size:25
Alignment explanation
Indices: 1673494--1673572 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 25
1673484 TGTGCTAAAC
1673494 TATTAAATAATTATTTTATTTTATTT
1 TATT-AATAATTATTTTATTTTATTT
1673520 TATT--T--TTATTTTATTTTTATTT
1 TATTAATAATTATTTTA-TTTTATTT
*
1673542 TATATAATAATTATTTAATTTTAGTTT
1 TAT-TAATAATTATTTTATTTTA-TTT
1673569 TATT
1 TATT
1673573 TCATTCAACG
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
21 8 0.18
22 11 0.24
23 2 0.04
25 1 0.02
26 10 0.22
27 13 0.29
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (25 bp):
TATTAATAATTATTTTATTTTATTT
Found at i:1673573 original size:11 final size:10
Alignment explanation
Indices: 1673504--1673573 Score: 68
Period size: 11 Copynumber: 6.6 Consensus size: 10
1673494 TATTAAATAA
1673504 TTATTTTATT
1 TTATTTTATT
1673514 TTATTTTATTT
1 TTATTTTA-TT
1673525 TTATTTTATTT
1 TTATTTTA-TT
*
1673536 TTATTTTATA
1 TTATTTTATT
* *
1673546 TAATAATTATT
1 TTAT-TTTATT
*
1673557 TAATTTTAGTT
1 TTATTTTA-TT
1673568 TTATTT
1 TTATTT
1673574 CATTCAACGA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
10 15 0.29
11 36 0.71
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (10 bp):
TTATTTTATT
Found at i:1675002 original size:21 final size:19
Alignment explanation
Indices: 1674962--1675002 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1674952 TCAAACAAAT
*
1674962 AAATATAAAAATATTTTTA
1 AAATATAAAAATATTATTA
1674981 AAATATAATAAATTATTATTA
1 AAATATAA-AAA-TATTATTA
1675002 A
1 A
1675003 TTAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATAAAAATATTATTA
Found at i:1675621 original size:15 final size:16
Alignment explanation
Indices: 1675601--1675630 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1675591 CGCACAAGTA
1675601 TTTTTTTTT-CTTTTT
1 TTTTTTTTTGCTTTTT
1675616 TTTTTTTTTGCTTTT
1 TTTTTTTTTGCTTTT
1675631 AAATTTTGAT
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:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (16 bp):
TTTTTTTTTGCTTTTT
Found at i:1677026 original size:14 final size:14
Alignment explanation
Indices: 1677001--1677049 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1676991 AATACTAAGT
1677001 TAATATATAATTTAA
1 TAATA-ATAATTTAA
*
1677016 TAATAATAATTAAA
1 TAATAATAATTTAA
1677030 TAA-AATTAATTTAA
1 TAATAA-TAATTTAA
*
1677044 AAATAA
1 TAATAA
1677050 CTAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.07
14 20 0.69
15 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAATAATTTAA
Found at i:1677043 original size:28 final size:27
Alignment explanation
Indices: 1677005--1677071 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
1676995 CTAAGTTAAT
*
1677005 ATATAATTTAATAATAATAATTAAATAA
1 ATATAATTTAATAATAATAACTAAA-AA
1677033 A-ATTAATTT-A-AA-AATAACTAAAAA
1 ATA-TAATTTAATAATAATAACTAAAAA
1677057 ATATAATTTAATAAT
1 ATATAATTTAATAAT
1677072 GTGTTTAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
24 9 0.27
25 11 0.33
26 4 0.12
27 2 0.06
28 7 0.21
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAATTTAATAATAATAACTAAAAA
Found at i:1678846 original size:2 final size:2
Alignment explanation
Indices: 1678839--1678868 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1678829 CACCAAAATC
1678839 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1678869 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1678873 original size:2 final size:2
Alignment explanation
Indices: 1678868--1678901 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1678858 ACACACACAC
1678868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1678902 GTAATGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1684045 original size:2 final size:2
Alignment explanation
Indices: 1684038--1684074 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1684028 GCTTTAAAGT
1684038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1684075 TAATTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1685080 original size:112 final size:111
Alignment explanation
Indices: 1684727--1685161 Score: 485
Period size: 112 Copynumber: 3.9 Consensus size: 111
1684717 AAGTAAAGTT
* *
1684727 GTAAATTATTTAATTT-AAGATCAAGTCTTAT-AAAATATATATTAGATAAAATAGATCTCACGA
1 GTAAATTATTTAATTTAAAG-TCAAGTCTTATAAAAATATATATTAAATAAAATAGATCTCA-TA
* * *
1684790 -GCTTATTTAATTAATCTGTTTAGGTTTATTTTATTTAATTATATCACG
64 TGCTTATTTAATTAATTTATTTAGGTCTATTTTATTTAATTATATCA-G
* * * *
1684838 TCATAAATTATTTAATTTAATA-CCAAGTCTTATAAAAATATATATTAAATAAAATAG--GTCAC
1 --GTAAATTATTTAATTTAA-AGTCAAGTCTTATAAAAATATATATTAAATAAAATAGATCTCAT
* * *
1684900 GTGCTTATTTAATT-ATTTATTTAGATCTA-TTTATTTCATTATATCA-
63 ATGCTTATTTAATTAATTTATTTAGGTCTATTTTATTTAATTATATCAG
* *
1684946 -TAAATTATTTAATTTAAGGTCAATTCTTATAAAAAATATATATTAAATAAAATAGATCTCATAT
1 GTAAATTATTTAATTTAAAGTCAAGTCTTAT-AAAAATATATATTAAATAAAATAGATCTCATAT
*
1685010 GCTTATTTAATTAATTTATTTAGGTCTATTTTATTTAATTATATTAG
65 GCTTATTTAATTAATTTATTTAGGTCTATTTTATTTAATTATATCAG
** * * *
1685057 GTAAATTATTTAATTTAAAGTCAAACCTTATAAAAAATATATATTAGATAAAATAAAACTCATAT
1 GTAAATTATTTAATTTAAAGTCAAGTCTTAT-AAAAATATATATTAAATAAAATAGATCTCATAT
* * * * * *
1685122 GCATATTTAAGTAACTTATTTGGGGCCTACTTTATTTAAT
65 GCTTATTTAATTAATTTATTT-AGGTCTATTTTATTTAAT
1685162 CATGTTGGAT
Statistics
Matches: 277, Mismatches: 32, Indels: 26
0.83 0.10 0.08
Matches are distributed among these distances:
105 26 0.09
106 24 0.09
108 16 0.06
109 14 0.05
110 31 0.11
111 11 0.04
112 91 0.33
113 40 0.14
114 23 0.08
115 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (111 bp):
GTAAATTATTTAATTTAAAGTCAAGTCTTATAAAAATATATATTAAATAAAATAGATCTCATATG
CTTATTTAATTAATTTATTTAGGTCTATTTTATTTAATTATATCAG
Found at i:1685131 original size:220 final size:217
Alignment explanation
Indices: 1684728--1685131 Score: 546
Period size: 220 Copynumber: 1.8 Consensus size: 217
1684718 AGTAAAGTTG
*
1684728 TAAATTATTTAATTTAAGATCAAGTCTTATAAAATATATATTAGATAAAATAGATCTCACGAGCT
1 TAAATTATTTAATTTAAGATCAAGTCTTATAAAATATATATTAAATAAAATAGATCTCACGAGCT
* *
1684793 TATTTAATTAATCTGTTTAGGTTTATTTTATTTAATTATATCACGTCATAAATTATTTAATTTAA
66 TATTTAATTAATCTATTTAGGTCTATTTTATTTAATTATATCACG-CATAAATTATTTAATTTAA
** ** * *
1684858 TACCAAGTCTTATAAAAATATATATTAAATAAAATAGGTCACGTGCTTATTTAATTATTTATTTA
130 TACCAAACCTTATAAAAATATATATTAAATAAAATAACTCACATGCATATTTAATTATTTATTTA
1684923 GATCTATTTATTTCATTATATCA
195 GATCTATTTATTTCATTATATCA
* * *
1684946 TAAATTATTTAATTTAAGGTCAATTCTTATAAAAAATATATATTAAATAAAATAGATCTCA-TAT
1 TAAATTATTTAATTTAAGATCAAGTCTTAT--AAAATATATATTAAATAAAATAGATCTCACGA-
* * *
1685010 GCTTATTTAATTAATTTATTTAGGTCTATTTTATTTAATTATATTA-G-GTAAATTATTTAATTT
63 GCTTATTTAATTAATCTATTTAGGTCTATTTTATTTAATTATATCACGCATAAATTATTTAATTT
* * *
1685073 AA-AGTCAAACCTTATAAAAAATATATATTAGATAAAATAAAACTCATATGCATATTTAA
128 AATA-CCAAACCTTAT-AAAAATATATATTAAATAAAAT--AACTCACATGCATATTTAA
1685132 GTAACTTATT
Statistics
Matches: 161, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
216 1 0.01
217 25 0.16
218 49 0.30
219 2 0.01
220 84 0.52
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (217 bp):
TAAATTATTTAATTTAAGATCAAGTCTTATAAAATATATATTAAATAAAATAGATCTCACGAGCT
TATTTAATTAATCTATTTAGGTCTATTTTATTTAATTATATCACGCATAAATTATTTAATTTAAT
ACCAAACCTTATAAAAATATATATTAAATAAAATAACTCACATGCATATTTAATTATTTATTTAG
ATCTATTTATTTCATTATATCA
Found at i:1689631 original size:15 final size:15
Alignment explanation
Indices: 1689586--1689632 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1689576 CACACTAATG
1689586 TTGTTTTAAAA-ATTA
1 TTGTTTTAAAATA-TA
*
1689601 TT-TATTAAAATGATA
1 TTGTTTTAAAAT-ATA
1689616 TTGTTTTAAAATATA
1 TTGTTTTAAAATATA
1689631 TT
1 TT
1689633 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.26
15 11 0.41
16 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTGTTTTAAAATATA
Found at i:1689637 original size:13 final size:14
Alignment explanation
Indices: 1689594--1689641 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
1689584 TGTTGTTTTA
1689594 AAAAT-TATTTATT
1 AAAATATATTTATT
*
1689607 AAAATGATATTGTTTT
1 AAAAT-ATATT-TATT
1689623 AAAATATA-TTATT
1 AAAATATATTTATT
1689636 AAAATA
1 AAAATA
1689642 ATACTGTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 14 0.47
14 1 0.03
15 7 0.23
16 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (14 bp):
AAAATATATTTATT
Found at i:1694510 original size:15 final size:15
Alignment explanation
Indices: 1694490--1694519 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1694480 TTTGAAAGTA
*
1694490 TCATAAGTTTTTTTC
1 TCATAAATTTTTTTC
1694505 TCATAAATTTTTTTC
1 TCATAAATTTTTTTC
1694520 GAGTCCAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.60
Consensus pattern (15 bp):
TCATAAATTTTTTTC
Found at i:1697589 original size:78 final size:78
Alignment explanation
Indices: 1697507--1697685 Score: 297
Period size: 78 Copynumber: 2.3 Consensus size: 78
1697497 TATCGAGATA
*
1697507 TTTCATGTTGAATGTGCACTTTAAAGGTAGGTTTTTCATTTCATGTTATTATTGAATCCATTAGC
1 TTTCATGTTGAATGTGCACTTTAAAAGTAGGTTTTTCATTTCATGTTATTATTGAATCCATTAGC
1697572 ATCACT-GAGATGT
66 ATCACTAGA-ATGT
*
1697585 TTTCATGTTGAATATGCACTTTAAAAGTAGGTTTTTCATTTCATGTTATTATTGAATCCATTAGC
1 TTTCATGTTGAATGTGCACTTTAAAAGTAGGTTTTTCATTTCATGTTATTATTGAATCCATTAGC
1697650 ATCACTAGAATGT
66 ATCACTAGAATGT
* * *
1697663 TTTCATGTCGAAGGTGTACTTTA
1 TTTCATGTTGAATGTGCACTTTA
1697686 GGAAACATTT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 92 0.98
79 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.44
Consensus pattern (78 bp):
TTTCATGTTGAATGTGCACTTTAAAAGTAGGTTTTTCATTTCATGTTATTATTGAATCCATTAGC
ATCACTAGAATGT
Found at i:1699376 original size:13 final size:13
Alignment explanation
Indices: 1699335--1699417 Score: 96
Period size: 13 Copynumber: 7.2 Consensus size: 13
1699325 CCGTTACAAG
1699335 CAATGTATCGATA
1 CAATGTATCGATA
1699348 CAAT-T-TC-AT-
1 CAATGTATCGATA
1699357 C-ATGTATCGATA
1 CAATGTATCGATA
1699369 CAATGTATCGATA
1 CAATGTATCGATA
1699382 CAAT-T-TC-AT-
1 CAATGTATCGATA
1699391 C-ATGTATCGATA
1 CAATGTATCGATA
1699403 CAATGTATCGATA
1 CAATGTATCGATA
1699416 CA
1 CA
1699418 TTGTCCCATA
Statistics
Matches: 60, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 8 0.13
11 8 0.13
12 4 0.07
13 32 0.53
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1699376 original size:34 final size:34
Alignment explanation
Indices: 1699335--1699417 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
1699325 CCGTTACAAG
1699335 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCATCATGTATCGATA
1699369 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCATCATGTATCGATA
1699403 CAATGTATCGATACA
1 CAATGTATCGATACA
1699418 TTGTCCCATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCATCATGTATCGATA
Found at i:1699511 original size:19 final size:20
Alignment explanation
Indices: 1699468--1699521 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1699458 TGCCAATCTC
**
1699468 ATGTATCGATACAATTGTCT
1 ATGTATCGATACAATTGAAT
1699488 ATGTATCGATACAATT-AAT
1 ATGTATCGATACAATTGAAT
1699507 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1699522 GTATCGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAT
Found at i:1699525 original size:13 final size:13
Alignment explanation
Indices: 1699507--1699533 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1699497 TACAATTAAT
1699507 ATGTATCGATACA
1 ATGTATCGATACA
1699520 ATGTATCGATACA
1 ATGTATCGATACA
1699533 A
1 A
1699534 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1699529 original size:32 final size:33
Alignment explanation
Indices: 1699488--1699552 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1699478 ACAATTGTCT
**
1699488 ATGTATCGATACAATTAAT-ATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
*
1699520 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
1699553 TTGGGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:1702036 original size:13 final size:14
Alignment explanation
Indices: 1702018--1702056 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
1702008 AAATAGTACC
1702018 CAATGTATCT-ATA
1 CAATGTATCTGATA
1702031 CAATGTAT-TGATA
1 CAATGTATCTGATA
1702044 CAATGTATC-GATA
1 CAATGTATCTGATA
1702057 TAAGGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 23 0.96
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (14 bp):
CAATGTATCTGATA
Found at i:1702256 original size:29 final size:33
Alignment explanation
Indices: 1702206--1702275 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 33
1702196 AAACAAACAT
* *
1702206 AATTCAATCATACAACATAACA-AA-CATC-AA
1 AATTCATTCATACAACAAAACAGAATCATCAAA
1702236 AATTCATTCA-ACAACAAAACATGAATCATCAAA
1 AATTCATTCATACAACAAAACA-GAATCATCAAA
1702269 AATTCAT
1 AATTCAT
1702276 AATATCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 10 0.29
30 9 0.26
31 2 0.06
32 4 0.12
33 9 0.26
ACGTcount: A:0.54, C:0.21, G:0.01, T:0.23
Consensus pattern (33 bp):
AATTCATTCATACAACAAAACAGAATCATCAAA
Found at i:1708359 original size:19 final size:20
Alignment explanation
Indices: 1708315--1708368 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1708305 CTGCCAATCT
**
1708315 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1708335 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
1708354 CATGTATCGATACAA
1 CATGTATCGATACAA
1708369 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1715829 original size:2 final size:2
Alignment explanation
Indices: 1715824--1715860 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1715814 CACACAAATG
1715824 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1715861 TAAATACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1717475 original size:12 final size:12
Alignment explanation
Indices: 1717458--1717485 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1717448 TTTGTTATAA
1717458 TATTAGGTTCTC
1 TATTAGGTTCTC
1717470 TATTAGGTTCTC
1 TATTAGGTTCTC
1717482 TATT
1 TATT
1717486 GTAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (12 bp):
TATTAGGTTCTC
Found at i:1722290 original size:27 final size:28
Alignment explanation
Indices: 1722258--1722331 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
1722248 TTATTAATGT
1722258 TATAAATTTTATATAAATAT-AAAA-TA
1 TATAAATTTTATATAAATATAAAAATTA
* *
1722284 TATTAAATATAAT-TATAATATAAAAATTA
1 TA-TAAATTTTATATA-AATATAAAAATTA
* *
1722313 TAGAAAATTTATATAAATA
1 TATAAATTTTATATAAATA
1722332 AATAAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
26 4 0.11
27 13 0.35
28 14 0.38
29 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
TATAAATTTTATATAAATATAAAAATTA
Found at i:1726345 original size:13 final size:13
Alignment explanation
Indices: 1726327--1726356 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1726317 ACAATTCTTC
*
1726327 ATGTATCGATACA
1 ATGTATCAATACA
1726340 ATGTATCAATACA
1 ATGTATCAATACA
1726353 ATGT
1 ATGT
1726357 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:1726352 original size:33 final size:33
Alignment explanation
Indices: 1726306--1726370 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1726296 CGTTGGGCAT
* *
1726306 AATGTATCGATACAAT-TCTTCATGTATCGATAC
1 AATGTATCAATACAATGTC-CCATGTATCGATAC
1726339 AATGTATCAATACAATGTCCCATGTATCGATA
1 AATGTATCAATACAATGTCCCATGTATCGATA
1726371 TATTTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (33 bp):
AATGTATCAATACAATGTCCCATGTATCGATAC
Found at i:1726427 original size:20 final size:20
Alignment explanation
Indices: 1726401--1726455 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1726391 CTATCAGTTT
*
1726401 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTAAG
*
1726421 TATGTATCGATACAA-TAAG
1 CATGTATCGATACAATTAAG
1726440 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1726456 GTATCAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTAAG
Found at i:1726512 original size:54 final size:52
Alignment explanation
Indices: 1726422--1726540 Score: 202
Period size: 54 Copynumber: 2.2 Consensus size: 52
1726412 ACAATTGAGT
*
1726422 ATGTATCGATACAATAAGCATGTATCGATACAATGTATCAATATAAAGCATA
1 ATGTATCGATACAATAAGCATGTATCGATACAATGTATCAATACAAAGCATA
*
1726474 ATGTATCGATACAATATGAGCATGTATCGATACAATGTATCGATACAAAGCATA
1 ATGTATCGATACAATA--AGCATGTATCGATACAATGTATCAATACAAAGCATA
1726528 ATGTATCGATACA
1 ATGTATCGATACA
1726541 TCTGGGTGTG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 16 0.25
54 47 0.75
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATAAGCATGTATCGATACAATGTATCAATACAAAGCATA
Found at i:1726513 original size:13 final size:13
Alignment explanation
Indices: 1726495--1726521 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1726485 CAATATGAGC
1726495 ATGTATCGATACA
1 ATGTATCGATACA
1726508 ATGTATCGATACA
1 ATGTATCGATACA
1726521 A
1 A
1726522 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1735130 original size:52 final size:52
Alignment explanation
Indices: 1735045--1735169 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1735035 ATATGAAAAG
* *
1735045 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1735097 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1735149 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1735170 AAGATCGGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1735182 original size:52 final size:52
Alignment explanation
Indices: 1735045--1735189 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 52
1735035 ATATGAAAAG
* *
1735045 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAAT
*** *
1735097 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAAT
*
1735149 TTGCCTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
1735190 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 4 0.05
52 79 0.95
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAAT
Found at i:1735196 original size:13 final size:13
Alignment explanation
Indices: 1735178--1735202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1735168 CAAAGATCGG
1735178 TGTATCGATACAA
1 TGTATCGATACAA
1735191 TGTATCGATACA
1 TGTATCGATACA
1735203 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1735284 original size:13 final size:13
Alignment explanation
Indices: 1735266--1735290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1735256 CAAAAAAATA
1735266 TGTATCGATACAT
1 TGTATCGATACAT
1735279 TGTATCGATACA
1 TGTATCGATACA
1735291 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1735286 original size:33 final size:33
Alignment explanation
Indices: 1735244--1735310 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1735234 AGTAGCTTAA
1735244 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1735277 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1735310 A
1 A
1735311 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1737227 original size:13 final size:13
Alignment explanation
Indices: 1737209--1737238 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1737199 ACAATTCTTC
1737209 ATGTATCAATACA
1 ATGTATCAATACA
*
1737222 ATGTATCGATACA
1 ATGTATCAATACA
1737235 ATGT
1 ATGT
1737239 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:1737230 original size:33 final size:33
Alignment explanation
Indices: 1737188--1737254 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1737178 CGTTGGGCAT
*
1737188 AATGTATCGATACAAT-TCTTCATGTATCAATAC
1 AATGTATCGATACAATGTC-CCATGTATCAATAC
*
1737221 AATGTATCGATACAATGTCCCATGTATCGATAC
1 AATGTATCGATACAATGTCCCATGTATCAATAC
1737254 A
1 A
1737255 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATGTCCCATGTATCAATAC
Found at i:1737337 original size:19 final size:19
Alignment explanation
Indices: 1737287--1737338 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1737277 CAGTTTCATT
*
1737287 TATCGATACAATTGAGTATG
1 TATCGATACAA-TGAGCATG
* *
1737307 TATCAATTCAATGAGCATG
1 TATCGATACAATGAGCATG
1737326 TATCGATACAATG
1 TATCGATACAATG
1737339 TATCGATACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TATCGATACAATGAGCATG
Found at i:1737341 original size:13 final size:13
Alignment explanation
Indices: 1737323--1737347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1737313 TTCAATGAGC
1737323 ATGTATCGATACA
1 ATGTATCGATACA
1737336 ATGTATCGATAC
1 ATGTATCGATAC
1737348 CAAGCATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1738564 original size:20 final size:20
Alignment explanation
Indices: 1738539--1738593 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
1738529 AATTACCTGT
* *
1738539 ATGTATCGATACATTGAAGA
1 ATGTATAGATACATTGAAAA
* ** *
1738559 ATGTATTGATGTAATGAAAA
1 ATGTATAGATACATTGAAAA
1738579 ATGTATAGATACATT
1 ATGTATAGATACATT
1738594 TGGGTCAAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (20 bp):
ATGTATAGATACATTGAAAA
Found at i:1738723 original size:20 final size:20
Alignment explanation
Indices: 1738680--1738753 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
1738670 TACATAGTCC
**
1738680 TGTATCGATACATTTCAAGAA
1 TGTATCGATACA-TTCACTAA
*
1738701 TGTATCGATACATTCACTCA
1 TGTATCGATACATTCACTAA
* * *
1738721 TGTATCAATATATT-ACCTTAT
1 TGTATCGATACATTCA-C-TAA
1738742 TGTATCGATACA
1 TGTATCGATACA
1738754 AATTGTTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 18 0.43
21 23 0.55
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTCACTAA
Found at i:1739239 original size:119 final size:119
Alignment explanation
Indices: 1739027--1739262 Score: 409
Period size: 119 Copynumber: 2.0 Consensus size: 119
1739017 TAGCCCAAAT
*
1739027 AAAATAAGGTGTCTACACTTTTTTTTTAACATGATGTTTCCTAAATAACTCTAAAGGACATGCGT
1 AAAATAAGGTGTCTACACTCTTTTTTTAACATGATGTTTCCTAAATAACTCTAAAGGACATGCGT
* **
1739092 CAACATAAAAATTCTTACATGATTCTATAAACTCGGTTTCAATGCAATGTTAAC
66 CAACATAAAAATTCTTACATAACCCTATAAACTCGGTTTCAATGCAATGTTAAC
* * *
1739146 AAAATGAGGTGTCTACAGTCTTTTTTTAACATGATGTTTCCTAAATAACTCTAAAGGACATGCTT
1 AAAATAAGGTGTCTACACTCTTTTTTTAACATGATGTTTCCTAAATAACTCTAAAGGACATGCGT
1739211 CAACATAAAAATTCTTACATAACCCTATAAACTCGGTTTCAATGCAATGTTA
66 CAACATAAAAATTCTTACATAACCCTATAAACTCGGTTTCAATGCAATGTTA
1739263 GCTAAATACC
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 110 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (119 bp):
AAAATAAGGTGTCTACACTCTTTTTTTAACATGATGTTTCCTAAATAACTCTAAAGGACATGCGT
CAACATAAAAATTCTTACATAACCCTATAAACTCGGTTTCAATGCAATGTTAAC
Found at i:1743546 original size:20 final size:20
Alignment explanation
Indices: 1743523--1743593 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
1743513 ATTTGTATCA
1743523 ATACATTTCATGATGTATTG
1 ATACATTTCATGATGTATTG
* *
1743543 ATACATTAGCCTATTATGTATTG
1 ATACATT--TC-ATGATGTATTG
* *
1743566 ATACATCATCATG-TGTATCG
1 ATACAT-TTCATGATGTATTG
1743586 ATACATTT
1 ATACATTT
1743594 GAAAAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
19 1 0.03
20 19 0.47
21 2 0.05
22 2 0.05
23 16 0.40
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (20 bp):
ATACATTTCATGATGTATTG
Found at i:1748761 original size:16 final size:16
Alignment explanation
Indices: 1748740--1748770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1748730 GAGATATTGC
*
1748740 TTTAATTTTCTTAAAT
1 TTTAATTTTATTAAAT
1748756 TTTAATTTTATTAAA
1 TTTAATTTTATTAAA
1748771 AATATAAATA
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:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTTTATTAAAT
Found at i:1749300 original size:39 final size:39
Alignment explanation
Indices: 1749242--1749318 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
1749232 CGGTTCTAAA
*
1749242 AAATTATGAAAATGTGTCTATACGTATACCTTCCACATG
1 AAATTATGAAAATGCGTCTATACGTATACCTTCCACATG
* * *
1749281 AAATTATGAAAATGCGTCTATAGGTGTACCTTTCACAT
1 AAATTATGAAAATGCGTCTATACGTATACCTTCCACAT
1749319 AAAAGCATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (39 bp):
AAATTATGAAAATGCGTCTATACGTATACCTTCCACATG
Found at i:1749781 original size:164 final size:162
Alignment explanation
Indices: 1749569--1749999 Score: 519
Period size: 164 Copynumber: 2.6 Consensus size: 162
1749559 ATTTTACCTT
* * * *
1749569 TAAAAACTAAAAATTGCTATTTAATCCCTAAACTTTTTAAATTTTCATTTCATACTTGACAAAAA
1 TAAAAAC-AAAAATTGCTATTTAGTCCCTAAACTTTTAAAAATTTCATTTCATACTCGA-AAAAA
* * ****
1749634 ACTAAAGGATAGGAAAAATTTTAAAAATTTTCTATACCACTACGGGTGGCCATAAAAATAATAAA
64 ACCAAAGGATA-GAAAAGTTTTAAAAATTTT-TATACCA-TACAAAAGGCCATAAAAATAATAAA
1749699 AATTTAAAGAAAATGACTAAGATAGC-AATTTT-TTC
126 AATTTAAAGAAAATGACTAAGATAGCGAATTTTCTTC
* * *
1749734 TAAAAACAAAAATTGCTATTTGGTCCTTAAACTTTTAAAAATTTCATTTCATACTCGATGAAAAA
1 TAAAAACAAAAATTGCTATTTAGTCCCTAAACTTTTAAAAATTTCATTTCATACTCGA-AAAAAA
* **
1749799 CCGAGAA-GATATAAAGAGTTTTAAAAA-TTTTATATCCATACAAAAGGCCATAGGAATAATAAA
65 CC-A-AAGGATAGAAA-AGTTTTAAAAATTTTTATA-CCATACAAAAGGCCATAAAAATAATAAA
* *
1749862 AATTTAAAGAAAATGACTAAGATAGCGATTTTTCTTT
126 AATTTAAAGAAAATGACTAAGATAGCGAATTTTCTTC
* * * **
1749899 TAAAAACCAAATTTGCTATTTAGTCCCTAAACTTTTAAAAATTTCATTTCATACCCGATGAAAAC
1 TAAAAACAAAAATTGCTATTTAGTCCCTAAACTTTTAAAAATTTCATTTCATACTCGAAAAAAAC
1749964 CAAGAGGATACGAAAAGTTTTAAAAATTTTTATACC
66 CAA-AGGATA-GAAAAGTTTTAAAAATTTTTATACC
1750000 CTTACAGAAG
Statistics
Matches: 229, Mismatches: 27, Indels: 21
0.83 0.10 0.08
Matches are distributed among these distances:
162 1 0.00
163 51 0.22
164 88 0.38
165 87 0.38
166 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.32
Consensus pattern (162 bp):
TAAAAACAAAAATTGCTATTTAGTCCCTAAACTTTTAAAAATTTCATTTCATACTCGAAAAAAAC
CAAAGGATAGAAAAGTTTTAAAAATTTTTATACCATACAAAAGGCCATAAAAATAATAAAAATTT
AAAGAAAATGACTAAGATAGCGAATTTTCTTC
Found at i:1750023 original size:165 final size:163
Alignment explanation
Indices: 1749466--1750029 Score: 570
Period size: 165 Copynumber: 3.4 Consensus size: 163
1749456 TACTTGACAA
* * * * * *
1749466 AAAACTAAGAGGATATGAAAAGTGTTAAAAATTTCTATATCCCTACGGAAGGTCATAGGAATAAT
1 AAAACCAAGAGGATA-GAAAAGTTTTAAAAATTTTTATA-CCCTACAGAAGGCCATAAGAATAAT
* * * * * *
1749531 AGAAATCCTT----AAAATGATTAAAAT-GATGATTTTACCTTTAAAAACTAAAAATTGCTATTT
64 AAAAAT--TTAAAGAAAATGACTAAGATAG-CGATTTTTCTTTTAAAAAC-AAAAATTGCTATTT
* * * * **
1749591 AATCCCTAAACTTTTTAAATTTTCATTTCATACTTGACAA
125 AGTCCCTAAACTTTTAAAAATTTCATTTCATACTCGA-TG
* * * ** *
1749631 AAAACTAA-AGGATAGGAAAAATTTTAAAAATTTTCTATACCACTACGGGTGGCCATAAAAATAA
1 AAAACCAAGAGGATA-GAAAAGTTTTAAAAATTTT-TATACC-CTACAGAAGGCCATAAGAATAA
* * *
1749695 TAAAAATTTAAAGAAAATGACTAAGATAGC-AATTTT-TTCTAAAAACAAAAATTGCTATTTGGT
63 TAAAAATTTAAAGAAAATGACTAAGATAGCGATTTTTCTTTTAAAAACAAAAATTGCTATTTAGT
*
1749758 CCTTAAACTTTTAAAAATTTCATTTCATACTCGATG
128 CCCTAAACTTTTAAAAATTTCATTTCATACTCGATG
* * * * * *
1749794 AAAAACCGAGAAGATATAAAGAGTTTTAAAAA-TTTTATATCCATACAAAAGGCCATAGGAATAA
1 -AAAACCAAGAGGATAGAAA-AGTTTTAAAAATTTTTATA-CCCTACAGAAGGCCATAAGAATAA
* *
1749858 TAAAAATTTAAAGAAAATGACTAAGATAGCGATTTTTCTTTTAAAAACCAAATTTGCTATTTAGT
63 TAAAAATTTAAAGAAAATGACTAAGATAGCGATTTTTCTTTTAAAAACAAAAATTGCTATTTAGT
*
1749923 CCCTAAACTTTTAAAAATTTCATTTCATACCCGATG
128 CCCTAAACTTTTAAAAATTTCATTTCATACTCGATG
* *
1749959 AAAACCAAGAGGATACGAAAAGTTTTAAAAATTTTTATACCCTTACAGAAGACAATAAGAATAAT
1 AAAACCAAGAGGATA-GAAAAGTTTTAAAAATTTTTATACCC-TACAGAAGGCCATAAGAATAAT
*
1750024 TAAAAT
64 AAAAAT
1750030 CTTTTAAAAT
Statistics
Matches: 330, Mismatches: 53, Indels: 32
0.80 0.13 0.08
Matches are distributed among these distances:
163 51 0.15
164 114 0.35
165 148 0.45
166 4 0.01
167 12 0.04
168 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (163 bp):
AAAACCAAGAGGATAGAAAAGTTTTAAAAATTTTTATACCCTACAGAAGGCCATAAGAATAATAA
AAATTTAAAGAAAATGACTAAGATAGCGATTTTTCTTTTAAAAACAAAAATTGCTATTTAGTCCC
TAAACTTTTAAAAATTTCATTTCATACTCGATG
Found at i:1750989 original size:21 final size:22
Alignment explanation
Indices: 1750951--1750992 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1750941 AAATTTAGTT
*
1750951 TTTTTTTCTTAGTGTTTTTGTAA
1 TTTTTTTCTTAG-CTTTTTGTAA
1750974 TTTTTTTCTTA-CTTTTTGT
1 TTTTTTTCTTAGCTTTTTGT
1750993 CTATGGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.74
Consensus pattern (22 bp):
TTTTTTTCTTAGCTTTTTGTAA
Found at i:1751761 original size:150 final size:149
Alignment explanation
Indices: 1751474--1751823 Score: 354
Period size: 150 Copynumber: 2.3 Consensus size: 149
1751464 TATATGCAAA
* * * * *
1751474 AAAAATTC-AAAACTCATAAAATAAATTTAATTTTCTAAAACTGATTTAATATGAATTCAATAAA
1 AAAAATTCTAAAACTCATAAAATAAATTGAATTTTTTAAAACTGATTTTATATAAATTCAAAAAA
* * *
1751538 AATATTTGATAAATTTTAAAAATTTTGAATTAAAAAATCAAACAAAAAAAATTACAAATTAAAAA
66 AATATTTGATAAA-TTTAAAAATTATAAATTAAAAAATCAAACAAAAAAAATTACAAAGTAAAAA
*
1751603 ACTCTGTAT-TTTGAAACAG
130 ACTCTGTATCTTAGAAACAG
*
1751622 AAACAATTCTAAAACTCATAAAATAAATTGAATTTTTTAAAAATGATTTTATATAAATT-AAAAA
1 AAA-AATTCTAAAACTCATAAAATAAATTGAATTTTTTAAAACTGATTTTATATAAATTCAAAAA
* * * * * *
1751686 ATAATATTTGGAT-AA-TTATAAATTATAAACTTAAAAAAATCCTACCGAAAAAATTTACAGAGT
65 A-AATATTT-GATAAATTTAAAAATTATAAA-TT-AAAAAAT-CAAACAAAAAAAATTACAAAGT
* * * * *
1751749 -AGAAATTTTGTATCTTAGTAATAG
125 AAAAAACTCTGTATCTTAGAAACAG
* * * * *
1751773 AAAAATTTTTAAATTCATAAAATTAATAG-ATTTTTTAAAACTGATTTTATA
1 AAAAATTCTAAAACTCATAAAATAAATTGAATTTTTTAAAACTGATTTTATA
1751824 GTGATTTAAG
Statistics
Matches: 167, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
148 14 0.08
149 33 0.20
150 91 0.54
151 29 0.17
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (149 bp):
AAAAATTCTAAAACTCATAAAATAAATTGAATTTTTTAAAACTGATTTTATATAAATTCAAAAAA
AATATTTGATAAATTTAAAAATTATAAATTAAAAAATCAAACAAAAAAAATTACAAAGTAAAAAA
CTCTGTATCTTAGAAACAG
Found at i:1753909 original size:20 final size:20
Alignment explanation
Indices: 1753881--1753955 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1753871 TTTTACCTAG
1753881 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1753901 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1753921 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
1753941 ATGTATCGATACATT
1 ATGTATCGATACATT
1753956 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1753941 original size:40 final size:39
Alignment explanation
Indices: 1753881--1753958 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
1753871 TTTTACCTAG
*
1753881 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
1753921 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
1753959 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:1754899 original size:20 final size:21
Alignment explanation
Indices: 1754867--1754906 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1754857 AGCCTTTGAC
*
1754867 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAATATGTTT
1754888 CATGCA-TTTTTAATATGTT
1 CATGCATTTTTTAATATGTT
1754907 CAGCATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:1767910 original size:17 final size:17
Alignment explanation
Indices: 1767884--1767923 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1767874 ATTATACTTG
*
1767884 AAGGGTGAAAACATGAA
1 AAGGGCGAAAACATGAA
1767901 AAGGGCGAAAACATGAA
1 AAGGGCGAAAACATGAA
1767918 AAGGGC
1 AAGGGC
1767924 ATCCTTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.07
Consensus pattern (17 bp):
AAGGGCGAAAACATGAA
Found at i:1767962 original size:19 final size:20
Alignment explanation
Indices: 1767935--1767973 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1767925 TCCTTTACAC
1767935 CCAAAAAAAA-AAAAAAAAA
1 CCAAAAAAAACAAAAAAAAA
*
1767954 CCAAGAAAAACAAAAAAAAA
1 CCAAAAAAAACAAAAAAAAA
1767974 GAAAGGGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.85, C:0.13, G:0.03, T:0.00
Consensus pattern (20 bp):
CCAAAAAAAACAAAAAAAAA
Found at i:1769236 original size:28 final size:28
Alignment explanation
Indices: 1769137--1770020 Score: 1159
Period size: 28 Copynumber: 31.0 Consensus size: 28
1769127 ATGTTCATCC
*
1769137 CTTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1769165 CTTTTTAAAGCCTACGAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1769194 CTTTTCAAAGCCCACAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
1769223 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1769251 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769279 CTTTCAAAGCCTACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769307 ATTTTCAAAG-CCACAAGTCAGTGGCA-T
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1769334 CCTTTCAAAGCCCACGCAAGTTAGTGGCACC
1 -CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
1769365 CTTTTAAAGCCCACGTAAGTCAGTGGCACC
1 CTTTCAAAGCCCAC--AAGTCAGTGGCACT
* *
1769395 CTTTTAAAG-CTACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1769421 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769450 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
1769479 CTTTCAAAGCCCACAAGTTAGTGACACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769507 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1769535 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769563 CTTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1769591 CTTTTAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1769619 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769647 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1769676 CTTTCAAAGCCCACAAGTTAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1769704 CTTTTCAAAGCCCACAAGTCAGTGGTACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1769733 CTTTCAAAGCTCACAAGTCAGTGGTACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1769761 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1769789 CTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1769817 CTTTCAAAGCCCACAAGTTAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1769845 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
** *
1769873 CGTTTCAAAGCCCATGAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
** *
1769902 CTTTCAAAGTGCACAAGTCAGTGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1769930 CTTTTCAAAGCCCACAAGCCAGTGGTAACT
1 C-TTTCAAAGCCCACAAGTCAGTGG-CACT
*
1769960 CTTTTCAAAGCCCACACAACTCAGTGGCAACT
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT
*
1769992 CTTTTCAATA-CCACACAAGTTAGTGGCAC
1 C-TTTCAA-AGCC-CACAAGTCAGTGGCAC
1770021 CATTTTTTTT
Statistics
Matches: 762, Mismatches: 72, Indels: 42
0.87 0.08 0.05
Matches are distributed among these distances:
27 29 0.04
28 448 0.59
29 185 0.24
30 60 0.08
31 17 0.02
32 22 0.03
33 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1769316 original size:85 final size:86
Alignment explanation
Indices: 1769136--1770020 Score: 1167
Period size: 85 Copynumber: 10.3 Consensus size: 86
1769126 AATGTTCATC
* * * *
1769136 CCTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTTAAAGCCTACGAGTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
*
1769201 AAGCCCACAAGTTAGTGGCACT
65 AAGCCCACAAGTCAGTGGCACT
1769223 -CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
*
1769286 AGCCTACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
** * *
1769307 ATTTTCAAAG-CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGCAAGTTAGTGGCACCCTTTT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTT
1769370 -AAAGCCCACGTAAGTCAGTGGCAC-
63 CAAAGCCCAC--AAGTCAGTGGCACT
* *
1769394 CCTTTTAAAG-CTACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
1769457 AAGCCCACAAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * *
1769478 CCTTTCAAAGCCCACAAGTTAGTGACACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
1769542 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* * *
1769563 -CTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
1769626 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* * *
1769647 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
*
1769712 AGCCCACAAGTCAGTGGTAC-
66 AGCCCACAAGTCAGTGGCACT
* * * *
1769732 CCTTTCAAAGCTCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCGA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
1769796 AGCCCACAAGTCAGTGGCAC-
66 AGCCCACAAGTCAGTGGCACT
* *
1769816 CCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCGTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
**
1769880 AAGCCCATGAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
** * * *
1769901 CCTTTCAAAGTGCACAAGTCAGTGGCATTCTTTTCAAAGCCCACAAGCCAGTGGTAACTCTTTTC
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGG-CACTCTTTTC
*
1769966 AAAGCCCACACAACTCAGTGGCAACT
64 AAAG-CC-CACAAGTCAGTGGC-ACT
* *
1769992 CTTTTCAATA-CCACACAAGTTAGTGGCAC
1 CCTTTCAA-AGCC-CACAAGTCAGTGGCAC
1770021 CATTTTTTTT
Statistics
Matches: 715, Mismatches: 60, Indels: 41
0.88 0.07 0.05
Matches are distributed among these distances:
83 1 0.00
84 235 0.33
85 292 0.41
86 87 0.12
87 50 0.07
88 15 0.02
89 11 0.02
90 2 0.00
91 7 0.01
92 15 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (86 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
AGCCCACAAGTCAGTGGCACT
Done.