Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_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: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1139823 original size:19 final size:19
Alignment explanation
Indices: 1139799--1139848 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1139789 AAATGCAGGG
1139799 TTAATTTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
1139818 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
1139837 ATAATTTTGTAT
1 TTAATTTTGTAT
1139849 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:1140784 original size:199 final size:199
Alignment explanation
Indices: 1140191--1140959 Score: 1314
Period size: 199 Copynumber: 3.9 Consensus size: 199
1140181 GGTAACTTAT
* *
1140191 GTGTCGATACATTTATAACAAGTGTCAATCCGAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
*
1140256 GGTAAATTAGCAATATAACCAGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
1140321 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1140386 AAAA
196 AAAA
*
1140390 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACAATC-AAAACCGTAATTATAATGTAAT
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAAC-ATCGAAAACCATAATTATAATGTAAT
*
1140454 AGGTAAATTAGC-A-ATAA-CGATCT-AATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGT
65 AGGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGT
*
1140515 ATCGACAAAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
130 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
1140580 AAAAA
195 AAAAA
*
1140585 GTGTCAATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
*
1140650 GGTAAATTAGCAATATAACTGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
* * * *
1140715 TCGACATAAATCCAACAAGTGTCGATACTTTTAGTCCATAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
1140780 AAAA
196 AAAA
* * *
1140784 GTGTCGATACATTTATAACAAGTGTCGATCTCAAAAACATCGAAACCCATAATGATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * * *
1140849 GGTAAATTAGCAATATAACCGGTGTAAATATACCGATTTTTTAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
*
1140914 TCGAAACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTAT
131 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTAT
1140960 CGACATAAAT
Statistics
Matches: 536, Mismatches: 28, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
194 3 0.01
195 177 0.33
196 5 0.01
197 8 0.01
198 5 0.01
199 335 0.62
200 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (199 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
AAAA
Found at i:1140976 original size:45 final size:45
Alignment explanation
Indices: 1140911--1141004 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
1140901 TGTACAAAAA
*
1140911 GTATCGAAACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAAT
1 GTATCGAAACAAATCAAACAAGTGTCGATACTTTTGGTCCACAAT
* * * * *
1140956 GTATCGACATAAATCCAACAAGTGTTGATACTTTTTGTCCACAAT
1 GTATCGAAACAAATCAAACAAGTGTCGATACTTTTGGTCCACAAT
1141001 GTAT
1 GTAT
1141005 TTCAAAACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (45 bp):
GTATCGAAACAAATCAAACAAGTGTCGATACTTTTGGTCCACAAT
Found at i:1141685 original size:15 final size:16
Alignment explanation
Indices: 1141646--1141702 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1141636 TTCTCAAATC
1141646 TCTTCTCAACCCACCT
1 TCTTCTCAACCCACCT
* *
1141662 T-TTCCCAACCCA-GT
1 TCTTCTCAACCCACCT
1141676 TCTTCTCAACCACAACCT
1 TCTTCTCAACC-C-ACCT
*
1141694 CCTTCTCAA
1 TCTTCTCAA
1141703 ACAATCGTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 2 0.06
15 18 0.56
16 2 0.06
17 1 0.03
18 9 0.28
ACGTcount: A:0.23, C:0.46, G:0.02, T:0.30
Consensus pattern (16 bp):
TCTTCTCAACCCACCT
Found at i:1143740 original size:19 final size:19
Alignment explanation
Indices: 1143716--1143760 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1143706 GCAAAAGGTG
1143716 GTAAAATACACGAGTATTT
1 GTAAAATACACGAGTATTT
* *
1143735 GTAAAATACGCTAGTATTT
1 GTAAAATACACGAGTATTT
*
1143754 GGAAAAT
1 GTAAAAT
1143761 TTGTTGAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (19 bp):
GTAAAATACACGAGTATTT
Found at i:1144441 original size:200 final size:200
Alignment explanation
Indices: 1144098--1146266 Score: 3635
Period size: 200 Copynumber: 10.8 Consensus size: 200
1144088 TACCTTTTTC
* * * *
1144098 AAATATACCGGTTTTTGAGAAAAAAAGTGTATAAAAAGTATCGACACAAATAAAAAAATTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
*
1144163 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATGCATTTAAAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
1144228 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
1144293 GGTCT
196 GGTCT
* **
1144298 AAATATACCAGTTTTTGAGAAAACAATTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* * *
1144363 TACATCTTGTACAAATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTAAAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* *
1144428 AGTGTCGATCCCGAAAAAATCGAAAAATATAATTATAATGTAATAGGTAAATTATTAATGTAACC
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
*
1144493 GATCT
196 GGTCT
1144498 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* *
1144563 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACGAAGTGTCGATGCATTTAAAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* * *
1144628 AGTGGCGATCCTGAAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTAATGTAACC
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
1144693 GGTCT
196 GGTCT
* *
1144698 AAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATTAAAAAAGTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* *
1144763 TACATCTTGTCCAAATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTAAAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* * *
1144828 AGTGTCGATCCCGAAAATATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAAAGTAACT
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
1144893 GGTCT
196 GGTCT
* *
1144898 AAATATACCGATTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTTGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* *
1144963 TACATCTTGTCCAGACTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATGCATTTAAAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* *
1145028 AGTGTCGATCCTGAAAACATTGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
1145093 GGTCT
196 GGTCT
* *
1145098 AAATATACCGGTTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAAT-AAAAAAGTGTCA
1 AAATATACCGG-TTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCG
*
1145162 ATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTAAAAC
65 ATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAAC
*
1145227 AAGTGTCGATCCCGAAAACATCGAAAAATATAATTATAATGTAATAGGTAAATTATTAATGTAAC
130 AAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAAC
1145292 CGGTCT
195 CGGTCT
1145298 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* *
1145363 TACATCTTGTCCATATTGTATTTTAAAAACCAAGTGCATAACAAAGTGTCGATACATTTAAAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* *
1145428 AGTGTCGATCCTGAAAACATCGAAAAACATAATTATAATGTAATAGCTAAATTATTAATGTAACC
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
1145493 GGTCT
196 GGTCT
* *
1145498 AAATATACCGGTTTTTGAGAAAAACAGGTGTA-AAACAAGTATTGACACAAATAAAACAAGTGTC
1 AAATATACCGGTTTTTGAG-AAAACAGGTGTACAAA-AAGTATCGACACAAATAAAAAAAGTGTC
* *
1145562 GATACATTTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACGTTTAAAA
64 GATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAA
* *
1145627 CAAGTGTCGATCCTGAAAACATCGAAAAGCATAATTATAATGTAATAGGTAAATTATTAATGTAA
129 CAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAA
*
1145692 CTGGTCT
194 CCGGTCT
* * *
1145699 AAATATACCGGTTTTTGAGAAAACATGTGTA-AAACAACTATCGACACAAATAAAACAAGTGTCG
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAA-AAGTATCGACACAAATAAAAAAAGTGTCG
* * * *
1145763 ATACATTTTGTCCAGATTGTATTTTAAAAACTAAGTACACAACAAAGTGTCGATACGTTTAAAAC
65 ATACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAAC
*
1145828 AAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAAG
130 AAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAAC
* *
1145893 CAGACT
195 CGGTCT
1145899 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* *
1145964 TACATCTTGTCTAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* *
1146029 AGTGTCGATCCTGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAATC
131 AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
1146094 GGTCT
196 GGTCT
* **
1146099 AAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAGCAAAAAAAGTGTCGA
1 AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
* * * *
1146164 TACATCTTGTCCAGATTGTATTTTAAAAACCAATTGCACAACAAAGTTTTGATACATTTATAACA
66 TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
* *
1146229 ATTCTCGATCCC-AAAATCATCGAAAAACATAATTATAA
131 AGTGTCGATCCCGAAAA-CATCGAAAAACATAATTATAA
1146267 CCAAATGTCT
Statistics
Matches: 1853, Mismatches: 110, Indels: 12
0.94 0.06 0.01
Matches are distributed among these distances:
199 43 0.02
200 1581 0.85
201 229 0.12
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (200 bp):
AAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTATCGACACAAATAAAAAAAGTGTCGA
TACATCTTGTCCAGATTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACA
AGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTAATGTAACC
GGTCT
Found at i:1149336 original size:23 final size:23
Alignment explanation
Indices: 1149286--1149330 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1149276 TGCCTATTTT
*
1149286 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1149309 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1149331 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1149371 original size:87 final size:87
Alignment explanation
Indices: 1149225--1149391 Score: 316
Period size: 87 Copynumber: 1.9 Consensus size: 87
1149215 AAATAGGTTA
* *
1149225 ATATAAGCGCTACTTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATGCCTATTTTATTA
1 ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
1149290 TATAAGCGCTACCTATTACATT
66 TATAAGCGCTACCTATTACATT
1149312 ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
1 ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
1149377 TATAAGCGCTACCTA
66 TATAAGCGCTACCTA
1149392 ATATGTTATT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
TATAAGCGCTACCTATTACATT
Found at i:1149377 original size:64 final size:64
Alignment explanation
Indices: 1149309--1149428 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
1149299 TACCTATTAC
1149309 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
1 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
*
1149373 ATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTCCGGTTAAATG
1 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
1149429 ATATAACATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (64 bp):
ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
Found at i:1149938 original size:3 final size:3
Alignment explanation
Indices: 1149932--1149959 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1149922 TCTTTTTTTA
1149932 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1149960 TAAGGTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1150670 original size:23 final size:23
Alignment explanation
Indices: 1150644--1150687 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1150634 AAAACACAGA
1150644 GGGGGTTTCGAAATAAAAAATAG
1 GGGGGTTTCGAAATAAAAAATAG
1150667 GGGGGTTTCGAAATAAAAAAT
1 GGGGGTTTCGAAATAAAAAAT
1150688 TGGGAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.30, T:0.23
Consensus pattern (23 bp):
GGGGGTTTCGAAATAAAAAATAG
Found at i:1153363 original size:12 final size:12
Alignment explanation
Indices: 1153346--1153375 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1153336 TCGCACTAGT
*
1153346 GGGAAACACAAA
1 GGGAAAAACAAA
1153358 GGGAAAAACAAA
1 GGGAAAAACAAA
1153370 GGGAAA
1 GGGAAA
1153376 GAGACAATCA
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:0.60, C:0.10, G:0.30, T:0.00
Consensus pattern (12 bp):
GGGAAAAACAAA
Found at i:1154315 original size:40 final size:40
Alignment explanation
Indices: 1154260--1154359 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 40
1154250 ACCAATATTG
1154260 TTCTTACAGTATCGATACCACATGAACAATACTGAAACTA
1 TTCTTACAGTATCGATACCACATGAACAATACTGAAACTA
* * * * *
1154300 TTCTTACAGTATCGATACCACATGAACATTATTGATATTG
1 TTCTTACAGTATCGATACCACATGAACAATACTGAAACTA
*
1154340 TTCTTACAGTATCAATACCA
1 TTCTTACAGTATCGATACCA
1154360 AAGGTAAGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (40 bp):
TTCTTACAGTATCGATACCACATGAACAATACTGAAACTA
Found at i:1159255 original size:15 final size:15
Alignment explanation
Indices: 1159235--1159264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1159225 CAATAATAAC
*
1159235 TCAGTAACAGCTAAA
1 TCAGTAACAACTAAA
1159250 TCAGTAACAACTAAA
1 TCAGTAACAACTAAA
1159265 AATAATAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (15 bp):
TCAGTAACAACTAAA
Found at i:1160038 original size:17 final size:16
Alignment explanation
Indices: 1160016--1160066 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
1160006 TATATAAATT
1160016 ATTATTTATTTATATA
1 ATTATTTATTTATATA
1160032 GATTA-TTATTAATATATA
1 -ATTATTTATT--TATATA
*
1160050 ATTATATTATTAATATA
1 ATTAT-TTATTTATATA
1160067 TAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
18 6 0.21
19 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTATTTATTTATATA
Found at i:1160059 original size:19 final size:19
Alignment explanation
Indices: 1160006--1160075 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
1159996 TTATATAGGT
*
1160006 TATATAAAT-TATTATTTATT
1 TATATAAATATATTA-TTA-A
*
1160026 TATATAGAT-TATTATTAA
1 TATATAAATATATTATTAA
*
1160044 TATATAATTATATTATTAA
1 TATATAAATATATTATTAA
1160063 TATATAAATATAT
1 TATATAAATATAT
1160076 AGATTCTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
18 7 0.16
19 24 0.55
20 13 0.30
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
TATATAAATATATTATTAA
Found at i:1160166 original size:19 final size:21
Alignment explanation
Indices: 1160123--1160163 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1160113 TTATATAGAA
*
1160123 TATAGATATATCCAACTTTTC
1 TATAGATATATACAACTTTTC
*
1160144 TATAGATATATAGAACTTTT
1 TATAGATATATACAACTTTT
1160164 ATAAGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
TATAGATATATACAACTTTTC
Found at i:1161713 original size:22 final size:22
Alignment explanation
Indices: 1161685--1161746 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
1161675 TTATGTATAT
1161685 TATAATATATTAGATTATTATC
1 TATAATATATTAGATTATTATC
*
1161707 TATAATAT-TCTAAATTATTATC
1 TATAATATAT-TAGATTATTATC
*
1161729 TAT-ATA-ATTAGATAATTA
1 TATAATATATTAGATTATTA
1161747 AATTAGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 8 0.23
21 5 0.14
22 22 0.63
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
TATAATATATTAGATTATTATC
Found at i:1164920 original size:13 final size:13
Alignment explanation
Indices: 1164902--1164926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1164892 ATCAATTATT
1164902 TAATATTTATTAA
1 TAATATTTATTAA
1164915 TAATATTTATTA
1 TAATATTTATTA
1164927 TTAAATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATTTATTAA
Found at i:1166958 original size:49 final size:49
Alignment explanation
Indices: 1166815--1167051 Score: 314
Period size: 49 Copynumber: 4.8 Consensus size: 49
1166805 AAATACTCTG
* *
1166815 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGATACCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * *
1166864 AAATGAAAGTT-AATGCATAATGGTGTATTTCGGCATAAAATGTGCCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * *
1166912 AAATGAAAGTTAAATGTATAACGGAGCATTTCAGCATAAAAGGTGCCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * * *
1166961 AAATGAAAGTTAAATGCAAAACGATCCATTTTGGCATAAAAAGTGCCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * *
1167010 TAATGAAAGTTAAATGCATAACAGTGCATTTTTGGCATAAAA
1 AAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAA
1167052 TGTACCACTC
Statistics
Matches: 162, Mismatches: 24, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
48 43 0.27
49 106 0.65
50 13 0.08
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (49 bp):
AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
Found at i:1171004 original size:3 final size:3
Alignment explanation
Indices: 1170998--1171059 Score: 54
Period size: 3 Copynumber: 20.0 Consensus size: 3
1170988 TCATTTAAAT
** * *
1170998 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA -TA TTA TAAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
1171043 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
1171060 AATATTACAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 2 0.04
3 37 0.79
4 8 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1171019 original size:18 final size:18
Alignment explanation
Indices: 1170992--1171027 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1170982 TTTTTTTCAT
*
1170992 TTAAATTTATTATTATTA
1 TTAAAATTATTATTATTA
1171010 TTAAAATTATTATTATTA
1 TTAAAATTATTATTATTA
1171028 GTATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAAATTATTATTATTA
Found at i:1177824 original size:18 final size:19
Alignment explanation
Indices: 1177793--1177830 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1177783 TCCAGCAAAG
* *
1177793 AAAAAAATAGAAA-GAAAA
1 AAAAAAACAAAAAGGAAAA
1177811 AAAAAAACAAAAAGGAAAA
1 AAAAAAACAAAAAGGAAAA
1177830 A
1 A
1177831 GAAGAAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (19 bp):
AAAAAAACAAAAAGGAAAA
Found at i:1182819 original size:20 final size:21
Alignment explanation
Indices: 1182782--1182834 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
1182772 ATCTACACTC
1182782 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATA-ATTCTCTT
*
1182804 TTTAAAGATGAT-ATTCTCTT
1 TTCAAAGATGATAATTCTCTT
1182824 TTCAAAGATGA
1 TTCAAAGATGA
1182835 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.62
22 11 0.38
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (21 bp):
TTCAAAGATGATAATTCTCTT
Found at i:1183663 original size:75 final size:76
Alignment explanation
Indices: 1183346--1183834 Score: 892
Period size: 76 Copynumber: 6.5 Consensus size: 76
1183336 CTATTTCCCA
*
1183346 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1183411 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
1183422 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1183487 ATCCTTCGGGT
66 AGCCTTCGGGT
*
1183498 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1183563 AGCCTTCGGGT
66 AGCCTTCGGGT
1183574 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1183638 AGCCTTCGGGT
66 AGCCTTCGGGT
1183649 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1183714 AGCCTTCGGGT
66 AGCCTTCGGGT
1183725 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1183789 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
1183800 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1183835 CATTTCCATC
Statistics
Matches: 406, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
75 140 0.34
76 266 0.66
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:1183706 original size:151 final size:151
Alignment explanation
Indices: 1183346--1183834 Score: 890
Period size: 151 Copynumber: 3.2 Consensus size: 151
1183336 CTATTTCCCA
*
1183346 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1183411 ATCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTT
*
1183476 GATGTTTTCAAATCCTTCGGGT
130 GATGTTTTCAAAGCCTTCGGGT
*
1183498 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1183563 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTT
1183627 GATGTTTTCAAAGCCTTCGGGT
130 GATGTTTTCAAAGCCTTCGGGT
1183649 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1183714 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAGCTTTTTG
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAGCTTTTTG
1183779 ATGTTTTCAAAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
* *
1183800 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1183835 CATTTCCATC
Statistics
Matches: 327, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
150 5 0.02
151 202 0.62
152 120 0.37
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (151 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAGCTTTTTG
ATGTTTTCAAAGCCTTCGGGT
Found at i:1183968 original size:3 final size:3
Alignment explanation
Indices: 1183962--1184024 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
1183952 TCATTTAAAT
** * *
1183962 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA -TA TTA TTA -TA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1184008 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
1184025 AATATTACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1183983 original size:18 final size:18
Alignment explanation
Indices: 1183956--1183991 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1183946 TTTTTTTCAT
*
1183956 TTAAATTTATTATTATTA
1 TTAAAATTATTATTATTA
1183974 TTAAAATTATTATTATTA
1 TTAAAATTATTATTATTA
1183992 GTATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAAATTATTATTATTA
Found at i:1184016 original size:18 final size:16
Alignment explanation
Indices: 1183963--1184024 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 16
1183953 CATTTAAATT
1183963 TATTATTATTATTA-A
1 TATTATTATTATTATA
*
1183978 AATTATTATTATTAGTA
1 TATTATTATTATTA-TA
1183995 TATTATTATAATATTATA
1 TATTATTAT--TATTATA
1184013 TATTATTTATTA
1 TATTA-TTATTA
1184025 AATATTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 13 0.32
17 11 0.28
18 7 0.17
19 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTATTATTATTATA
Found at i:1191041 original size:48 final size:49
Alignment explanation
Indices: 1190928--1191123 Score: 331
Period size: 49 Copynumber: 4.0 Consensus size: 49
1190918 AACTGTTCTG
1190928 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* *
1190977 AAATGAAAGTTAAATGCATAACGGTGCATTTCAGCAT-AAATGTGCCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* *
1191025 AAATGAAAGTTAAATGCATATCGGTGCATTTCGGCATAAAAGGTACCAC
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
*
1191074 TAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCAC
1 AAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAAGGTGCCAC
1191124 TCATGGTATT
Statistics
Matches: 136, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
48 45 0.33
49 71 0.52
50 20 0.15
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (49 bp):
AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
Found at i:1191042 original size:97 final size:99
Alignment explanation
Indices: 1190928--1191123 Score: 333
Period size: 97 Copynumber: 2.0 Consensus size: 99
1190918 AACTGTTCTG
*
1190928 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACAAATGAAAGTTAAATG
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATG
*
1190993 CATAACGGTGCA-TTTCAGCAT-AAATGTGCCAC
66 CATAACGGTGCATTTTCAGCATAAAAGGTGCCAC
* *
1191025 AAATGAAAGTTAAATGCATATCGGTGCATTTCGGCATAAAAGGTACCACTAATGAAAGTTAAATG
1 AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATG
*
1191090 CATAACGGTGCATTTTCGGCATAAAAGGTGCCAC
66 CATAACGGTGCATTTTCAGCATAAAAGGTGCCAC
1191124 TCATGGTATT
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 74 0.80
98 8 0.09
99 10 0.11
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (99 bp):
AAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATG
CATAACGGTGCATTTTCAGCATAAAAGGTGCCAC
Found at i:1201018 original size:39 final size:40
Alignment explanation
Indices: 1200973--1201053 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 40
1200963 ATTACATGTT
* *
1200973 TTTATTCTTTTTTTA-TTCATTAC-CATTGTTTCTT-TTGTC
1 TTTATTCTTATTATATTTCATTACTC-TTG-TTCTTATTGTC
1201012 TTTATTCTTATTATATTTCATTACTCTTGTTCTTATTGTC
1 TTTATTCTTATTATATTTCATTACTCTTGTTCTTATTGTC
1201052 TT
1 TT
1201054 AATCACATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 18 0.49
40 18 0.49
41 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.65
Consensus pattern (40 bp):
TTTATTCTTATTATATTTCATTACTCTTGTTCTTATTGTC
Found at i:1206351 original size:11 final size:10
Alignment explanation
Indices: 1206337--1206394 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
1206327 CACTTTTTTA
*
1206337 AAAAATAAAT
1 AAAAATGAAT
1206347 AAAAATGCAAT
1 AAAAATG-AAT
1206358 AAAAATGAATT
1 AAAAATGAA-T
1206369 AAAAATGAAT
1 AAAAATGAAT
* *
1206379 AAAATTCAAT
1 AAAAATGAAT
1206389 AAAAAT
1 AAAAAT
1206395 ATAATGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.52
11 20 0.48
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:1206362 original size:21 final size:20
Alignment explanation
Indices: 1206337--1206394 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1206327 CACTTTTTTA
1206337 AAAAATAAATAAAAATGCAAT
1 AAAAATAAATAAAAATG-AAT
*
1206358 AAAAATGAATTAAAAATGAAT
1 AAAAAT-AAATAAAAATGAAT
* *
1206379 AAAATTCAATAAAAAT
1 AAAAATAAATAAAAAT
1206395 ATAATGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.25
21 14 0.44
22 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAATAAATAAAAATGAAT
Found at i:1206841 original size:29 final size:28
Alignment explanation
Indices: 1206796--1206862 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1206786 TTAATTATTA
* *
1206796 TTTTTTAACAACAATTAATAATATTTAT-T
1 TTTTTTAATAACAATTAA-AAT-TTAATAT
1206825 TATTTTTAATAA-AATTAAAATTTAATAT
1 T-TTTTTAATAACAATTAAAATTTAATAT
1206853 TTTTTTAATA
1 TTTTTTAATA
1206863 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 13 0.38
28 5 0.15
29 7 0.21
30 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTTTAATAACAATTAAAATTTAATAT
Found at i:1206957 original size:11 final size:10
Alignment explanation
Indices: 1206928--1206987 Score: 66
Period size: 10 Copynumber: 5.8 Consensus size: 10
1206918 CTTTACATTA
1206928 TATTTTTATT
1 TATTTTTATT
* *
1206938 GAATTTTATT
1 TATTTTTATT
1206948 TATTTATTATT
1 TATTT-TTATT
1206959 TATTTTTATT
1 TATTTTTATT
* *
1206969 GCATTTTTTTT
1 -TATTTTTATT
1206980 TATTTTTA
1 TATTTTTA
1206988 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 22 0.55
11 18 0.45
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1206965 original size:21 final size:21
Alignment explanation
Indices: 1206928--1206987 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1206918 CTTTACATTA
* *
1206928 TATTTTTATTGAATTTTATT-
1 TATTTTTATTTATTTTTATTG
1206948 TATTTATTATTTATTTTTATTG
1 TATTT-TTATTTATTTTTATTG
* *
1206970 CATTTTTTTTTATTTTTA
1 TATTTTTATTTATTTTTA
1206988 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.15
21 25 0.74
22 4 0.12
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (21 bp):
TATTTTTATTTATTTTTATTG
Found at i:1210051 original size:83 final size:85
Alignment explanation
Indices: 1209933--1210087 Score: 192
Period size: 83 Copynumber: 1.8 Consensus size: 85
1209923 CGTTTTAACA
* * * *
1209933 TAAACGCCTCTATAAACACGTACTTTTATGGCGTTT-T-TATACAAATGTCGCTATAGAAT-CAT
1 TAAACGCCTCTATAAACACATACTTTTATGACGTTTATGTATACAAACGCCGCTATAG-ATGCAT
1209995 ACTTTAGTGTCATTTCAATAC
65 ACTTTAGTGTCATTTCAATAC
* * * *
1210016 TAAACGCCTCTATAGACTCATAC-TTTAGTGACGTTTATGTTTACAAACGCCGCTATAGATGCGT
1 TAAACGCCTCTATAAACACATACTTTTA-TGACGTTTATGTATACAAACGCCGCTATAGATGCAT
1210080 ACTTTAGT
65 ACTTTAGT
1210088 AGCGTTTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 4 0.07
83 27 0.45
84 3 0.05
85 26 0.43
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (85 bp):
TAAACGCCTCTATAAACACATACTTTTATGACGTTTATGTATACAAACGCCGCTATAGATGCATA
CTTTAGTGTCATTTCAATAC
Found at i:1210100 original size:85 final size:81
Alignment explanation
Indices: 1209891--1210106 Score: 195
Period size: 85 Copynumber: 2.6 Consensus size: 81
1209881 GCAATTGTAA
* * * *
1209891 ACAAACGCCACTATAGACTCAG-ACTTTCGTTGCGTTTTAACA-TAAACGCCTCTATAAACACGT
1 ACAAACGCCGCTATAGA-TC-GTACTTTAG-TGCGTTTTAATACTAAACGCCTCTATAAACACAT
*
1209954 ACTTTTATGGCGTTTTTAT
63 ACTTTTATGACGTTTTTAT
* * * * * * *
1209973 ACAAATGTCGCTATAGAATCATACTTTAGTGTCATTTCAATACTAAACGCCTCTATAGACTCATA
1 ACAAACGCCGCTATAG-ATCGTACTTTAGTG-CGTTTTAATACTAAACGCCTCTATAAACACATA
*
1210038 C-TTTAGTGACGTTTATGTTT
64 CTTTTA-TGACGTTT-T-TAT
*
1210058 ACAAACGCCGCTATAGATGCGTACTTTAGTAGCGTTTTAATACCAAACG
1 ACAAACGCCGCTATAGAT-CGTACTTTAGT-GCGTTTTAATACTAAACG
1210107 TCGCAATTGT
Statistics
Matches: 106, Mismatches: 19, Indels: 15
0.76 0.14 0.11
Matches are distributed among these distances:
81 2 0.02
82 32 0.30
83 28 0.26
84 3 0.03
85 40 0.38
86 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (81 bp):
ACAAACGCCGCTATAGATCGTACTTTAGTGCGTTTTAATACTAAACGCCTCTATAAACACATACT
TTTATGACGTTTTTAT
Found at i:1216453 original size:45 final size:45
Alignment explanation
Indices: 1216374--1216472 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 45
1216364 ATAACTAATG
*
1216374 AATAAAA-AATAATAACAAACTAAACATGTCTTAACTCTAA-TTCCT
1 AATAAAATAATAATAACAAAC-AAACATGTCTTAACTC-AACCTCCT
*
1216419 AATAAAATAATAATAACTAAA-AATA-ATGTTTTAACTCAACCTCCT
1 AATAAAATAATAATAAC-AAACAA-ACATGTCTTAACTCAACCTCCT
1216464 AATAAAATA
1 AATAAAATA
1216473 TAAATCTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
44 2 0.04
45 33 0.69
46 10 0.21
47 3 0.06
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (45 bp):
AATAAAATAATAATAACAAACAAACATGTCTTAACTCAACCTCCT
Found at i:1219358 original size:13 final size:13
Alignment explanation
Indices: 1219340--1219370 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1219330 ACTGAAATTA
*
1219340 ATTATTAATTATT
1 ATTATTAAGTATT
1219353 ATTATTAAGTATT
1 ATTATTAAGTATT
1219366 ATTAT
1 ATTAT
1219371 CATTATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
ATTATTAAGTATT
Found at i:1220920 original size:2 final size:2
Alignment explanation
Indices: 1220913--1220940 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1220903 ATTGTGCTTA
1220913 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
1220941 TTGTATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1221126 original size:2 final size:2
Alignment explanation
Indices: 1221119--1221146 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1221109 ATTGTGCTTA
1221119 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
1221147 TTGTATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1226958 original size:16 final size:16
Alignment explanation
Indices: 1226937--1226982 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1226927 TATTTGTCAG
1226937 ATGCCTAATATCAAAA
1 ATGCCTAATATCAAAA
*
1226953 ATGCCTAATATAAAAA
1 ATGCCTAATATCAAAA
*
1226969 ATGTCTAATATCAA
1 ATGCCTAATATCAA
1226983 GTTTCTGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (16 bp):
ATGCCTAATATCAAAA
Found at i:1228479 original size:45 final size:45
Alignment explanation
Indices: 1228413--1228537 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 45
1228403 ATCCAATATT
1228413 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCA-TTATT-ACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
1228460 TTACCATT-TGTACCATAAGCTTGTAAGCTTATTTTACCAATATAC
1 TTACCATTAT-TACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
1228505 TTGCCATTATT-CTATAAGCTCGTAAGCTTATTT
1 TTACCATTATTACCATAAGCTCGTAAGCTTATTT
1228538 GCATGCTTAC
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
44 20 0.28
45 41 0.58
46 4 0.06
47 6 0.08
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
TTACCATTATTACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:1228698 original size:40 final size:40
Alignment explanation
Indices: 1228619--1228699 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
1228609 ATAGGAGTCA
* * * * *
1228619 AATATTGCACCGCAGTGCTGAGGTCGAGTTTTGCTCACCT
1 AATAATGCACCGCAGTGCTAAGGTCGAGATTTACCCACCT
*
1228659 AATAATGCACCGTAGTGCTAAGGTC-AGGATTTACCCACCT
1 AATAATGCACCGCAGTGCTAAGGTCGA-GATTTACCCACCT
1228699 A
1 A
1228700 GTACACCGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
AATAATGCACCGCAGTGCTAAGGTCGAGATTTACCCACCT
Found at i:1235533 original size:21 final size:20
Alignment explanation
Indices: 1235505--1235579 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
1235495 TCGTAAGCTT
1235505 ATTTTACCAAAATACTTACC
1 ATTTTACCAAAATACTTACC
* * *
1235525 ATTTGTACCATAAGCT-CGTAAGCTT
1 ATTT-TACCA-AA-ATAC-TTA-C-C
1235550 ATTTTACCAAAATACTTACC
1 ATTTTACCAAAATACTTACC
1235570 ATTTGTACCA
1 ATTT-TACCA
1235580 TAAGCTCGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 15
0.66 0.10 0.24
Matches are distributed among these distances:
20 8 0.20
21 11 0.27
22 6 0.15
23 6 0.15
24 6 0.15
25 4 0.10
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.36
Consensus pattern (20 bp):
ATTTTACCAAAATACTTACC
Found at i:1235640 original size:44 final size:45
Alignment explanation
Indices: 1235486--1235642 Score: 255
Period size: 45 Copynumber: 3.5 Consensus size: 45
1235476 CCATTTATTA
1235486 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
1235531 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
* * *
1235576 ACCATAAGCTCGTAAGCTTATTTTACCCATATACTTGCCATTAT-T
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATT-TGT
*
1235621 -CCATAAGCTCCTAAGCTTATTT
1 ACCATAAGCTCGTAAGCTTATTT
1235643 GCATGCTTAC
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
44 21 0.20
45 85 0.79
46 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (45 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
Found at i:1235803 original size:40 final size:40
Alignment explanation
Indices: 1235724--1235804 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
1235714 ATAGGAGTCA
* * * *
1235724 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
* *
1235764 AATAATGCACCGTAGTGCTGAGGTATG-GATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGT-CGAGATTTACCCACCT
1235804 A
1 A
1235805 GTACACCGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
Found at i:1236760 original size:14 final size:14
Alignment explanation
Indices: 1236741--1236776 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1236731 AGTTGACCAA
1236741 CAGAATCTATTTTG
1 CAGAATCTATTTTG
1236755 CAGAATCTATTTTG
1 CAGAATCTATTTTG
*
1236769 CATAATCT
1 CAGAATCT
1236777 GTTGTCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (14 bp):
CAGAATCTATTTTG
Found at i:1239250 original size:99 final size:99
Alignment explanation
Indices: 1238990--1239305 Score: 404
Period size: 99 Copynumber: 3.1 Consensus size: 99
1238980 TCTGTCACCT
** *
1238990 TTGAGATTG-TTTCTCTCCAAACAAATTTCATCTCGCTTGAGACAGGTTTTCCTCGAAACACAAA
1 TTGAGATTGTTTTC-CTAAAAACAAATTTCATCTCGCTTGAGACA--TTTTCCTCGAAACAAAAA
1239054 TTTTGAAATTGTTTCACTTAAAACAAAATTTATCTCAC
63 TTTTGAAATTGTTTCAC-TAAAACAAAATTTATCTCAC
*
1239092 TTGAGATTGTTTTCCTAAAAGCAAATTTCATCTCGCTTGAGATCATTTTCCCTCGAAACAAAAAT
1 TTGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGA-CATTTT-CCTCGAAACAAAAAT
*
1239157 TTTGAAATTGTTTCACT-AAA-AAAATTGATCTCAC
64 TTTGAAATTGTTTCACTAAAACAAAATTTATCTCAC
* * **
1239191 TTGAGATTGTTTTCCTAAAAACAAATATCGTCTCGCTTGAGACACTTTTACCTTTAAACAAAAAT
1 TTGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGACA-TTTT-CCTCGAAACAAAAAT
* *
1239256 TTTGAAATTGTTTCCCTCGAAACAAAATTTTATCTCAC
64 TTTGAAATTGTTTCACT-AAAACAAAA-TTTATCTCAC
* *
1239294 ATGAGATAGTTT
1 TTGAGATTGTTT
1239306 CTTTGGAAAC
Statistics
Matches: 191, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
98 2 0.01
99 85 0.45
100 3 0.02
101 8 0.04
102 68 0.36
103 25 0.13
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (99 bp):
TTGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGACATTTTCCTCGAAACAAAAATTT
TGAAATTGTTTCACTAAAACAAAATTTATCTCAC
Found at i:1239776 original size:139 final size:139
Alignment explanation
Indices: 1239556--1240784 Score: 1400
Period size: 139 Copynumber: 8.9 Consensus size: 139
1239546 TTTCAAAGAT
** * * * * *
1239556 AAATTATCTCCAAATACAACTATATGTCCTCAACACTAAAGAACAATGTAGTCCACCAACCAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* * * * * *
1239621 CTCCTCAACGTGAAGGAACAGTGTCATCCTTAGACAATTAGACTTCCTCAACGTGAAGGAATCGT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
*
1239686 GTTGTCTTC
131 GTTGTCTCC
* * * * ** ** *
1239695 AAATTATCTCCAAATACGGCTAGACATCCTCAACACGAACGAATAATGCCGTATACTGACTAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* * * * *
1239760 CTCCTGAACACGAAGGAGTAGTGCCATCCTCAGACAATCAGACTTCCTCAACACGAAGGAACCGT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
1239825 GTTGTCTCC
131 GTTGTCTCC
*
1239834 AAATTATCTCCAAATACGGCTAGACGTCCCCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* ** * * * * * **
1239899 CTCCTCAACGCGAAGAAGTTGTGTTATTCTTAAACAATCAGACTTCCTCAATGTTAAGGAACCGT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
1239964 GTTGTCTCC
131 GTTGTCTCC
* * * ** * *
1239973 AAATTATCTCCAAATATGGCTAGACGTCCTCAAAACAAAGGAACAATGTCGTCGTCCGACCAAAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* * ** **
1240038 CTCCTCAACGTGAAGGAGCGGTGTCATCCTCAGACAATCAGACTTTTTCAACGCGAAGGAACATT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
* *
1240103 ATTGTCTAC
131 GTTGTCTCC
* * *
1240112 ATATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCATAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
** * * * *
1240177 CTCCTCAACATGAAGGAGCAATGTCATCCTCAGACAATTAGACTTCCTCAACGCGAATGAATCGT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
* *
1240242 GTTGTTTTC
131 GTTGTCTCC
* * * * * * * *
1240251 AAATTATCTCTAAATACGGCTAAACATCCTCAACACGAACGAATAACGCCGTCCACTAACCAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* * *
1240316 CTCCTCAACGTGAAGGAACAGTGTCATCCTCAGACAATCAGACTTCCTCAACGAGAAGGAACCGT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
1240381 GTTG--T-C
131 GTTGTCTCC
* *
1240387 ------TCT--AAATACGGCTATACGTCCTCAACACGAAGGAACAATGTCATCCACCAACCAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
** * * * * *
1240444 CTCCTCAACGCGAAGGAGTTGTGTCATCCTTAAACAATCAGACTTTCTCAACGCAAAGGAACCCT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
1240509 GTTGTCTCC
131 GTTGTCTCC
* * *
1240518 AAATTATCTCCAAATACGACTAGACGTCCTTAACACGAAGGAACAATGTCGTCCACCAACCAAAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* * * * * ***
1240583 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCGGACAATCAGACTTCTTTAATGGGAAGGAATTAT
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
*
1240648 GTTTTCTCC
131 GTTGTCTCC
* * * * * **
1240657 AAATTATCTCCAAATATGGCTAGACGTCCTTAGCACGAAAGAACAATGTCGTCCACCGAGTAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
* * * * *
1240722 CTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTTAACACGAAGGAACC
66 CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACC
1240785 ACATTGTCTT
Statistics
Matches: 909, Mismatches: 170, Indels: 22
0.83 0.15 0.02
Matches are distributed among these distances:
128 105 0.12
130 4 0.00
131 1 0.00
136 1 0.00
137 4 0.00
139 794 0.87
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (139 bp):
AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACCAACCAGAT
CTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGT
GTTGTCTCC
Found at i:1240680 original size:545 final size:549
Alignment explanation
Indices: 1239556--1240782 Score: 1696
Period size: 545 Copynumber: 2.2 Consensus size: 549
1239546 TTTCAAAGAT
** * * * *
1239556 AAATTATCTCCAAATACAACTATATGTCCTCAACACTAAAGAACAATGTAGTCCACCAACCAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCAGAT
* * *
1239621 CTCCTCAACGTGAAGGAACAGTGTCATCCTTAGACAATTAGACTTCCTCAACGTGAAGGAATCGT
66 CTCCTCAACGTGAAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTCAACGCGAAGGAATCGT
* * *
1239686 GTTGTCTTCAAATTATCTCCAAATACGGCTAGACATCCTCAACACGAACGAATAATGCCGTATAC
131 GTTGTCTTCAAATTATCTCCAAATACGGCTAAACATCCTCAACACGAACGAATAACGCCGTACAC
* * * **
1239751 TGACTAGATCTCCTGAACACGAAGGAGTAGTGCCATCCTCAGACAATCAGACTTCCTCAACACGA
196 TAACCAGATCTCCTCAACACGAAGGAACAGTGCCATCCTCAGACAATCAGACTTCCTCAACACGA
1239816 AGGAACCGTGTTGTCTCCAAATTATCTCCAAATACGGCTAGACGTCCCCAACACGAAGGAACAAT
261 AGGAACCGTGTTG-CTCC-----ATCT-CAAATACGGCTAGACGTCCCCAACACGAAGGAACAAT
* * *
1239881 GTCGTCCACCAACCAGATCTCCTCAACGCGAAGAAGTTGTGTTATTCTTAAACAATCAGACTTCC
319 GTCATCCACCAACCAGATCTCCTCAACGCGAAGAAGTTGTGTCATCCTTAAACAATCAGACTTCC
* ** * * *
1239946 TCAATGTTAAGGAACCGTGTTGTCTCCAAATTATCTCCAAATATGGCTAGACGTCCTCAAAACAA
384 TCAACGCAAAGGAACCCTGTTGTCTCCAAATTATCTCCAAATACGACTAGACGTCCTCAAAACAA
** * * *
1240011 AGGAACAATGTCGTCGTCCGACCAAATCTCCTCAACGTGAAGGAGCGGTGTCATCCTCAGACAAT
449 AGGAACAATGTCGTCCACCAACCAAATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAAT
1240076 CAGACTTTTTCAACGCGAAGGAACATTATTGTCTAC
514 CAGACTTTTTCAACGCGAAGGAACATTATTGTCTAC
* *
1240112 ATATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCATAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCAGAT
* * *
1240177 CTCCTCAACATGAAGGAGCAATGTCATCCTCAGACAATTAGACTTCCTCAACGCGAATGAATCGT
66 CTCCTCAACGTGAAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTCAACGCGAAGGAATCGT
* * *
1240242 GTTGTTTTCAAATTATCTCTAAATACGGCTAAACATCCTCAACACGAACGAATAACGCCGTCCAC
131 GTTGTCTTCAAATTATCTCCAAATACGGCTAAACATCCTCAACACGAACGAATAACGCCGTACAC
** *
1240307 TAACCAGATCTCCTCAACGTGAAGGAACAGTGTCATCCTCAGACAATCAGACTTCCTCAACGA-G
196 TAACCAGATCTCCTCAACACGAAGGAACAGTGCCATCCTCAGACAATCAGACTTCCTCAAC-ACG
* *
1240371 AAGGAACCGTGTTG-T-C-TCT-AAATACGGCTATACGTCCTCAACACGAAGGAACAATGTCATC
260 AAGGAACCGTGTTGCTCCATCTCAAATACGGCTAGACGTCCCCAACACGAAGGAACAATGTCATC
* *
1240432 CACCAACCAGATCTCCTCAACGCGAAGGAGTTGTGTCATCCTTAAACAATCAGACTTTCTCAACG
325 CACCAACCAGATCTCCTCAACGCGAAGAAGTTGTGTCATCCTTAAACAATCAGACTTCCTCAACG
* * *
1240497 CAAAGGAACCCTGTTGTCTCCAAATTATCTCCAAATACGACTAGACGTCCTTAACACGAAGGAAC
390 CAAAGGAACCCTGTTGTCTCCAAATTATCTCCAAATACGACTAGACGTCCTCAAAACAAAGGAAC
*
1240562 AATGTCGTCCACCAACCAAATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCGGACAATCAGACT
455 AATGTCGTCCACCAACCAAATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACT
* * * *
1240627 TCTTT-AATGGGAAGG-A-ATTATGTTTTCTCC
520 T-TTTCAACGCGAAGGAACATTA--TTGTCTAC
* * * * **
1240657 AAATTATCTCCAAATATGGCTAGACGTCCTTAGCACGAAAGAACAATGTCGTCCACCGAGTAGAT
1 AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCAGAT
* * * ** * *
1240722 CTCCTCAATGCGAAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTTAACACGAAGGAA
66 CTCCTCAACGTGAAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTCAACGCGAAGGAA
1240783 CCACATTGTC
Statistics
Matches: 595, Mismatches: 72, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
543 4 0.01
544 1 0.00
545 338 0.57
546 3 0.01
547 3 0.01
553 1 0.00
554 1 0.00
556 243 0.41
557 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (549 bp):
AAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCAGAT
CTCCTCAACGTGAAGGAGCAGTGTCATCCTCAGACAATTAGACTTCCTCAACGCGAAGGAATCGT
GTTGTCTTCAAATTATCTCCAAATACGGCTAAACATCCTCAACACGAACGAATAACGCCGTACAC
TAACCAGATCTCCTCAACACGAAGGAACAGTGCCATCCTCAGACAATCAGACTTCCTCAACACGA
AGGAACCGTGTTGCTCCATCTCAAATACGGCTAGACGTCCCCAACACGAAGGAACAATGTCATCC
ACCAACCAGATCTCCTCAACGCGAAGAAGTTGTGTCATCCTTAAACAATCAGACTTCCTCAACGC
AAAGGAACCCTGTTGTCTCCAAATTATCTCCAAATACGACTAGACGTCCTCAAAACAAAGGAACA
ATGTCGTCCACCAACCAAATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTT
TTTCAACGCGAAGGAACATTATTGTCTAC
Found at i:1241748 original size:21 final size:22
Alignment explanation
Indices: 1241722--1241763 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1241712 ATTCGAAGGA
1241722 AGAAAAAAGAAAAA-CAGAGAG
1 AGAAAAAAGAAAAATCAGAGAG
*
1241743 AGAAAAATGAAAAATCAGAGA
1 AGAAAAAAGAAAAATCAGAGA
1241764 AGATAAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.69, C:0.05, G:0.21, T:0.05
Consensus pattern (22 bp):
AGAAAAAAGAAAAATCAGAGAG
Found at i:1243376 original size:17 final size:18
Alignment explanation
Indices: 1243344--1243377 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1243334 TAACGCAGAT
*
1243344 CAATTTTTGTCTTAAAAA
1 CAATTTTTGTCGTAAAAA
1243362 CAATTTTT-TCGTAAAA
1 CAATTTTTGTCGTAAAA
1243378 TTATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (18 bp):
CAATTTTTGTCGTAAAAA
Found at i:1265356 original size:30 final size:29
Alignment explanation
Indices: 1265320--1265397 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 29
1265310 CATTTTCATT
*
1265320 TAAGTACTTAAAAGTATTTTTTGGTCAAAA
1 TAAGTACCT-AAAGTATTTTTTGGTCAAAA
*
1265350 TAAGTACCTAAAGTTATCTTTTTGGTCTAAA
1 TAAGTACCTAAAG-TAT-TTTTTGGTCAAAA
*
1265381 TAGGTACCTAAAGTATT
1 TAAGTACCTAAAGTATT
1265398 CAATTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.12
30 14 0.33
31 24 0.56
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTGGTCAAAA
Found at i:1265515 original size:23 final size:23
Alignment explanation
Indices: 1265488--1265532 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1265478 TGAATAGTTT
*
1265488 AGGTACTTATTTTGACTAAAAAG
1 AGGTACTTATTTTGACCAAAAAG
*
1265511 AGGTATTTATTTTGACCAAAAA
1 AGGTACTTATTTTGACCAAAAA
1265533 ATACTTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
AGGTACTTATTTTGACCAAAAAG
Found at i:1267717 original size:21 final size:21
Alignment explanation
Indices: 1267691--1267732 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1267681 AGTATAATTA
1267691 ACAACTAAATTAAATTTTATG
1 ACAACTAAATTAAATTTTATG
1267712 ACAACTAAATTAAATTTTATG
1 ACAACTAAATTAAATTTTATG
1267733 TAATTCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
ACAACTAAATTAAATTTTATG
Found at i:1269549 original size:13 final size:14
Alignment explanation
Indices: 1269532--1269596 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 14
1269522 ATCGTTATTT
1269532 TTTTATATTATTAC
1 TTTTATATTATTAC
1269546 -TTTATA-TATATAC
1 TTTTATATTAT-TAC
1269559 GTATTTCATATT-TTAC
1 -T-TTT-ATATTATTAC
1269575 TTTTATATTATTAC
1 TTTTATATTATTAC
1269589 TTTT-TATT
1 TTTTATATT
1269597 TCGTTTACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
12 3 0.07
13 18 0.41
14 11 0.25
15 1 0.02
16 6 0.14
17 4 0.09
18 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTTATATTATTAC
Found at i:1269595 original size:15 final size:15
Alignment explanation
Indices: 1269531--1269595 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
1269521 AATCGTTATT
1269531 TTTTTATATTATTAC
1 TTTTTATATTATTAC
*
1269546 TTTATATA-TA-TAC
1 TTTTTATATTATTAC
*
1269559 GTATTTCATATT-TTAC
1 -T-TTTTATATTATTAC
1269575 -TTTTATATTATTAC
1 TTTTTATATTATTAC
1269589 TTTTTAT
1 TTTTTAT
1269596 TTCGTTTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
13 11 0.28
14 7 0.17
15 18 0.45
16 4 0.10
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.63
Consensus pattern (15 bp):
TTTTTATATTATTAC
Found at i:1269685 original size:2 final size:2
Alignment explanation
Indices: 1269678--1269739 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
1269668 TTTTACTCAT
1269678 TA TA TA TA TA T- TA TA TA TA TA -A TA TA TA TA TA T- 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
1269717 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1269740 TATTTTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 54 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1269756 original size:20 final size:21
Alignment explanation
Indices: 1269682--1269773 Score: 56
Period size: 22 Copynumber: 4.5 Consensus size: 21
1269672 ACTCATTATA
*
1269682 TATATATTATA-TATATAATAT
1 TATATATTATATTAT-TATTAT
1269703 ATATATATTATA-TATATATATAT
1 -TATATATTATATTAT-TAT-TAT
1269726 ATATATATATATATTATT-TTAT
1 -TATATAT-TATATTATTATTAT
*
1269748 T-T-TATTATA-TGTTA-TAT
1 TATATATTATATTATTATTAT
1269765 TAT-TATTAT
1 TATATATTAT
1269774 GTGTACATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 14
0.80 0.03 0.18
Matches are distributed among these distances:
17 7 0.11
18 11 0.17
19 3 0.05
20 1 0.02
21 1 0.02
22 20 0.32
23 12 0.19
24 5 0.08
25 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
TATATATTATATTATTATTAT
Found at i:1269903 original size:4 final size:4
Alignment explanation
Indices: 1269894--1269920 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1269884 TTATTAATAT
1269894 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1269921 TACTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1272176 original size:25 final size:27
Alignment explanation
Indices: 1272137--1272191 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
1272127 TATATTTCTC
* *
1272137 TTAAAAATTTTAAATTATTA-T-ATAA
1 TTAAAAATATAAAATTATTATTGATAA
*
1272162 TTAAAAATATAAAATTTTTATTGATAA
1 TTAAAAATATAAAATTATTATTGATAA
1272189 TTA
1 TTA
1272192 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.68
26 1 0.04
27 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TTAAAAATATAAAATTATTATTGATAA
Found at i:1275337 original size:20 final size:20
Alignment explanation
Indices: 1275312--1275349 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1275302 ATGGGTTTTG
* *
1275312 TATCGATACTGGATGAACAA
1 TATCGAGACTAGATGAACAA
1275332 TATCGAGACTAGATGAAC
1 TATCGAGACTAGATGAAC
1275350 TAGGACAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (20 bp):
TATCGAGACTAGATGAACAA
Found at i:1276903 original size:77 final size:78
Alignment explanation
Indices: 1276816--1276962 Score: 192
Period size: 77 Copynumber: 1.9 Consensus size: 78
1276806 AATTAAAATG
*
1276816 TTATTTAATTAATT-CAAATTAAATATCCATT-AAAGACTTATAATCCGAATTACA-ATCTTTAA
1 TTATTTAATT-ATTCCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTACATAT-TTTAA
1276878 TGTTTATTTAAACTC
64 TGTTTATTTAAACTC
* * * * *
1276893 TTATTTAATTATTCCGAATTAAATTTCTATTAAAAGAGTTGTAATCAGAATTACATTATTTTAAT
1 TTATTTAATTATTCCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTACA-TATTTTAAT
1276958 GTTTA
65 GTTTA
1276963 CTTACTATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
76 3 0.05
77 24 0.40
78 20 0.33
79 11 0.18
80 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (78 bp):
TTATTTAATTATTCCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTACATATTTTAATG
TTTATTTAAACTC
Found at i:1279662 original size:19 final size:19
Alignment explanation
Indices: 1279634--1279670 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1279624 ACCTATACAA
*
1279634 AAATAAATAATGAATATAT
1 AAATAAATAATAAATATAT
*
1279653 AAATATATAATAAATATA
1 AAATAAATAATAAATATA
1279671 ATATATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAAATAATAAATATAT
Found at i:1292294 original size:19 final size:19
Alignment explanation
Indices: 1292266--1292302 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1292256 CCTATACAAC
*
1292266 AAATAAATAATGAATATAT
1 AAATAAATAATCAATATAT
*
1292285 AAATATATAATCAATATA
1 AAATAAATAATCAATATA
1292303 ATATATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAAATAATCAATATAT
Found at i:1294218 original size:17 final size:17
Alignment explanation
Indices: 1294184--1294228 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1294174 CTTTTCCCTT
* *
1294184 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
1294200 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
1294217 TCGTTCGAGAAA
1 TCTTTCGAGAAA
1294229 CAAACACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:1295508 original size:45 final size:41
Alignment explanation
Indices: 1295458--1295554 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 41
1295448 GCTAAAGTTC
*
1295458 GCGGCGTTTGATAACAAAAAACGCCGCAATAGGTCAAGATCTATA
1 GCGGCGTTTG-TAAC--AAAA-GCCGCAAAAGGTCAAGATCTATA
* *
1295503 GCGGCGTTTTTGTAACAAAAGCCGCAAAAGGTCGATATCTATA
1 GCGGCG--TTTGTAACAAAAGCCGCAAAAGGTCAAGATCTATA
1295546 GCGGCGTTT
1 GCGGCGTTT
1295555 TTTGGAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
41 3 0.06
43 26 0.55
44 4 0.09
45 6 0.13
46 4 0.09
47 4 0.09
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (41 bp):
GCGGCGTTTGTAACAAAAGCCGCAAAAGGTCAAGATCTATA
Found at i:1295660 original size:84 final size:84
Alignment explanation
Indices: 1295476--1295766 Score: 257
Period size: 85 Copynumber: 3.4 Consensus size: 84
1295466 TGATAACAAA
* * * * * * *
1295476 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTT-TGTAACAAAAGCCGCAAAAGGTC-GAT
1 AAACGCCGCAAAATGT-TAGATCTATAGCGGTGTTTTCAG-AACAAACGCCGCAAAATGTCAGAT
* * *
1295539 ATCTATAGCGGCGTTTTTTGGAAC
64 A--TATAACGAC-ATTTTTGGAAC
* * * * *
1295563 AAACGCCGTAAAATGTCAGATATATAGCGGTGTTTTCAGAACAAGCGCCGTAAAATGTCAGATAT
1 AAACGCCGCAAAATGTTAGATCTATAGCGGTGTTTTCAGAACAAACGCCGCAAAATGTCAGATAT
* **
1295628 ATAGCGGTATTTTTGGAAC
66 ATAACGACATTTTTGGAAC
* ** *
1295647 AAACGCCACAAAATGTTAGATCTATAGCGGCCT-TTTTTGGAACAAACGCTGCAAAATGTCAGAT
1 AAACGCCGCAAAATGTTAGATCTATAGCGG--TGTTTTCAGAACAAACGCCGCAAAATGTCAGAT
* *
1295711 CTATAACGACGTTTTTGGAAC
64 ATATAACGACATTTTTGGAAC
* *
1295732 AAACGCCGCAAAA-GTTAGATCTATAACGGCGTTTT
1 AAACGCCGCAAAATGTTAGATCTATAGCGGTGTTTT
1295767 TTTAAACAAA
Statistics
Matches: 169, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
83 4 0.02
84 51 0.30
85 62 0.37
86 34 0.20
87 18 0.11
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (84 bp):
AAACGCCGCAAAATGTTAGATCTATAGCGGTGTTTTCAGAACAAACGCCGCAAAATGTCAGATAT
ATAACGACATTTTTGGAAC
Found at i:1295732 original size:127 final size:128
Alignment explanation
Indices: 1295476--1295767 Score: 327
Period size: 127 Copynumber: 2.3 Consensus size: 128
1295466 TGATAACAAA
* * * * * * *
1295476 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGTAACAAAAGCCGCAAAAGGTCGATAT
1 AAACGCCGCAAAATGTC-AGATATATAGCGGCATTTTTGGAACAAAAGCCACAAAAGGTCGAGAT
* * * **
1295541 CTATAGCGGCGTTTTTTGGAACAAACGCCGTAAAATGTCAGATATATAGCGGTGTTTTCAGAAC
65 CTATAGCGGCCTTTTTTGGAACAAACGCCGCAAAATGTCAGATATATAACGACGTTTTCAGAAC
* * * * * *
1295605 AAGCGCCGTAAAATGTCAGATATATAGCGGTATTTTTGGAACAAACGCCACAAAATGT-TAGATC
1 AAACGCCGCAAAATGTCAGATATATAGCGGCATTTTTGGAACAAAAGCCACAAAAGGTCGAGATC
* * **
1295669 TATAGCGGCCTTTTTTGGAACAAACGCTGCAAAATGTCAGATCTATAACGACGTTTTTGGAAC
66 TATAGCGGCCTTTTTTGGAACAAACGCCGCAAAATGTCAGATATATAACGACGTTTTCAGAAC
* * * *
1295732 AAACGCCGCAAAA-GTTAGATCTATAACGGCGTTTTT
1 AAACGCCGCAAAATGTCAGATATATAGCGGCATTTTT
1295768 TTAAACAAAC
Statistics
Matches: 134, Mismatches: 29, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
126 18 0.13
127 69 0.51
128 34 0.25
129 13 0.10
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (128 bp):
AAACGCCGCAAAATGTCAGATATATAGCGGCATTTTTGGAACAAAAGCCACAAAAGGTCGAGATC
TATAGCGGCCTTTTTTGGAACAAACGCCGCAAAATGTCAGATATATAACGACGTTTTCAGAAC
Found at i:1295743 original size:42 final size:42
Alignment explanation
Indices: 1295476--1295782 Score: 328
Period size: 42 Copynumber: 7.2 Consensus size: 42
1295466 TGATAACAAA
* * *
1295476 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAATGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * *
1295519 AAAAGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTTGGAAC
1 AAACGCCGCAAAATGTC-AGATCTATAGCGGCG-TTTTTGGAAC
* * * **
1295563 AAACGCCGTAAAATGTCAGATATATAGCGGTGTTTTCAGAAC
1 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * **
1295605 AAGCGCCGTAAAATGTCAGATATATAGCGGTATTTTTGGAAC
1 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAAC
* * *
1295647 AAACGCCACAAAATGTTAGATCTATAGCGGCCTTTTTTGGAAC
1 AAACGCCGCAAAATGTCAGATCTATAGCGG-CGTTTTTGGAAC
* * *
1295690 AAACGCTGCAAAATGTCAGATCTATAACGACGTTTTTGGAAC
1 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAAC
* * **
1295732 AAACGCCGCAAAA-GTTAGATCTATAACGGCGTTTTTTTAAAC
1 AAACGCCGCAAAATGTCAGATCTATAGCGGCG-TTTTTGGAAC
1295774 AAACGCCGC
1 AAACGCCGC
1295783 TAATTACCTT
Statistics
Matches: 226, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.07
42 111 0.49
43 76 0.34
44 23 0.10
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:1299099 original size:13 final size:13
Alignment explanation
Indices: 1299081--1299122 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1299071 TATAATCAGC
1299081 AAAGTGAATATCA
1 AAAGTGAATATCA
1299094 AAAGTGAATATCA
1 AAAGTGAATATCA
*
1299107 AAAGTTAATATCA
1 AAAGTGAATATCA
1299120 AAA
1 AAA
1299123 CTAAACTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.24
Consensus pattern (13 bp):
AAAGTGAATATCA
Found at i:1300715 original size:40 final size:41
Alignment explanation
Indices: 1300465--1300975 Score: 460
Period size: 41 Copynumber: 12.4 Consensus size: 41
1300455 GTTTGTAAAC
* * * ** *
1300465 AAAAATGCCACTAAAGTACGAGTCTATAGTGGTATTTTTAT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * *
1300506 AAAAA--CCACTAAAGTTA-TGAGTCTTTAACGGTGTTTGTAT
1 AAAAACGCCACTAAAG-TACT-AGTCTATAGCGGCGTTTGTAT
* * * *
1300546 ACAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTTCAAA
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTG-T--AT
1300590 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* *
1300631 AAAAAAACGCCACTAAAGTACTAGTCTATAGCGGCATTTTTAT
1 --AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * * *
1300674 AAACACGCCACTAAAGTAC-AGTCTTTGGCTGCGTTTGTAT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * *
1300714 -AAAACTGCCACTAACGTACTAGTCTATAGCAGCGTTTAATAT
1 AAAAAC-GCCACTAAAGTACTAGTCTATAGCGGCGTTT-GTAT
*
1300756 AAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * * * *
1300797 AAAAATGCCACAAAAGTACTAGTCTTTAGCGGCGTTTTTTCT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCG-TTTGTAT
** * * * **
1300839 AAAAACATCACTTAAGTAC-ATTCTTTAGCGGATTTTGTAT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * **
1300879 AAAAACACCACTAAAGTA-TAGTCTTTAGCGGCGTTTGTCC
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * * * * *
1300919 AAAAACGCCACTAAAGTTCAAGTGTTTTGCGGCGTTTGTTCT
1 AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTG-TAT
*
1300961 AAAAACGCCGCTAAA
1 AAAAACGCCACTAAA
1300976 AATGTCGATA
Statistics
Matches: 387, Mismatches: 65, Indels: 35
0.79 0.13 0.07
Matches are distributed among these distances:
39 13 0.03
40 103 0.27
41 114 0.29
42 76 0.20
43 45 0.12
44 36 0.09
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
Found at i:1300750 original size:41 final size:40
Alignment explanation
Indices: 1300466--1300935 Score: 394
Period size: 40 Copynumber: 11.4 Consensus size: 40
1300456 TTTGTAAACA
* * * ** *
1300466 AAAATGCCACTAAAGTACGAGTCTATAGTGGTATTTTTAT
1 AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * * *
1300506 AAAA-ACCACTAAAGTTA-TGAGTCTTTAACGGTGTTTGTAT
1 AAAACGCCACTAAAG-TACT-AGTCTATAGCGGCGTTTGTAT
* * *
1300546 ACAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTTCAAAA
1 A-AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTG-T---AT
1300591 AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
1 AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* *
1300631 AAAAAAACGCCACTAAAGTACTAGTCTATAGCGGCATTTTTAT
1 ---AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * *
1300674 AAACACGCCACTAAAGTAC-AGTCTTTGGCTGCGTTTGTAT
1 AAA-ACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * *
1300714 AAAACTGCCACTAACGTACTAGTCTATAGCAGCGTTTAATAT
1 AAAAC-GCCACTAAAGTACTAGTCTATAGCGGCGTTT-GTAT
*
1300756 AAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAT
1 -AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* * * * *
1300797 AAAAATGCCACAAAAGTACTAGTCTTTAGCGGCGTTTTTTCT
1 -AAAACGCCACTAAAGTACTAGTCTATAGCGGCG-TTTGTAT
** * * * **
1300839 AAAAACATCACTTAAGTAC-ATTCTTTAGCGGATTTTGTAT
1 -AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
* *
1300879 AAAAACACCACTAAAGTA-TAGTCTTTAGCGGCGTTTGTCCA-
1 -AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGT--AT
1300920 AAAACGCCACTAAAGT
1 AAAACGCCACTAAAGT
1300936 TCAAGTGTTT
Statistics
Matches: 354, Mismatches: 55, Indels: 42
0.78 0.12 0.09
Matches are distributed among these distances:
39 11 0.03
40 110 0.31
41 92 0.26
42 61 0.17
43 44 0.12
44 34 0.10
45 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (40 bp):
AAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT
Found at i:1309959 original size:20 final size:20
Alignment explanation
Indices: 1309923--1310069 Score: 161
Period size: 20 Copynumber: 7.2 Consensus size: 20
1309913 AAGCGTATTT
*
1309923 ATACTTTCCCAAAGAGTATCG
1 ATACTTTACC-AAGAGTATCG
1309944 ATACTTTACCAAGAGTATCG
1 ATACTTTACCAAGAGTATCG
* * *
1309964 ATAGTTTACCAATAGTATCA
1 ATACTTTACCAAGAGTATCG
* *
1309984 ATACTTTCCCAAATAGTATCG
1 ATACTTTACC-AAGAGTATCG
* *
1310005 ATACTTTCCCCAAGAGTATGG
1 ATACTTT-ACCAAGAGTATCG
*
1310026 ATACTTT-CCAAGAGTATCA
1 ATACTTTACCAAGAGTATCG
* *
1310045 ATAATTTACCTAGAGTATCG
1 ATACTTTACCAAGAGTATCG
1310065 ATACT
1 ATACT
1310070 GAGAGTACTT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
19 16 0.15
20 49 0.45
21 40 0.37
22 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (20 bp):
ATACTTTACCAAGAGTATCG
Found at i:1310042 original size:61 final size:61
Alignment explanation
Indices: 1309923--1310069 Score: 199
Period size: 61 Copynumber: 2.4 Consensus size: 61
1309913 AAGCGTATTT
* *
1309923 ATACTTTCCCAAAGAGTATCGATACTTTACCAAGAGTATCGATAGTTTACCAATAGTATCA
1 ATACTTTCCCAAAGAGTATCGATACTTTACCAAGAGTATCGATACTTTACCAAGAGTATCA
* * *
1309984 ATACTTTCCCAAATAGTATCGATACTTTCCCCAAGAGTATGGATACTTT-CCAAGAGTATCA
1 ATACTTTCCCAAAGAGTATCGATACTTT-ACCAAGAGTATCGATACTTTACCAAGAGTATCA
* * *
1310045 ATAATTTACC-TAGAGTATCGATACT
1 ATACTTTCCCAAAGAGTATCGATACT
1310070 GAGAGTACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
60 13 0.17
61 46 0.61
62 17 0.22
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (61 bp):
ATACTTTCCCAAAGAGTATCGATACTTTACCAAGAGTATCGATACTTTACCAAGAGTATCA
Found at i:1311156 original size:18 final size:20
Alignment explanation
Indices: 1311133--1311185 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 20
1311123 CCAAAATTTG
1311133 GTATCGATACTCA-ATCA-A
1 GTATCGATACTCACATCATA
1311151 GTATCGATACCTCAACATCATA
1 GTATCGATA-CTC-ACATCATA
*
1311173 GTATTGATACTCA
1 GTATCGATACTCA
1311186 TACTAGAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.30
19 3 0.10
20 2 0.07
21 7 0.23
22 9 0.30
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (20 bp):
GTATCGATACTCACATCATA
Found at i:1314406 original size:85 final size:85
Alignment explanation
Indices: 1314313--1314491 Score: 229
Period size: 85 Copynumber: 2.1 Consensus size: 85
1314303 TGACGCGCAA
* * * *
1314313 TTGTGTGTCATAAATATATGACACGCATTTATGACGCT-CATTGCGCGTCATTGAATCCCCCGTC
1 TTGTGTGTCATAAATATATGACACGCATGTATGAC-CTACATTGCGCGTCATTGAAGCACACGTC
*
1314377 A-TAAATGAAGATGACACACAT
65 ATTAAA-AAAGATGACACACAT
* * *
1314398 TTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCA
1 TTGTGTGTCATAAATATATGACACGCATGTATGACCTACATTGCGCGTCATTGAAGCACACGTCA
*
1314463 TTAAAAAATATGACACACAT
66 TTAAAAAAGATGACACACAT
1314483 TCT-TGTGTC
1 T-TGTGTGTC
1314492 GTGATTGTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
84 1 0.01
85 76 0.93
86 5 0.06
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (85 bp):
TTGTGTGTCATAAATATATGACACGCATGTATGACCTACATTGCGCGTCATTGAAGCACACGTCA
TTAAAAAAGATGACACACAT
Found at i:1320486 original size:64 final size:62
Alignment explanation
Indices: 1320370--1320530 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 62
1320360 GCATCCCTTG
* *
1320370 ACGGGTGCATCGATGCACTGTCTATGCATCGGTGCATAAATCCTATTCGATGTTT-ATATTTTA
1 ACGGGTGCATCGATGCACTCT-TATGCATCGATGCATAAATCCTATTCGATGTTTCAT-TTTTA
* *
1320433 AGCGGGTGCATCGATGCACTCCTTATGCATCGATGCACT-AATGGC-ATTTGATGTTTCCATTTT
1 A-CGGGTGCATCGATGCACT-CTTATGCATCGATGCA-TAAAT-CCTATTCGATGTTT-CATTTT
1320496 TA
61 TA
** * *
1320498 ATAGGTGCATCGATGCACTTCATGTGCATCGAT
1 ACGGGTGCATCGATGCAC-TCTTATGCATCGAT
1320531 ACACACTGAA
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 70 0.84
65 10 0.12
66 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (62 bp):
ACGGGTGCATCGATGCACTCTTATGCATCGATGCATAAATCCTATTCGATGTTTCATTTTTA
Found at i:1325343 original size:20 final size:20
Alignment explanation
Indices: 1325307--1325348 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1325297 TTTTAAGCCC
1325307 CTATCATGACATTAAACTCAA
1 CTATCATGACATTAAAC-CAA
*
1325328 CTATCATTAC-TTAAACCAA
1 CTATCATGACATTAAACCAA
1325347 CT
1 CT
1325349 TATATCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.31
Consensus pattern (20 bp):
CTATCATGACATTAAACCAA
Found at i:1331705 original size:21 final size:20
Alignment explanation
Indices: 1331666--1331797 Score: 160
Period size: 20 Copynumber: 6.5 Consensus size: 20
1331656 CTAGCTAAGT
*
1331666 GTATCGTTACTTTCCCAAGA
1 GTATCGATACTTTCCCAAGA
*
1331686 GTATTGATACTTTCCCCAAGA
1 GTATCGATACTTT-CCCAAGA
*
1331707 GTATTGATACTTTCCCAAGA
1 GTATCGATACTTTCCCAAGA
*
1331727 GTATCAATACTTTCCCCAAGA
1 GTATCGATACTTT-CCCAAGA
*
1331748 GTATGGATACTTT-CCAAGA
1 GTATCGATACTTTCCCAAGA
*
1331767 GTATCGATACATT-CCATAGA
1 GTATCGATACTTTCCCA-AGA
*
1331787 GTATCTATACT
1 GTATCGATACT
1331798 GAGGGTACAT
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 20 0.20
20 41 0.41
21 38 0.38
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (20 bp):
GTATCGATACTTTCCCAAGA
Found at i:1331730 original size:41 final size:41
Alignment explanation
Indices: 1331673--1331781 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
1331663 AGTGTATCGT
* *
1331673 TACTTTCCCAAGAGTATTGATACTTTCCCCAAGAGTATTGA
1 TACTTTCCCAAGAGTATCGATACTTTCCCCAAGAGTATGGA
*
1331714 TACTTTCCCAAGAGTATCAATACTTTCCCCAAGAGTATGGA
1 TACTTTCCCAAGAGTATCGATACTTTCCCCAAGAGTATGGA
*
1331755 TACTTT-CCAAGAGTATCGATACATTCC
1 TACTTTCCCAAGAGTATCGATACTTTCC
1331782 ATAGAGTATC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
40 19 0.30
41 44 0.70
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (41 bp):
TACTTTCCCAAGAGTATCGATACTTTCCCCAAGAGTATGGA
Found at i:1335548 original size:22 final size:22
Alignment explanation
Indices: 1335501--1335542 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1335491 ATTGATCGTT
* *
1335501 ATATATGATGTTTAACGTGAAC
1 ATATATGATGATTAACATGAAC
1335523 ATATATGAT-ATTAACATGAA
1 ATATATGATGATTAACATGAA
1335543 TGATATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (22 bp):
ATATATGATGATTAACATGAAC
Found at i:1335795 original size:26 final size:26
Alignment explanation
Indices: 1335759--1335808 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1335749 AGTGCATATG
*
1335759 GTGGGCACGACCTTATGTGTATTATA
1 GTGGGCACGACCGTATGTGTATTATA
*
1335785 GTGGGTACGACCGTATGTGTATTA
1 GTGGGCACGACCGTATGTGTATTA
1335809 ACACTTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (26 bp):
GTGGGCACGACCGTATGTGTATTATA
Found at i:1342638 original size:275 final size:275
Alignment explanation
Indices: 1342147--1342681 Score: 1007
Period size: 275 Copynumber: 1.9 Consensus size: 275
1342137 TAACTTAAAT
*
1342147 AATTTACAAATTCTAATCCTAAACAAATTAATTTACTTGAATTAATAATTATTTTAATTAAAAAT
1 AATTTACAAATTCTAATCCTAAACAAATTAATTTACTTGAATTAATAATTATTTTAATTAAAAAG
1342212 CATAATTTAATTATAATTATATTAAATCTAAAACTAAATTTTAATTAATAATTAATTTTTAAAAA
66 CATAATTTAATTATAATTATATTAAATCTAAAACTAAATTTTAATTAATAATTAATTTTTAAAAA
* * *
1342277 AATCTTATACTTTTAATATTTACATAATAAGGATAAATTTATTTGTTGTGTGTTTCGGTATGTTG
131 AATCTTATACTTTTAATATTTACATAATAAGGACAAATTTATTTGTCGTGTGTCTCGGTATGTTG
*
1342342 TTTTAGTGATACATTATGGTATACGACGTGCACTGTAGACTCTTCATATATATATATATATATAT
196 CTTTAGTGATACATTATGGTATACGACGTGCACTGTAGACTCTTCATATATATATATATATATAT
1342407 ATATTATGAGTCTAC
261 ATATTATGAGTCTAC
1342422 AATTTACAAATTCTAATCCTAAACAAATTAATTTACTTGAATTAATAATTATTTTAATTAAAAAG
1 AATTTACAAATTCTAATCCTAAACAAATTAATTTACTTGAATTAATAATTATTTTAATTAAAAAG
*
1342487 CATAATTTAATTATAATTATATTAAATCTAAAACTAAATTTTAATTAATGATTAATTTTTAAAAA
66 CATAATTTAATTATAATTATATTAAATCTAAAACTAAATTTTAATTAATAATTAATTTTTAAAAA
1342552 AATCTTATACTTTTAATATTTACATAATAAGGACAAATTTATTTGTCGTGTGTCTCGGTATGTTG
131 AATCTTATACTTTTAATATTTACATAATAAGGACAAATTTATTTGTCGTGTGTCTCGGTATGTTG
*
1342617 CTTTAGTGATACATTATGGTATACGACGTGCACTGTAGACTCTTTATATATATATATATATATAT
196 CTTTAGTGATACATTATGGTATACGACGTGCACTGTAGACTCTTCATATATATATATATATATAT
1342682 GAGTCTACAG
Statistics
Matches: 253, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
275 253 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (275 bp):
AATTTACAAATTCTAATCCTAAACAAATTAATTTACTTGAATTAATAATTATTTTAATTAAAAAG
CATAATTTAATTATAATTATATTAAATCTAAAACTAAATTTTAATTAATAATTAATTTTTAAAAA
AATCTTATACTTTTAATATTTACATAATAAGGACAAATTTATTTGTCGTGTGTCTCGGTATGTTG
CTTTAGTGATACATTATGGTATACGACGTGCACTGTAGACTCTTCATATATATATATATATATAT
ATATTATGAGTCTAC
Found at i:1346855 original size:33 final size:34
Alignment explanation
Indices: 1346779--1346866 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
1346769 AATGGTAATA
*
1346779 AACAAAATTAATCAAAATACATTAACAAAAAGTCC
1 AACAAAATTAA-CAAAATAAATTAACAAAAAGTCC
1346814 AACAAAATTAACAAAATAAATTAA-AATAAA-TCC
1 AACAAAATTAACAAAATAAATTAACAA-AAAGTCC
1346847 AAGC-AAATTAA-AGAAATAAA
1 AA-CAAAATTAACA-AAATAAA
1346867 GTAAGTATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
32 1 0.02
33 21 0.43
34 16 0.33
35 11 0.22
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.19
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAACAAAAAGTCC
Found at i:1349122 original size:28 final size:29
Alignment explanation
Indices: 1349075--1349142 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
1349065 AAAAAATTAA
* *
1349075 TTAAATAAAATATTAAAAATTTTAAATAC
1 TTAAATAAAATATAAAAAATATTAAATAC
*
1349104 TTAAATAAATTA-AAAAAATATTAAATA-
1 TTAAATAAAATATAAAAAATATTAAATAC
1349131 -T-AATAAAATATA
1 TTAAATAAAATATA
1349143 CCTTAAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 8 0.24
26 2 0.06
28 13 0.38
29 11 0.32
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
TTAAATAAAATATAAAAAATATTAAATAC
Found at i:1349137 original size:20 final size:21
Alignment explanation
Indices: 1349098--1349151 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1349088 TAAAAATTTT
1349098 AAATACTTAAATAAATTAAAA
1 AAATACTTAAATAAATTAAAA
1349119 AAATA-TTAAATATAA-T-AAA
1 AAATACTTAAATA-AATTAAAA
*
1349138 ATATACCTTAAATA
1 AAATA-CTTAAATA
1349152 GTTATAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 7 0.24
20 8 0.28
21 14 0.48
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATACTTAAATAAATTAAAA
Found at i:1349140 original size:17 final size:17
Alignment explanation
Indices: 1349065--1349141 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 17
1349055 TATATCTGCA
* *
1349065 AAAAAATTAATTA-AAT
1 AAAATATTAAATATAAT
* *
1349081 AAAATATTAAAAAT-TT
1 AAAATATTAAATATAAT
* *
1349097 TAAATACTTAAATAAATTAAA
1 AAAATA-TTAAAT--A-TAAT
1349118 AAAATATTAAATATAAT
1 AAAATATTAAATATAAT
1349135 AAAATAT
1 AAAATAT
1349142 ACCTTAAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
16 16 0.36
17 15 0.33
18 1 0.02
19 1 0.02
20 7 0.16
21 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATATTAAATATAAT
Found at i:1350545 original size:17 final size:18
Alignment explanation
Indices: 1350525--1350564 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1350515 AAAGGTCACT
*
1350525 TTTTCTCAAAT-CGTGCC
1 TTTTCGCAAATACGTGCC
*
1350542 TTTTCGCAAATAGGTGCC
1 TTTTCGCAAATACGTGCC
1350560 TTTTC
1 TTTTC
1350565 ATGAGGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (18 bp):
TTTTCGCAAATACGTGCC
Found at i:1352799 original size:57 final size:55
Alignment explanation
Indices: 1352738--1352867 Score: 129
Period size: 56 Copynumber: 2.3 Consensus size: 55
1352728 ATAAAACGTC
* * *
1352738 AAATTTACTTTCTTGGAAATCTTGAACGATT-TCATTTTGAGAAGGAAATAAATTGTT
1 AAATTTA-TTTCTTGGAAATATTGAACGATTCT-ATTTTGAAAAAGAAATAAATT-TT
* * * * *
1352795 AAATTTATTTTCATAG-AATATTGTATGATTCTGTTTTGAAAAAGAAATAAATTTT
1 AAATTTA-TTTCTTGGAAATATTGAACGATTCTATTTTGAAAAAGAAATAAATTTT
*
1352850 GAATTTATTTCTTGGAAA
1 AAATTTATTTCTTGGAAA
1352868 ATTATGGTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
54 6 0.10
55 10 0.17
56 29 0.49
57 14 0.24
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (55 bp):
AAATTTATTTCTTGGAAATATTGAACGATTCTATTTTGAAAAAGAAATAAATTTT
Found at i:1355138 original size:20 final size:20
Alignment explanation
Indices: 1355113--1355153 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1355103 TTTTTATTTC
1355113 TTAATAAACTCATCCCAAAA
1 TTAATAAACTCATCCCAAAA
1355133 TTAATAAACTCATCCCAAAA
1 TTAATAAACTCATCCCAAAA
1355153 T
1 T
1355154 ACTATCACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAATAAACTCATCCCAAAA
Found at i:1358780 original size:37 final size:37
Alignment explanation
Indices: 1358737--1358951 Score: 107
Period size: 37 Copynumber: 5.6 Consensus size: 37
1358727 TATAATATAG
*
1358737 TATAGTTTTTGAAAATATTTTCAAAAAACGTATAACA
1 TATAGTTTTTGAAAATATTTTCAAAAAACGTATAATA
* *** * *
1358774 TATAGTTGTT-AAAACGGTTTCGAAAATACGATTTAAAAACATA
1 TATAGTTTTTGAAAATATTTTC-AAAAAACG---T--ATA-ATA
** * **
1358817 TATTA-TATAATTTGAAAATATTTTTGAAACATATATAATA
1 TA-TAGT-T--TTTGAAAATATTTTCAAAAAACGTATAATA
* * **
1358857 TATAGTTTTTTG-CAATCATTTTGAAAAAATATATAATA
1 TATAG-TTTTTGAAAAT-ATTTTCAAAAAACGTATAATA
* *
1358895 TATAG-TTTTGAAAATATTTTTGAAAATACGTATAATA
1 TATAGTTTTTGAAAATA-TTTTCAAAAAACGTATAATA
1358932 TATAG-TTTTGAAAATATTTT
1 TATAGTTTTTGAAAATATTTT
1358952 TGGAAACATA
Statistics
Matches: 136, Mismatches: 25, Indels: 35
0.69 0.13 0.18
Matches are distributed among these distances:
36 18 0.13
37 55 0.40
38 27 0.20
39 2 0.01
40 7 0.05
41 3 0.02
42 2 0.01
43 6 0.04
44 3 0.02
46 6 0.04
47 7 0.05
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (37 bp):
TATAGTTTTTGAAAATATTTTCAAAAAACGTATAATA
Found at i:1358952 original size:37 final size:35
Alignment explanation
Indices: 1358809--1359028 Score: 225
Period size: 37 Copynumber: 6.1 Consensus size: 35
1358799 ATACGATTTA
* * *
1358809 AAAACATATATTATATA-ATTTGAAAATATTTTTG
1 AAAATATATAATATATAGTTTTGAAAATATTTTTG
*
1358843 AAACATATATAATATATAGTTTTTTG-CAATCA-TTTTG
1 AAA-ATATATAATATATAG--TTTTGAAAAT-ATTTTTG
1358880 AAAAAATATATAATATATAGTTTTGAAAATATTTTTG
1 --AAAATATATAATATATAGTTTTGAAAATATTTTTG
1358917 AAAATACGTATAATATATAGTTTTGAAAATATTTTTG
1 AAAATA--TATAATATATAGTTTTGAAAATATTTTTG
* *
1358954 GAAACATAT--TATATAGTTTTGAAAATAATTTTTG
1 AAAATATATAATATATAGTTTTGAAAAT-ATTTTTG
* * *
1358988 AAAATATATATTATATAATTTTGAACAAACATTTTTG
1 AAAATATATAATATATAGTTTTG-A-AAATATTTTTG
1359025 AAAA
1 AAAA
1359029 CATTTTGAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 29
0.80 0.06 0.15
Matches are distributed among these distances:
33 17 0.11
34 17 0.11
35 21 0.13
36 17 0.11
37 61 0.38
38 23 0.14
39 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (35 bp):
AAAATATATAATATATAGTTTTGAAAATATTTTTG
Found at i:1358962 original size:14 final size:12
Alignment explanation
Indices: 1358900--1358994 Score: 54
Period size: 12 Copynumber: 8.0 Consensus size: 12
1358890 TAATATATAG
1358900 TTTTGAAAATAT
1 TTTTGAAAATAT
*
1358912 TTTTGAAAATAC
1 TTTTGAAAATAT
* * *
1358924 GTAT-AATATATAG
1 TTTTGAA-A-ATAT
1358937 TTTTGAAAATAT
1 TTTTGAAAATAT
* *
1358949 TTTTGGAAACA-
1 TTTTGAAAATAT
* * *
1358960 TATT--ATATAG
1 TTTTGAAAATAT
1358970 TTTTGAAAATAAT
1 TTTTGAAAAT-AT
1358983 TTTTGAAAATAT
1 TTTTGAAAATAT
1358995 ATATTATATA
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
9 3 0.05
10 3 0.05
11 5 0.08
12 31 0.51
13 17 0.28
14 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:1359091 original size:2 final size:2
Alignment explanation
Indices: 1359084--1359115 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1359074 ATATTTTCGA
1359084 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
1359116 GACTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1366601 original size:28 final size:27
Alignment explanation
Indices: 1366527--1366605 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
1366517 CTTTTTATTA
*
1366527 TTTATTTATATATTTGTTTATTTCCTTT
1 TTTATTTA-ATATTTATTTATTTCCTTT
* * * *
1366555 TAATTTTTTATTA-TCATTTTTTTCCTCTT
1 T--TTATTTAATATTTATTTATTTCCT-TT
1366584 TTTATTTAATATTTATTTATTT
1 TTTATTTAATATTTATTTATTT
1366606 GTTTCTATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
27 8 0.21
28 19 0.50
29 5 0.13
30 6 0.16
ACGTcount: A:0.20, C:0.08, G:0.01, T:0.71
Consensus pattern (27 bp):
TTTATTTAATATTTATTTATTTCCTTT
Found at i:1372732 original size:86 final size:85
Alignment explanation
Indices: 1372489--1372735 Score: 341
Period size: 85 Copynumber: 2.9 Consensus size: 85
1372479 CTATTACAGT
* * * *
1372489 ATAACTCAAGGCGAGAAAGGCTATCTGTCAACAAAAACCTTCAAGTTCGATTTCATTCAGCTCAA
1 ATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTACATTCAGCTCAA
*
1372554 GGCCATATCAAATTTATAAC
66 GGACATATCAAATTTATAAC
* * * *
1372574 ATAACTCAAGGCAAGAAGAGCTATCAGTCAACAAAAACTTTCGAGTTCGATTCCATTCAGCTCAA
1 ATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTACATTCAGCTCAA
* * *
1372639 GGGCATATTAAATTTATATC
66 GGACATATCAAATTTATAAC
* * *
1372659 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAAACTTTCGAGTTCGATTACATTCAGCTCG
1 ATAACTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACTTTCGAGTTCGATTACATTCAGCTCA
*
1372724 ATGACATATCAA
65 AGGACATATCAA
1372736 CCACATGGTA
Statistics
Matches: 141, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 102 0.72
86 39 0.28
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (85 bp):
ATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTACATTCAGCTCAA
GGACATATCAAATTTATAAC
Found at i:1379166 original size:54 final size:51
Alignment explanation
Indices: 1379106--1379209 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
1379096 GATCATAAGC
1379106 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTA
** * * *
1379160 TTATTTTTTTCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
1379210 TTCATGGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 23 0.51
53 2 0.04
54 20 0.44
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (51 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTA
Found at i:1381901 original size:14 final size:12
Alignment explanation
Indices: 1381876--1382037 Score: 66
Period size: 12 Copynumber: 13.0 Consensus size: 12
1381866 TATTATATAA
1381876 TTTTGAAAATAT
1 TTTTGAAAATAT
1381888 TTTTGAAAACATAT
1 TTTTG-AAA-ATAT
*
1381902 ATTATAT-ATAAT-T
1 -TT-T-TGAAAATAT
*
1381915 TTTTGAAAACA-
1 TTTTGAAAATAT
1381926 TTTTGAAAATAT
1 TTTTGAAAATAT
* * *
1381938 ATATT-ATATATAG
1 -TTTTGA-AAATAT
1381951 TTTTGAAAATAT
1 TTTTGAAAATAT
*
1381963 TTTTGAAAATAC
1 TTTTGAAAATAT
* *
1381975 ATAT-AATATATAT
1 TTTTGAA-A-ATAT
**
1381988 TTTTGAAAACGT
1 TTTTGAAAATAT
* *
1382000 ATAT-AATATATAGT
1 TTTTGAA-A-ATA-T
1382014 TTTTGAAAATAT
1 TTTTGAAAATAT
1382026 TTTTGAAAATAT
1 TTTTGAAAATAT
1382038 ATTATATAGT
Statistics
Matches: 108, Mismatches: 24, Indels: 36
0.64 0.14 0.21
Matches are distributed among these distances:
10 1 0.01
11 18 0.17
12 47 0.44
13 22 0.20
14 12 0.11
15 6 0.06
16 1 0.01
17 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:1381956 original size:75 final size:71
Alignment explanation
Indices: 1381858--1381997 Score: 208
Period size: 75 Copynumber: 1.9 Consensus size: 71
1381848 ATACGATTTA
* *
1381858 AAAACATATATTATATAATTTTGAAAATATTTTTGAAAACATATATTATATATAATTTTTTGAAA
1 AAAACATATATTATATAATTTTGAAAATATTTTTGAAAACACATATAATATAT-A-TTTTTGAAA
1381923 ACATTTTG
64 ACATTTTG
* *
1381931 AAAATATATATTATATATAGTTTTGAAAATATTTTTGAAAATACATATAATATATATTTTTGAAA
1 AAAACATATATTATATA-A-TTTTGAAAATATTTTTGAAAACACATATAATATATATTTTTGAAA
1381996 AC
64 AC
1381998 GTATATAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
73 27 0.44
74 2 0.03
75 32 0.52
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (71 bp):
AAAACATATATTATATAATTTTGAAAATATTTTTGAAAACACATATAATATATATTTTTGAAAAC
ATTTTG
Found at i:1381984 original size:37 final size:37
Alignment explanation
Indices: 1381857--1381996 Score: 167
Period size: 37 Copynumber: 3.8 Consensus size: 37
1381847 AATACGATTT
* *
1381857 AAAA-ACATATATTATATAATTTTGAAAATATTTTTG
1 AAAATACATATAATATATATTTTTGAAAATATTTTTG
* * * *
1381893 AAAACATATATTATATATAATTTTTTGAAAACA-TTTTG
1 AAAATACATATAATATAT-A-TTTTTGAAAATATTTTTG
* * *
1381931 AAAATATATATTATATATAGTTTTGAAAATATTTTTG
1 AAAATACATATAATATATATTTTTGAAAATATTTTTG
1381968 AAAATACATATAATATATATTTTTGAAAA
1 AAAATACATATAATATATATTTTTGAAAA
1381997 CGTATATAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
36 14 0.16
37 42 0.47
38 23 0.26
39 10 0.11
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATACATATAATATATATTTTTGAAAATATTTTTG
Found at i:1381991 original size:25 final size:25
Alignment explanation
Indices: 1381959--1382024 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
1381949 AGTTTTGAAA
1381959 ATATTTTTGAAAATACATATAATAT
1 ATATTTTTGAAAATACATATAATAT
***
1381984 ATATTTTTGAAAACGTATATAATAT
1 ATATTTTTGAAAATACATATAATAT
1382009 ATAGTTTTTGAAAATA
1 ATA-TTTTTGAAAATA
1382025 TTTTTGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 25 0.71
26 10 0.29
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (25 bp):
ATATTTTTGAAAATACATATAATAT
Found at i:1381996 original size:62 final size:59
Alignment explanation
Indices: 1381926--1382055 Score: 181
Period size: 62 Copynumber: 2.2 Consensus size: 59
1381916 TTTGAAAACA
* * *
1381926 TTTTGAAAATATATATTATATATAG-TTTTGAAAATATTTTTGAAAATACATATAATATATAT
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAATATTTTTGAAAAT--ATAT--TATATAG
*
1381988 TTTTGAAAACGTATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATTATATAG
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATTATATAG
1382047 TTTTGAAAA
1 TTTTGAAAA
1382056 AACATTTTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
59 15 0.24
61 4 0.06
62 22 0.35
63 22 0.35
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (59 bp):
TTTTGAAAACATATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATTATATAG
Found at i:1382003 original size:100 final size:97
Alignment explanation
Indices: 1381884--1382069 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 97
1381874 AATTTTGAAA
* *
1381884 ATATTTTTGAAAACATATATTATATATAATTTTTTGAAAACA-TTTTGAAAATATATATTATATA
1 ATATTTTTGAAAACATATATAATATAT-AGTTTTTGAAAACATTTTTG-AAA-ATATA-T-TATA
*
1381948 TAGTTTTG-AAAATATTTTTGAAAATACATATAATAT
61 TAGTTTTGAAAAACATTTTTGAAAATACATATAATAT
* *
1381984 ATATTTTTGAAAACGTATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATTATATAGTT
1 ATATTTTTGAAAACATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATTATATAGTT
1382049 TTGAAAAAACATTTTTGAAAA
66 TTG-AAAAACATTTTTGAAAA
1382070 CATTTTGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
96 12 0.15
97 1 0.01
98 20 0.26
99 15 0.19
100 30 0.38
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (97 bp):
ATATTTTTGAAAACATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATTATATAGTT
TTGAAAAACATTTTTGAAAATACATATAATAT
Found at i:1382044 original size:34 final size:36
Alignment explanation
Indices: 1381984--1382095 Score: 108
Period size: 35 Copynumber: 3.1 Consensus size: 36
1381974 CATATAATAT
1381984 ATATTTTTGAAAACGTATATAATATATAGTTTTTG-AAA
1 ATATTTTTGAAAAC-TATAT-ATATATAG-TTTTGAAAA
1382022 ATATTTTTGAAAA-TATAT-TATATAGTTTTGAAAAA
1 ATATTTTTGAAAACTATATATATATAGTTTTG-AAAA
* * * *
1382057 ACATTTTTGAAAAC-AT-TTTGAAATCGTTTTGAAAA
1 ATATTTTTGAAAACTATATAT-ATATAGTTTTGAAAA
1382092 ATAT
1 ATAT
1382096 ATAATATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
33 5 0.08
34 8 0.12
35 25 0.38
36 14 0.22
38 13 0.20
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (36 bp):
ATATTTTTGAAAACTATATATATATAGTTTTGAAAA
Found at i:1382235 original size:17 final size:17
Alignment explanation
Indices: 1382215--1382259 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1382205 TTTTTTCCTC
1382215 TTTTATTTTTTATTTAT
1 TTTTATTTTTTATTTAT
*
1382232 TTTTATTATTTATTTAT
1 TTTTATTTTTTATTTAT
*
1382249 TTTTCTTTTTT
1 TTTTATTTTTT
1382260 TAGGGTCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTTTATTTAT
Found at i:1382420 original size:12 final size:12
Alignment explanation
Indices: 1382394--1382438 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1382384 TATTATATAG
*
1382394 TTTTGAAAATAAT
1 TTTTGAAAA-CAT
1382407 TTTTGAAAACAT
1 TTTTGAAAACAT
*
1382419 TTTTGAAAAC-G
1 TTTTGAAAACAT
1382430 TTTTGAAAA
1 TTTTGAAAA
1382439 ATATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 9 0.30
12 12 0.40
13 9 0.30
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.42
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:1382437 original size:347 final size:337
Alignment explanation
Indices: 1382025--1382670 Score: 1019
Period size: 347 Copynumber: 1.9 Consensus size: 337
1382015 TTTGAAAATA
*
1382025 TTTTTGAAAATATATTATATAGTTTTGAAAAAACATTTTTGAAAACATTTTGAAATCGTTTTGAA
1 TTTTTGAAAATATATTATATAGTTTTGAAAAAACATTTTTGAAAACATTTTGAAAACGTTTTGAA
1382090 AAATATATAATATATAATTTAGAAAATATTGTCGAATATATATATATATATATAATATATGACTT
66 AAATATATAATATATAATTTAGAAAATATTGTCG-A-ATATATATATATATAT-ATATATGACTT
1382155 TGAAAACACTTTTTAAAATATATGTAGTATGTAATTTTCATTACATTTTATTTTTTCCTCTTTTA
128 TGAAAACACTTTTTAAAATATATGTAGTATGTAATTTTCATTACATTTTA---TTT-CT-TTTT-
* * * * *
1382220 TTT-TTTA-TTTATTTTTATTATTTATTTATTTTTCTTTTTTTAGGGTCCAAAACAGCCCAATCG
187 TTTCCTCATTTTATTTAT-TTATTTATTTA--TCTCTTCTTTTAGGGTCCAAAACAGCCCAATCG
** *
1382283 GGTTTGGGCCTGAACCAGCCCAGTAAAGGTCCAAGGTTTTCACGTTTCAGCAAAGGCGTCGCACA
249 GGTTTGGGCCTGAACCAGCCCAACAAAGGTCCAAGGTTTTCACGCTTCAGCAAAGGCGTCGCACA
1382348 AATGAGGATTTATTTTCGATTTTT
314 AATGAGGATTTATTTTCGATTTTT
*
1382372 TTTTTGAAAATATATTATATAGTTTTGAAAATA-ATTTTTGAAAACATTTTTGAAAACGTTTTGA
1 TTTTTGAAAATATATTATATAGTTTTGAAAAAACATTTTTGAAAACA-TTTTGAAAACGTTTTGA
*
1382436 AAAATATATAATATATAATTTAGAAAATATTTTCGAATATATATATATATATATATATGACTTTG
65 AAAATATATAATATATAATTTAGAAAATATTGTCGAATATATATATATATATATATATGACTTTG
1382501 AAAACACTTTTTAAAATATATGTAGTATGTAATTTTCATTACATTTTATTTCTTTTTTTTCCTCA
130 AAAACACTTTTTAAAATATATGTAGTATGTAATTTTCATTACATTTTATTTCTTTTTTTTCCTCA
*
1382566 TTTTATTTATTTATTTATTTATCTCTTCTTTTAGGGTCCAAAATAGCCCAATCGGGTTTGGGCCT
195 TTTTATTTATTTATTTATTTATCTCTTCTTTTAGGGTCCAAAACAGCCCAATCGGGTTTGGGCCT
* * *
1382631 GAACCAGCCCAACAGAGGTCTAGGGTTTTCACGCTTCAGC
260 GAACCAGCCCAACAAAGGTCCAAGGTTTTCACGCTTCAGC
1382671 CGAGGCACTG
Statistics
Matches: 281, Mismatches: 15, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
337 75 0.27
338 3 0.01
339 17 0.06
340 10 0.04
341 3 0.01
344 61 0.22
345 16 0.06
346 14 0.05
347 82 0.29
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (337 bp):
TTTTTGAAAATATATTATATAGTTTTGAAAAAACATTTTTGAAAACATTTTGAAAACGTTTTGAA
AAATATATAATATATAATTTAGAAAATATTGTCGAATATATATATATATATATATATGACTTTGA
AAACACTTTTTAAAATATATGTAGTATGTAATTTTCATTACATTTTATTTCTTTTTTTTCCTCAT
TTTATTTATTTATTTATTTATCTCTTCTTTTAGGGTCCAAAACAGCCCAATCGGGTTTGGGCCTG
AACCAGCCCAACAAAGGTCCAAGGTTTTCACGCTTCAGCAAAGGCGTCGCACAAATGAGGATTTA
TTTTCGATTTTT
Found at i:1383043 original size:21 final size:21
Alignment explanation
Indices: 1383019--1383060 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1383009 TGAACCATCC
*
1383019 GAGATAACCGGGAACAACCCT
1 GAGATAACCAGGAACAACCCT
* *
1383040 GAGATAATCAGGAGCAACCCT
1 GAGATAACCAGGAACAACCCT
1383061 AAAATAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (21 bp):
GAGATAACCAGGAACAACCCT
Found at i:1384187 original size:18 final size:17
Alignment explanation
Indices: 1384133--1384181 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1384123 TTGGATCCTT
* *
1384133 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1384151 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1384169 AGTGCATTCGATG
1 AGTGCA-TCGATG
1384182 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1384286 original size:65 final size:64
Alignment explanation
Indices: 1384127--1384312 Score: 209
Period size: 65 Copynumber: 2.9 Consensus size: 64
1384117 TGACCGTTGG
*
1384127 ATCCTTAGTGCATCGGTGCACTAAG-A-GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAA
1 ATCCTTAGTGCATCGGTGCA-T--GTATGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAA
1384189 AT
63 AT
** ** * *
1384191 AGGCAGAGTGCATCGATGCATGTCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTTAGTGCATCGGTGCATGTAT-GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
1384256 -
64 T
* *
1384256 ATCCTTAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATACATTCGATGTT
1 ATCCTTAGTGCATCGGTGCAT-GTATGTGCATCGATGCATCAAATGCATTCGATGTT
1384313 CAATTTAATT
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
61 1 0.01
63 1 0.01
64 43 0.43
65 50 0.50
66 6 0.06
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
ATCCTTAGTGCATCGGTGCATGTATGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:1384351 original size:65 final size:65
Alignment explanation
Indices: 1384127--1384362 Score: 202
Period size: 65 Copynumber: 3.7 Consensus size: 65
1384117 TGACCGTTGG
* * * * *
1384127 ATCCTTAGTGCATCGGTGCA--CTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AA
1 ATCCTTAGTGCATCGATGCATGGTATG-GTGCATCGATGCATCAAATACATTCGATGTTTCATAA
1384189 A
65 A
** ** * *
1384190 TAGGCAGAGTGCATCGATGCAT-GTCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATA
1 -ATCCTTAGTGCATCGATGCATGGTATGGTGCATCGATGCATCAAATACATTCGATG-TTTCATA
1384254 AA
64 AA
* * *
1384256 ATCCTTAGTGCATCGGTGCATGGTAT-GTGCATCGATGCATGAAATACATTCGATG-TTCAATTT
1 ATCCTTAGTGCATCGATGCATGGTATGGTGCATCGATGCATCAAATACATTCGATGTTTC-A-TA
1384319 AA
64 AA
* *
1384321 TTCAC-T-GTGCATCGATGCATGG-ATTGGTGCATCGGTGCATCA
1 ATC-CTTAGTGCATCGATGCATGGTA-TGGTGCATCGATGCATCA
1384363 CTCTGAAAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 17
0.78 0.12 0.09
Matches are distributed among these distances:
63 4 0.03
64 60 0.43
65 70 0.50
66 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
ATCCTTAGTGCATCGATGCATGGTATGGTGCATCGATGCATCAAATACATTCGATGTTTCATAAA
Found at i:1390888 original size:22 final size:21
Alignment explanation
Indices: 1390846--1390885 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1390836 AAGACTATTT
1390846 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1390867 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1390886 ATAGAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1394371 original size:34 final size:35
Alignment explanation
Indices: 1394333--1394400 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 35
1394323 AGTTTGTCCA
1394333 TCTAATTTAAAATCCTACGTC-GTCCATGTATGTC
1 TCTAATTTAAAATCCTACGTCGGTCCATGTATGTC
1394367 TCTAATTTAAAATCCTACGTCGGTCCATGTATGT
1 TCTAATTTAAAATCCTACGTCGGTCCATGTATGT
1394401 AGTTGGGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (35 bp):
TCTAATTTAAAATCCTACGTCGGTCCATGTATGTC
Found at i:1396447 original size:20 final size:20
Alignment explanation
Indices: 1396400--1396447 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1396390 AAACTTGAAT
*
1396400 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1396420 TCACAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1396440 TCGCAACG
1 TCGCAACG
1396448 TGATTTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1398039 original size:42 final size:41
Alignment explanation
Indices: 1397980--1398075 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
1397970 CCCCACTTCG
* * * *
1397980 AGAGCCATCACCTGATCGAACCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCGAACCGA-TATACACCTCCACAACC
* *
1398022 AGAGCCATCACCTGATCGAGCCGATATACACCTCCACAACG
1 AGAGCCATCACCTGATCGAACCGATATACACCTCCACAACC
1398063 AGAGCCATCACCT
1 AGAGCCATCACCT
1398076 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 25 0.52
42 23 0.48
ACGTcount: A:0.30, C:0.38, G:0.17, T:0.16
Consensus pattern (41 bp):
AGAGCCATCACCTGATCGAACCGATATACACCTCCACAACC
Found at i:1398216 original size:21 final size:21
Alignment explanation
Indices: 1398189--1398241 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1398179 GTTAGGGGAG
*
1398189 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * **
1398210 TTGCGTGAGGAGGTTGGTACT
1 TTACGTGATGAGGTCAGTACT
1398231 TTACGTGATGA
1 TTACGTGATGA
1398242 CAATGGTGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Done.