Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, whole genome shotgun sequence
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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 4 of 20
Found at i:1233409 original size:23 final size:23
Alignment explanation
Indices: 1233380--1233501 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 23
1233370 ATAACGCGAC
*
1233380 TCCATATTTACTACTCACGTGAT
1 TCCATATTTACTAGTCACGTGAT
*
1233403 TCCATATTTACTAGTCGCGTGAT
1 TCCATATTTACTAGTCACGTGAT
* ****
1233426 TCCA-ATTCTA-TGACTCAAACAAT
1 TCCATATT-TACT-AGTCACGTGAT
* *
1233449 TTCATATTAACTAGTCACGTGAT
1 TCCATATTTACTAGTCACGTGAT
* * *
1233472 TCAAAATTTAGTAGTCACGTGAT
1 TCCATATTTACTAGTCACGTGAT
1233495 TCCATAT
1 TCCATAT
1233502 CAAATACTTG
Statistics
Matches: 73, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
22 4 0.05
23 65 0.89
24 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (23 bp):
TCCATATTTACTAGTCACGTGAT
Found at i:1241478 original size:2 final size:2
Alignment explanation
Indices: 1241471--1241501 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1241461 TCACAGAATT
1241471 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 T
1241502 TCACTTTGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1251586 original size:8 final size:8
Alignment explanation
Indices: 1251575--1251606 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1251565 GCTCAGATGC
1251575 ATGATATA
1 ATGATATA
1251583 ATGATATA
1 ATGATATA
1251591 ATGATAT-
1 ATGATATA
1251598 ATGATATA
1 ATGATATA
1251606 A
1 A
1251607 CTTATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (8 bp):
ATGATATA
Found at i:1251603 original size:15 final size:16
Alignment explanation
Indices: 1251575--1251606 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1251565 GCTCAGATGC
1251575 ATGATATAATGATATA
1 ATGATATAATGATATA
1251591 ATGATAT-ATGATATA
1 ATGATATAATGATATA
1251606 A
1 A
1251607 CTTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGATATAATGATATA
Found at i:1251916 original size:30 final size:28
Alignment explanation
Indices: 1251866--1251944 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
1251856 ATAATAACTA
* * *
1251866 ATTATAAACAATATGTTATTAAATCTAAGGTG
1 ATTATAAATAA-A-GTTATTAAATATAA--TC
1251898 ATTATAAATAAAGTTATTAAATATAATC
1 ATTATAAATAAAGTTATTAAATATAATC
1251926 A-TATAAATAAAGTCTATTA
1 ATTATAAATAAAGT-TATTA
1251945 TAAGTTATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
27 12 0.28
28 7 0.16
30 13 0.30
31 1 0.02
32 10 0.23
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (28 bp):
ATTATAAATAAAGTTATTAAATATAATC
Found at i:1251992 original size:24 final size:24
Alignment explanation
Indices: 1251965--1252012 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1251955 TAATGCTTGT
1251965 ATATGAATTAAATATATATATATA
1 ATATGAATTAAATATATATATATA
* * *
1251989 ATATGACTTTATTATATATATATA
1 ATATGAATTAAATATATATATATA
1252013 TAATTAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATGAATTAAATATATATATATA
Found at i:1252108 original size:210 final size:207
Alignment explanation
Indices: 1251598--1252204 Score: 623
Period size: 210 Copynumber: 2.9 Consensus size: 207
1251588 ATAATGATAT
* * *
1251598 ATGATATAACTTATATATTATAATATTTTATATCAAAATTTGTATAAATAATAACTAACTATAAA
1 ATGACATAACTTATATATTATAATGTTTTATATCAAAATTTGTATAAATAATAACTAATTATAAA
* * * *
1251663 CAATATATTTTAATATCTAA-GTGATAGCCAATAAAATTATTAAGTGTAATCATATAAATAAAGT
66 CAATATATTATAAAATCTAAGGTGATAG-TAATAAAGTTATTAAGTGTAATCATATAAATAAAGT
* ********* * *
1251727 TTATTATAAGTTATAATAATGCTTNNNNNNNNNNTAAATATATGTATATATAATATATTAGTTTA
130 TTATTATAAGTTATAGTAATGCTT-GATATGAATTAAATATA-GTATATAT-A-ATATGACTTTA
1251792 TTATATATATAAAATTA
191 TTATATATATAAAATTA
* * **********
1251809 ATGATGCA-AA-TTATATGTTAAAATGTTTTATATCAANNNNNNNNNNAATAATAACTAATTATA
1 ATGA--CATAACTTATATATTATAATGTTTTATATCAAAATTTGTATAAATAATAACTAATTATA
* * * *
1251872 AACAATATGTTATTAAATCTAAGGTGATTA-TAAATAAAGTTATTAAATATAATCATATAAATAA
64 AACAATATATTATAAAATCTAAGGTGA-TAGT-AATAAAGTTATTAAGTGTAATCATATAAATAA
*
1251936 AGTCTATTATAAGTTATAGTAATGCTTGTATATGAATTAAATATA-TATATATAATATGACTTTA
127 AGTTTATTATAAGTTATAGTAATGCTTG-ATATGAATTAAATATAGTATATATAATATGACTTTA
1252000 TTATATATATATATAATTA
191 TTATATATATA-A-AATTA
* * *
1252019 ATGACATAACTTATATTTTATAATGTTTTATATCAAAGTTTGTATAAATAACAACTAATTATAAA
1 ATGACATAACTTATATATTATAATGTTTTATATCAAAATTTGTATAAATAATAACTAATTATAAA
* * * *
1252084 TAATATATTATAAAATATAAGGTGATAGCTAATAAAGTTATTGAGTGTCATCATATAAATAAAGT
66 CAATATATTATAAAATCTAAGGTGATAG-TAATAAAGTTATTAAGTGTAATCATATAAATAAAGT
* *
1252149 TTATTATAAATTATAGTAATG-TTGATGTGTAAATTAAATATATGTATATATAATAT
130 TTATTATAAGTTATAGTAATGCTTGATATG--AATTAAATATA-GTATATATAATAT
1252205 ATTTATACAA
Statistics
Matches: 320, Mismatches: 60, Indels: 31
0.78 0.15 0.08
Matches are distributed among these distances:
208 26 0.08
209 9 0.03
210 140 0.44
211 62 0.19
212 80 0.25
213 3 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.40
Consensus pattern (207 bp):
ATGACATAACTTATATATTATAATGTTTTATATCAAAATTTGTATAAATAATAACTAATTATAAA
CAATATATTATAAAATCTAAGGTGATAGTAATAAAGTTATTAAGTGTAATCATATAAATAAAGTT
TATTATAAGTTATAGTAATGCTTGATATGAATTAAATATAGTATATATAATATGACTTTATTATA
TATATAAAATTA
Found at i:1252198 original size:2 final size:2
Alignment explanation
Indices: 1252186--1252234 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
1252176 TGTAAATTAA
* * *
1252186 AT AT AT GT AT AT AT A- AT AT AT TT AT AC A- AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1252225 AT AT AT AT AT
1 AT AT AT AT AT
1252235 TCATAACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1254821 original size:19 final size:20
Alignment explanation
Indices: 1254797--1254837 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1254787 CTACTACACC
1254797 TTTTTAT-TTTTT-TGTTTAT
1 TTTTTATGTTTTTAT-TTTAT
1254816 TTTTTATGTTTTTATTTTAT
1 TTTTTATGTTTTTATTTTAT
1254836 TT
1 TT
1254838 AATATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 12 0.60
21 1 0.05
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (20 bp):
TTTTTATGTTTTTATTTTAT
Found at i:1254825 original size:13 final size:13
Alignment explanation
Indices: 1254799--1254835 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1254789 ACTACACCTT
1254799 TTTATTTTTT-TG
1 TTTATTTTTTATG
1254811 TTTATTTTTTATG
1 TTTATTTTTTATG
1254824 TTT-TTATTTTAT
1 TTTATT-TTTTAT
1254836 TTAATATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTATTTTTTATG
Found at i:1255183 original size:24 final size:24
Alignment explanation
Indices: 1255156--1255203 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1255146 AGTTAAAAAC
1255156 TAAGTCAAATTAAAATATAAATTT
1 TAAGTCAAATTAAAATATAAATTT
*
1255180 TAAGTCAAATTAGAATATAAATTT
1 TAAGTCAAATTAAAATATAAATTT
1255204 CAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAGTCAAATTAAAATATAAATTT
Found at i:1255537 original size:15 final size:15
Alignment explanation
Indices: 1255517--1255568 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1255507 ATTTATATTT
1255517 TTTAATTTTTTTAAA
1 TTTAATTTTTTTAAA
*
1255532 TTTAA-TTTTTAAATA
1 TTTAATTTTTTTAA-A
* *
1255547 TTTCAATTTTGTTCAA
1 TTT-AATTTTTTTAAA
1255563 TTTAAT
1 TTTAAT
1255569 CTCTGTAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.23
15 12 0.40
16 6 0.20
17 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTAATTTTTTTAAA
Found at i:1258365 original size:28 final size:28
Alignment explanation
Indices: 1258333--1258403 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
1258323 TGGTTCGCAA
*
1258333 GTAACAACAATATTTTAGGCAT-TAAAAT
1 GTAACAACAATATTTT-GGAATATAAAAT
* * **
1258361 GTAACAA-AATGTTTTTGAATATAACGT
1 GTAACAACAATATTTTGGAATATAAAAT
1258388 GTAACAACAATATTTT
1 GTAACAACAATATTTT
1258404 TTTTCAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 3 0.09
27 18 0.51
28 14 0.40
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (28 bp):
GTAACAACAATATTTTGGAATATAAAAT
Found at i:1258466 original size:45 final size:44
Alignment explanation
Indices: 1258417--1258569 Score: 155
Period size: 45 Copynumber: 3.4 Consensus size: 44
1258407 TCAATATGGT
* * * *
1258417 GTGTAACAACGTAACCATGATGTGTCATATGTTTTTGTTCATGAA
1 GTGTAACAACTTAATCAT-ATGTGTCACATGTTTTTGTACATGAA
* * * **
1258462 GTGTAATAACTTAATCATAGTGTGTAACATATTTTTGTACATGGT
1 GTGTAACAACTTAATCATA-TGTGTCACATGTTTTTGTACATGAA
* *
1258507 GTGTAACAACTTAATCATAACGTATCACATGTTTTTGTACAT-AA
1 GTGTAACAACTTAATCAT-ATGTGTCACATGTTTTTGTACATGAA
*
1258551 CGTGTAACAATTTAATCAT
1 -GTGTAACAACTTAATCAT
1258570 GACGTGTAAC
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
44 1 0.01
45 86 0.98
46 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.39
Consensus pattern (44 bp):
GTGTAACAACTTAATCATATGTGTCACATGTTTTTGTACATGAA
Found at i:1258577 original size:90 final size:90
Alignment explanation
Indices: 1258412--1258580 Score: 216
Period size: 90 Copynumber: 1.9 Consensus size: 90
1258402 TTTTTTCAAT
* * * * * *
1258412 ATGGTGTGTAACAACGTAACCATGATGTGTCATATGTTTTTGTTCATGAAGTGTAATAACTTAAT
1 ATGGTGTGTAACAACGTAACCATAACGTATCACATGTTTTTGTACATGAAGTGTAACAACTTAAT
*
1258477 CATAGTGTGTAACATATTTTTGTAC
66 CATAGCGTGTAACATATTTTTGTAC
* * *
1258502 ATGGTGTGTAACAACTTAATCATAACGTATCACATGTTTTTGTACAT-AACGTGTAACAATTTAA
1 ATGGTGTGTAACAACGTAACCATAACGTATCACATGTTTTTGTACATGAA-GTGTAACAACTTAA
1258566 TCAT-GACGTGTAACA
65 TCATAG-CGTGTAACA
1258581 ACTTAATCAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 3 0.04
90 64 0.96
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (90 bp):
ATGGTGTGTAACAACGTAACCATAACGTATCACATGTTTTTGTACATGAAGTGTAACAACTTAAT
CATAGCGTGTAACATATTTTTGTAC
Found at i:1258599 original size:21 final size:21
Alignment explanation
Indices: 1258550--1258591 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1258540 TTTGTACATA
*
1258550 ACGTGTAACAATTTAATCATG
1 ACGTGTAACAACTTAATCATG
1258571 ACGTGTAACAACTTAATCATG
1 ACGTGTAACAACTTAATCATG
1258592 GTGTGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (21 bp):
ACGTGTAACAACTTAATCATG
Found at i:1258653 original size:111 final size:111
Alignment explanation
Indices: 1258455--1258668 Score: 304
Period size: 111 Copynumber: 1.9 Consensus size: 111
1258445 ATGTTTTTGT
* * *
1258455 TCATGAAGTGTAATAACTTAATCATAGTGTGTAACATATTTTTGTACATGGTGTGTAACAACTTA
1 TCATGAAGTGTAACAACTTAATCATAGTGTGTAACATATTTTTGTACATGGTGTATAACAACCTA
*
1258520 ATCATAACGTATCACATGTTTTTGTACATAACGTGTAACAATTTAA
66 ATCATAACGTATCACATATTTTTGTACATAACGTGTAACAATTTAA
* * * *
1258566 TCATGACGTGTAACAACTTAATCATGGTGTGTAATATTTTTTTGTACATGGTGTATAACAACCTA
1 TCATGAAGTGTAACAACTTAATCATAGTGTGTAACATATTTTTGTACATGGTGTATAACAACCTA
* * * *
1258631 A-CTATGATGTGTCACATATTTTTGTACATGACGTGTAA
66 ATC-ATAACGTATCACATATTTTTGTACATAACGTGTAA
1258669 TATGTTTTTG
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
110 1 0.01
111 89 0.99
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (111 bp):
TCATGAAGTGTAACAACTTAATCATAGTGTGTAACATATTTTTGTACATGGTGTATAACAACCTA
ATCATAACGTATCACATATTTTTGTACATAACGTGTAACAATTTAA
Found at i:1258661 original size:24 final size:24
Alignment explanation
Indices: 1258634--1258695 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
1258624 CAACCTAACT
* *
1258634 ATGATGTGTCACATATTTTTGTAC
1 ATGACGTGTAACATATTTTTGTAC
* * *
1258658 ATGACGTGTAATATGTTTTTGTAT
1 ATGACGTGTAACATATTTTTGTAC
*
1258682 ATAACGTGTAACAT
1 ATGACGTGTAACAT
1258696 CATGACATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.44
Consensus pattern (24 bp):
ATGACGTGTAACATATTTTTGTAC
Found at i:1258728 original size:27 final size:27
Alignment explanation
Indices: 1258698--1258751 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1258688 TGTAACATCA
1258698 TGACATGTAATCATTAAAAGTAATTTT
1 TGACATGTAATCATTAAAAGTAATTTT
1258725 TGACATGTAATCATTAAAAGTAATTTT
1 TGACATGTAATCATTAAAAGTAATTTT
1258752 ATCTAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (27 bp):
TGACATGTAATCATTAAAAGTAATTTT
Found at i:1266536 original size:21 final size:21
Alignment explanation
Indices: 1266512--1266551 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1266502 ATTTTAGAAT
1266512 GGATATTGCTTGTTAATGATG
1 GGATATTGCTTGTTAATGATG
* *
1266533 GGATATTGGTTGTTGATGA
1 GGATATTGCTTGTTAATGA
1266552 AGATATGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.42
Consensus pattern (21 bp):
GGATATTGCTTGTTAATGATG
Found at i:1267813 original size:67 final size:67
Alignment explanation
Indices: 1267698--1267830 Score: 171
Period size: 67 Copynumber: 2.0 Consensus size: 67
1267688 TTAGATTTTA
* * *
1267698 GGTTTTGGTTGATCCCTTGAAAAATCATTGTTAAAGGCTATGGTTGAGCCTT-TAAAAAACCATT
1 GGTTTTGGCTGATCCCGTGAAAAATCATTGTTAAAGGCTATGGCTGAG-CTTGTAAAAAACCATT
1267762 GTG
65 GTG
* * * *
1267765 GGTTTTGGCTGATCCCGTGAAAAA-CTATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAGCCATT
1 GGTTTTGGCTGATCCCGTGAAAAATC-ATTGTTAAAGGCTATGGCTGAGCTTGTAAAAAACCATT
1267829 GT
65 GT
1267831 AAAAGCTTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 4 0.07
67 53 0.93
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (67 bp):
GGTTTTGGCTGATCCCGTGAAAAATCATTGTTAAAGGCTATGGCTGAGCTTGTAAAAAACCATTG
TG
Found at i:1280916 original size:28 final size:28
Alignment explanation
Indices: 1280833--1280952 Score: 140
Period size: 28 Copynumber: 4.4 Consensus size: 28
1280823 CTAACAATAA
*
1280833 GAATAC-TTTAACCTACCAAGAATGGAT
1 GAATACTTTTAACCCACCAAGAATGGAT
1280860 GAATAC-TTTAACCCACCAAGAATGGAT
1 GAATACTTTTAACCCACCAAGAATGGAT
* *
1280887 GAATACTTTTAACCCA-CAATGATTGAAT
1 GAATACTTTTAACCCACCAA-GAATGGAT
* *
1280915 GAAAAGTTTTAACCCA-CAAGGAATGGAT
1 GAATACTTTTAACCCACCAA-GAATGGAT
*
1280943 GACTACTTTT
1 GAATACTTTT
1280953 TATTGGTCTC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
27 35 0.44
28 45 0.56
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (28 bp):
GAATACTTTTAACCCACCAAGAATGGAT
Found at i:1286021 original size:15 final size:15
Alignment explanation
Indices: 1286003--1286035 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1285993 TTTTGATCCA
1286003 CATCTTTTCCTTTAT
1 CATCTTTTCCTTTAT
*
1286018 CATCTTTTTCTTTAT
1 CATCTTTTCCTTTAT
1286033 CAT
1 CAT
1286036 AGGAGTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (15 bp):
CATCTTTTCCTTTAT
Found at i:1293604 original size:19 final size:20
Alignment explanation
Indices: 1293577--1293616 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1293567 CTTGGATTAC
1293577 TCCAATGAAAT-AGAATATT
1 TCCAATGAAATGAGAATATT
*
1293596 TCCACTGAAATGAGAATATT
1 TCCAATGAAATGAGAATATT
1293616 T
1 T
1293617 ATTAACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TCCAATGAAATGAGAATATT
Found at i:1295008 original size:5 final size:5
Alignment explanation
Indices: 1294998--1295030 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
1294988 GAACCAAAAC
1294998 CAAAT CAAAT CAAAT CAAAT CAAAAT CAAAT CA
1 CAAAT CAAAT CAAAT CAAAT C-AAAT CAAAT CA
1295031 CTATCATCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (5 bp):
CAAAT
Found at i:1298811 original size:22 final size:22
Alignment explanation
Indices: 1298759--1298814 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
1298749 TATTGGTCCA
**
1298759 AAGTCACGCAATACATAACAAC
1 AAGTCACATAATACATAACAAC
1298781 AAGTCACATAATACATAACAACC
1 AAGTCACATAATACATAACAA-C
1298804 AA-TCACATAAT
1 AAGTCACATAAT
1298815 GCCTAAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.52, C:0.25, G:0.05, T:0.18
Consensus pattern (22 bp):
AAGTCACATAATACATAACAAC
Found at i:1298951 original size:52 final size:52
Alignment explanation
Indices: 1298894--1298995 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
1298884 TCAGCCTCAC
* *
1298894 AATACCTAACAATAAGTCACACAATGCCTAATATCTGCTTACGTTATGCCAA
1 AATACCTAACAATAAGTCACACAATGCCTAATATCCGCTCACGTTATGCCAA
*
1298946 AATACCTAACAATAAGTCACGCAATGCCTAATATCCGCTCACGTTATGCC
1 AATACCTAACAATAAGTCACACAATGCCTAATATCCGCTCACGTTATGCC
1298996 TAATATACGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.25
Consensus pattern (52 bp):
AATACCTAACAATAAGTCACACAATGCCTAATATCCGCTCACGTTATGCCAA
Found at i:1299116 original size:22 final size:22
Alignment explanation
Indices: 1299091--1299132 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1299081 ACTAAACACA
*
1299091 CAATGCCTAATATCCATTCATG
1 CAATGCATAATATCCATTCATG
1299113 CAATGCATAATATCCATTCA
1 CAATGCATAATATCCATTCA
1299133 CATAATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (22 bp):
CAATGCATAATATCCATTCATG
Found at i:1299139 original size:22 final size:22
Alignment explanation
Indices: 1299087--1299140 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1299077 AATAACTAAA
*
1299087 CACACAATGCCTAATATCCATT
1 CACACAATGCATAATATCCATT
**
1299109 CATGCAATGCATAATATCCATT
1 CACACAATGCATAATATCCATT
*
1299131 CACATAATGC
1 CACACAATGC
1299141 CTATAAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.28
Consensus pattern (22 bp):
CACACAATGCATAATATCCATT
Found at i:1300041 original size:22 final size:22
Alignment explanation
Indices: 1300016--1300061 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1300006 ACAACTCATG
*
1300016 CAATTCCAAAAATCTAGTCTCA
1 CAATGCCAAAAATCTAGTCTCA
** *
1300038 CAATGCCTCATATCTAGTCTCA
1 CAATGCCAAAAATCTAGTCTCA
1300060 CA
1 CA
1300062 TTGTTTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.07, T:0.28
Consensus pattern (22 bp):
CAATGCCAAAAATCTAGTCTCA
Found at i:1320949 original size:15 final size:14
Alignment explanation
Indices: 1320929--1320965 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
1320919 GTTATATATA
1320929 TTATAATTAATAATT
1 TTATAATT-ATAATT
1320944 TTATAAGTTATAATT
1 TTATAA-TTATAATT
1320959 TTATAAT
1 TTATAAT
1320966 GTTAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TTATAATTATAATT
Found at i:1324934 original size:10 final size:10
Alignment explanation
Indices: 1324919--1324972 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1324909 TTTAAAATGA
1324919 AATAATATAT
1 AATAATATAT
1324929 AATAATAGTAT
1 AATAATA-TAT
* *
1324940 TATTAT-TA-
1 AATAATATAT
*
1324948 AAAAATA-AT
1 AATAATATAT
1324957 AATAATATAT
1 AATAATATAT
1324967 AATAAT
1 AATAAT
1324973 CCTATCGACC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.12
9 8 0.24
10 15 0.44
11 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (10 bp):
AATAATATAT
Found at i:1338137 original size:171 final size:170
Alignment explanation
Indices: 1337833--1338241 Score: 509
Period size: 171 Copynumber: 2.4 Consensus size: 170
1337823 AATAATTAGT
* *
1337833 TCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAA
1 TCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAA
* ** * * * ** *
1337898 TGGGTGACTCTAAATGGACTTTTCTTGTTGATAAATGCTTGTTTCTTTACGTTTTTCGAGGCAGA
66 TGAGTGACGATAAATGGACTTTTCTTCTTAATAAATGCTTGTCTCTACACGTTTTAC-AGGCAGA
* *
1337963 CATTCAATTATAGTCTGTTTTAA-AGAAAACTGTAAAAAAAA
130 CATTCAATTATAGTCTGTTTTAACA-AAAAATATAAAAAAAA
* * *
1338004 TCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGTGAGCAATTAGCCTTTTGAAGGAA
1 TCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAA
* * * * * *
1338069 TTAGTGACGATAAATGTACTTTTCTTCTTAATGAATGGCTT-TCTCTACATGTCTCTTAC-TGTA
66 TGAGTGACGATAAATGGACTTTTCTTCTTAATAAAT-GCTTGTCTCTACACGT-T-TTACAGGCA
* *
1338132 GACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAACAAT
128 GACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAAA
* * *
1338175 TCAGCTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGCAAGTAAGAAGCCTTTTGAAGGAA
1 TCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAA
1338240 TG
66 TG
1338242 GGTNNNNNNN
Statistics
Matches: 203, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
171 194 0.96
172 6 0.03
173 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (170 bp):
TCAACTTAAAATCAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAA
TGAGTGACGATAAATGGACTTTTCTTCTTAATAAATGCTTGTCTCTACACGTTTTACAGGCAGAC
ATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAAA
Found at i:1339006 original size:11 final size:11
Alignment explanation
Indices: 1338990--1339014 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1338980 TTTTCATTTT
1338990 CCACATCAATG
1 CCACATCAATG
1339001 CCACATCAATG
1 CCACATCAATG
1339012 CCA
1 CCA
1339015 TGTAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (11 bp):
CCACATCAATG
Found at i:1339689 original size:2 final size:2
Alignment explanation
Indices: 1339682--1339709 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1339672 ACATACATAC
1339682 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
1339710 GGATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1343131 original size:21 final size:22
Alignment explanation
Indices: 1343105--1343155 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1343095 TAATTTATTT
1343105 AATTTAAAATAAAAAT-ATAAA
1 AATTTAAAATAAAAATGATAAA
* *
1343126 AATTT-AATTAAATATGATAAA
1 AATTTAAAATAAAAATGATAAA
*
1343147 AAATTAAAA
1 AATTTAAAA
1343156 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.33
21 14 0.58
22 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AATTTAAAATAAAAATGATAAA
Found at i:1344352 original size:16 final size:16
Alignment explanation
Indices: 1344331--1344362 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1344321 CAAATACTTA
1344331 TAAGATTCGGGTTAAG
1 TAAGATTCGGGTTAAG
1344347 TAAGATTCGGGTTAAG
1 TAAGATTCGGGTTAAG
1344363 GTATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (16 bp):
TAAGATTCGGGTTAAG
Found at i:1345384 original size:18 final size:19
Alignment explanation
Indices: 1345361--1345409 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1345351 TTCGATTTGG
*
1345361 AAGAAAAGGGGAAAATA-A
1 AAGAAAAGGAGAAAATAGA
*
1345379 AAGAAAAAGAGAAAATAGA
1 AAGAAAAGGAGAAAATAGA
1345398 AAGACAAAGGAG
1 AAGA-AAAGGAG
1345410 TTGAACGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 15 0.58
19 5 0.19
20 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (19 bp):
AAGAAAAGGAGAAAATAGA
Found at i:1346269 original size:36 final size:36
Alignment explanation
Indices: 1346229--1346315 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
1346219 AGAAGAACCC
*
1346229 AAAGTCGAAACTGAAGGAAAATCTGAAGCCTCTGAA
1 AAAGTCGAAACTGAAGAAAAATCTGAAGCCTCTGAA
* **
1346265 AAAGTCGAAACTCAAGAAAAATCTGAAGCCTCTTCA
1 AAAGTCGAAACTGAAGAAAAATCTGAAGCCTCTGAA
1346301 AAAGTCGAAACTGAA
1 AAAGTCGAAACTGAA
1346316 ACACCCGCCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (36 bp):
AAAGTCGAAACTGAAGAAAAATCTGAAGCCTCTGAA
Found at i:1353938 original size:2 final size:2
Alignment explanation
Indices: 1353931--1353972 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1353921 GATCATGATA
1353931 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1353972 T
1 T
1353973 TGACATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1361641 original size:55 final size:54
Alignment explanation
Indices: 1361570--1361673 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 54
1361560 TTGCACCATA
* * *
1361570 GTTCAACTAATTTAAATTAATTTTATATTAATTAGTTTACAAAAAAGGTAAGTTG
1 GTTCAACTAATATAAATTAATATTACATTAATTAGTTTAC-AAAAAGGTAAGTTG
* *
1361625 GTTCATCTAATATAAATTAATATTACATTTATTAGTTTACAAAAAGGTA
1 GTTCAACTAATATAAATTAATATTACATTAATTAGTTTACAAAAAGGTA
1361674 GATTGATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 9 0.20
55 35 0.80
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (54 bp):
GTTCAACTAATATAAATTAATATTACATTAATTAGTTTACAAAAAGGTAAGTTG
Found at i:1364285 original size:13 final size:13
Alignment explanation
Indices: 1364267--1364299 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1364257 CCGAATCAGA
1364267 CGAGACTGACAGC
1 CGAGACTGACAGC
1364280 CGAGACTGACAGC
1 CGAGACTGACAGC
1364293 CGAGACT
1 CGAGACT
1364300 CTTCCCCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.30, T:0.09
Consensus pattern (13 bp):
CGAGACTGACAGC
Found at i:1368250 original size:4 final size:4
Alignment explanation
Indices: 1368243--1368271 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1368233 TTATATATAT
1368243 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1368272 AACCTGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1372141 original size:33 final size:33
Alignment explanation
Indices: 1372104--1372177 Score: 85
Period size: 36 Copynumber: 2.2 Consensus size: 33
1372094 ACCGCTACAG
**
1372104 TTGCTGCTGCTGGGGCTGGTGGTTCTTCTTCCT
1 TTGCTGCTGCTGCAGCTGGTGGTTCTTCTTCCT
* *
1372137 TTGCTTTTTCTGTTGCAGCTGGTGGTTCTTCTTCCT
1 TTGC---TGCTGCTGCAGCTGGTGGTTCTTCTTCCT
1372173 TTGCT
1 TTGCT
1372178 TTCTCTGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
33 5 0.15
36 29 0.85
ACGTcount: A:0.01, C:0.23, G:0.27, T:0.49
Consensus pattern (33 bp):
TTGCTGCTGCTGCAGCTGGTGGTTCTTCTTCCT
Found at i:1372158 original size:36 final size:36
Alignment explanation
Indices: 1372118--1372196 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
1372108 TGCTGCTGGG
* **
1372118 GCTGGTGGTTCTTCTTCCTTTGCTTTTTCTGTTGCA
1 GCTGGTGGTTCTTCTTCCTTTGCTTTCTCTGTCACA
1372154 GCTGGTGGTTCTTCTTCCTTTGCTTTCTCTGTCACA
1 GCTGGTGGTTCTTCTTCCTTTGCTTTCTCTGTCACA
1372190 GCTGGTG
1 GCTGGTG
1372197 ATTCAGATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.04, C:0.24, G:0.24, T:0.48
Consensus pattern (36 bp):
GCTGGTGGTTCTTCTTCCTTTGCTTTCTCTGTCACA
Found at i:1376251 original size:22 final size:23
Alignment explanation
Indices: 1376208--1376253 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1376198 ATAGAGAGTT
1376208 ATTTAGGCTTAATTTTGATAGTA
1 ATTTAGGCTTAATTTTGATAGTA
*
1376231 ATTTA-GCTTAGTTCTTG-TAGTA
1 ATTTAGGCTTAATT-TTGATAGTA
1376253 A
1 A
1376254 AACATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (23 bp):
ATTTAGGCTTAATTTTGATAGTA
Found at i:1379893 original size:21 final size:20
Alignment explanation
Indices: 1379864--1379902 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1379854 TTAATTATTA
* *
1379864 TATTTATTAGTTTTTAAATTT
1 TATTAATTA-TTTATAAATTT
1379885 TATTAATTATTTATAAAT
1 TATTAATTATTTATAAAT
1379903 AAGTCTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTAATTATTTATAAATTT
Found at i:1380526 original size:28 final size:29
Alignment explanation
Indices: 1380482--1380538 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1380472 TTAGTAAAAA
*
1380482 ATATTTAAATAATTTTTTAT-TTTTTATT
1 ATATTTAAATAAATTTTTATATTTTTATT
1380510 ATATTT-AATCAAATTTTTATATTTTTATT
1 ATATTTAAAT-AAATTTTTATATTTTTATT
1380539 TAAAATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 15 0.58
29 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
ATATTTAAATAAATTTTTATATTTTTATT
Found at i:1380545 original size:26 final size:25
Alignment explanation
Indices: 1380483--1380549 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
1380473 TAGTAAAAAA
*
1380483 TATTT-AAAT-AATTTTTTATTTTT
1 TATTTAAAATCAAATTTTTATTTTT
*
1380506 TATTATATTTAATCAAATTTTTATATTTT
1 TATT-TA--AAATCAAATTTTTAT-TTTT
1380535 TATTTAAAATCAAAT
1 TATTTAAAATCAAAT
1380550 AAACCTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
23 4 0.11
24 1 0.03
26 8 0.23
27 3 0.09
28 11 0.31
29 8 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTAAAATCAAATTTTTATTTTT
Found at i:1380847 original size:31 final size:29
Alignment explanation
Indices: 1380812--1380905 Score: 120
Period size: 29 Copynumber: 3.2 Consensus size: 29
1380802 TTATAAGAGT
1380812 TTATTTAACTCAAAATTAAAAATATAAAAAA
1 TTATTTAACT-AAAA-TAAAAATATAAAAAA
1380843 TTATTT-ACTTAAAATAAAAATATAAAAAA
1 TTATTTAAC-TAAAATAAAAATATAAAAAA
* *
1380872 TTGATTGAA-TATAATAAAAATATAAAAAA
1 TT-ATTTAACTAAAATAAAAATATAAAAAA
1380901 TTATT
1 TTATT
1380906 CAATTTTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
28 3 0.05
29 38 0.66
30 9 0.16
31 8 0.14
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (29 bp):
TTATTTAACTAAAATAAAAATATAAAAAA
Found at i:1383811 original size:13 final size:13
Alignment explanation
Indices: 1383793--1383817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1383783 ATCTCTATAA
1383793 GAAAGTTTATTTT
1 GAAAGTTTATTTT
1383806 GAAAGTTTATTT
1 GAAAGTTTATTT
1383818 AGTTCTCTGT
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:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
GAAAGTTTATTTT
Found at i:1386544 original size:15 final size:16
Alignment explanation
Indices: 1386524--1386556 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1386514 TAACTGCCAT
1386524 TAAAAAAAAT-ATTTA
1 TAAAAAAAATAATTTA
*
1386539 TAAAAAAGATAATTTA
1 TAAAAAAAATAATTTA
1386555 TA
1 TA
1386557 TTTCAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAAAAAAATAATTTA
Found at i:1386663 original size:45 final size:45
Alignment explanation
Indices: 1386599--1386692 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
1386589 TTATAAAAAT
1386599 CTTCTTTTTCTATTTTCAAGGGGCACTTGTTGAATCACCAACCCA
1 CTTCTTTTTCTATTTTCAAGGGGCACTTGTTGAATCACCAACCCA
1386644 CTTCTTTTTCTATTTTCAAGGGGCACTTGTTGAATCACCAACCCA
1 CTTCTTTTTCTATTTTCAAGGGGCACTTGTTGAATCACCAACCCA
1386689 CTTC
1 CTTC
1386693 ATGTTTAGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (45 bp):
CTTCTTTTTCTATTTTCAAGGGGCACTTGTTGAATCACCAACCCA
Found at i:1387067 original size:20 final size:19
Alignment explanation
Indices: 1387042--1387082 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1387032 TATATACTTT
* *
1387042 ATTAATATTTACTCTATATA
1 ATTAATATATAAT-TATATA
1387062 ATTAATATATAATTATATA
1 ATTAATATATAATTATATA
1387081 AT
1 AT
1387083 ATAAGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATATATAATTATATA
Found at i:1390500 original size:93 final size:93
Alignment explanation
Indices: 1390341--1390526 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
1390331 GGTACTGCAT
1390341 TATAAATCTAAAGACTCCGTTGAGTTCAGCAGAAGAAAAGCCAAAGCTCTTAGAAGTTATTATAT
1 TATAAATCTAAAGACTCCGTTGAGTTCAGCAGAAGAAAAGCCAAAGCTCTTAGAAGTTATTATAT
1390406 TATAAGAAAGACAATTCTTCAATAAAGC
66 TATAAGAAAGACAATTCTTCAATAAAGC
1390434 TATAAATCTAAAGACTCCGTTGAGTTCAGCAGAAGAAAAGCCAAAGCTCTTAGAAGTTATTATAT
1 TATAAATCTAAAGACTCCGTTGAGTTCAGCAGAAGAAAAGCCAAAGCTCTTAGAAGTTATTATAT
1390499 TATAAGAAAGACAATTCTTCAATAAAGC
66 TATAAGAAAGACAATTCTTCAATAAAGC
1390527 AAATGTAATG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (93 bp):
TATAAATCTAAAGACTCCGTTGAGTTCAGCAGAAGAAAAGCCAAAGCTCTTAGAAGTTATTATAT
TATAAGAAAGACAATTCTTCAATAAAGC
Found at i:1392171 original size:29 final size:29
Alignment explanation
Indices: 1392126--1392184 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1392116 GTATGGTATC
* *
1392126 AAATGTTAGCTCGGTAGGGTGATAAGTTG
1 AAATGTTAGCTCAGTAGGGTGATAAATTG
1392155 AAATGTTAGCTCAGTAGGGTGATAAATTG
1 AAATGTTAGCTCAGTAGGGTGATAAATTG
1392184 A
1 A
1392185 TTAAGCTAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.31
Consensus pattern (29 bp):
AAATGTTAGCTCAGTAGGGTGATAAATTG
Found at i:1410915 original size:24 final size:24
Alignment explanation
Indices: 1410882--1410928 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1410872 GGTGATTCTC
*
1410882 AATTCTTATAATTACGTTAATTAT
1 AATTCATATAATTACGTTAATTAT
1410906 AATTCATATAATTACGTTAATTA
1 AATTCATATAATTACGTTAATTA
1410929 ATAAGAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (24 bp):
AATTCATATAATTACGTTAATTAT
Found at i:1413018 original size:24 final size:24
Alignment explanation
Indices: 1412986--1413031 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1412976 GTGATTCTTC
* *
1412986 ATTCTTATAATTACGTTAATTATA
1 ATTCCTATAATTACATTAATTATA
*
1413010 ATTCCTATAATTGCATTAATTA
1 ATTCCTATAATTACATTAATTA
1413032 ATAAAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTCCTATAATTACATTAATTATA
Found at i:1416355 original size:32 final size:32
Alignment explanation
Indices: 1416291--1416355 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1416281 AACAATGTTA
** * *
1416291 AATTTTCACTAAAATGGTAATAAGATCTTTAT
1 AATTTTCACTAAAATGACAATAAGACCCTTAT
1416323 AATTTTCACTAGAAAT-ACAATAAGACCCTTAT
1 AATTTTCACTA-AAATGACAATAAGACCCTTAT
1416355 A
1 A
1416356 TTTAAAAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (32 bp):
AATTTTCACTAAAATGACAATAAGACCCTTAT
Found at i:1422209 original size:46 final size:46
Alignment explanation
Indices: 1422120--1422214 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
1422110 CGAATCCCGT
* * *
1422120 TCCCGGTTCCCCCTTCGGCCCTGCCCCCCTCCCACAGTCCCACGAG
1 TCCCGATTCCCCCTGCGGCCCTGCCCCCCTCCCACAGGCCCACGAG
* * *
1422166 TCCCGATTCCCCCTGCGGCCCTGCCGCCC-CCCTCCGGCTCCACGAG
1 TCCCGATTCCCCCTGCGGCCCTGCCCCCCTCCCACAGGC-CCACGAG
1422212 TCC
1 TCC
1422215 TTGTGGGTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 6 0.14
46 36 0.86
ACGTcount: A:0.07, C:0.57, G:0.19, T:0.17
Consensus pattern (46 bp):
TCCCGATTCCCCCTGCGGCCCTGCCCCCCTCCCACAGGCCCACGAG
Found at i:1422268 original size:21 final size:19
Alignment explanation
Indices: 1422234--1422274 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1422224 ATTCCCGATT
1422234 CCCCCCGCGCCCCCCACCCC
1 CCCCCCGCGCCCCCC-CCCC
*
1422254 CCCCTCCGGGCCCCCCCCCC
1 CCCC-CCGCGCCCCCCCCCC
1422274 C
1 C
1422275 ACTCAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.02, C:0.83, G:0.12, T:0.02
Consensus pattern (19 bp):
CCCCCCGCGCCCCCCCCCC
Found at i:1422528 original size:8 final size:8
Alignment explanation
Indices: 1422515--1422559 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
1422505 AAAGAAGAAA
1422515 GGGAGTTG
1 GGGAGTTG
*
1422523 GGGAGTCG
1 GGGAGTTG
*
1422531 GGGAG-TC
1 GGGAGTTG
*
1422538 GGGACTTG
1 GGGAGTTG
1422546 GGGAGTTG
1 GGGAGTTG
1422554 GGGAGT
1 GGGAGT
1422560 CGGGTAACCG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
7 4 0.13
8 26 0.87
ACGTcount: A:0.13, C:0.07, G:0.60, T:0.20
Consensus pattern (8 bp):
GGGAGTTG
Found at i:1422546 original size:23 final size:23
Alignment explanation
Indices: 1422515--1422563 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1422505 AAAGAAGAAA
*
1422515 GGGAGTTGGGGAGTCGGGGAGTC
1 GGGACTTGGGGAGTCGGGGAGTC
*
1422538 GGGACTTGGGGAGTTGGGGAGTC
1 GGGACTTGGGGAGTCGGGGAGTC
1422561 GGG
1 GGG
1422564 TAACCGGGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.08, G:0.61, T:0.18
Consensus pattern (23 bp):
GGGACTTGGGGAGTCGGGGAGTC
Found at i:1430195 original size:18 final size:18
Alignment explanation
Indices: 1430131--1430200 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
1430121 TTGTGAATGG
*
1430131 ATATATTTGTTCAAATAG
1 ATATATTTGTTCAAATAA
* *** *
1430149 TTATATCCATTTAAA-AA
1 ATATATTTGTTCAAATAA
*
1430166 ATTATTTTTGTTCAAATAA
1 A-TATATTTGTTCAAATAA
*
1430185 ATATATTTGTTTAAAT
1 ATATATTTGTTCAAAT
1430201 GGTTATGGTC
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
17 1 0.03
18 32 0.89
19 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
ATATATTTGTTCAAATAA
Found at i:1430224 original size:54 final size:55
Alignment explanation
Indices: 1430131--1430249 Score: 134
Period size: 54 Copynumber: 2.2 Consensus size: 55
1430121 TTGTGAATGG
* * ** *
1430131 ATATATTTGTTCAAATAGTTATATCCATTTAAAAAATTATTTTTGTTCAAATAA-
1 ATATATTTGTTCAAATAGTTATATCCATTCAAAAAATTATATTTGTAAAAAAAAT
* * * *
1430185 ATATATTTGTTTAAATGGTTATGGT-CATTCAAAATATTATATTTGTAAAAAAAAT
1 ATATATTTGTTCAAATAGTTAT-ATCCATTCAAAAAATTATATTTGTAAAAAAAAT
1430240 ATATATTTGT
1 ATATATTTGT
1430250 CTATAAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
54 43 0.80
55 11 0.20
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (55 bp):
ATATATTTGTTCAAATAGTTATATCCATTCAAAAAATTATATTTGTAAAAAAAAT
Found at i:1433179 original size:24 final size:23
Alignment explanation
Indices: 1433136--1433203 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
1433126 TGCAACTATC
* *
1433136 TATTTTCAATAGACACAATTGTT
1 TATTTTCAATAAACATAATTGTT
*
1433159 TATTTTCTAATAAACATAATTATT
1 TATTTTC-AATAAACATAATTGTT
*
1433183 TGTTTTC---AAACATAATTGTT
1 TATTTTCAATAAACATAATTGTT
1433203 T
1 T
1433204 GAATAAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.33
23 7 0.18
24 19 0.49
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (23 bp):
TATTTTCAATAAACATAATTGTT
Found at i:1433216 original size:18 final size:18
Alignment explanation
Indices: 1433167--1433224 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1433157 TTTATTTTCT
*
1433167 AATAAACATAATTATTTG
1 AATAAACATAATTGTTTG
**
1433185 TTTTCAAACATAATTGTTTG
1 -AAT-AAACATAATTGTTTG
*
1433205 AATAAACTTAATTGTTTG
1 AATAAACATAATTGTTTG
1433223 AA
1 AA
1433225 CAAATATAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 16 0.50
19 2 0.06
20 14 0.44
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (18 bp):
AATAAACATAATTGTTTG
Found at i:1433595 original size:20 final size:21
Alignment explanation
Indices: 1433555--1433595 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1433545 TGGTGAATCC
1433555 TTTATTGAGCATCTAATATAA
1 TTTATTGAGCATCTAATATAA
* *
1433576 TTTATTTAGCATGT-ATATAA
1 TTTATTGAGCATCTAATATAA
1433596 CCCAATGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTATTGAGCATCTAATATAA
Found at i:1439234 original size:2 final size:2
Alignment explanation
Indices: 1439221--1439254 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1439211 TTAATTAAAG
*
1439221 AT AT AT AC 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
1439255 TTGTGTGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1444338 original size:18 final size:19
Alignment explanation
Indices: 1444315--1444351 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1444305 TCGTTACTAA
*
1444315 TTAG-TTAATTAATCATTT
1 TTAGTTTAAATAATCATTT
1444333 TTAGTTTAAATAATCATTT
1 TTAGTTTAAATAATCATTT
1444352 GAAATCTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAGTTTAAATAATCATTT
Found at i:1453468 original size:16 final size:17
Alignment explanation
Indices: 1453442--1453473 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1453432 ACTCTTGTTA
1453442 TTTTGGGTTGGCTTTTG
1 TTTTGGGTTGGCTTTTG
1453459 TTTT-GGTTGGCTTTT
1 TTTTGGGTTGGCTTTT
1453474 ATTGAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.06, G:0.31, T:0.62
Consensus pattern (17 bp):
TTTTGGGTTGGCTTTTG
Found at i:1456532 original size:20 final size:19
Alignment explanation
Indices: 1456509--1456554 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1456499 TTTTTATATT
1456509 TTTTTATAAT-TCTTTAACAA
1 TTTTTATAATAT-TTTAA-AA
1456529 TTTTTAATAATATTTTAAAA
1 TTTTT-ATAATATTTTAAAA
1456549 TTTTTA
1 TTTTTA
1456555 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 10 0.42
22 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTATAATATTTTAAAA
Found at i:1456555 original size:20 final size:22
Alignment explanation
Indices: 1456508--1456562 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1456498 TTTTTTATAT
*
1456508 TTTTTTATAAT-TCTTTAACAA
1 TTTTTAATAATATCTTTAACAA
1456529 TTTTTAATAATAT-TTTAA-AA
1 TTTTTAATAATATCTTTAACAA
1456549 TTTTTAATATATAT
1 TTTTTAATA-ATAT
1456563 ATATAGCGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.35
21 19 0.61
22 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAATAATATCTTTAACAA
Found at i:1458218 original size:2 final size:2
Alignment explanation
Indices: 1458211--1458236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1458201 TAAGTATAAG
1458211 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1458237 GAACTTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1461986 original size:21 final size:21
Alignment explanation
Indices: 1461962--1462004 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1461952 AAACTGCAAT
1461962 TCTTTACACAGTTGAAAGAGG
1 TCTTTACACAGTTGAAAGAGG
1461983 TCTTTACACAGTTGAAAGAGG
1 TCTTTACACAGTTGAAAGAGG
1462004 T
1 T
1462005 TTACATCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (21 bp):
TCTTTACACAGTTGAAAGAGG
Found at i:1462009 original size:19 final size:20
Alignment explanation
Indices: 1461963--1462009 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
1461953 AACTGCAATT
1461963 CTTTACACAGTTGAAAGAGG
1 CTTTACACAGTTGAAAGAGG
1461983 TCTTTACACAGTTGAAAGAGG
1 -CTTTACACAGTTGAAAGAGG
1462004 -TTTACA
1 CTTTACA
1462010 TCACCTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.23
21 20 0.77
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (20 bp):
CTTTACACAGTTGAAAGAGG
Found at i:1478284 original size:22 final size:22
Alignment explanation
Indices: 1478259--1478300 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1478249 AAATATTTTA
*
1478259 TATTATAA-TTATTAATAAAATT
1 TATT-TAATTTATAAATAAAATT
1478281 TATTTAATTTATAAATAAAA
1 TATTTAATTTATAAATAAAA
1478301 ATATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTAATTTATAAATAAAATT
Found at i:1478377 original size:15 final size:15
Alignment explanation
Indices: 1478350--1478391 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
1478340 TAATTTTAAT
1478350 AATATTGAATAATTTA
1 AATATT-AATAATTTA
1478366 AATATTAATAA-TTA
1 AATATTAATAATTTA
1478380 AA-ATTAA-AATTT
1 AATATTAATAATTT
1478392 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 7 0.28
14 5 0.20
15 5 0.20
16 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATTAATAATTTA
Found at i:1478403 original size:22 final size:24
Alignment explanation
Indices: 1478370--1478416 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1478360 AATTTAAATA
1478370 TTAATAATTAAA-ATTAAAATTTT
1 TTAATAATTAAATATTAAAATTTT
*
1478393 TTAA-AATTAAATATTAATATTTT
1 TTAATAATTAAATATTAAAATTTT
1478416 T
1 T
1478417 AATTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATAATTAAATATTAAAATTTT
Found at i:1488715 original size:2 final size:2
Alignment explanation
Indices: 1488710--1488735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1488700 AAAAAAAGGT
1488710 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1488736 GAACCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1489334 original size:15 final size:15
Alignment explanation
Indices: 1489313--1489466 Score: 68
Period size: 15 Copynumber: 10.8 Consensus size: 15
1489303 TAGGATATAA
1489313 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
* *
1489328 GTTTAAATTTAAATT
1 ATTTAAATTTAATTT
* **
1489343 ATCT--A-TCCATTAT
1 ATTTAAATTTAATT-T
1489356 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
1489371 GTTTAAATTTAA---
1 ATTTAAATTTAATTT
1489383 A--TAAGGA-TTAATTAT
1 ATTTAA--ATTTAATT-T
1489398 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
1489413 GTTTAAATTTAA---
1 ATTTAAATTTAATTT
1489425 A--TAAGGA-TTAATTAT
1 ATTTAA--ATTTAATT-T
1489440 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
1489455 GTTTAAATTTAA
1 ATTTAAATTTAA
1489467 ACATAATATC
Statistics
Matches: 102, Mismatches: 15, Indels: 44
0.63 0.09 0.27
Matches are distributed among these distances:
10 6 0.06
11 8 0.08
12 5 0.05
13 5 0.05
15 56 0.55
16 16 0.16
17 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:1489334 original size:21 final size:21
Alignment explanation
Indices: 1489310--1489467 Score: 112
Period size: 21 Copynumber: 7.5 Consensus size: 21
1489300 CAATAGGATA
1489310 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
**
1489331 TAAATTTAAA-TT-ATCTATCCAT
1 TAAATTTAAATTTAAT-T-T-GTT
*
1489353 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* **
1489374 TAAATTTAAA--TAAGGATTAAT
1 TAAATTTAAATTTAA--TTTGTT
*
1489395 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* **
1489416 TAAATTTAAA--TAAGGATTAAT
1 TAAATTTAAATTTAA--TTTGTT
*
1489437 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
1489458 TAAATTTAAA
1 TAAATTTAAA
1489468 CATAATATCC
Statistics
Matches: 102, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
19 8 0.08
20 3 0.03
21 69 0.68
22 11 0.11
23 9 0.09
24 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:1489410 original size:42 final size:42
Alignment explanation
Indices: 1489313--1489467 Score: 256
Period size: 42 Copynumber: 3.7 Consensus size: 42
1489303 TAGGATATAA
*** **
1489313 ATTTAAATTTAATTTGTTTAAATTTAAATTATCTATCCATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAA-TAAGGATTAATTAT
1489356 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
1489398 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
1489440 ATTTAAATTTAATTTGTTTAAATTTAAA
1 ATTTAAATTTAATTTGTTTAAATTTAAA
1489468 CATAATATCC
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 79 0.74
43 28 0.26
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (42 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
Found at i:1495821 original size:21 final size:21
Alignment explanation
Indices: 1495795--1495867 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
1495785 AGATAGGATA
1495795 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* **
1495816 TAAATTTAAA--TAAGGATTAAT
1 TAAATTTAAATTTAA--TTTGTT
*
1495837 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
*
1495858 TAAATGTAAA
1 TAAATTTAAA
1495868 CATAATATCC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 3 0.08
21 33 0.85
23 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:1499659 original size:15 final size:17
Alignment explanation
Indices: 1499630--1499667 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1499620 TAAAGGTATA
1499630 TATATAATTAGTAA-TTT
1 TATA-AATTAGTAATTTT
1499647 TATAAATTA-TAATTTT
1 TATAAATTAGTAATTTT
1499663 TATAA
1 TATAA
1499668 CGTTAACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 13 0.65
17 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATAAATTAGTAATTTT
Found at i:1502638 original size:8 final size:8
Alignment explanation
Indices: 1502625--1502673 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
1502615 TATAATGATG
1502625 AAAAAAGA
1 AAAAAAGA
1502633 AAAAAAGA
1 AAAAAAGA
1502641 AAAAAA-A
1 AAAAAAGA
**
1502648 TTAAAAGA
1 AAAAAAGA
*
1502656 AAGAAAGA
1 AAAAAAGA
*
1502664 AAGAAAGA
1 AAAAAAGA
1502672 AA
1 AA
1502674 TTATTCATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 5 0.14
8 30 0.86
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1503393 original size:35 final size:35
Alignment explanation
Indices: 1503354--1503423 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1503344 ACATTATAGA
* *
1503354 AATAAACTTTTATCATATATATGAAAGTAGAAGTT
1 AATAAACTTTTATCATATATATGAAAATAAAAGTT
1503389 AATAAACTTTTATCATATATATGAAAATAAAAGTT
1 AATAAACTTTTATCATATATATGAAAATAAAAGTT
1503424 TACAAGGGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (35 bp):
AATAAACTTTTATCATATATATGAAAATAAAAGTT
Found at i:1512594 original size:34 final size:34
Alignment explanation
Indices: 1512556--1512623 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1512546 GAGAGAATGG
*
1512556 GGCAGAGAAGGGGTAGCCACGCAGAAGAGAGAGT
1 GGCAGAGAAGGGGCAGCCACGCAGAAGAGAGAGT
** *
1512590 GGCAGAGAAGGGGCAGCGGCGCAGGAGAGAGAGT
1 GGCAGAGAAGGGGCAGCCACGCAGAAGAGAGAGT
1512624 AGGAAAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.49, T:0.04
Consensus pattern (34 bp):
GGCAGAGAAGGGGCAGCCACGCAGAAGAGAGAGT
Found at i:1514833 original size:34 final size:32
Alignment explanation
Indices: 1514781--1514866 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 32
1514771 AAAAAAATCA
*
1514781 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
1514816 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAAT-AAAATAAAATATAAAAAATTATAATAAG
1514849 AAATAAAAATAAAATATA
1 AAAT-AAAATAAAATATA
1514867 TGACATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 19 0.42
34 15 0.33
35 5 0.11
36 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATAAAATAAAATATAAAAAATTATAATAAG
Found at i:1515117 original size:16 final size:15
Alignment explanation
Indices: 1515080--1515122 Score: 77
Period size: 15 Copynumber: 2.8 Consensus size: 15
1515070 TTATTTTTCC
1515080 TGCAATCACATTACT
1 TGCAATCACATTACT
1515095 TGCAATCACATTACT
1 TGCAATCACATTACT
1515110 TGGCAATCACATT
1 T-GCAATCACATT
1515123 GCATGTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (15 bp):
TGCAATCACATTACT
Found at i:1516071 original size:461 final size:449
Alignment explanation
Indices: 1515210--1516118 Score: 1388
Period size: 461 Copynumber: 2.0 Consensus size: 449
1515200 GAAAACACAC
1515210 TAAATTAAGACACATAAACGAACAAATTTGTTCTAACATCCTATGTGTTGATAAAAAAAATCAAC
1 TAAATTAAGACACATAAACGAACAAATTTGTTCTAACATCCTATGTGTTGATAAAAAAAATCAAC
1515275 ACATGTATAATTTTTGTCAAAGTGATTTTTTTTAAAAACAATCTTTTGATCCTTACTTTACATAG
66 ACATGTATAATTTTTGTCAAAGTGATTTTTTTTAAAAACAATCTTTTGATCCTTACTTTACATAG
* **
1515340 TTTTATATTCTTTTTTTATTATATTTCATATTTATCAATAATCAATGAAGGGGGAAAAAGTGAAA
131 TTTTATATTCTTTTTTTATTATATTTCATATTTACCAATAATCAATGAAGGGAAAAAAAGTGAAA
*
1515405 GAAAAGAAAATTTGGAAAAAATCCAAGCGAATAGTGGCAAGAAGTGTGGTTGGAAAGATCATTTT
196 GAAAAGAAAATTTGAAAAAAATCCAAGCGAATAGTGGCAAGAAGTGTGGTTGGAAAGATCATTTT
* * * * *
1515470 CTGATAAAGTTTTAGAGAGAGAAAGAGGCAAAGAAAGGGTAACGATGTAGGTAAGAGAGGGAGTG
261 CTGATAAAGTTTTAAAGAGAAAAAGAGGCAAAGAAAGGGTAACGATGCAAGTAAGAGAGAGAGTG
*
1515535 GGAAAATAAAACAAGGTTAGGGTTTCACAATTAGGTTTATAAATGTGGTTGGAACGACACTATGT
326 GGAAAATAAAACAAGGTTAGGGTTTCACAATTAGGTTTATAAATGTGGTTGAAACGACACTATGT
* * *
1515600 AGATAATGAAGAAAAGAGAAAATAAAGGGGAAAGAAGTAAATGGCTGAGGCACTTAGAG
391 AGATAATGAAGAAAAGAGAAAATAAAAGGGAAAGAAGTAAACGACTGAGGCACTTAGAG
* *
1515659 TAAATTAAGACACATGAACGAACAAATTTGTTCTAACATCCTATTTGTTGATAAAAAAAATCAAC
1 TAAATTAAGACACATAAACGAACAAATTTGTTCTAACATCCTATGTGTTGATAAAAAAAATCAAC
** *
1515724 ATGTGTATAATTTTTGTCGAAGTGATCTTTTTTTGAAAAA-AATCTTTTGATCCTTACTTTACAT
66 ACATGTATAATTTTTGTCAAAGTGAT-TTTTTTT-AAAAACAATCTTTTGATCCTTACTTTACAT
*
1515788 AGTTTTATATTCTTTTATTTTTTATTATCATATTTCATATTTACCAATAATTAATGAAAGGGAAA
129 AGTTTTATATTC---T-TTTTTTA-T-T-ATATTTCATATTTACCAATAATCAATG-AAGGGAAA
* * * **
1515853 AAAAGTGACAGAGAAGAGAAAATTTGAAAAAAATCCAAGTGAATGGTGGCGTGAAGTGTGGTTGG
186 AAAAGTGA-A-AGAAAAGAAAATTTGAAAAAAATCCAAGCGAATAGTGGCAAGAAGTGTGGTTGG
* * *
1515918 AAGGATCATTTTCTGATAAAGTTTTAAAGAGAAAAAGAGGTAGAGAAAAGGGTAACGATGCAAGT
249 AAAGATCATTTTCTGATAAAGTTTTAAAGAGAAAAAGAGGCAAAG-AAAGGGTAACGATGCAAGT
* * *
1515983 AGGAGAGAGTGTGGGAAAATAAAATAAGGTTAGGGTTTCACAATTAGGTTTATAAATGTGGTTGA
313 AAGAGAGAGAGTGGGAAAATAAAACAAGGTTAGGGTTTCACAATTAGGTTTATAAATGTGGTTGA
* * * *
1516048 AACGACACTGTGTGGATAATGAAGAAAAGCGAAAATAAAAGGGAAAGAAGTAAACGATTGAGGCA
378 AACGACACTATGTAGATAATGAAGAAAAGAGAAAATAAAAGGGAAAGAAGTAAACGACTGAGGCA
1516113 CTTAGA
443 CTTAGA
1516119 CTAATCAAAT
Statistics
Matches: 413, Mismatches: 34, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
449 86 0.21
450 43 0.10
451 5 0.01
453 1 0.00
454 7 0.02
455 1 0.00
456 1 0.00
457 25 0.06
458 14 0.03
459 1 0.00
460 88 0.21
461 141 0.34
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.30
Consensus pattern (449 bp):
TAAATTAAGACACATAAACGAACAAATTTGTTCTAACATCCTATGTGTTGATAAAAAAAATCAAC
ACATGTATAATTTTTGTCAAAGTGATTTTTTTTAAAAACAATCTTTTGATCCTTACTTTACATAG
TTTTATATTCTTTTTTTATTATATTTCATATTTACCAATAATCAATGAAGGGAAAAAAAGTGAAA
GAAAAGAAAATTTGAAAAAAATCCAAGCGAATAGTGGCAAGAAGTGTGGTTGGAAAGATCATTTT
CTGATAAAGTTTTAAAGAGAAAAAGAGGCAAAGAAAGGGTAACGATGCAAGTAAGAGAGAGAGTG
GGAAAATAAAACAAGGTTAGGGTTTCACAATTAGGTTTATAAATGTGGTTGAAACGACACTATGT
AGATAATGAAGAAAAGAGAAAATAAAAGGGAAAGAAGTAAACGACTGAGGCACTTAGAG
Found at i:1516837 original size:28 final size:28
Alignment explanation
Indices: 1516773--1516837 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1516763 TAAATTATTA
1516773 ATAAATTATAGTAATATAGTATAACTTAT
1 ATAAATTATAGTAATATAG-ATAACTTAT
* * *
1516802 AT-AGTTATATTAATATAG-TAAGTTAT
1 ATAAATTATAGTAATATAGATAACTTAT
1516828 ATTAAATTAT
1 A-TAAATTAT
1516838 TAATATTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 8 0.27
27 1 0.03
28 19 0.63
29 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (28 bp):
ATAAATTATAGTAATATAGATAACTTAT
Found at i:1517102 original size:20 final size:20
Alignment explanation
Indices: 1517077--1517116 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1517067 CTAACTAGTC
*
1517077 AATAACAATTTACTATTATA
1 AATAACAATATACTATTATA
*
1517097 AATAACAATATACTGTTATA
1 AATAACAATATACTATTATA
1517117 TAGTATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
AATAACAATATACTATTATA
Found at i:1519575 original size:14 final size:14
Alignment explanation
Indices: 1519558--1519587 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1519548 AATTAAAATT
*
1519558 AACTAATTAACTAA
1 AACTAATTAACCAA
1519572 AACTAATTAACCAA
1 AACTAATTAACCAA
1519586 AA
1 AA
1519588 TTTAAACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (14 bp):
AACTAATTAACCAA
Found at i:1520929 original size:13 final size:13
Alignment explanation
Indices: 1520913--1520937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1520903 CACATAACAC
1520913 TCATTTATAACTA
1 TCATTTATAACTA
1520926 TCATTTATAACT
1 TCATTTATAACT
1520938 CAACACATAT
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:0.00, T:0.48
Consensus pattern (13 bp):
TCATTTATAACTA
Found at i:1523676 original size:34 final size:35
Alignment explanation
Indices: 1523633--1523700 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
1523623 TCCATTTAAT
* **
1523633 CCTTTAACTTTT-TTTATTTT-CAATTTAGTCCTTC
1 CCTTAAACTTTTCTTT-TTTTGCAATCAAGTCCTTC
1523667 CCTTAAACTTTTCTTTTTTTGCAATCAAGTCCTT
1 CCTTAAACTTTTCTTTTTTTGCAATCAAGTCCTT
1523701 GCAATTGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.54
Consensus pattern (35 bp):
CCTTAAACTTTTCTTTTTTTGCAATCAAGTCCTTC
Found at i:1523832 original size:43 final size:43
Alignment explanation
Indices: 1523706--1523873 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 43
1523696 TCCTTGCAAT
* * *
1523706 TGAGAATTAATTCTTTCTTTACAAGGTGTTGGTTCTTCTTACC
1 TGAGAATTAATTCTTTCTCTACTAGGTGTTGGTTCTTCTTGCC
* * * * * *
1523749 CGAGGATCAATTCTTTCTCCACCAGGTATTGGTTCTTCTTGCC
1 TGAGAATTAATTCTTTCTCTACTAGGTGTTGGTTCTTCTTGCC
* * * **
1523792 TGAAAATTGATTCTTTCTCTACTAGGTGTTTGTTCTTCTTGTT
1 TGAGAATTAATTCTTTCTCTACTAGGTGTTGGTTCTTCTTGCC
* * *
1523835 TGAGAATTGATTCTCTCTCTACTCGGTGTTGGTTCTTCT
1 TGAGAATTAATTCTTTCTCTACTAGGTGTTGGTTCTTCT
1523874 CACTTGAGAA
Statistics
Matches: 102, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.46
Consensus pattern (43 bp):
TGAGAATTAATTCTTTCTCTACTAGGTGTTGGTTCTTCTTGCC
Found at i:1525048 original size:79 final size:79
Alignment explanation
Indices: 1524878--1525077 Score: 231
Period size: 79 Copynumber: 2.5 Consensus size: 79
1524868 TATGAAATTT
* * *
1524878 TCAACACATACATCTCATGACATACATTTCATAATCTCATAATTAATTCCCAAGCTTAGCCCATA
1 TCAACACATACATCTTATGGCATACATGTCATAATCTCATAATTAATT-CCAAGCTTAGCCCATA
1524943 GTGTACATAACATAA
65 GTGTACATAACATAA
* * * * *
1524958 TCAAAACATACATCTTATGGCATTCATGTCATAATCTCATAATTCATT-TAATGCTTAGCCTATA
1 TCAACACATACATCTTATGGCATACATGTCATAATCTCATAATTAATTCCAA-GCTTAGCCCATA
* * **
1525022 GTGTACATGATATTC
65 GTGTACATAACATAA
* * * *
1525037 TCCACACATACATCTTGTGGGATACATGTCATAACCTCATA
1 TCAACACATACATCTTATGGCATACATGTCATAATCTCATA
1525078 GAAAAGAACT
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
78 2 0.02
79 57 0.56
80 42 0.42
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (79 bp):
TCAACACATACATCTTATGGCATACATGTCATAATCTCATAATTAATTCCAAGCTTAGCCCATAG
TGTACATAACATAA
Found at i:1531756 original size:8 final size:8
Alignment explanation
Indices: 1531743--1531819 Score: 57
Period size: 9 Copynumber: 8.9 Consensus size: 8
1531733 TCTGTTCCTT
1531743 TTTTTTTA
1 TTTTTTTA
1531751 TTTTTTTA
1 TTTTTTTA
1531759 GTTTTTATTA
1 -TTTTT-TTA
*
1531769 ATTTTTTA
1 TTTTTTTA
1531777 TTTTTATTA
1 TTTTT-TTA
*
1531786 TATTATATTA
1 T-TT-TTTTA
1531796 TTTATTTT-
1 TTT-TTTTA
*
1531804 TATTTTTA
1 TTTTTTTA
1531812 CTTTTTTT
1 -TTTTTTT
1531820 TAGGGAATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.07
8 17 0.30
9 25 0.45
10 9 0.16
11 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1531773 original size:17 final size:16
Alignment explanation
Indices: 1531742--1531821 Score: 60
Period size: 16 Copynumber: 5.0 Consensus size: 16
1531732 CTCTGTTCCT
*
1531742 TTTTTTTTATTTTTTTA
1 TTTTTATTA-TTTTTTA
1531759 GTTTTTATTAATTTTTTA
1 -TTTTTATT-ATTTTTTA
* *
1531777 TTTTTATTATATTATA
1 TTTTTATTATTTTTTA
*
1531793 -TTAT-TTA-TTTTTA
1 TTTTTATTATTTTTTA
1531806 TTTTTACTT-TTTTTTA
1 TTTTTA-TTATTTTTTA
1531822 GGGAATAGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
13 4 0.08
14 6 0.12
15 3 0.06
16 14 0.28
17 8 0.16
18 14 0.28
19 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTTATTATTTTTTA
Found at i:1531798 original size:26 final size:26
Alignment explanation
Indices: 1531744--1531810 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
1531734 CTGTTCCTTT
*
1531744 TTTTTTATTTTTTTAGTTTTTATTAA
1 TTTTTTATTTTTTTAGTTTATATTAA
*
1531770 TTTTTTATTTTTATTA-TATTATATTATT
1 TTTTTTATTTTT-TTAGT-TTATATTA-A
1531798 TATTTTTATTTTT
1 T-TTTTTATTTTT
1531811 ACTTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 13 0.37
27 10 0.29
28 1 0.03
29 11 0.31
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTTTATTTTTTTAGTTTATATTAA
Found at i:1531799 original size:23 final size:22
Alignment explanation
Indices: 1531764--1531807 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1531754 TTTTAGTTTT
*
1531764 TATTAATTTTTTATTTTTATTA
1 TATTAATTATTTATTTTTATTA
1531786 TATTATATTATTTATTTTTATT
1 TATTA-ATTATTTATTTTTATT
1531808 TTTACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTAATTATTTATTTTTATTA
Found at i:1532096 original size:62 final size:62
Alignment explanation
Indices: 1531999--1533100 Score: 908
Period size: 61 Copynumber: 17.9 Consensus size: 62
1531989 AAATTTTCTC
* * * * * * *
1531999 GTGCCAAGATAACTGGGCTTAAACGTCTTAGATGCCAACTAAATTGGGCTTGAACTCTTTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * *
1532061 GTGCCAATATAACTGAACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAACTCTTTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * * * *
1532123 GTGTCAACGTAACTAGACTTATACATCTTAGATGACAGTTTAATTGGGCTTAAACTCTTTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * * * *
1532185 GT-CTAAACATAACCGGGCTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAACTCCTTTT
1 GTGC-CAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * *
1532247 GTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGAGCTTAATCATCTTTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAC-TCTTTTT
** * * * **
1532310 GTGCCAATGTAGCTAGG-TTTAAACATCTTGGATGTTAGCTAAATTGGGCTTAAACTCTTTTT
1 GTGCCAACATAACT-GGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * ***
1532372 GTGCCAACATAGCTAGG-TTTAAACATCTTGGATGCTAGCTAAATCAAGCTTAAACTCTTTTT
1 GTGCCAACATAACT-GGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * ** **
1532434 GTGTCAACATAACTGGACTTATACTTCTTGGATGCCAATTAAATTGGGCTT-AA-TCATCATT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
* * * * *
1532495 GTGCCAATATAACTGGGCTTAAACATCTTGGTTGCCAGCTTAATTGGGCTTAAACTCTTTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * * * * ** *
1532557 GTACTAACGTAACTGGACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAAATC-AATG
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* ** * * *
1532618 GTGCCAACATAACTCGG-CTTAAATGTCTTGGATACCAGCTAAATTTGGCTT-AA-TCATCTTT
1 GTGCCAACATAACT-GGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
** ** * ** *
1532679 GTGCCAATGTAACTGGACTTATACATCTTGGATGCCAATTTAATTTAGCTTAAACTCATCTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
* * * * *
1532742 GTACCAATATAACTGGACTTAAACATCTTAGATGCCAGCTAAATTGGGCTT-AA-TCATCTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
* * * *
1532803 GTGCCAACGTAACTGGATTTATACATCTTGGATGCCAGCTAAATTGGGGTT-AA-TCATCTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
* * * * * * * * ** *
1532864 GTGCCAATATAATTGGGCTTAAACTTTTTGGATGCTAGCTAAATTAGGCTT-AA-TCAACTTC
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
* * ** * ** *
1532925 GTGCCAATATAACTAGG-CTTAAATGTCTTGGATGCCAGCTAAATTGGACTTAAACT-AATTC
1 GTGCCAACATAACT-GGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * ** *
1532986 GTGCCAACATAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAA-TCTCTTT
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
* * * * *
1533047 GTGCTAATATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTAGGCTTAAA
1 GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAA
1533101 ACCTCTCATG
Statistics
Matches: 851, Mismatches: 170, Indels: 39
0.80 0.16 0.04
Matches are distributed among these distances:
59 2 0.00
60 9 0.01
61 371 0.44
62 365 0.43
63 102 0.12
64 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (62 bp):
GTGCCAACATAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTTTT
Found at i:1532155 original size:124 final size:123
Alignment explanation
Indices: 1531999--1533100 Score: 949
Period size: 124 Copynumber: 8.9 Consensus size: 123
1531989 AAATTTTCTC
* * * * *
1531999 GTGCCAAGATAACTGGGCTTAAACGTCTTAGATGCCAACTAAATTGGGCTTGAACTCTTTTTGTG
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTT-AACTCTTTTTGTG
* * *
1532064 CCAATATAACTGAACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAACTCTTTTT
65 CCAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTCTCTTT
* * * * * * * *
1532123 GTGTCAACGTAACTAGACTTATACATCTTAGATGACAGTTTAATTGGGCTTAAACTCTTTTTGT-
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTT-AACTCTTTTTGTG
* * * * *
1532187 CTAAACATAACCGGGCTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAACTC-CTTTT
65 C-CAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTCTC-TTT
* * * * *
1532247 GTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGAGCTTAATCATCTTTTTGT
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAA-C-TCTTTTTGT
* * * * * ** * *
1532312 GCCAATGTAGCTAGG-TTTAAACATCTTGGATGTTAGCTAAATTGGGCTTAAACTCTTTTT
64 GCCAATATAACT-GGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTCTCTTT
* * * ***
1532372 GTGCCAACATAGCTAGG-TTTAAACATCTTGGATGCTAGCTAAATCAAGCTTAAACTCTTTTTGT
1 GTGCCAACATAACT-GGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTT-AACTCTTTTTGT
* * * *
1532436 GTCAACATAACTGGACTTATACTTCTTGGATGCCAATTAAATTGGGCTT-AA-TCATCATT
64 GCCAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTC-TCTTT
* * * * *
1532495 GTGCCAATATAACTGGGCTTAAACATCTTGGTTGCCAGCTTAATTGGGCTTAAACTCTTTTTGTA
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTT-AACTCTTTTTGTG
* ** * * ** *
1532560 CTAACGTAACTGGACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAAATC-AATG
65 CCAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTCTCTTT
** * * *
1532618 GTGCCAACATAACTCGG-CTTAAATGTCTTGGATACCAGCTAAATTTGGCTTAA-TCATCTTTGT
1 GTGCCAACATAACT-GGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAACTC-TTTTTGT
* * * * **
1532681 GCCAATGTAACTGGACTTATACATCTTGGATGCCAATTTAATTTAGCTTAAACTCATCTTT
64 GCCAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTC-TCTTT
* * * *
1532742 GTACCAATATAACTGGACTTAAACATCTTAGATGCCAGCTAAATTGGGCTTAA-TCATCTTTGTG
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAACTC-TTTTTGTG
** * * * *
1532806 CCAACGTAACTGGATTTATACATCTTGGATGCCAGCTAAATTGGGGTT-AA-TCATCTTT
65 CCAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTC-TCTTT
* * * * * * * ** *
1532864 GTGCCAATATAATTGGGCTTAAACTTTTTGGATGCTAGCTAAATTAGGCTTAA-TCAACTTCGTG
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAACTC-TTTTTGTG
* * * ** *
1532928 CCAATATAACTAGG-CTTA-AATGTCTTGGATGCCAGCTAAATTGGACTTAAACT-AATTC
65 CCAATATAACT-GGACTTATACT-TCTTGGATGCCAGTTAAATTGGGCTTAAACTCTCTTT
* * * ** * *
1532986 GTGCCAACATAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAATCTCTTTGTGC
1 GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAACTCTTTTTGTGC
* * * * * *
1533051 TAATATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTAGGCTTAAA
66 CAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAA
1533101 ACCTCTCATG
Statistics
Matches: 804, Mismatches: 148, Indels: 54
0.80 0.15 0.05
Matches are distributed among these distances:
121 5 0.01
122 249 0.31
123 159 0.20
124 292 0.36
125 92 0.11
126 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (123 bp):
GTGCCAACATAACTGGACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAACTCTTTTTGTGC
CAATATAACTGGACTTATACTTCTTGGATGCCAGTTAAATTGGGCTTAAACTCTCTTT
Found at i:1532234 original size:31 final size:31
Alignment explanation
Indices: 1532199--1532298 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
1532189 AAACATAACC
1532199 GGGCTTATACTTCTTGGATGCCAGTTTAATT
1 GGGCTTATACTTCTTGGATGCCAGTTTAATT
* * * *** *
1532230 GGGCTTAAACTCCTTTTG-TGCCAACGTAACT
1 GGGCTTATACTTC-TTGGATGCCAGTTTAATT
* *
1532261 GGACTTATACTTCTTGGATGCCAGTTAAATT
1 GGGCTTATACTTCTTGGATGCCAGTTTAATT
*
1532292 GAGCTTA
1 GGGCTTA
1532299 ATCATCTTTT
Statistics
Matches: 49, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
30 3 0.06
31 43 0.88
32 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (31 bp):
GGGCTTATACTTCTTGGATGCCAGTTTAATT
Found at i:1532502 original size:30 final size:31
Alignment explanation
Indices: 1532459--1533100 Score: 112
Period size: 31 Copynumber: 20.9 Consensus size: 31
1532449 GACTTATACT
* *
1532459 TCTTGGATGCCAATTAAATTGGGCTTAATCA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
*
1532490 TCATT-G-TGCCAA-TATAACTGGGCTTAAACA
1 TC-TTGGTTGCCAATTA-AATTGGGCTTAAACA
*
1532520 TCTTGGTTGCCAGCTT-AATTGGGCTTAAAC-
1 TCTTGGTTGCCA-ATTAAATTGGGCTTAAACA
* * * * * * *
1532550 TCTT-TTTGTACTAACGT-AACTGGACTTATACT
1 TCTTGGTTG--CCAA-TTAAATTGGGCTTAAACA
* * *
1532582 TCTTGGATGCCAGTTTAATTGGGCTTAAA-A
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
* * * * **
1532612 TCAATGG-TGCCAA-CATAACTCGGCTTAAATG
1 TC-TTGGTTGCCAATTA-AATTGGGCTTAAACA
* * ** * *
1532643 TCTTGGATACCAGCTAAATTTGGCTTAATCA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
* * * *
1532674 TCTTTG-TGCCAATGT-AACTGGACTTATACA
1 TCTTGGTTGCCAAT-TAAATTGGGCTTAAACA
* * **
1532704 TCTTGGATGCCAATTTAATTTAGCTTAAACTCA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAA--CA
* * * *
1532737 TCTTTG-TACCAA-TATAACTGGACTTAAACA
1 TCTTGGTTGCCAATTA-AATTGGGCTTAAACA
* * ** *
1532767 TCTTAGATGCCAGCTAAATTGGGCTTAATCA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
* * * ** *
1532798 TCTTTG-TGCCAACGT-AACTGGATTTATACA
1 TCTTGGTTGCCAA-TTAAATTGGGCTTAAACA
* ** * *
1532828 TCTTGGATGCCAGCTAAATTGGGGTTAATCA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
* *
1532859 TCTTTG-TGCCAA-TATAATTGGGCTTAAACT
1 TCTTGGTTGCCAATTA-AATTGGGCTTAAACA
* * * ** * *
1532889 TTTTGGATGCTAGCTAAATTAGGCTTAATCA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
* * * * **
1532920 ACTTCG-TGCCAA-TATAACTAGGCTTAAATG
1 TCTTGGTTGCCAATTA-AATTGGGCTTAAACA
* ** *
1532950 TCTTGGATGCCAGCTAAATTGGACTTAAAC-
1 TCTTGGTTGCCAATTAAATTGGGCTTAAACA
* * * * * *
1532980 TAATTCG-TGCCAA-CATAACTGGACTTATACA
1 T-CTTGGTTGCCAATTA-AATTGGGCTTAAACA
* * * **
1533011 TCTTGGATGCTAGTTTGATTGGGCTTAAATC-
1 TCTTGGTTGCCAATTAAATTGGGCTTAAA-CA
* * *
1533042 TCTTTG-TGCTAA-TATAACTGGGCTTAAACA
1 TCTTGGTTGCCAATTA-AATTGGGCTTAAACA
* ** *
1533072 TCTTGGATGCCAGCTAAATTAGGCTTAAA
1 TCTTGGTTGCCAATTAAATTGGGCTTAAA
1533101 ACCTCTCATG
Statistics
Matches: 433, Mismatches: 134, Indels: 88
0.66 0.20 0.13
Matches are distributed among these distances:
29 14 0.03
30 178 0.41
31 201 0.46
32 30 0.07
33 10 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
TCTTGGTTGCCAATTAAATTGGGCTTAAACA
Found at i:1539380 original size:13 final size:13
Alignment explanation
Indices: 1539362--1539386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1539352 TGAAGACTCT
1539362 TTTTTTTCTTTCC
1 TTTTTTTCTTTCC
1539375 TTTTTTTCTTTC
1 TTTTTTTCTTTC
1539387 AAAAGACCTC
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTTTCC
Found at i:1542529 original size:21 final size:21
Alignment explanation
Indices: 1542504--1542591 Score: 82
Period size: 20 Copynumber: 4.4 Consensus size: 21
1542494 CGCTCACCTT
1542504 TTTCTTTTTCTCTCTTTTCTC
1 TTTCTTTTTCTCTCTTTTCTC
*
1542525 TTTC-TTTTC-CCCTTTCTCTC
1 TTTCTTTTTCTCTCTTT-TCTC
1542545 TTT-TTCTTTCT-TCTTTTCTC
1 TTTCTT-TTTCTCTCTTTTCTC
* *
1542565 ---CTCTTTCTCTCTTTTTTC
1 TTTCTTTTTCTCTCTTTTCTC
1542583 TTTCTTTTT
1 TTTCTTTTT
1542592 TCTTATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
17 5 0.09
18 9 0.17
19 5 0.09
20 17 0.32
21 17 0.32
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTTTTCTCTCTTTTCTC
Found at i:1542558 original size:29 final size:31
Alignment explanation
Indices: 1542510--1542594 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
1542500 CCTTTTTCTT
*
1542510 TTTCTCTC-TTTTCTCT-TTCTTTTC-CC-C
1 TTTCTCTCTTTTTCTTTCTTCTTTTCTCCTC
1542537 TTTCTCTCTTTTTCTTTCTTCTTTTCTCCTC
1 TTTCTCTCTTTTTCTTTCTTCTTTTCTCCTC
1542568 TTTCTCTCTTTTTTCTTTCTT-TTTTCT
1 TTTCTCTC-TTTTTCTTTCTTCTTTTCT
1542595 TATTTTTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
27 8 0.15
28 7 0.13
29 8 0.15
30 2 0.04
31 15 0.29
32 12 0.23
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTCTCTCTTTTTCTTTCTTCTTTTCTCCTC
Found at i:1542577 original size:25 final size:22
Alignment explanation
Indices: 1542536--1542613 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 22
1542526 TTCTTTTCCC
*
1542536 CTTTCTCTCTTTT-TCT-TTCTT
1 CTTTCT-TCTTTTCTCTCTTTTT
*
1542557 CTTTTCTCCTCTTTCTCTCTTTTTT
1 C-TTTCTTCT-TTTCTCTC-TTTTT
* *
1542582 CTTTCTT-TTTTCTTATTTTTTT
1 CTTTCTTCTTTTC-TCTCTTTTT
1542604 CTTTCTTCTT
1 CTTTCTTCTT
1542614 CCCTTCCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.07
22 24 0.53
23 8 0.18
24 5 0.11
25 5 0.11
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (22 bp):
CTTTCTTCTTTTCTCTCTTTTT
Found at i:1542730 original size:4 final size:4
Alignment explanation
Indices: 1542723--1542750 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1542713 TTCCAAACTC
1542723 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1542751 TTTTCAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1542984 original size:31 final size:31
Alignment explanation
Indices: 1542948--1543020 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
1542938 AAAGGAATGG
*
1542948 GTTTTTGTTTGTTGTTGAATCTTGGCTTTTT
1 GTTTTTCTTTGTTGTTGAATCTTGGCTTTTT
* *
1542979 GTTTTTCTTTGTTGTTGAATCTTTGTTTTTT
1 GTTTTTCTTTGTTGTTGAATCTTGGCTTTTT
1543010 GTTTTTCTTTG
1 GTTTTTCTTTG
1543021 CTAGATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.05, C:0.07, G:0.19, T:0.68
Consensus pattern (31 bp):
GTTTTTCTTTGTTGTTGAATCTTGGCTTTTT
Found at i:1543215 original size:23 final size:23
Alignment explanation
Indices: 1543189--1543233 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1543179 TGAACTTTTT
*
1543189 TATTA-ATTTTTTAATTTTTATTA
1 TATTATATTATTT-ATTTTTATTA
1543212 TATTATATTATTTATTTTTATT
1 TATTATATTATTTATTTTTATT
1543234 TTTGGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTATATTATTTATTTTTATTA
Found at i:1543424 original size:49 final size:49
Alignment explanation
Indices: 1543349--1543448 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
1543339 TTCTTCATAA
* *
1543349 GTAAAACCAGTGCACCCAATGGTGAGACATTAGGTTGAATATAGCCCTT
1 GTAAAACCAGTGCACCCAATGATGAGACATTAGGTTGAATAAAGCCCTT
*
1543398 GTAAAACCAGTGCACCCAATGATGAGACATTAGGTTGAATAAAGCCTTT
1 GTAAAACCAGTGCACCCAATGATGAGACATTAGGTTGAATAAAGCCCTT
1543447 GT
1 GT
1543449 TTAACAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (49 bp):
GTAAAACCAGTGCACCCAATGATGAGACATTAGGTTGAATAAAGCCCTT
Found at i:1555079 original size:17 final size:17
Alignment explanation
Indices: 1555059--1555091 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1555049 GGTTGATAAT
1555059 TGATATGTACTGATTGA
1 TGATATGTACTGATTGA
*
1555076 TGATATGTATTGATTG
1 TGATATGTACTGATTG
1555092 TATATTTGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.45
Consensus pattern (17 bp):
TGATATGTACTGATTGA
Found at i:1556906 original size:68 final size:68
Alignment explanation
Indices: 1556834--1556999 Score: 197
Period size: 68 Copynumber: 2.4 Consensus size: 68
1556824 AGAAAATACG
* * * *** *
1556834 TCATATACATAATCTCATGGCATTCATCATGCTTTCTTAGTCATCTCATATGGTATATGGAATTT
1 TCATATACATAATCTTATGGCATTCATCATGCATACTTAAAAATCTCATATGGTATATGGAATTC
1556899 ACA
66 ACA
* * * * * *
1556902 TCATATACACAATCTTATAGTATACATCATGCATACTTAAAAATCTCGTATGGTGTATGGAATTC
1 TCATATACATAATCTTATGGCATTCATCATGCATACTTAAAAATCTCATATGGTATATGGAATTC
*
1556967 ATA
66 ACA
*
1556970 TCATATACCTAATCTTATGGCATTCATCAT
1 TCATATACATAATCTTATGGCATTCATCAT
1557000 ACCATACATG
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (68 bp):
TCATATACATAATCTTATGGCATTCATCATGCATACTTAAAAATCTCATATGGTATATGGAATTC
ACA
Found at i:1560464 original size:29 final size:30
Alignment explanation
Indices: 1560432--1560497 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1560422 AGAAATTCTA
* *
1560432 TTGGAAAAACTTTTCCAACAG-AAATTTCG
1 TTGGAAAAACTTCTCCAACAGAAAATTCCG
** *
1560461 TTGGAAATGCTTCTCCAACGGAAAATTCCG
1 TTGGAAAAACTTCTCCAACAGAAAATTCCG
1560491 TTGGAAA
1 TTGGAAA
1560498 TTTTTGACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (30 bp):
TTGGAAAAACTTCTCCAACAGAAAATTCCG
Found at i:1560469 original size:83 final size:83
Alignment explanation
Indices: 1560371--1560533 Score: 202
Period size: 83 Copynumber: 2.0 Consensus size: 83
1560361 ATTCCTATGG
* * ** *
1560371 AATTTCATTGGAAATGCTTTTCTAACGAAAAATTTTGTTAAAAATTTTTGA-AGAAATTCTATTG
1 AATTTCATTGGAAATGCTTCTCCAACGAAAAATTCCGTTAAAAATTTTTGACAG-AATTCTATTA
*
1560435 GAAAAACTTTTCCAACAGA
65 GAAAAACATTTCCAACAGA
* * ** * *
1560454 AATTTCGTTGGAAATGCTTCTCCAACGGAAAATTCCGTTGGAAATTTTTGACCGAATTCTGTTAG
1 AATTTCATTGGAAATGCTTCTCCAACGAAAAATTCCGTTAAAAATTTTTGACAGAATTCTATTAG
1560519 AAAAACATTTCCAAC
66 AAAAACATTTCCAAC
1560534 GGAATTGATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 66 0.99
84 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (83 bp):
AATTTCATTGGAAATGCTTCTCCAACGAAAAATTCCGTTAAAAATTTTTGACAGAATTCTATTAG
AAAAACATTTCCAACAGA
Found at i:1561624 original size:28 final size:29
Alignment explanation
Indices: 1561561--1561629 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
1561551 GTAATATTGT
*
1561561 AGAGATTATGCTTGAGCCTTGAAAAAGTAA
1 AGAGATTATGCTTGAGCATTG-AAAAGTAA
* *
1561591 ATAGATTATGCTTCG-GCATTG-AAAGTAG
1 AGAGATTATGCTT-GAGCATTGAAAAGTAA
1561619 AGAGATTATGC
1 AGAGATTATGC
1561630 CTTAACCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 16 0.47
30 17 0.50
31 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (29 bp):
AGAGATTATGCTTGAGCATTGAAAAGTAA
Found at i:1561892 original size:35 final size:35
Alignment explanation
Indices: 1561853--1561919 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
1561843 TTCTATTCTC
1561853 TTTCACTT-TT-TGAACTTGTGCATTTTCTCTTTACT
1 TTTCACTTCTTCT-AACTTGTGCATTTT-TCTTTACT
1561888 TTTCACTTCTTCTAACTTGTGCATTTTTCTTT
1 TTTCACTTCTTCTAACTTGTGCATTTTTCTTT
1561920 GTTGTGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
35 13 0.43
36 16 0.53
37 1 0.03
ACGTcount: A:0.13, C:0.21, G:0.07, T:0.58
Consensus pattern (35 bp):
TTTCACTTCTTCTAACTTGTGCATTTTTCTTTACT
Done.