Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000885.1 Hibiscus syriacus cultivar Beakdansim tig00001728_pilon, 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: 1639497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:1011116 original size:16 final size:17
Alignment explanation
Indices: 1011088--1011141 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
1011078 CAATCAATAA
*
1011088 AAAT-TCAATCTAAAAC
1 AAATGTCAAGCTAAAAC
1011104 AAATG-CAAGCTAAAAC
1 AAATGTCAAGCTAAAAC
*
1011120 AAA-GTCAATCTAAAAC
1 AAATGTCAAGCTAAAAC
1011136 ATAATG
1 A-AATG
1011142 GAAGTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 28 0.88
17 2 0.06
18 1 0.03
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.20
Consensus pattern (17 bp):
AAATGTCAAGCTAAAAC
Found at i:1011823 original size:13 final size:13
Alignment explanation
Indices: 1011805--1011891 Score: 108
Period size: 13 Copynumber: 6.7 Consensus size: 13
1011795 TCAATTATTC
1011805 CAATATGCAATAA
1 CAATATGCAATAA
1011818 CAATATGC-ATGAA
1 CAATATGCAAT-AA
*
1011831 CAATATGTAATAA
1 CAATATGCAATAA
*
1011844 CAGTATGC-ATGAA
1 CAATATGCAAT-AA
1011857 CAATATGCAATAA
1 CAATATGCAATAA
1011870 C-ATCATGCAATAA
1 CAAT-ATGCAATAA
1011883 CAATATGCA
1 CAATATGCA
1011892 TGAAGAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
12 6 0.09
13 52 0.81
14 6 0.09
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.24
Consensus pattern (13 bp):
CAATATGCAATAA
Found at i:1011842 original size:26 final size:26
Alignment explanation
Indices: 1011805--1011891 Score: 124
Period size: 26 Copynumber: 3.3 Consensus size: 26
1011795 TCAATTATTC
1011805 CAATATGCAATAACAATATGCATGAA
1 CAATATGCAATAACAATATGCATGAA
* *
1011831 CAATATGTAATAACAGTATGCATGAA
1 CAATATGCAATAACAATATGCATGAA
1011857 CAATATGCAATAAC-ATCATGCAAT-AA
1 CAATATGCAATAACAAT-ATGC-ATGAA
1011883 CAATATGCA
1 CAATATGCA
1011892 TGAAGAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
25 1 0.02
26 52 0.95
27 2 0.04
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.24
Consensus pattern (26 bp):
CAATATGCAATAACAATATGCATGAA
Found at i:1011862 original size:39 final size:39
Alignment explanation
Indices: 1011805--1011902 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 39
1011795 TCAATTATTC
*
1011805 CAATATGCAAT-AACAATATGC-ATGAACAAT-ATGTAATAA
1 CAATATGC-ATGAACAATATGCAAT-AAC-ATCATGCAATAA
*
1011844 CAGTATGCATGAACAATATGCAATAACATCATGCAATAA
1 CAATATGCATGAACAATATGCAATAACATCATGCAATAA
*
1011883 CAATATGCATGAAGAATATG
1 CAATATGCATGAACAATATG
1011903 TATTAGCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
38 4 0.08
39 46 0.88
40 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.24
Consensus pattern (39 bp):
CAATATGCATGAACAATATGCAATAACATCATGCAATAA
Found at i:1011900 original size:13 final size:12
Alignment explanation
Indices: 1011805--1011902 Score: 90
Period size: 13 Copynumber: 7.6 Consensus size: 12
1011795 TCAATTATTC
1011805 CAATATGCAATAA
1 CAATATGC-ATAA
1011818 CAATATGCATGAA
1 CAATATGCAT-AA
*
1011831 CAATATGTAATAA
1 CAATATG-CATAA
*
1011844 CAGTATGCATGAA
1 CAATATGCAT-AA
1011857 CAATATGCAATAA
1 CAATATGC-ATAA
1011870 C-ATCATGCAATAA
1 CAAT-ATGC-ATAA
1011883 CAATATGCATGAA
1 CAATATGCAT-AA
*
1011896 GAATATG
1 CAATATG
1011903 TATTAGCAAG
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
12 8 0.11
13 59 0.81
14 6 0.08
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.24
Consensus pattern (12 bp):
CAATATGCATAA
Found at i:1013817 original size:30 final size:30
Alignment explanation
Indices: 1013783--1013856 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
1013773 ATCAATTTCA
*
1013783 GGTTCATTAATTTCTGGCACAACTGGTTCT
1 GGTTCATTAATTTCTAGCACAACTGGTTCT
* **
1013813 GGTTCACTAATTTCTAGTTCAACTGGTTCT
1 GGTTCATTAATTTCTAGCACAACTGGTTCT
* *
1013843 GCTTCATCAATTTC
1 GGTTCATTAATTTC
1013857 AGTTTCATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (30 bp):
GGTTCATTAATTTCTAGCACAACTGGTTCT
Found at i:1014905 original size:10 final size:10
Alignment explanation
Indices: 1014890--1014916 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1014880 ATAAACCCAC
1014890 TAAACTCATA
1 TAAACTCATA
1014900 TAAACTCATA
1 TAAACTCATA
1014910 TAAACTC
1 TAAACTC
1014917 CCTAACATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAACTCATA
Found at i:1014935 original size:12 final size:12
Alignment explanation
Indices: 1014918--1014947 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1014908 TATAAACTCC
*
1014918 CTAACATCTATA
1 CTAACATATATA
1014930 CTAACATATATA
1 CTAACATATATA
1014942 CTAACA
1 CTAACA
1014948 GTAAATCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (12 bp):
CTAACATATATA
Found at i:1016400 original size:20 final size:19
Alignment explanation
Indices: 1016370--1016408 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 19
1016360 TTGAACTCTT
1016370 TTTTAATGGGCCTCTTTTTAG
1 TTTTAATGGG-CT-TTTTTAG
1016391 TTTT-ATGGGCTTTTTTAG
1 TTTTAATGGGCTTTTTTAG
1016409 AATATGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 5 0.28
21 4 0.22
ACGTcount: A:0.13, C:0.10, G:0.21, T:0.56
Consensus pattern (19 bp):
TTTTAATGGGCTTTTTTAG
Found at i:1020142 original size:14 final size:14
Alignment explanation
Indices: 1020106--1020143 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1020096 TTTTGGTTTA
1020106 AGTGTTATGTAATC
1 AGTGTTATGTAATC
1020120 AGT-TCTATGTAATC
1 AGTGT-TATGTAATC
1020134 AGTGTTATGT
1 AGTGTTATGT
1020144 TGTAAACAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (14 bp):
AGTGTTATGTAATC
Found at i:1023588 original size:55 final size:55
Alignment explanation
Indices: 1023463--1023624 Score: 193
Period size: 55 Copynumber: 3.0 Consensus size: 55
1023453 CAAACTCATT
* * * * * * * * *
1023463 ACACATAGTGACAATACGGTAATTCACAAACTCAGTATAAATTACT-T-AGGTTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATCAATT-TTGTGGGGTTAC
1023517 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATCAATTTTGTGGGGTTAC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATCAATTTTGTGGGGTTAC
* * *
1023572 ACACATAGTGCTAATACGGAAATTCATAAACTCATTATGAATTTTGTGGGGTT
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATCAATTTTGTGGGGTT
1023625 GTTAACTGTA
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 38 0.40
55 55 0.59
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (55 bp):
ACACATAGTGCCAATACAGAAATTCATAAACTCATTATCAATTTTGTGGGGTTAC
Found at i:1035769 original size:17 final size:18
Alignment explanation
Indices: 1035747--1035784 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1035737 ACCGTTGGAA
*
1035747 CACTTA-GTGCATCGGTG
1 CACTTAGGTGCATCGATG
1035764 CACTTAGGGTGCATCGATG
1 CACTTA-GGTGCATCGATG
1035783 CA
1 CA
1035785 TAAAATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (18 bp):
CACTTAGGTGCATCGATG
Found at i:1035821 original size:64 final size:63
Alignment explanation
Indices: 1035772--1035926 Score: 217
Period size: 64 Copynumber: 2.4 Consensus size: 63
1035762 TGCACTTAGG
1035772 GTGCATCGATGCATAAAATGCATTCGATG-TTTC--AAACAAGCCTGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAC-A-CCTGAGTGCATCGATGCATGG-
*
1035834 CT
63 -A
* *
1035836 GTGCATCGATACATAAAATGCATTCGATGTTTTCATAAACACCTGAGTGCATCGATGTATGGAA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAACACCTGAGTGCATCGATGCATGG-A
1035900 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
1035927 AATGGTGAGT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
64 54 0.65
65 24 0.29
66 1 0.01
67 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAACACCTGAGTGCATCGATGCATGGA
Found at i:1044514 original size:20 final size:20
Alignment explanation
Indices: 1044489--1044526 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1044479 TTCGAAATGG
1044489 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
1044509 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
1044527 GCTTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:1055042 original size:19 final size:19
Alignment explanation
Indices: 1054989--1055035 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1054979 TACCCCTTAA
*
1054989 AAAATAAG-ATATTAAAAG
1 AAAATAAGAATAATAAAAG
*
1055007 AAAATAATAATAATAAAAG
1 AAAATAAGAATAATAAAAG
*
1055026 AAAGTAAGAA
1 AAAATAAGAA
1055036 AACTAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (19 bp):
AAAATAAGAATAATAAAAG
Found at i:1055274 original size:22 final size:23
Alignment explanation
Indices: 1055226--1055310 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 23
1055216 GAAACTAAAA
*
1055226 ATATAATGAAAATAA-ATAAATAGT
1 ATATAAT-AAAATAATAAAAATA-T
1055250 ATA-AATAAAATAATAAAAATAT
1 ATATAATAAAATAATAAAAATAT
*
1055272 ATATAA-AAAAAATATAAAAATGTAT
1 ATATAATAAAATA-ATAAAAA--TAT
*
1055297 GTATAATAAAATAA
1 ATATAATAAAATAA
1055311 AATACTAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
22 16 0.31
23 18 0.35
24 3 0.06
25 9 0.18
26 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (23 bp):
ATATAATAAAATAATAAAAATAT
Found at i:1055283 original size:24 final size:24
Alignment explanation
Indices: 1055236--1055310 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
1055226 ATATAATGAA
1055236 AATAAATAA-ATAGTATAAATAAAAT
1 AATAAA-AATATA-TATAAATAAAAT
*
1055261 AATAAAAATATATATAAAAAAAAT
1 AATAAAAATATATATAAATAAAAT
* *
1055285 -ATAAAAATGTATGTATAATAAAAT
1 AATAAAAATATATATA-AATAAAAT
1055309 AA
1 AA
1055311 AATACTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
23 13 0.30
24 20 0.47
25 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
AATAAAAATATATATAAATAAAAT
Found at i:1055363 original size:2 final size:2
Alignment explanation
Indices: 1055356--1055391 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1055346 TGAAGTAAGA
1055356 AT 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 AT
1055392 GTTAGGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1055451 original size:2 final size:2
Alignment explanation
Indices: 1055446--1055476 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1055436 TAAAAAAATA
1055446 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
1055477 GGAAAATAAT
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:1055470 original size:82 final size:83
Alignment explanation
Indices: 1055364--1055560 Score: 235
Period size: 82 Copynumber: 2.4 Consensus size: 83
1055354 GAATATATAT
* * * *
1055364 ATATATATATATATATATATATATATATGTTAGGAAAAT-ATAGTAA-ATAA-ATAGTAAATAAG
1 ATATATATATATATATATATATATATAT-ATAGGAAAATAATA-TAATATAACACA-CAAAAAAG
*
1055426 TA-AACGTA-GATAAA-AAAATA
63 -AGAAC-TATAATAAATAAAATA
1055446 ATATATATATATATATATATATATATATATAGGAAAATAATATAATATAACACACAAAAAAGAGA
1 ATATATATATATATATATATATATATATATAGGAAAATAATATAATATAACACACAAAAAAGAGA
*
1055511 ACTATAATAAATAAATTAA
66 ACTATAATAAATAAAAT-A
*
1055530 ATATATATATATATATATATATATACATATA
1 ATATATATATATATATATATATATATATATA
1055561 AATAATAAGG
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
81 15 0.15
82 49 0.49
83 6 0.06
84 31 0.31
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (83 bp):
ATATATATATATATATATATATATATATATAGGAAAATAATATAATATAACACACAAAAAAGAGA
ACTATAATAAATAAAATA
Found at i:1055537 original size:2 final size:2
Alignment explanation
Indices: 1055530--1055560 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1055520 AATAAATTAA
*
1055530 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1055561 AATAATAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1056050 original size:37 final size:37
Alignment explanation
Indices: 1056009--1056101 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1055999 ATGCTTGTGG
* * *
1056009 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
1056046 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
1056083 ATCATATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
1056102 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:1057318 original size:207 final size:205
Alignment explanation
Indices: 1056883--1057481 Score: 760
Period size: 207 Copynumber: 2.9 Consensus size: 205
1056873 TCCTCCGTCG
* ** * *
1056883 TGAAGTTGAAATTGGCTCTGGAACCGAGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTG
* *
1056948 AAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG---GGAA--A
66 AAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGCTCTGAATGA
** * * * *
1057008 TTTTTTGTTGACAACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATA
131 AATTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAGA
*
1057073 TCCTTTGCTA
196 TCCTTCGCTA
*
1057083 TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTTGT
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCG-TTGT
*
1057148 GAAGTTGAACTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAT
65 GAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG-CTCTGAAT
* * * * * * *
1057213 GAAATTTTGTTGACAATCAGCCGCCCCTTTGTCGTGAAGTTGAGCTTGTGTTATCTTGGGTCCAA
129 GAAATTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAA
1057278 GATCCTTCGCTGA
194 GATCCTTCGCT-A
** * * *
1057291 -GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGTCAACCGCCCCTTCGCTGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTG
* * * *
1057355 AAGTTGAGCTTGTGCTATATTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAAC
66 AAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT-GCTCTG-AA-
* *
1057420 TGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
128 T--GAAA-T-TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTC
1057482 AGATGGCGCG
Statistics
Matches: 342, Mismatches: 42, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
200 54 0.16
201 58 0.17
205 3 0.01
206 58 0.17
207 118 0.35
208 2 0.01
210 4 0.01
211 1 0.00
212 44 0.13
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (205 bp):
TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTG
AAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGCTCTGAATGA
AATTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAGA
TCCTTCGCTA
Found at i:1057363 original size:106 final size:106
Alignment explanation
Indices: 1056995--1057481 Score: 601
Period size: 106 Copynumber: 4.6 Consensus size: 106
1056985 GCTGTGAAGT
* * * *
1056995 TGAAATTGGGAAATTTTTTGTTGACAACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTAT
*
1057060 CTCGAGTCCAATATCCTTTGCT-ATGAAGTTGAAATTGGCTC
66 CTCGAGTCCAATATCCTTCGCTGA-GAAGTTGAAATTGGCTC
* * * *
1057101 TGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTTGTGAAGTTGAACTTGTGCTG
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCG-TTGTGAAGTTGAACTTGTGTTA
* * *
1057166 TCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTC
65 TCTCGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTC
* * * * *
1057208 TG-AA-T--GAAA-T-TTTGTTGACAATCAGCCGCCCCTTTGTCGTGAAGTTGAGCTTGTGTTAT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTAT
* * *
1057267 CTTGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTC
66 CTCGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTC
* ** * * * * *
1057308 TGAAATTGGGAAGTTGTTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTAT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTAT
* * *
1057373 ATTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTCGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTC
* * *
1057414 TGAAACTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTAT
1057479 CTC
66 CTC
1057482 AGATGGCGCG
Statistics
Matches: 324, Mismatches: 49, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
100 56 0.17
101 24 0.07
102 2 0.01
103 3 0.01
104 3 0.01
105 2 0.01
106 174 0.54
107 60 0.19
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
TGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTAT
CTCGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTC
Found at i:1057389 original size:313 final size:304
Alignment explanation
Indices: 1056862--1057481 Score: 800
Period size: 313 Copynumber: 2.0 Consensus size: 304
1056852 AGCATTGTTC
*
1056862 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGGAA-C-AGAAATTGTTTGTTGACA
* * * * *
1056927 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
64 ACCAGCCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAGATCCTTCGCTGAGA
* * *
1056992 AGTTGAAATTGGGAAATTTTTTGTTGACAACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGT
129 AGTTGAAATTGGGAAATTTTTTGTTGACAACCAACCGCCCCTTCACTGTGAAGTTGAACTTGTGC
* * * * *
1057057 TGTCTCGAGTCCAATATCCTTTGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGT
194 TATATCGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGT
1057122 TGACAACCAGTCGTCCCTTCGTTTGTGAAGTTGAACTTGTGCTGTCT
259 TGACAACCAGTCGTCCCTTCG-TTGTGAAGTTGAACTTGTGCTGTCT
* * *
1057169 CGAGTCTAATATCCTTCG-CTGTGAAGTTGAAATTGACTCT-GAA-TGAAA-T-TTTGTTGACAA
1 CGAGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGACTCTGGAACAGAAATTGTTTGTTGACAA
* * * * *
1057229 TCAGCCGCCCCTTTGTCGTGAAGTTGAGCTTGTGTTATCTTGGGTCCAAGATCCTTCGCTGAGAA
65 CCAGCCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAGATCCTTCGCTGAGAA
** *
1057294 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGT
130 GTTGAAATTGG----GAAA-T------TT-TTTGTTGACAACCAACCGCCCCTTCACTGTGAAGT
* * *
1057359 TGAGCTTGTGCTATATTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
183 TGAACTTGTGCTATATCGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAACTGGG
*
1057424 AAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
248 AAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
1057481 C
1 C
1057482 AGATGGCGCG
Statistics
Matches: 271, Mismatches: 29, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
301 77 0.28
302 1 0.00
303 4 0.01
305 4 0.01
306 5 0.02
307 35 0.13
312 27 0.10
313 118 0.44
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (304 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGGAACAGAAATTGTTTGTTGACAAC
CAGCCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTCGAGTCCAAGATCCTTCGCTGAGAAG
TTGAAATTGGGAAATTTTTTGTTGACAACCAACCGCCCCTTCACTGTGAAGTTGAACTTGTGCTA
TATCGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTG
ACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
Found at i:1057551 original size:43 final size:44
Alignment explanation
Indices: 1057490--1057609 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 44
1057480 TCAGATGGCG
* *
1057490 CGATATCCTCCATTGTGGAGTTGAAATCGTGGATGTGT-GGAAA
1 CGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGAAA
*
1057533 CGATATCCTCCGTCGTGGAGTTGAAATCATGGATGTGTGGGAAA
1 CGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGAAA
* *
1057577 -AATATCCTCCG-CATGGAGTTGAAATCGTGGATG
1 CGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
1057610 ACCCCTTCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
42 20 0.29
43 45 0.64
44 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (44 bp):
CGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGAAA
Found at i:1058429 original size:36 final size:37
Alignment explanation
Indices: 1058375--1058450 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
1058365 GAAATGATTT
*
1058375 CAAAGGTTTTTTCTAAGGGAAACTGTCTCAAGGGAGA
1 CAAAGGTTTTTTCTAAGGGAAACTGTCTCAAGAGAGA
1058412 CAAA-GTTTGTTTC-AAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTT-TTTCTAAGGGAAACTGTCTCAAGAGAGA
1058448 CAA
1 CAA
1058451 TGGTGGACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 29 0.78
37 8 0.22
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (37 bp):
CAAAGGTTTTTTCTAAGGGAAACTGTCTCAAGAGAGA
Found at i:1059138 original size:24 final size:24
Alignment explanation
Indices: 1059111--1059172 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
1059101 AATATCAAAA
1059111 AAGAGTTTTAAAAGATGTTTAATC
1 AAGAGTTTTAAAAGATGTTTAATC
* *
1059135 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTAAAAGATGTTTAATC
*
1059159 AAAAGTTTTGAAAA
1 AAGAGTTTT-AAAA
1059173 TATTGTCCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (24 bp):
AAGAGTTTTAAAAGATGTTTAATC
Found at i:1060020 original size:21 final size:22
Alignment explanation
Indices: 1059999--1060056 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1059989 TTGTCCCTTT
1059999 TTCTTTTGATTTTTT-CTTTTTTG
1 TTCTTTT--TTTTTTCCTTTTTTG
1060022 TTCTTTTTTTTTTCC-TTTTTG
1 TTCTTTTTTTTTTCCTTTTTTG
*
1060043 CTTCTTTTCTTTTT
1 -TTCTTTTTTTTTT
1060057 GTTCTTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 12 0.38
22 13 0.41
23 7 0.22
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (22 bp):
TTCTTTTTTTTTTCCTTTTTTG
Found at i:1060055 original size:23 final size:21
Alignment explanation
Indices: 1059999--1060056 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
1059989 TTGTCCCTTT
*
1059999 TTCTTTTGATTTTTTCTTTTTTG
1 TTCTTTT--TTTTTTCCTTTTTG
1060022 TTCTTTTTTTTTTCCTTTTTG
1 TTCTTTTTTTTTTCCTTTTTG
*
1060043 CTTCTTTTCTTTTT
1 -TTCTTTTTTTTTT
1060057 GTTCTTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 13 0.41
22 12 0.38
23 7 0.22
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (21 bp):
TTCTTTTTTTTTTCCTTTTTG
Found at i:1068302 original size:36 final size:36
Alignment explanation
Indices: 1068260--1068335 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
1068250 TTATAGCTAA
*
1068260 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1068296 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1068332 AAAA
1 AAAA
1068336 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:1068867 original size:37 final size:37
Alignment explanation
Indices: 1068782--1068875 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
1068772 GGATCCTATC
* ** * *
1068782 TTTAGGAGTTTAAATAATAGTAAAAATCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGCAAAAATCTATCATATT
*
1068819 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGCAAAAATCTATCATATT
1068856 TTTAGGAGTTTGAATCCTAG
1 TTTAGGAGTTTGAATCCTAG
1068876 TAGGACGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGCAAAAATCTATCATATT
Found at i:1071518 original size:21 final size:21
Alignment explanation
Indices: 1071494--1071546 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1071484 CGGTGGGTTG
*
1071494 GTATCGATACTGATTCAAATA
1 GTATCGATACTGATTAAAATA
1071515 GTATCGATACTGATTAAAATA
1 GTATCGATACTGATTAAAATA
1071536 GTATCGATACT
1 GTATCGATACT
1071547 AAAGGTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATCGATACTGATTAAAATA
Found at i:1073539 original size:16 final size:16
Alignment explanation
Indices: 1073518--1073552 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
1073508 GCTTTCAAAA
1073518 TTGAAAAAAGAAATTT
1 TTGAAAAAAGAAATTT
1073534 TTG-AAAAAGAAATTT
1 TTGAAAAAAGAAATTT
1073549 TTGA
1 TTGA
1073553 TTTGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (16 bp):
TTGAAAAAAGAAATTT
Found at i:1074483 original size:43 final size:45
Alignment explanation
Indices: 1074374--1074499 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 45
1074364 TATAAAATCT
*
1074374 CTTACTATTTATCTCATAAGCTCGTAAGCTTATTTTACCAAAAATA
1 CTTACCATTTAT-TCATAAGCTCGTAAGCTTATTTTACCAAAAATA
* * *
1074420 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATC-AATATA
1 CTTACCATTT--ATT-CATAAGCTCGTAAGCTTATTTTACCAAAAATA
*
1074467 CTTGCCA-TTATTCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCATAAGCTCGTAAGCTTATTT
1074500 GCATACTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
43 21 0.30
44 3 0.04
46 10 0.14
47 11 0.15
48 26 0.37
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCATAAGCTCGTAAGCTTATTTTACCAAAAATA
Found at i:1074507 original size:38 final size:41
Alignment explanation
Indices: 1074382--1074513 Score: 117
Period size: 48 Copynumber: 3.0 Consensus size: 41
1074372 CTCTTACTAT
* *
1074382 TTATCTCATAAGCTCGTAAGCTTATTTTACCAAAAATATTTACCA
1 TTAT-TCATAAGCTCGTAAGCTTATTTTAGC---AATACTTACCA
* *
1074427 TTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA
1 -TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATACTTACCA
1074474 TTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATACTTACCA
1 TTATTCATAAGCTCGTAAGCTTATTTTAGCAATACTTACCA
1074512 TT
1 TT
1074514 TATTAACCAA
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
38 11 0.14
41 1 0.01
42 3 0.04
43 18 0.23
44 3 0.04
46 6 0.08
47 9 0.12
48 26 0.34
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (41 bp):
TTATTCATAAGCTCGTAAGCTTATTTTAGCAATACTTACCA
Found at i:1078445 original size:17 final size:17
Alignment explanation
Indices: 1078425--1078476 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
1078415 CTCTCATCTT
1078425 TTTCTCTTTTTCTTTTC
1 TTTCTCTTTTTCTTTTC
* *
1078442 TTTCTCATTTTCATTT-
1 TTTCTCTTTTTCTTTTC
*
1078458 TTTCTTCTTCTTCGTTTTC
1 TTTC-TCTTTTTC-TTTTC
1078477 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 4 0.15
17 20 0.74
18 3 0.11
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTCTCTTTTTCTTTTC
Found at i:1078465 original size:23 final size:23
Alignment explanation
Indices: 1078432--1078487 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
1078422 CTTTTTCTCT
1078432 TTTTCTTTTCTTTC-TCATTTTCA
1 TTTT-TTTTCTTTCTTCATTTTCA
*
1078455 TTTTTTCTTC-TTCTTCGTTTTCA
1 TTTTTT-TTCTTTCTTCATTTTCA
1078478 TTTTTTTTCT
1 TTTTTTTTCT
1078488 ATTTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTTTTCTTTCTTCATTTTCA
Found at i:1078511 original size:16 final size:15
Alignment explanation
Indices: 1078478--1078520 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
1078468 TTCGTTTTCA
1078478 TTTTTT-TTC-TATT
1 TTTTTTCTTCTTATT
1078491 TTTTTTCTTCTTATGT
1 TTTTTTCTTCTTAT-T
1078507 TTTTTTCTTCTTAT
1 TTTTTTCTTCTTAT
1078521 AAAATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.22
14 3 0.11
15 3 0.11
16 15 0.56
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTCTTATT
Found at i:1079675 original size:46 final size:45
Alignment explanation
Indices: 1079619--1079725 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
1079609 TGCACATACC
* * * *
1079619 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGAACTTG
* * *
1079665 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATTAACTTG
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGAACTTG
*
1079710 ATACATCGATGCACTC
1 ATGCATCGATGCACTC
1079726 TTAGTGCACC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
45 30 0.58
46 19 0.37
47 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGAACTTG
Found at i:1088179 original size:21 final size:21
Alignment explanation
Indices: 1088153--1088192 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1088143 CAGAACCCCA
*
1088153 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1088174 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1088193 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1096460 original size:65 final size:63
Alignment explanation
Indices: 1096330--1096481 Score: 184
Period size: 65 Copynumber: 2.4 Consensus size: 63
1096320 AATTAAATTG
* *
1096330 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTAATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTT-ATGA
* * *
1096394 AAGCATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-T
1 AA-CATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTCAGG--ATTTAT
1096457 GA
62 GA
1096459 AACATCGAATGC-TCTTGATGCAT
1 AACATCGAATGCAT-TTGATGCAT
1096482 TGATACACTC
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
63 1 0.01
64 21 0.27
65 50 0.64
66 2 0.03
67 4 0.05
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTTATGA
Found at i:1099294 original size:48 final size:43
Alignment explanation
Indices: 1099235--1099344 Score: 130
Period size: 43 Copynumber: 2.4 Consensus size: 43
1099225 ATTTATCCCG
* *
1099235 TAAGCTTGTAAGCTTATTTTACCAAAAATATTTACCATTTAAATTCCA
1 TAAGCTCGTAAGCTTATTTTACC-AAAATACTTACCA-TT--ATT-CA
* * *
1099283 TAAGCTCGTAAGCTTATTTTATCAATATACTTGCCATTATTCA
1 TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCA
1099326 TAAGCTCGTAAGCTTATTT
1 TAAGCTCGTAAGCTTATTT
1099345 GCATACTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
43 21 0.37
44 3 0.05
46 2 0.04
47 10 0.18
48 21 0.37
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (43 bp):
TAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCA
Found at i:1099328 original size:43 final size:47
Alignment explanation
Indices: 1099219--1099344 Score: 145
Period size: 48 Copynumber: 2.8 Consensus size: 47
1099209 TATAAAATCT
* * *
1099219 CTTACCATTT-ATCCCGTAAGCTTGTAAGCTTATTTTACCAAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAAATA
* * *
1099265 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATC-AATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAAATA
*
1099312 CTTGCCA-TT-ATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
1099345 GCATACTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
43 21 0.30
44 3 0.04
46 11 0.16
47 10 0.14
48 25 0.36
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (47 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAAATA
Found at i:1110690 original size:32 final size:34
Alignment explanation
Indices: 1110635--1110699 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
1110625 ATGATCTGAC
*
1110635 AATGTTATATAATAACATAACATATTC-AAACTA
1 AATGTTATATAATAACATAACATAATCTAAACTA
*
1110668 AATGTTAGTATCA-AAC-TAACATAATCTAAACT
1 AATGTTA-TATAATAACATAACATAATCTAAACT
1110700 TAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 9 0.32
33 15 0.54
34 4 0.14
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (34 bp):
AATGTTATATAATAACATAACATAATCTAAACTA
Found at i:1116993 original size:54 final size:54
Alignment explanation
Indices: 1116929--1117306 Score: 243
Period size: 55 Copynumber: 6.9 Consensus size: 54
1116919 TACCAAATAG
* *
1116929 GCACTAAGTGTGAATTCTACGAAATTCATCTTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGAATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * *
1116983 GCAGTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCGTTTTA
1 GCACTAAGTGTGAATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCA
* * ** *
1117037 GCACTAAGTGTGCATTTCAC-ATAATTCATCCTATGTTAATGAATAACCG-TACA
1 GCACTAAGTGTGAATTCCACGA-AATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * *
1117090 TGCACTATGTGTGCAAATCCACGAAATTCATCATGA-GTTGATGAATAA-C-TATACA
1 -GCACTAAGTGTG-AATTCCACGAAATTCATCCT-ATGTGGATGAATAACCGT-TTCA
* * * * * * **
1117145 TGCACTATGTGTGCAAATCCAC-AGAATTCATCATAAGTTGATGAATAATCG-TAGA
1 -GCACTAAGTGTG-AATTCCACGA-AATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * * * **
1117200 GGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCG-TAAA
1 -GCACTAAGTGTG-AATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * *
1117255 GGCACTATGTGTGCAAATCCACAAAATTCATCATGA-GTTGATGAATAACCGT
1 -GCACTAAGTGTG-AATTCCACGAAATTCATCCT-ATGTGGATGAATAACCGT
1117307 ACAGGCACGA
Statistics
Matches: 287, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
53 2 0.01
54 105 0.37
55 175 0.61
56 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
GCACTAAGTGTGAATTCCACGAAATTCATCCTATGTGGATGAATAACCGTTTCA
Found at i:1117145 original size:55 final size:55
Alignment explanation
Indices: 1117075--1117378 Score: 416
Period size: 55 Copynumber: 5.5 Consensus size: 55
1117065 TCCTATGTTA
* *
1117075 ATGAATAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTG
1 ATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
** * * *
1117130 ATGAATAACTATACATGCACTATGTGTGCAAATCCACAGAATTCATCATAAGTTG
1 ATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
* * *
1117185 ATGAATAATCGTAGAGGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTG
1 ATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
*
1117240 ATGAATAACCGTAAAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
1 ATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
* * **
1117295 ATGAATAACCGTACAGGCACGATGTGTGC-AACCCACTGAATTCATCATGAGTTG
1 ATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
* *
1117349 ATGAACT-ACCGTATAAGCACTACT-TGTGCA
1 ATGAA-TAACCGTACAGGCACTA-TGTGTGCA
1117379 TCTTAATAAA
Statistics
Matches: 224, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
54 44 0.20
55 180 0.80
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (55 bp):
ATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTG
Found at i:1117221 original size:110 final size:110
Alignment explanation
Indices: 1116927--1117353 Score: 429
Period size: 110 Copynumber: 3.9 Consensus size: 110
1116917 ATTACCAAAT
* * * * * * * * * *
1116927 AGGCACTAAGTGTG-AATTCTACGAAATTCATCTTATGTGGATGAATAACCGTTTCA-GCAGTAA
1 AGGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCG-TACAGGCACTAT
* * * * * **
1116990 GTGTGC-ATTCCACGGAATTCATCCT-ATGTGGATGAATAACCGTTTT
65 GTGTGCAAATCCACGAAATTCATCATGA-GTTGATGAATAACC-ATAA
* * * * * * * *
1117036 A-GCACTAAGTGTGC-ATTTCACATAATTCATCCTATGTTAATGAATAACCGTACATGCACTATG
1 AGGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATG
* *
1117099 TGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACTATAC
66 TGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATAA
* * * *
1117144 ATGCACTATGTGTGCAAATCCACAGAATTCATCATAAGTTGATGAATAATCGTAGAGGCACTATG
1 AGGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATG
* * *
1117209 TGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCGTAA
66 TGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATAA
* *
1117254 AGGCACTATGTGTGCAAATCCACAAAATTCATCATGAGTTGATGAATAACCGTACAGGCACGATG
1 AGGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATG
*
1117319 TGTGC-AACCCACTG-AATTCATCATGAGTTGATGAA
66 TGTGCAAATCCAC-GAAATTCATCATGAGTTGATGAA
1117354 CTACCGTATA
Statistics
Matches: 269, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
107 3 0.01
108 54 0.20
109 67 0.25
110 145 0.54
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (110 bp):
AGGCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATG
TGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATAA
Found at i:1117263 original size:165 final size:163
Alignment explanation
Indices: 1117037--1117353 Score: 463
Period size: 165 Copynumber: 1.9 Consensus size: 163
1117027 AACCGTTTTA
* * * * * * *
1117037 GCACTAAGTGTGCATTTCACATAATTCATCCTATGTTAATGAATAACCGTACATGCACTATGTGT
1 GCACTAAGTGTGCAATCCACAAAATTCATCATAAGTTAATGAATAACCGTAAAGGCACTATGTGT
* * * * *
1117102 GCAAATCCACGAAATTCATCATGAGTTGATGAATAACTATACATGCACTATGTGTGCAAATCCAC
66 GCAAATCCACAAAATTCATCATGAGTTGATGAATAACCATACAGGCACGATGTGTGC-AACCCAC
1117167 AGAATTCATCATAAGTTGATGAATAATCGTAGAG
130 AGAATTCATCATAAGTTGATGAATAATCGTAGAG
* *
1117201 GCACTATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAACCGTAAAGGCACTATGTG
1 GCACTAAGTGTGC-AATCCACAAAATTCATCATAAGTTAATGAATAACCGTAAAGGCACTATGTG
*
1117266 TGCAAATCCACAAAATTCATCATGAGTTGATGAATAACCGTACAGGCACGATGTGTGCAACCCAC
65 TGCAAATCCACAAAATTCATCATGAGTTGATGAATAACCATACAGGCACGATGTGTGCAACCCAC
* *
1117331 TGAATTCATCATGAGTTGATGAA
130 AGAATTCATCATAAGTTGATGAA
1117354 CTACCGTATA
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
164 39 0.29
165 96 0.71
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (163 bp):
GCACTAAGTGTGCAATCCACAAAATTCATCATAAGTTAATGAATAACCGTAAAGGCACTATGTGT
GCAAATCCACAAAATTCATCATGAGTTGATGAATAACCATACAGGCACGATGTGTGCAACCCACA
GAATTCATCATAAGTTGATGAATAATCGTAGAG
Found at i:1117666 original size:45 final size:45
Alignment explanation
Indices: 1117616--1117754 Score: 199
Period size: 45 Copynumber: 3.1 Consensus size: 45
1117606 TAGATGGATA
* * *
1117616 GAAATGCATAATGGTGTATAAAAGGTATAAAAGGATGTCATAAAT
1 GAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGTCATAAAT
*
1117661 GAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
1 GAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGTCATAAAT
* * *
1117706 GAAATGTATCATGGTGTCTAAAAGGCATGAAAGGATAT-ATAAAT
1 GAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGTCATAAAT
*
1117750 AAAAT
1 GAAAT
1117755 TAATAAATAA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
44 10 0.12
45 75 0.88
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (45 bp):
GAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGTCATAAAT
Found at i:1128923 original size:2 final size:2
Alignment explanation
Indices: 1128916--1128949 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1128906 AAGTCATTTA
1128916 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
1128950 CAACTCATGC
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:1135336 original size:12 final size:12
Alignment explanation
Indices: 1135321--1135366 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1135311 TTCATAGCAT
1135321 TTTTTATTTTAC
1 TTTTTATTTTAC
1135333 TTTTTATTTT--
1 TTTTTATTTTAC
1135343 TTTTATAGTTTTAC
1 TTTT-TA-TTTTAC
*
1135357 TTGTTATTTT
1 TTTTTATTTT
1135367 CCTTATCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
10 4 0.14
11 2 0.07
12 18 0.62
13 2 0.07
14 3 0.10
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTATTTTAC
Found at i:1135354 original size:24 final size:22
Alignment explanation
Indices: 1135320--1135366 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
1135310 TTTCATAGCA
*
1135320 TTTTTTATTTTACTTTTTATTT
1 TTTTTTATTTTACTTGTTATTT
1135342 TTTTTATAGTTTTACTTGTTATTT
1 TTTTT-TA-TTTTACTTGTTATTT
1135366 T
1 T
1135367 CCTTATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 2 0.09
24 15 0.68
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTTTATTTTACTTGTTATTT
Found at i:1135378 original size:24 final size:24
Alignment explanation
Indices: 1135327--1135372 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1135317 GCATTTTTTA
* **
1135327 TTTTACTTTTTATTTTTTTTATAG
1 TTTTACTTGTTATTTTCCTTATAG
1135351 TTTTACTTGTTATTTTCCTTAT
1 TTTTACTTGTTATTTTCCTTAT
1135373 CTTTTTCATA
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:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTACTTGTTATTTTCCTTATAG
Found at i:1140030 original size:20 final size:20
Alignment explanation
Indices: 1140001--1140039 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1139991 AGAGCTCATA
*
1140001 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1140021 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1140040 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1144678 original size:20 final size:22
Alignment explanation
Indices: 1144643--1144683 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1144633 TATAAATATC
1144643 ATTTTTAAGCTCAAAACACTTG
1 ATTTTTAAGCTCAAAACACTTG
1144665 ATTTTT-AG-TCAAAACACTT
1 ATTTTTAAGCTCAAAACACTT
1144684 TCCAGTCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 2 0.11
22 6 0.32
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (22 bp):
ATTTTTAAGCTCAAAACACTTG
Found at i:1150143 original size:36 final size:35
Alignment explanation
Indices: 1150102--1150199 Score: 142
Period size: 36 Copynumber: 2.7 Consensus size: 35
1150092 ATGTTTCTCC
*
1150102 AAGGGTGTTATAGATGTTGGTCTTGAATGATTATTA
1 AAGGGTGTCATAGATGTTGGTCTTGAA-GATTATTA
* *
1150138 GAGGGTATCATAGATGTTGGTCTTGTAAGATTATTA
1 AAGGGTGTCATAGATGTTGGTCTTG-AAGATTATTA
*
1150174 AAGAGTGTCATAGATGTTGGTCTTGA
1 AAGGGTGTCATAGATGTTGGTCTTGA
1150200 CGGACTCTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.02
36 52 0.95
37 2 0.04
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.39
Consensus pattern (35 bp):
AAGGGTGTCATAGATGTTGGTCTTGAAGATTATTA
Found at i:1154190 original size:3 final size:3
Alignment explanation
Indices: 1154177--1154235 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
1154167 TTATTTGCAA
* * *
1154177 TAT TAT T-T TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
1154220 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
1154236 TATATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1154233 original size:26 final size:28
Alignment explanation
Indices: 1154177--1154235 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
1154167 TTATTTGCAA
*
1154177 TATTATTTTATTATTATTATTGCTTTAAT
1 TATTATTTCATTATTATTATT-CTTTAAT
1154206 TATTATTTCATTATTATTATT-TTT-AT
1 TATTATTTCATTATTATTATTCTTTAAT
1154232 TATT
1 TATT
1154236 TATATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 3 0.10
29 20 0.69
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTATTTCATTATTATTATTCTTTAAT
Found at i:1159418 original size:2 final size:2
Alignment explanation
Indices: 1159411--1159436 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1159401 TTATCCTTTA
1159411 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
1159437 CCTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1159750 original size:14 final size:15
Alignment explanation
Indices: 1159731--1159763 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1159721 TCATCCAGTA
*
1159731 AAAAAAGAAGAA-GG
1 AAAAAAGAAAAATGG
1159745 AAAAAAGAAAAATGG
1 AAAAAAGAAAAATGG
1159760 AAAA
1 AAAA
1159764 GCAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAATGG
Found at i:1159794 original size:15 final size:15
Alignment explanation
Indices: 1159730--1159794 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
1159720 CTCATCCAGT
* *
1159730 AAAAAAAGAAGAAGG
1 AAAAGAAGAAAAAGG
1159745 AAAA-AAGAAAAATGG
1 AAAAGAAGAAAAA-GG
* **
1159760 AAAAGCAAAAAAAAAA
1 AAAAG-AAGAAAAAGG
1159776 AAAAGAAGAAAAAGG
1 AAAAGAAGAAAAAGG
1159791 AAAA
1 AAAA
1159795 TTGAATCAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
14 7 0.17
15 21 0.52
16 5 0.12
17 7 0.17
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (15 bp):
AAAAGAAGAAAAAGG
Found at i:1162169 original size:4 final size:4
Alignment explanation
Indices: 1162160--1162184 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1162150 CTTACCTTGC
1162160 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
1162185 AGGCATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:1166242 original size:63 final size:65
Alignment explanation
Indices: 1166124--1166250 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 65
1166114 AGATATTTAT
* * *
1166124 TATCTATTTAACTTTGAATATTAAAAATATAATTATATACTTTTAAATATTTTAAATTAAAATAA
1 TATCTATTTAACTTTAAATAGTAAAAAGATAATTATATACTTTTAAATATTTTAAATTAAAATAA
* * * *
1166189 TATCTATTTAAGTTTAAATAGTAAAAGGA-ATTTATAT-CTTTTGAATATTTTAAATTAAAATA
1 TATCTATTTAACTTTAAATAGTAAAAAGATAATTATATACTTTTAAATATTTTAAATTAAAATA
1166251 TATTAGTATC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 24 0.44
64 7 0.13
65 24 0.44
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (65 bp):
TATCTATTTAACTTTAAATAGTAAAAAGATAATTATATACTTTTAAATATTTTAAATTAAAATAA
Found at i:1172786 original size:71 final size:67
Alignment explanation
Indices: 1172694--1172889 Score: 199
Period size: 64 Copynumber: 2.9 Consensus size: 67
1172684 AGTAGGATAA
* *
1172694 TTAT-TCTTTTGAATATGTCAAATTTAAAAGGTATTTATTATCTATTTAACTTTGAGTATTAAAA
1 TTATATCTTTTGAATATTTCAAA-TTAAAA-GTA-TTATTATCTATTTAAATTTGAGTATTAAAA
*
1172758 GATAG-
63 -AGAGT
* * *
1172763 TTATATACTTTTGAATATTTCAAATTAAAA-TA--A-TATCTATTTAAGTTTGAATAATAAAAAG
1 TTATAT-CTTTTGAATATTTCAAATTAAAAGTATTATTATCTATTTAAATTTGAGTATTAAAAAG
1172824 AGT
65 AGT
* * *
1172827 TTATATCTTTTGAATATTTCAAAATAAAAGATATTATTATATGTTTAAATTTG-GATATTAAAA
1 TTATATCTTTTGAATATTTCAAATTAAAAG-TATTATTATCTATTTAAATTTGAG-TATTAAAA
1172890 TATATCTGGT
Statistics
Matches: 107, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
63 25 0.23
64 29 0.27
65 3 0.03
67 1 0.01
68 22 0.21
69 4 0.04
70 7 0.07
71 16 0.15
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTATATCTTTTGAATATTTCAAATTAAAAGTATTATTATCTATTTAAATTTGAGTATTAAAAAGA
GT
Found at i:1175916 original size:55 final size:55
Alignment explanation
Indices: 1175825--1176034 Score: 253
Period size: 55 Copynumber: 3.8 Consensus size: 55
1175815 TACCGAATGA
* *
1175825 GCACTATGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTCAAAAAATTCATAATAAGTTTATGAATTTCCGTATTG
* ** * *
1175879 ACACTATGTGTGCAACCTCATTAAATTAATAATAAGTTTATGAATTTCTGTATTG
1 GCACTATGTGTGCAACCTCAAAAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * *
1175934 GCACTATGTGTGCAACCTCACAAAATTCATAACGAA-TTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAACCTCAAAAAATTCATAA-TAAGTTTATGAATTTCCGTATTG
* *** * *
1175989 GCACTATGTGTGCAACCCCACGTAATTCATAATGAGTTTGTGAATT
1 GCACTATGTGTGCAACCTCAAAAAATTCATAATAAGTTTATGAATT
1176035 ACTGTATCAA
Statistics
Matches: 134, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
54 15 0.11
55 117 0.87
56 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (55 bp):
GCACTATGTGTGCAACCTCAAAAAATTCATAATAAGTTTATGAATTTCCGTATTG
Found at i:1176021 original size:110 final size:109
Alignment explanation
Indices: 1175825--1176041 Score: 287
Period size: 110 Copynumber: 2.0 Consensus size: 109
1175815 TACCGAATGA
* *
1175825 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGACACTATGTGT
1 GCACTATGTGTGCAACTCAAGAAATTCATAAGAAGTTTATGAATTTCCGTATTGACACTATGTGT
* * *
1175890 GCAACCTCATTAAATTAATAATAAGTTTATGAATTTCTGTATTG
66 GCAACCCCAGTAAATTAATAATAAGTTTATGAATTACTGTATTG
* *
1175934 GCACTATGTGTGCAACCTCACA-AAATTCATAACGAA-TTTATGAATTTTCGTATTGGCACTATG
1 GCACTATGTGTGCAA-CTCA-AGAAATTCATAA-GAAGTTTATGAATTTCCGTATTGACACTATG
* * *
1175997 TGTGCAACCCCACGT-AATTCATAATGAGTTTGTGAATTACTGTAT
63 TGTGCAACCCCA-GTAAATTAATAATAAGTTTATGAATTACTGTAT
1176042 CAACACTAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
109 15 0.16
110 75 0.80
111 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (109 bp):
GCACTATGTGTGCAACTCAAGAAATTCATAAGAAGTTTATGAATTTCCGTATTGACACTATGTGT
GCAACCCCAGTAAATTAATAATAAGTTTATGAATTACTGTATTG
Found at i:1179252 original size:22 final size:22
Alignment explanation
Indices: 1179199--1179252 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1179189 AAACGTTCTC
* *
1179199 CTTC-ATGTTGCTCTTTCATTG
1 CTTCAATGTTTCTCCTTCATTG
1179220 CTTCAATGTTTCTCCTTCATTG
1 CTTCAATGTTTCTCCTTCATTG
1179242 CTTCAATGTTT
1 CTTCAATGTTT
1179253 ATCCATAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.13, C:0.24, G:0.11, T:0.52
Consensus pattern (22 bp):
CTTCAATGTTTCTCCTTCATTG
Found at i:1183611 original size:55 final size:54
Alignment explanation
Indices: 1183462--1183692 Score: 275
Period size: 55 Copynumber: 4.3 Consensus size: 54
1183452 TACCGAATAT
* * * * * *
1183462 GCACTATG-GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCACCTCACGAAATTCATATTGAGTTTATGAATTTCCGTATCG
*
1183515 GCACTATGTGTGCACCTCACGAAATTCATATTAAGTTTATGAATTTCCGTATCG
1 GCACTATGTGTGCACCTCACGAAATTCATATTGAGTTTATGAATTTCCGTATCG
* * * *
1183569 GTACTATGTGTGACACCTCACAAAAATCATATTGAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTG-CACCTCACGAAATTCATATTGAGTTTATGAATTTCCGTATCG
* * * * * *
1183624 GCACTATGTGTGCAACCCCACGTAATTCGTAATGAGTTTATGAATTACTGTATCG
1 GCACTATGTGTGC-ACCTCACGAAATTCATATTGAGTTTATGAATTTCCGTATCG
*
1183679 GCACTACGTGTGCA
1 GCACTATGTGTGCA
1183693 GAACAATGGA
Statistics
Matches: 154, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
53 8 0.05
54 53 0.34
55 93 0.60
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (54 bp):
GCACTATGTGTGCACCTCACGAAATTCATATTGAGTTTATGAATTTCCGTATCG
Found at i:1183716 original size:110 final size:108
Alignment explanation
Indices: 1183482--1183716 Score: 276
Period size: 110 Copynumber: 2.1 Consensus size: 108
1183472 GCAACTTAAG
* * *
1183482 AAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCACCTCACGAAATTCATATT
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCACCCCACGAAATTCATAAT
* * * **
1183547 AAGTTTATGAATTTCCGTATCGGTACTATGTGTGACACCTCACA
66 AAGTTTATGAATTACCGTATCGGCACTACGTGTGACA-CGAACA
* * * *
1183591 AAAATCATATTGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCCCACGTAATTCGTAA
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGC-ACCCCACGAAATTCATAA
* *
1183656 TGAGTTTATGAATTACTGTATCGGCACTACGTGTG-CA-GAACA
65 TAAGTTTATGAATTACCGTATCGGCACTACGTGTGACACGAACA
*
1183698 ATGGAATTTATAATGAGTT
1 A---AATTCATAATGAGTT
1183717 GAAATATTCA
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
107 4 0.04
109 45 0.43
110 56 0.53
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (108 bp):
AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCACCCCACGAAATTCATAAT
AAGTTTATGAATTACCGTATCGGCACTACGTGTGACACGAACA
Found at i:1186337 original size:55 final size:55
Alignment explanation
Indices: 1186216--1186338 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
1186206 AAAGCCGATA
* ** *
1186216 AAGTTTATGAATTTCCGTATTGGTACTATGTGTACAACGTTATGAAATTCATAAT
1 AAGTTTATGAATTTCCGTATTGGTACTATATGTACAACGCCACGAAATTCATAAT
* * * * *
1186271 GAGATTATGAATTTTCGTATTGGTACTATATGTGCAACGCCACGTAATTCATAAT
1 AAGTTTATGAATTTCCGTATTGGTACTATATGTACAACGCCACGAAATTCATAAT
*
1186326 AAGTTTGTGAATT
1 AAGTTTATGAATT
1186339 ACTGTACTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (55 bp):
AAGTTTATGAATTTCCGTATTGGTACTATATGTACAACGCCACGAAATTCATAAT
Found at i:1191448 original size:55 final size:55
Alignment explanation
Indices: 1191355--1191557 Score: 250
Period size: 55 Copynumber: 3.7 Consensus size: 55
1191345 TTACCGAATG
* * *
1191355 GGCACTATGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATGAATTTCCGTATT
1191409 GGCACTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * * * * *
1191464 GACACTATGTGTGCAACCCCA-CATAATTCATAGTGAGTTTGTGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTCATGA-AATTCATAATGAGTTTATGAATTTCCGTATT
* * * *
1191519 GGCACTACGTGTGCAAAAC-CATGGAATTTATAATGAGTT
1 GGCACTATGTGTGC-AACCTCATGAAATTCATAATGAGTT
1191558 GAAATATTCA
Statistics
Matches: 129, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
54 17 0.13
55 109 0.84
56 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATGAATTTCCGTATT
Found at i:1195290 original size:10 final size:10
Alignment explanation
Indices: 1195219--1195292 Score: 50
Period size: 9 Copynumber: 7.8 Consensus size: 10
1195209 ATAAAATAAA
1195219 ATTATTTT-T
1 ATTATTTTAT
*
1195228 ATTATATTAT
1 ATTATTTTAT
1195238 ATTATATTTA-
1 ATTAT-TTTAT
*
1195248 ATTATTTGA-
1 ATTATTTTAT
* *
1195257 ATAAATTT-T
1 ATTATTTTAT
**
1195266 ATTATACTA-
1 ATTATTTTAT
1195275 ATTATTTTAT
1 ATTATTTTAT
1195285 ATTATTTT
1 ATTATTTT
1195293 TGCGGTTGTA
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
9 26 0.54
10 19 0.40
11 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:1197652 original size:46 final size:46
Alignment explanation
Indices: 1197601--1197697 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
1197591 ATTATTCTTT
* *
1197601 ATTTTCATTGA-GAGCATCCATTCATACTTATAATTCA-CCATTATGC
1 ATTTTCATTGATG-GCATCCATTCATACTGATAATGCACCCA-TATGC
* * *
1197647 ATTTTCATTTATGGCATCCTTTCATGCTGATAATGCACCCATATGC
1 ATTTTCATTGATGGCATCCATTCATACTGATAATGCACCCATATGC
1197693 ATTTT
1 ATTTT
1197698 ATTTATACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
46 40 0.91
47 4 0.09
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (46 bp):
ATTTTCATTGATGGCATCCATTCATACTGATAATGCACCCATATGC
Found at i:1197764 original size:46 final size:46
Alignment explanation
Indices: 1197692--1197837 Score: 186
Period size: 46 Copynumber: 3.2 Consensus size: 46
1197682 CACCCATATG
* * * *
1197692 CATTTTATTTAT-ACATCCTTTCATGCCCTTTTATACGATATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
* * *
1197737 CATTTCATTTATGGCATCCTTTTATGCCCTTTTATAATCTATTACA
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
* * *
1197783 CACTTCATTTATGGCATCCTTTCATGCCCTTTTATATGCTATTATG
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
1197829 CATTGTCAT
1 CATT-TCAT
1197838 ACCTCTAGGC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 11 0.13
46 70 0.82
47 4 0.05
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.47
Consensus pattern (46 bp):
CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
Found at i:1197947 original size:81 final size:81
Alignment explanation
Indices: 1197847--1198001 Score: 267
Period size: 81 Copynumber: 1.9 Consensus size: 81
1197837 TACCTCTAGG
* *
1197847 CTTTTACTCAAAGGCATTTAACCTTTCATCTAACT-TGCATAATTGACACCTTTCTGTCAAATTC
1 CTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGT-CATAATTGACACATTTCTGTCAAATGC
1197911 ACAGCTAGGCTATTAAT
65 ACAGCTAGGCTATTAAT
*
1197928 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCA
1197993 CAGCTAGGC
66 CAGCTAGGC
1198002 CTTAAAGGCA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 69 0.99
82 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (81 bp):
CTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCA
CAGCTAGGCTATTAAT
Found at i:1198050 original size:68 final size:68
Alignment explanation
Indices: 1197934--1198410 Score: 638
Period size: 68 Copynumber: 7.0 Consensus size: 68
1197924 TAATCTTTTA
* * * *
1197934 CTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACA-CATTTCTGTCAAATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATC-TTTCTGTCAAATGCACAGCT
1197998 AGGC
65 AGGC
* * *
1198002 CTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTTAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTA
1198067 GGC
66 GGC
* * * * * * *
1198070 CTCAAAGACACTTATCCTTTCATCTAACTAGCATAATTGACACCTTTATGTCAAATGTACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTA
*
1198135 AGC
66 GGC
* * *
1198138 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAACTGACACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTA
*
1198203 AGC
66 GGC
* * * * *
1198206 CTCAAAGGAACTTAACATTTCATCTAACTGGCATAATTGACATCTTTCGGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTA
1198271 GGC
66 GGC
*
1198274 CTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACA-CATTTCTGTCAAATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATC-TTTCTGTCAAATGCACAGCT
1198338 AGGC
65 AGGC
* * *
1198342 CTCAAAGGCACTTAGCCTATCATCTAACTGTCATAATTGATACAT-TTT-TGTCAAATGCACAAC
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTG--ACATCTTTCTGTCAAATGCACAGC
1198405 TAGGC
64 TAGGC
1198410 C
1 C
1198411 ATTAATCTTT
Statistics
Matches: 361, Mismatches: 43, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
67 1 0.00
68 353 0.98
69 4 0.01
70 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTA
GGC
Found at i:1198295 original size:204 final size:204
Alignment explanation
Indices: 1197934--1198402 Score: 704
Period size: 204 Copynumber: 2.3 Consensus size: 204
1197924 TAATCTTTTA
* * *
1197934 CTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCACAGCTA
* * * * * * *
1197999 GGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACATCTTTCTGTTAAATGCACAA
66 AGCCTCAAAGGAACTTAACATTTCATCTAACTGGCATAATTGACATCTTTCGGTCAAATGCACAA
* * *
1198064 CTAGGCCTCAAAGACACTTATCCTTTCATCTAACTAGCATAATTGACACCTTTATGTCAAATGTA
131 CTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTAGCATAATTGACACATTTATGTCAAATGCA
*
1198129 CAGTTAAGC
196 CAGCTAAGC
* * * *
1198138 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAACTGACACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCACAGCTA
1198203 AGCCTCAAAGGAACTTAACATTTCATCTAACTGGCATAATTGACATCTTTCGGTCAAATGCACAA
66 AGCCTCAAAGGAACTTAACATTTCATCTAACTGGCATAATTGACATCTTTCGGTCAAATGCACAA
* * * *
1198268 CTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
131 CTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTAGCATAATTGACACATTTATGTCAAATGCA
*
1198333 CAGCTAGGC
196 CAGCTAAGC
* * *
1198342 CTCAAAGGCACTTAGCCTATCATCTAACTGTCATAATTGATACATTTTTGTCAAATGCACA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCACA
1198403 ACTAGGCCAT
Statistics
Matches: 236, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
204 236 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (204 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGTCATAATTGACACATTTCTGTCAAATGCACAGCTA
AGCCTCAAAGGAACTTAACATTTCATCTAACTGGCATAATTGACATCTTTCGGTCAAATGCACAA
CTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTAGCATAATTGACACATTTATGTCAAATGCA
CAGCTAAGC
Found at i:1198858 original size:59 final size:56
Alignment explanation
Indices: 1198585--1198902 Score: 386
Period size: 57 Copynumber: 5.6 Consensus size: 56
1198575 AAATTCATAA
* * * * *
1198585 AATTTCTT-AGTTTTTGCACATAAAGTTCTTATACGGGAATTCATAAACAAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGC-CATACGGAAATTCATAAACAAATTATG
* * *
1198641 AATTTCTTAACTTTTTGCACTCGAAGTGCCTATACGGAAATTCATAAATAAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCC-ATACGGAAATTCATAAACAAATTATG
* * *
1198698 AATTTCTTAACTTTTTGCACTCGAAGTGCCTATACGGAAATTCATAAATAAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCC-ATACGGAAATTCATAAACAAATTATG
* * * *
1198755 ATTTTCGTAACTTTTTGCACACAAAGTGCCCATTCGAAAATTCATAAACAAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTG-CCATACGGAAATTCATAAACAAATTATG
* *
1198812 AATTTCTTAACTTTTTTTGCACACAAAGTGCTCATACGAAAATTCATAAAAAAATTATG
1 AATTTCTTAAC--TTTTTGCACACAAAGTGC-CATACGGAAATTCATAAACAAATTATG
* **
1198871 AATTTCTTAACTTTTTACACACTCAGTGCCAT
1 AATTTCTTAACTTTTTGCACACAAAGTGCCAT
1198903 TATGTAATCA
Statistics
Matches: 234, Mismatches: 22, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
56 11 0.05
57 167 0.71
58 3 0.01
59 53 0.23
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (56 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCATACGGAAATTCATAAACAAATTATG
Found at i:1199343 original size:20 final size:20
Alignment explanation
Indices: 1199318--1199370 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1199308 GTTAACAATG
*
1199318 GTATCGATACCATCCTCATA
1 GTATCGATACCACCCTCATA
* *
1199338 GTATCGATACTC-CCCTCTTG
1 GTATCGATAC-CACCCTCATA
1199358 GTATCGATACCAC
1 GTATCGATACCAC
1199371 TTGAATCGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (20 bp):
GTATCGATACCACCCTCATA
Found at i:1201833 original size:125 final size:123
Alignment explanation
Indices: 1201654--1201929 Score: 340
Period size: 125 Copynumber: 2.2 Consensus size: 123
1201644 AGTAGTATTT
*
1201654 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACGCC
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCC
* * * * *
1201719 GGTATAGAATTGTACTTTAGTGGCGTTTTTATACAAACGCCGTTATACACATGTACTA
66 GCTAAAGAATCGTACTTTAGTGACATTTTTATACAAACGCCGTTATACACATGTACTA
* * *
1201777 TAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCATAATTTAGTGGCGTTTTTATACAAACG
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACG
* * * * * * *
1201842 CCGCTAAAGACTCGTACTTTATTGATATTTTTATACAAACACCGCTAAAGAC-TCGTACT-
64 CCGCTAAAGAATCGTACTTTAGTGACATTTTTATACAAACGCCGTTATACACAT-GTACTA
* *
1201901 TCAGTGGCATTTTTATTCAAACGCCGCTA
1 T-AGTGGCGTTTTTATACAAACGCCGCTA
1201930 TACACTTGTA
Statistics
Matches: 129, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
123 24 0.19
124 4 0.03
125 101 0.78
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (123 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCC
GCTAAAGAATCGTACTTTAGTGACATTTTTATACAAACGCCGTTATACACATGTACTA
Found at i:1201836 original size:166 final size:166
Alignment explanation
Indices: 1201609--1201968 Score: 510
Period size: 166 Copynumber: 2.2 Consensus size: 166
1201599 ATAGGTTCAT
* * *
1201609 CTATAGTGGCGTTT-T-TTCAACAAACGCCGCAAAAGAGTAGTATTTTAGTGGCGTTTTTATACA
1 CTATAGTGGCGTTTGTGTT-TACAAACGCCGCAAAAGACTAGTAATTTAGTGGCGTTTTTATACA
* * * * * *
1201672 AACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACGCCGGTATAGAATTGTACTTT
65 AACGCCGCTAAAGACTCGTAATTTAGTGACATTTTTATACAAACACCGCTAAAGAATCGTACTTC
* *
1201737 AGTGGCGTTTTTATACAAACGCCGTTATACACATGTA
130 AGTGGCATTTTTATACAAACGCCGCTATACACATGTA
* *
1201774 CTATAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCA-TAATTTAGTGGCGTTTTTATACA
1 CTATAGTGGCGTTTGTGTTTACAAACGCCGCAAAAGACT-AGTAATTTAGTGGCGTTTTTATACA
* * * *
1201838 AACGCCGCTAAAGACTCGTACTTTATTGATATTTTTATACAAACACCGCTAAAGACTCGTACTTC
65 AACGCCGCTAAAGACTCGTAATTTAGTGACATTTTTATACAAACACCGCTAAAGAATCGTACTTC
* *
1201903 AGTGGCATTTTTATTCAAACGCCGCTATACACTTGTA
130 AGTGGCATTTTTATACAAACGCCGCTATACACATGTA
1201940 CTATAGTGGCGTTTGTGTTTACAAACGCC
1 CTATAGTGGCGTTTGTGTTTACAAACGCC
1201969 TCAAGTTTAC
Statistics
Matches: 172, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
165 14 0.08
166 155 0.90
167 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (166 bp):
CTATAGTGGCGTTTGTGTTTACAAACGCCGCAAAAGACTAGTAATTTAGTGGCGTTTTTATACAA
ACGCCGCTAAAGACTCGTAATTTAGTGACATTTTTATACAAACACCGCTAAAGAATCGTACTTCA
GTGGCATTTTTATACAAACGCCGCTATACACATGTA
Found at i:1201941 original size:41 final size:41
Alignment explanation
Indices: 1201568--1201968 Score: 360
Period size: 41 Copynumber: 9.7 Consensus size: 41
1201558 ACAAATGGTA
** * ** *
1201568 ACTTTAGCAGCGTTTTTATAAAAACGCCGC-AATAGGTTCAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAA-AGACTCGT
* * * *
1201609 -CTATAGTGGCGTTTTT-TCAACAAACGCCGCAAAAGAGTAGT
1 ACTTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTCGT
*
1201650 ATTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * * * * *
1201691 AATTTAGTGGCATTTTTATACAAACGCCGGTATAGAATTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * *
1201732 ACTTTAGTGGCGTTTTTATACAAACGCCGTTATACACAT-GT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TCGT
* * * *
1201773 ACTATAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCAT
1 ACTTTAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGT
*
1201816 AATTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* *** *
1201857 ACTTTATTGATATTTTTATACAAACACCGCTAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * * * * *
1201898 ACTTCAGTGGCATTTTTATTCAAACGCCGCTATACACTTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* *
1201939 ACTATAGTGGCGTTTGTGTTTACAAACGCC
1 ACTTTAGTGGCGTTT-T-TATACAAACGCC
1201969 TCAAGTTTAC
Statistics
Matches: 293, Mismatches: 56, Indels: 20
0.79 0.15 0.05
Matches are distributed among these distances:
39 1 0.00
40 13 0.04
41 217 0.74
42 21 0.07
43 41 0.14
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
Found at i:1205849 original size:43 final size:43
Alignment explanation
Indices: 1205796--1206232 Score: 399
Period size: 43 Copynumber: 10.2 Consensus size: 43
1205786 AAGGTAATTA
* *
1205796 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTT
** *
1205839 GCGATGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTT
* *
1205882 GCGGCGTTTGT-TCTAAAAACGCCAG-TATAGGTCT-TCTCTTTT
1 GCGGCGTTTGTATCCAAAAACGCC-GCTATAGGTCTGAC-CTTTT
* * * *
1205924 GCGGCGTTTGTGTTCAAAAACGTCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTT
* * *
1205967 ACGGCATTTGTATCCAAAAATGCCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTT
* ** *
1206010 GCGGCGTTTGT-TCTAAAAGTGCCAG-TATAGGTCT-TCTCTTTT
1 GCGGCGTTTGTATCCAAAAACGCC-GCTATAGGTCTGAC-CTTTT
* *
1206052 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTT
* * * ** * *
1206095 GCGGCGTTT-TTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTC-TGACCTTTT
* * * * * *
1206138 GTGGCGTTTAT-TGCAAAAATGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCT-GACCTTTT
* * * *
1206181 GCGGCGTTTGT-TCAAAAAACGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGCT-ATAGGT-CTGACCTTTT
1206224 GCGGCGTTT
1 GCGGCGTTT
1206233 TTTGTTCTCA
Statistics
Matches: 325, Mismatches: 54, Indels: 30
0.79 0.13 0.07
Matches are distributed among these distances:
41 2 0.01
42 94 0.29
43 225 0.69
44 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTT
Found at i:1205942 original size:85 final size:86
Alignment explanation
Indices: 1205796--1206232 Score: 412
Period size: 85 Copynumber: 5.1 Consensus size: 86
1205786 AAGGTAATTA
* * ** *
1205796 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGCGATG-TTTGTGTCCAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTGT-TCTAAAAAC
1205860 GCCGCTATAGGTCTGACCTTTT
65 GCCGCTATAGGTCTGACCTTTT
* *
1205882 GCGGCGTTTGT-TCTAAAAACGCCAG-TATAGGTCT-TCTCTTTTGCGGCGTTTGTGTTC-AAAA
1 GCGGCGTTTGTATCCAAAAACGCC-GCTATAGGTCTGAC-CTTTTGCGGCGTTT-TGTTCTAAAA
* *
1205943 ACGTCGTTATAGGTCTGACCTTTT
63 ACGCCGCTATAGGTCTGACCTTTT
* * * **
1205967 ACGGCATTTGTATCCAAAAATGCCGCTATAGGTCTGACCTTTTGCGGCG-TTTGTTCTAAAAGTG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTGTTCTAAAAACG
*
1206031 CCAG-TATAGGTCT-TCTCTTTT
66 CC-GCTATAGGTCTGAC-CTTTT
* * *
1206052 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTTT-TTCTAGAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTGTTCTAAAAACG
** * *
1206116 CCGCTATATATCATAACTTTTT
66 CCGCTATAGGTC-TGACCTTTT
* * * * * * *
1206138 GTGGCGTTTAT-TGCAAAAATGCCGCTATAGATATCGACCTTTTGCGGCG-TTTGTTCAAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCT-GACCTTTTGCGGCGTTTTGTTCTAAAAAC
* * *
1206201 GCCG-TAATAGATATTGACCTATT
65 GCCGCT-ATAGGT-CTGACCTTTT
1206224 GCGGCGTTT
1 GCGGCGTTT
1206233 TTTGTTCTCA
Statistics
Matches: 292, Mismatches: 41, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
84 8 0.03
85 170 0.58
86 109 0.37
87 5 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (86 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTTGTTCTAAAAACG
CCGCTATAGGTCTGACCTTTT
Found at i:1206138 original size:128 final size:128
Alignment explanation
Indices: 1205796--1206232 Score: 483
Period size: 128 Copynumber: 3.4 Consensus size: 128
1205786 AAGGTAATTA
* * ** *
1205796 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGCGATGTTTGTGTCCAAAAACG
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTTCCAAAAACG
*
1205861 CCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCAGTATAGGTCTTCTCTTTT
66 CCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAATGCCAGTATAGGTCTTCTCTTTT
* * * * * * * *
1205924 GCGGCGTTTGTGTTC-AAAAACGTCGTTATAGGTCTGACCTTTTACGGCATTTGTATCCAAAAAT
1 GCGGCGTTTGT-ATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTTCCAAAAAC
*
1205988 GCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAGTGCCAGTATAGGTCTTCTCTTTT
65 GCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAATGCCAGTATAGGTCTTCTCTTTT
* * * *
1206052 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTT-TTTCTAGAAACG
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTTCCAAAAACG
** * * * * * * *
1206116 CCGCTATATATCATAACTTTTTGTGGCGTTTATTGC-AAAAATGCC-GCTATAGAT-ATCGACCT
66 CCGCTATAGGTC-TGACCTTTTGCGGCGTTTGTT-CTAAAAATGCCAG-TATAGGTCTTC--TCT
1206178 TTT
126 TTT
* *
1206181 GCGGCGTTTGT-TCAAAAAACGCCG-TAATAGATATTGACCTATTGCGGCGTTT
1 GCGGCGTTTGTATCAAAAAACGCCGCT-ATAGAT-CTGACCTTTTGCGGCGTTT
1206233 TTTGTTCTCA
Statistics
Matches: 265, Mismatches: 35, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
127 24 0.09
128 204 0.77
129 37 0.14
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (128 bp):
GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTTCCAAAAACG
CCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAATGCCAGTATAGGTCTTCTCTTTT
Found at i:1206419 original size:2 final size:2
Alignment explanation
Indices: 1206412--1206458 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1206402 ACATAAAAGC
1206412 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1206454 TA TA T
1 TA TA T
1206459 TTCTAACATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1215136 original size:45 final size:45
Alignment explanation
Indices: 1215071--1215163 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
1215061 CATTATGTAT
* *
1215071 TTTCATTTATGACATTATTTCATGCCAATAATGCACCCATATGCA
1 TTTCAATTATGACATCATTTCATGCCAATAATGCACCCATATGCA
* *
1215116 TTTCAATTATGGCATCATTTCATGCCGATAATGCACCCATATGCA
1 TTTCAATTATGACATCATTTCATGCCAATAATGCACCCATATGCA
1215161 TTT
1 TTT
1215164 TACTTAAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (45 bp):
TTTCAATTATGACATCATTTCATGCCAATAATGCACCCATATGCA
Found at i:1215225 original size:46 final size:46
Alignment explanation
Indices: 1215171--1215304 Score: 223
Period size: 46 Copynumber: 2.9 Consensus size: 46
1215161 TTTTACTTAA
* *
1215171 GCATCCTTTCTTGCCCTTTTATGCGCTATTATACATTTCATTTATG
1 GCATCCTTTCATGCCCTTTTATACGCTATTATACATTTCATTTATG
*
1215217 GCATCCTTTCATGCCCTTTTATACGCTATTATACACTTCATTTATG
1 GCATCCTTTCATGCCCTTTTATACGCTATTATACATTTCATTTATG
*
1215263 GCATCCTTTCATGCCCTTTTATACGCTATTATGCATTGTCAT
1 GCATCCTTTCATGCCCTTTTATACGCTATTATACATT-TCAT
1215305 ACCTCTAGTC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 78 0.95
47 4 0.05
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.45
Consensus pattern (46 bp):
GCATCCTTTCATGCCCTTTTATACGCTATTATACATTTCATTTATG
Found at i:1215398 original size:81 final size:81
Alignment explanation
Indices: 1215313--1215465 Score: 243
Period size: 81 Copynumber: 1.9 Consensus size: 81
1215303 ATACCTCTAG
* * *
1215313 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAATTGGCATAATTGACATCTTTATGTTAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACAACTTTATGTCAAATGC
1215378 ACAGCTAACCTATTAA
66 ACAGCTAACCTATTAA
* * * *
1215394 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGATAACTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACAACTTTATGTCAAATGC
1215459 ACAGCTA
66 ACAGCTA
1215466 GGCCTCAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACAACTTTATGTCAAATGC
ACAGCTAACCTATTAA
Found at i:1215517 original size:68 final size:68
Alignment explanation
Indices: 1215401--1215809 Score: 568
Period size: 68 Copynumber: 6.0 Consensus size: 68
1215391 TAATCTTTTA
* * * * *
1215401 CTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGATA-ACTTTCTGTCAAATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACA-TTTCTGTCAAATGCACAGCT
1215465 AGGC
65 AGGC
* * *
1215469 CTCAAAGGCACTTAGCCTTTCATCTAACTGCCATAATTGACATATTTCTGTCAAATGCACAGCGA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTA
1215534 GGC
66 GGC
* * * * * *
1215537 CTCAAAGGCACTTAGCCTTTCATTTAATTGGCATAATTGAAATATTTCTATCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTA
*
1215602 GAC
66 GGC
* *
1215605 CTCAAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTA
1215670 GGC
66 GGC
* * *
1215673 CTCAAAGACACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTA
1215738 GGC
66 GGC
* * * * * *
1215741 CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAAATGACACCTTTATGTCAAATACACATCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTA
1215806 GGC
66 GGC
1215809 C
1 C
1215810 ATTAATATTT
Statistics
Matches: 307, Mismatches: 33, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
68 306 1.00
69 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTA
GGC
Found at i:1215751 original size:204 final size:204
Alignment explanation
Indices: 1215401--1215776 Score: 635
Period size: 204 Copynumber: 1.8 Consensus size: 204
1215391 TAATCTTTTA
* * * *
1215401 CTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGATAACTTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGAATAATTGACAACTTTCTGTCAAATGCACAGCTA
* *
1215466 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGCCATAATTGACATATTTCTGTCAAATGCACAG
66 GGCCTCAAAGACACTTAGCCTTTCATCTAACTGCCATAATTGACACATTTCTGTCAAATGCACAG
*
1215531 CGAGGCCTCAAAGGCACTTAGCCTTTCATTTAATTGGCATAATTGAAATATTTCTATCAAATGCA
131 CGAGGCCTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGAAATATTTCTATCAAATGCA
1215596 CAGTTAGAC
196 CAGTTAGAC
* *
1215605 CTCAAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGAATAATTGACAACTTTCTGTCAAATGCACAGCTA
* * *
1215670 GGCCTCAAAGACACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAG
66 GGCCTCAAAGACACTTAGCCTTTCATCTAACTGCCATAATTGACACATTTCTGTCAAATGCACAG
*
1215735 CTAGGCCTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAA
131 CGAGGCCTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAA
1215777 ATGACACCTT
Statistics
Matches: 159, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
204 159 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (204 bp):
CTCAAAGGCACTTAACCTTTCATCTAACTGGAATAATTGACAACTTTCTGTCAAATGCACAGCTA
GGCCTCAAAGACACTTAGCCTTTCATCTAACTGCCATAATTGACACATTTCTGTCAAATGCACAG
CGAGGCCTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGAAATATTTCTATCAAATGCA
CAGTTAGAC
Found at i:1216083 original size:57 final size:57
Alignment explanation
Indices: 1216022--1216282 Score: 389
Period size: 57 Copynumber: 4.6 Consensus size: 57
1216012 TATATAGGAT
* * *
1216022 TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACCCGAAGTGCTCATACAAAAA
1 TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAAAAA
* * *
1216079 TTCATAAACAAATTATTAATTTTTTAACTTTTTGCACTCAAAGTGCCCATACAAAAA
1 TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAAAAA
* * *
1216136 TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTACCCATTCAGAAA
1 TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAAAAA
* * **
1216193 TTCATAAACAAATTATGAATTTTTTAACTTTTTTGCACACAAAGTGCTCATACGGAAA
1 TTCATAAACAAATTATGAATTTCTTAAC-TTTTTGCACACAAAGTGCCCATACAAAAA
1216251 TTCATAAA-AAATTATGAATTTCTTAACTTTTT
1 TTCATAAACAAATTATGAATTTCTTAACTTTTT
1216283 ATACACTCAG
Statistics
Matches: 186, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
56 5 0.03
57 148 0.80
58 33 0.18
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (57 bp):
TTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACAAAAA
Found at i:1216668 original size:22 final size:19
Alignment explanation
Indices: 1216636--1216688 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
1216626 TACCCTTACC
*
1216636 ATGGTATCGATACTACTATACT
1 ATGGTACCGATACT-CTAT--T
1216658 ATGGTACCGATACTCTATT
1 ATGGTACCGATACTCTATT
*
1216677 ATAGTACCGATA
1 ATGGTACCGATA
1216689 ACATTTATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
21 4 0.14
22 13 0.45
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGGTACCGATACTCTATT
Found at i:1220683 original size:182 final size:182
Alignment explanation
Indices: 1220314--1220725 Score: 605
Period size: 182 Copynumber: 2.3 Consensus size: 182
1220304 ACACAAATAT
* * * * * *
1220314 AAATGTATCGAGCCATAGCAATATAGCAGGTAAAAATATGACAAAACCGGTTTCATTATGACAAA
1 AAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCATAATGACAAA
*
1220379 ACCGGTAAAGTGCTACCAGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTTTT
66 ACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTTTT
* *
1220444 AGAATTTAAAAGAGAAGTAGTAATATCGCCTATAAAGTGTCGATAATTTATA
131 AGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTATA
* *
1220496 AAATGTATCGATTCATAACAATATAACAGGTAAAAATATGACAAAACTAGTCTCGA-AATGACAA
1 AAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTC-ATAATGACAA
* * * *
1220560 AACTGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGACACTT
65 AACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATCGACACTT
* *
1220623 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAA
129 TTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTAT-A
* *
1220678 AAATGTATCGATCCAAAATAATATAACAGGTAAAAATATGACAAAACC
1 AAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
1220726 GGTAAAGCGC
Statistics
Matches: 206, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
180 4 0.02
181 67 0.33
182 134 0.65
183 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
AAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCATAATGACAAA
ACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTAGATTGAAATAAGTATCGACACTTTT
AGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTATA
Found at i:1220820 original size:162 final size:162
Alignment explanation
Indices: 1220553--1220931 Score: 659
Period size: 162 Copynumber: 2.3 Consensus size: 162
1220543 TAGTCTCGAA
* * *
1220553 ATGACAAAACTGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTTGATACTTTAATATAAGTATCGA
*
1220618 CACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTATAAAAATG
*
1220683 TATCGATCCAAAATAATATAACAGGTAAAAAT
131 TATCGATCCAAAACAATATAACAGGTAAAAAT
*
1220715 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTTTTGATACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTTGATACTTTAATATAAGTATCGA
*
1220780 CACTTTTTGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTATAAAAATG
* *
1220845 TATCGATCCATAACAATATAACATGTAAAAAT
131 TATCGATCCAAAACAATATAACAGGTAAAAAT
* *
1220877 ATGACAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGGTGATACTTTAATA
1 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTTGATACTTTAATA
1220932 AGTACGTGTA
Statistics
Matches: 205, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 205 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (162 bp):
ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTTGATACTTTAATATAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAATTTATAAAAATG
TATCGATCCAAAACAATATAACAGGTAAAAAT
Found at i:1221708 original size:20 final size:19
Alignment explanation
Indices: 1221670--1221708 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1221660 CGAAACTGAT
*
1221670 AATTACAATGTAATAGGTA
1 AATTACAATGTAACAGGTA
*
1221689 AATTAACAATGTAACCGGTA
1 AATT-ACAATGTAACAGGTA
1221709 GAAATATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AATTACAATGTAACAGGTA
Found at i:1221918 original size:200 final size:199
Alignment explanation
Indices: 1221576--1221983 Score: 627
Period size: 200 Copynumber: 2.0 Consensus size: 199
1221566 TAGGTAGAAA
*
1221576 ATACTTTTTGTCCATAATGAATGACAAACGAGGTGCACAAATAAAGTGTCGATACATTTAAAATT
1 ATACTTTTTGTCCAGAATGAATGACAAACGAGGTGCACAAATAAAGTGTCGATACATTTAAAATT
* * *
1221641 ATATCGATCCAAAAAACATCGAAACTGATAATTACAATGTAATAGGTAAATTAACAATGTAACCG
66 ATATCGATCCAAAAAACATCGAAACCGATAATTACAATGCAATAGGTAAATTAACAATGTAACCA
** * * *
1221706 GTAGAAATATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATTGACACTTTCTAAATTTAT
131 GTAGAAATATACCAATTTTATGAGAAAATAGGTCTAAATAAAGTATCGACACTTTCTAAATTTAT
1221771 GTCG
196 GTCG
* **
1221775 ATACTTTTTGTCCAGAATGAATGTCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTAAAAT
1 ATACTTTTTGTCCAGAATGAATG-ACAAACGAGGTGCACAAATAAAGTGTCGATACATTTAAAAT
* * * *
1221840 TGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGCAATAGGTAAATTAATAATGTAACT
65 TATATCGATCCAAAAAACATCGAAACCGATAATTACAATGCAATAGGTAAATTAACAATGTAACC
* * *
1221905 AGTAGAAATATACCAATTTTATGAGAAAATAGGTCTACATAAAGTATCGACACTTTTTAAGTTTA
130 AGTAGAAATATACCAATTTTATGAGAAAATAGGTCTAAATAAAGTATCGACACTTTCTAAATTTA
1221970 TGTCG
195 TGTCG
*
1221975 ATATTTTTT
1 ATACTTTTT
1221984 TAATTTACGC
Statistics
Matches: 188, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
199 22 0.12
200 166 0.88
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
ATACTTTTTGTCCAGAATGAATGACAAACGAGGTGCACAAATAAAGTGTCGATACATTTAAAATT
ATATCGATCCAAAAAACATCGAAACCGATAATTACAATGCAATAGGTAAATTAACAATGTAACCA
GTAGAAATATACCAATTTTATGAGAAAATAGGTCTAAATAAAGTATCGACACTTTCTAAATTTAT
GTCG
Found at i:1222856 original size:17 final size:19
Alignment explanation
Indices: 1222809--1222851 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1222799 TGTACGGGAG
*
1222809 ATTTTGTATACGATTCATA
1 ATTTTGTATATGATTCATA
*
1222828 ATTTTGTATATGATTTATA
1 ATTTTGTATATGATTCATA
1222847 ATTTT
1 ATTTT
1222852 ATATGTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (19 bp):
ATTTTGTATATGATTCATA
Found at i:1225304 original size:12 final size:12
Alignment explanation
Indices: 1225287--1225316 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1225277 TCAATAGGAT
1225287 GTGGTATTGGTA
1 GTGGTATTGGTA
1225299 GTGGTATTGGTA
1 GTGGTATTGGTA
1225311 GTGGTA
1 GTGGTA
1225317 GTTGAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (12 bp):
GTGGTATTGGTA
Found at i:1226013 original size:200 final size:199
Alignment explanation
Indices: 1225631--1226325 Score: 866
Period size: 200 Copynumber: 3.5 Consensus size: 199
1225621 AACATATATA
* *
1225631 TCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCAAAAAC-AGTAATTATAATGTAATAG
1 TCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCAAAACCGA-TAATTATAATGTAATAG
* * * * * *
1225694 GTAAATTAACAATGTAACCGGTATAAAGATACCGG-TTAATTAGAAAACAAGTCAACATAATGTA
64 GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTA
* ** * *
1225758 TCGACACTTGTGGAATTTGTGTTGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGC
129 TCGACACTTTTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATG-CCAAACGAGGTGCACGA
1225823 ATAAAGTG
192 ATAAAGTG
* *
1225831 TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATATGT
1 TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGT
* * *
1225896 AAATTTATAATGTAATCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATC
66 AAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATC
*
1225961 G-CTACTTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGAGGTGCACGAAT
131 GAC-ACTTTTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACGAAT
1226025 AAAGTG
194 AAAGTG
* * *
1226031 TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACTGATAATTACAATGTAATATGT
1 TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGT
* * * * * * *
1226096 AAATTTACAATGTACCCGGTAGAAATATACTGATTTTACGATAAAATAGGTCTACATAATGTATC
66 AAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATC
* * * * *
1226161 GACACTTTTTAAGTTTGTGTCGATAC-TTTGTTTCAGAATGAATGCCCAACGAGATGCACAAATA
131 GACACTTTTTAAATTTGTGTCGATACTTTTG-TCCAGAATGAATGCCAAACGAGGTGCACGAATA
1226225 AAGTG
195 AAGTG
* * * * *
1226230 TCGATATATTTA--AAATTA-TATCGATCCCAAAAACAGCGAAACTGATAATTATAATATAATAG
1 TCGATACATTTATTAAA--AGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAG
* * * *
1226292 GTAAATTTGCAATGTTACCTGTACAAATATACCG
64 GTAAATTTACAATGTAACCGGTATAAATATACCG
1226326 ATTTAGTTAG
Statistics
Matches: 436, Mismatches: 50, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
197 3 0.01
198 71 0.16
199 45 0.10
200 250 0.57
201 65 0.15
202 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (199 bp):
TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGT
AAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATC
GACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGAATAA
AGTG
Found at i:1226449 original size:87 final size:87
Alignment explanation
Indices: 1226347--1226508 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
1226337 AAATATGTTA
* * * *
1226347 ATATAAGTGCTACCTATTACATTATATAAGCATTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCAACCTATTACATTATATAAGCACTACCTAATATATTATTGTACTTAATAATATTT
*
1226412 CCGGTTAAATGTATATTTTAAT
66 CCAGTTAAATGTATATTTTAAT
* * * * *
1226434 ATATAAGCGCAACCTATTTCATTATATAAGCGCTACCTGATATATTATTGTATTTGATAATATTT
1 ATATAAGCGCAACCTATTACATTATATAAGCACTACCTAATATATTATTGTACTTAATAATATTT
*
1226499 TCAGTTAAAT
66 CCAGTTAAAT
1226509 AATATAACAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCAACCTATTACATTATATAAGCACTACCTAATATATTATTGTACTTAATAATATTT
CCAGTTAAATGTATATTTTAAT
Found at i:1226480 original size:23 final size:23
Alignment explanation
Indices: 1226433--1226481 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1226423 TATATTTTAA
*
1226433 TATATAAGCGCAACCTATTTCAT
1 TATATAAGCGCAACCTATATCAT
*
1226456 TATATAAGCGCTACCTGATAT-AT
1 TATATAAGCGCAACCT-ATATCAT
1226479 TAT
1 TAT
1226482 TGTATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (23 bp):
TATATAAGCGCAACCTATATCAT
Found at i:1226997 original size:26 final size:26
Alignment explanation
Indices: 1226968--1227043 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
1226958 TTGTCACTGC
*
1226968 GTATCTTCTTCTCCCTTTGCCTTTGT
1 GTATCTTCTTCTCCCTTTGCCTCTGT
1226994 GTATCTTCTTCTCCCTTTGCCTCTGT
1 GTATCTTCTTCTCCCTTTGCCTCTGT
*
1227020 GTATCTTCTTCTCCCCTTGCCTCT
1 GTATCTTCTTCTCCCTTTGCCTCT
1227044 ACGAAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.04, C:0.36, G:0.11, T:0.50
Consensus pattern (26 bp):
GTATCTTCTTCTCCCTTTGCCTCTGT
Found at i:1233870 original size:15 final size:15
Alignment explanation
Indices: 1233850--1233883 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1233840 CAACAAATAA
1233850 ATTTTTTATATAAAT
1 ATTTTTTATATAAAT
*
1233865 ATTTTTTATTTAAAT
1 ATTTTTTATATAAAT
1233880 ATTT
1 ATTT
1233884 AGAATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTTATATAAAT
Found at i:1247485 original size:39 final size:40
Alignment explanation
Indices: 1247430--1247536 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 40
1247420 AATTACTCCT
* *
1247430 AGATA-AAGTTATAATTAATTTAAACTACTAAATCAAAT-
1 AGATATAAGTTCTAATTAATCTAAACTACTAAATCAAATA
1247468 AG-TATAGAGTTCTAATTAATCTAAACTACTAAATCAAATA
1 AGATATA-AGTTCTAATTAATCTAAACTACTAAATCAAATA
*
1247508 AGATATAA-TTCTAGTTAATCTAAACTACT
1 AGATATAAGTTCTAATTAATCTAAACTACT
1247537 GCTATTTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
37 2 0.03
38 3 0.05
39 50 0.81
40 3 0.05
41 4 0.06
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.35
Consensus pattern (40 bp):
AGATATAAGTTCTAATTAATCTAAACTACTAAATCAAATA
Found at i:1250306 original size:24 final size:24
Alignment explanation
Indices: 1250278--1250336 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1250268 CAGTCAAAGC
* * *
1250278 TGCCATGTAGAATTTGCACTGAAG
1 TGCCACGTAGAATATGCACCGAAG
1250302 TGCCACGTAGAATATGCACCGAAG
1 TGCCACGTAGAATATGCACCGAAG
*
1250326 TGCCGCGTAGA
1 TGCCACGTAGA
1250337 TTTGTCCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCGAAG
Found at i:1250382 original size:23 final size:23
Alignment explanation
Indices: 1250333--1250406 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
1250323 AAGTGCCGCG
* * * * *
1250333 TAGATTTGTCCCCAAGGACCGCG
1 TAGAATTGTCCCGAAGAACCACA
*
1250356 TAGAATTGTCCCGAATAACCACA
1 TAGAATTGTCCCGAAGAACCACA
* *
1250379 TAGAATTGTCCTGTAGAACCACA
1 TAGAATTGTCCCGAAGAACCACA
1250402 TAGAA
1 TAGAA
1250407 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGAACCACA
Found at i:1259659 original size:20 final size:20
Alignment explanation
Indices: 1259621--1259659 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1259611 TGTTCATCCG
* *
1259621 ATTCATACAGTATCGATACT
1 ATTCATACAGTACCAATACT
*
1259641 ATTCTTACAGTACCAATAC
1 ATTCATACAGTACCAATAC
1259660 CCATGCCCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTCATACAGTACCAATACT
Found at i:1266551 original size:22 final size:23
Alignment explanation
Indices: 1266513--1266558 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1266503 TTATTTTTAA
1266513 AAAATAATTATAAA-TTTAAAAT
1 AAAATAATTATAAATTTTAAAAT
*
1266535 AAAATATTTA-AATATTTTAAAAT
1 AAAATAATTATAA-ATTTTAAAAT
1266558 A
1 A
1266559 TTTAGATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.48
23 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATAATTATAAATTTTAAAAT
Found at i:1266557 original size:18 final size:18
Alignment explanation
Indices: 1266534--1266577 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1266524 AAATTTAAAA
1266534 TAAAATATTTAAATATTT
1 TAAAATATTTAAATATTT
*
1266552 TAAAATATTTAGATATTT
1 TAAAATATTTAAATATTT
1266570 TAAAATAT
1 TAAAATAT
1266578 CATATCTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAAAATATTTAAATATTT
Found at i:1266559 original size:10 final size:10
Alignment explanation
Indices: 1266534--1266577 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
1266524 AAATTTAAAA
1266534 TAAAATA-TT
1 TAAAATATTT
1266543 T-AAATATTT
1 TAAAATATTT
1266552 TAAAATA-TT
1 TAAAATATTT
*
1266561 T-AGATATTT
1 TAAAATATTT
1266570 TAAAATAT
1 TAAAATAT
1266578 CATATCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
8 9 0.31
9 10 0.34
10 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TAAAATATTT
Found at i:1267008 original size:29 final size:28
Alignment explanation
Indices: 1266955--1267060 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 28
1266945 CAGTGTTGGC
*
1266955 GTAGGTCGCCAGGGCATC-CCAGCGACATG
1 GTAGGTCGCCA-TGCA-CGCCAGCGACATG
1266984 GTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCATGCACGCCA-GCGACATG
* *
1267013 GTAGGTCGCCATGCACGCCCAGCGACCTT
1 GTAGGTCGCCATGCACG-CCAGCGACATG
*
1267042 ATAGGTCGCCATGCACGCC
1 GTAGGTCGCCATGCACGCC
1267061 CGGCGGCCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
27 1 0.01
28 8 0.11
29 58 0.83
30 3 0.04
ACGTcount: A:0.20, C:0.34, G:0.31, T:0.15
Consensus pattern (28 bp):
GTAGGTCGCCATGCACGCCAGCGACATG
Found at i:1267034 original size:58 final size:58
Alignment explanation
Indices: 1266955--1267065 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
1266945 CAGTGTTGGC
* *
1266955 GTAGGTCGCCAGGGCATCCCAGCGACATGGTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCAGGGCAGCCCAGCGACATGATAGGTCGCCATGCACGCCAGGCGACATG
* * * *
1267013 GTAGGTCGCCA-TGCACGCCCAGCGACCTTATAGGTCGCCATGCACGCCCGGCG
1 GTAGGTCGCCAGGGCA-GCCCAGCGACATGATAGGTCGCCATGCACGCCAGGCG
1267066 GCCAACGTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.07
58 43 0.93
ACGTcount: A:0.19, C:0.34, G:0.32, T:0.14
Consensus pattern (58 bp):
GTAGGTCGCCAGGGCAGCCCAGCGACATGATAGGTCGCCATGCACGCCAGGCGACATG
Found at i:1267570 original size:28 final size:28
Alignment explanation
Indices: 1267539--1267606 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1267529 GATATGAGGG
* *
1267539 GTTTAGGGTATAA-ATTATTAGTTTGTTA
1 GTTTAAGGTATAATA-TATTAATTTGTTA
* *
1267567 GTTTAAGTTATATTATATTAATTTGTTA
1 GTTTAAGGTATAATATATTAATTTGTTA
*
1267595 GTTTAAGTTATA
1 GTTTAAGGTATA
1267607 TATTAGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 34 0.97
29 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (28 bp):
GTTTAAGGTATAATATATTAATTTGTTA
Found at i:1267607 original size:28 final size:28
Alignment explanation
Indices: 1267554--1267607 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1267544 GGGTATAAAT
*
1267554 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
1267582 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
1267608 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:1270742 original size:60 final size:60
Alignment explanation
Indices: 1270671--1271695 Score: 1011
Period size: 60 Copynumber: 18.2 Consensus size: 60
1270661 GTATTTATAA
* *
1270671 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGAGTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1270731 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1270791 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
1270851 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
1270900 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1270960 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
1271020 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
* *
1271069 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAAT-ATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1271128 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A--TGAT--T--T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1271178 GA--TAGTAATGATTAGTAATAATGAAATTATTATTAA-ATTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA-TTTAATGATTTGATAGTAAT
* *
1271236 GATTTAGTAATGATTAGTATTAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1271296 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * * * * * *
1271356 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGTTT--TGA-TAG-TAATGATT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAATATTTAATGATTTGATAGT-AAT
* * * * *
1271409 TA-GTAATGAT---TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * * *
1271465 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATACTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
*
1271514 GA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1271573 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1271633 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1271681 GATTTAGTAATGATT
1 GATTTAGTAATGATT
1271696 TGATAGTAAT
Statistics
Matches: 810, Mismatches: 78, Indels: 159
0.77 0.07 0.15
Matches are distributed among these distances:
48 66 0.08
49 44 0.05
50 21 0.03
51 13 0.02
52 43 0.05
53 46 0.06
54 28 0.03
55 19 0.02
56 55 0.07
57 27 0.03
58 13 0.02
59 82 0.10
60 352 0.43
61 1 0.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:1270748 original size:21 final size:21
Alignment explanation
Indices: 1270671--1270811 Score: 68
Period size: 21 Copynumber: 7.0 Consensus size: 21
1270661 GTATTTATAA
1270671 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
1270692 GA--T-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* *
1270710 -ATTTAATGAGTTGA-TAGTAAT
1 GATTTAGT-A-ATGATTAGTAAT
1270731 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * * *
1270752 -A-AT-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
1270770 -ATTTAATGATTTGA-TATTAAT
1 GATTTAGT-A-ATGATTAGTAAT
1270791 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
1270812 AATGAAATTA
Statistics
Matches: 85, Mismatches: 22, Indels: 26
0.64 0.17 0.20
Matches are distributed among these distances:
17 1 0.01
18 25 0.29
19 4 0.05
20 7 0.08
21 32 0.38
22 16 0.19
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
GATTTAGTAATGATTAGTAAT
Found at i:1270888 original size:35 final size:34
Alignment explanation
Indices: 1270847--1271009 Score: 101
Period size: 35 Copynumber: 5.2 Consensus size: 34
1270837 GATTTAATAG
1270847 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * * *
1270882 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
1270907 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
1270942 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
1270967 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
1271002 TAATGATT
1 TAATGATT
1271010 TGATAGTAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 40
0.62 0.11 0.27
Matches are distributed among these distances:
25 16 0.17
27 6 0.07
28 4 0.04
29 14 0.15
30 4 0.04
31 14 0.15
32 4 0.04
33 6 0.07
35 24 0.26
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:1270909 original size:11 final size:10
Alignment explanation
Indices: 1270893--1270980 Score: 51
Period size: 10 Copynumber: 8.7 Consensus size: 10
1270883 AATGATTTGA
1270893 TAGTAATGATT
1 TAGTAATGA-T
1270904 TAGTAATGAT
1 TAGTAATGAT
*
1270914 TAGTAAT-AA
1 TAGTAATGAT
* *
1270923 T-GAAATTAT
1 TAGTAATGAT
*
1270932 TATTAAT-AT
1 TAGTAATGAT
1270941 T--TAATGATTT
1 TAGTAATGA--T
1270951 GATAGTAATGATT
1 --TAGTAATGA-T
1270964 TAGTAATGAT
1 TAGTAATGAT
1270974 TAGTAAT
1 TAGTAAT
1270981 AATGAAATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.06
8 5 0.08
9 7 0.11
10 20 0.32
11 18 0.29
12 1 0.02
13 2 0.03
14 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (10 bp):
TAGTAATGAT
Done.