Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 21
Found at i:1386689 original size:18 final size:18
Alignment explanation
Indices: 1386637--1386692 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1386627 TCTTATTAAG
* * *
1386637 TTAATTAGATATATATTA
1 TTAATTATAAATATATTT
* *
1386655 TTCATTTTAAA-ATATTT
1 TTAATTATAAATATATTT
1386672 TTAATTATAAATATATTT
1 TTAATTATAAATATATTT
1386690 TTA
1 TTA
1386693 TCGGATGTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTAATTATAAATATATTT
Found at i:1387244 original size:35 final size:36
Alignment explanation
Indices: 1387194--1387313 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
1387184 TGGCAACCAA
1387194 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
1387231 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
1387266 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1387303 -GTTGAAAAATG
1 CTTTGAAAAATG
1387314 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
35 32 0.41
36 18 0.23
37 28 0.36
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1391860 original size:37 final size:38
Alignment explanation
Indices: 1391814--1391899 Score: 122
Period size: 37 Copynumber: 2.3 Consensus size: 38
1391804 TGGAAACCAA
*
1391814 CTTTGAAAAATTG-GTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTGTTTTCAAAGTTTGGTAAATGTTT
* *
1391851 CTTTGAAAAATAGTTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTGTTTTCAAAGTTTGGTAAATGTTT
*
1391889 -GTTGAAAAATA
1 CTTTGAAAAATA
1391900 ATAATGGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 22 0.50
38 22 0.50
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (38 bp):
CTTTGAAAAATAGTGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1393619 original size:22 final size:21
Alignment explanation
Indices: 1393593--1393648 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1393583 AATGATCTAT
*
1393593 TTTAAAGTTAAATAAATAATTA
1 TTTAAA-TTAAATAAATAATAA
1393615 TTTAAA-TAAATTAAATAATAA
1 TTTAAATTAAA-TAAATAATAA
*
1393636 TTTTAATTAAATA
1 TTTAAATTAAATA
1393649 TTAAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 16 0.53
22 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAAATTAAATAAATAATAA
Found at i:1393631 original size:21 final size:22
Alignment explanation
Indices: 1393591--1393647 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1393581 CTAATGATCT
*
1393591 ATTTTAAAGTTAAA-TAAATAATT
1 ATTTTAAA--TAAATTAAATAATA
1393614 A-TTTAAATAAATTAAATAATA
1 ATTTTAAATAAATTAAATAATA
*
1393635 ATTTTAATTAAAT
1 ATTTTAAATAAAT
1393648 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 16 0.53
23 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTTAAATAAATTAAATAATA
Found at i:1393657 original size:17 final size:17
Alignment explanation
Indices: 1393623--1393657 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1393613 TATTTAAATA
*
1393623 AATTAAATAATAATTTT
1 AATTAAATAATAAATTT
*
1393640 AATTAAATATTAAATTT
1 AATTAAATAATAAATTT
1393657 A
1 A
1393658 TGGTTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATAAATTT
Found at i:1397201 original size:3 final size:3
Alignment explanation
Indices: 1397193--1397230 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1397183 GATTTTCATT
1397193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1397231 TGGTATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1397614 original size:42 final size:42
Alignment explanation
Indices: 1397551--1397631 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
1397541 ATGATGATCT
* *
1397551 TGGACGAGCGAAATAATGATGTTGATCCAACTTCTTATGTGA
1 TGGACGAGCAAAATAATGATGTTGATCCAACTACTTATGTGA
* *
1397593 TGGATGAGCAAAATGATGATGTTGATCCAACTACTTATG
1 TGGACGAGCAAAATAATGATGTTGATCCAACTACTTATG
1397632 CAATGGGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (42 bp):
TGGACGAGCAAAATAATGATGTTGATCCAACTACTTATGTGA
Found at i:1397921 original size:202 final size:203
Alignment explanation
Indices: 1397642--1398412 Score: 989
Period size: 202 Copynumber: 3.9 Consensus size: 203
1397632 CAATGGGATT
* *
1397642 GAGCTAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATA-AGTTCTTCT
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGA-AGAGTTCTTCT
* * *
1397706 CATTATGAACTCTCCACTAGAAATGTTGATCCTCC-CCTTTTTGTGATAGAATCGAACAAAGTGA
65 CATTATGAACTCTCCACTGGAAATGTTGATCCACCTCC-TTCTGTGATAGAATCGAACAAAGTGA
* * * *
1397770 TCA-GC-AGATCCAACTTCATATTG-GATGGATGAGCCAAGTATTAGTGTTGTTCTAACTCCTTA
129 TGATGCTA-ATCCAACTCCATA-TGCGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTA
1397832 TGTGATGGAAAC
192 TGTGATGGAAAC
* *
1397844 GAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATCGGAAGAGTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAAGAGTTCTTCTC
* * * * *
1397909 ATTATTAACTCTCCACTGGAAATGTTGATCTACCTCCTTCTGTGATGGAATCGAAAAAAGTGATT
66 ATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGATG
* * * *
1397974 ATGCTAATCCAACTCCACAT-AGATGGATGAGCCAAGCATTTGTGTTGTTCCAACTCCTTATGTG
131 ATGCTAATCCAACTCCATATGCGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATGTG
1398038 ATGGAAAC
196 ATGGAAAC
* * * *
1398046 AATCTAAGGTTGAACAAG---TTCTC-TTATGAACTTCTTCTCCCTCATCGGACGACTTCTTCTC
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAAGAGTTCTTCTC
* * * * *
1398107 A-T-T--A-TCTCCAATGGAAATGTTGATCCACCACTTTCTGTGATGGAATCAAACAAAGTGATG
66 ATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGATG
* * *
1398167 ATGCTAATCCAACTCCCTATGCGATGGATGATCCAAGTATTTGTGTTGTTCAAACTCTTTATGTG
131 ATGCTAATCCAACTCCATATGCGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATGTG
*
1398232 ATGGAAAA
196 ATGGAAAC
* * *
1398240 TAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-AGTAGGACGAGTTCTTCT
1 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCA-TCGGAAGAGTTCTTCT
* * * *
1398304 CATTATGAACCCTCCATTGGAAATGTTGATCCACCTCCTTCTGTGTTAGAATAGAACAAAGTGAT
65 CATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGAT
* * * *
1398369 GATGCTGATCCAACTCCATGTGCGATGGATGAGCAAAGTGTTTG
130 GATGCTAATCCAACTCCATATGCGATGGATGAGCCAAGTATTTG
1398413 CACAAGTTCT
Statistics
Matches: 497, Mismatches: 56, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
193 67 0.13
194 63 0.13
196 1 0.00
197 7 0.01
198 70 0.14
199 6 0.01
200 1 0.00
201 1 0.00
202 180 0.36
203 100 0.20
204 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (203 bp):
GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAAGAGTTCTTCTC
ATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATAGAATCGAACAAAGTGATG
ATGCTAATCCAACTCCATATGCGATGGATGAGCCAAGTATTTGTGTTGTTCAAACTCCTTATGTG
ATGGAAAC
Found at i:1398626 original size:117 final size:116
Alignment explanation
Indices: 1398417--1398688 Score: 438
Period size: 117 Copynumber: 2.3 Consensus size: 116
1398407 TGTTTGCACA
* * * *
1398417 AGTTCTTCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCCCCTTCTGTGATGTATCGAC
1 AGTTCTTCTCATTATGAAC-TCTCCACTGGAAATGTTGATCCACCCCCTTCTGTGATGAATCGAC
* *
1398482 CAAAGGTTTAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATG
65 CAAAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCGGATG
* *
1398534 AGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCCCCTTCTGTGAT-GAATCG-A
1398599 CC-AAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCGGATG
64 CCAAAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCGGATG
1398651 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
1398689 CTGGTTAATC
Statistics
Matches: 144, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
116 32 0.22
117 109 0.76
118 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (116 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCCCCTTCTGTGATGAATCGACC
AAAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCATCGGATG
Found at i:1399887 original size:56 final size:58
Alignment explanation
Indices: 1399820--1399932 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 58
1399810 ATTGATAACA
1399820 TTGAATTCAGCC-CCAAGCTTTGCATTGATTTTTTCC-AAGTTCTATCGCCCATTTAT
1 TTGAATTCAGCCTCCAAGCTTTGCATTGATTTTTTCCAAAGTTCTATCGCCCATTTAT
1399876 TTGAATTCAGCCTCCAAGCTTTGCATTGATTTTTTCCAAAGTTCTATCGCCCATTTA
1 TTGAATTCAGCCTCCAAGCTTTGCATTGATTTTTTCCAAAGTTCTATCGCCCATTTA
1399933 GTCGAAAGAG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 12 0.22
57 24 0.44
58 19 0.35
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (58 bp):
TTGAATTCAGCCTCCAAGCTTTGCATTGATTTTTTCCAAAGTTCTATCGCCCATTTAT
Found at i:1400345 original size:41 final size:41
Alignment explanation
Indices: 1400288--1400394 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
1400278 GCCCGAAGGT
*
1400288 CTTATAGAT-AGCCCGAATGACTTA-TCATCTTGCTCGAAA-A
1 CTTATAGATGA-CCCGAATGACTTAGT-ATCATGCTCGAAAGA
* *
1400328 GCTTATAGATGACCCGAAGGATTTAGGTATCATGCTCGAAAGA
1 -CTTATAGATGACCCGAATGACTTA-GTATCATGCTCGAAAGA
*
1400371 CTTACT-GATGGCCCGAATGACTTA
1 CTTA-TAGATGACCCGAATGACTTA
1400395 CTAAGTAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
41 20 0.36
42 32 0.58
43 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTATAGATGACCCGAATGACTTAGTATCATGCTCGAAAGA
Found at i:1400618 original size:242 final size:238
Alignment explanation
Indices: 1400151--1400785 Score: 927
Period size: 242 Copynumber: 2.7 Consensus size: 238
1400141 GAGGCTGAAA
* * *
1400151 GACTTACTAAGTAAGTATTTTGGAAATCGTTTTCTTACTTTTAAAAAAATCAATTTTCAGAAAAG
1 GACTTACTAAGTAAGAACTTTGGAAATTGTTTTCTTACTTTTAAAAAAATCAATTTTCAGAAAAG
1400216 ATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACATCCTGCC
66 ATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACATCCTGCC
* * * * * *
1400281 CGAAGGTCTTATAGATAGCCCGAATGACTTATCATCTTGCTCGAAAAGCTTATAGATGACCCGAA
131 CGAAGGTCTTATGGATGGCCCGAAGGAATTATCATCTTGCTCGAAAAGCTTATAGATCACACGAA
* * *
1400346 GGATTTAGGTATCATGCTCGAAAGACTTACTGATGGCCCGAA-T
196 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCC-AAGG
*
1400389 GACTTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAAAAAATTAATTTTCAGA
1 GACTTACTAAGTAAG-AACTTTGGAAATTGTTTTCTTACTTTT---AAAAAAATCAATTTTCAGA
* * * **
1400454 AAAGATTTAAATGAGAAGTTTTGGAAATCGCTTTCTCATTTTTTTAAAATCACGTGAAAACATTA
62 AAAGATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACATCC
* *
1400519 TGCCCGAAGGACTTATGGATGGCCCGGAGGAATTATCATCTTGCTCG-AAAGACTTATAGATCAC
127 TGCCCGAAGGTCTTATGGATGGCCCGAAGGAATTATCATCTTGCTCGAAAAG-CTTATAGATCAC
1400583 ACGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAGG
191 ACGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAGG
* *
1400631 GACTTACTAAGTAAGAACTTTGGGAATTGTTTTCTTACTTTT--AAAAATCAATTTCCAGAAAAG
1 GACTTACTAAGTAAGAACTTTGGAAATTGTTTTCTTACTTTTAAAAAAATCAATTTTCAGAAAAG
* * * *
1400694 ATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTTGAAAATAATGTGAAAACATCCTGCC
66 ATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACATCCTGCC
** *
1400759 TAAAGGTCTTACGGATGGCCCGAAGGA
131 CGAAGGTCTTATGGATGGCCCGAAGGA
1400786 CTTACTAATC
Statistics
Matches: 355, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
236 98 0.28
238 15 0.04
239 24 0.07
241 32 0.09
242 186 0.52
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (238 bp):
GACTTACTAAGTAAGAACTTTGGAAATTGTTTTCTTACTTTTAAAAAAATCAATTTTCAGAAAAG
ATTTAAATGAGAAGCTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACATCCTGCC
CGAAGGTCTTATGGATGGCCCGAAGGAATTATCATCTTGCTCGAAAAGCTTATAGATCACACGAA
GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAGG
Found at i:1400944 original size:61 final size:61
Alignment explanation
Indices: 1400853--1401008 Score: 190
Period size: 59 Copynumber: 2.6 Consensus size: 61
1400843 TTAAGTAATC
* * * * * *** *
1400853 GTCAAGAAAACTATGAAAATCAAACCTAGTTTCTTTTTTAAAATTTTTTTGAAAACATCAT
1 GTCAAGAAACCTCTGAAAATCAGACATAGTTTCTTTTTAAAAATGCATTTGAAAACACCAT
* * *
1400914 GTCAAGAAACCTCTAAAAATCAGACTTAGTTTC--TTTAAAAATGCATTTGAAAATACCAT
1 GTCAAGAAACCTCTGAAAATCAGACATAGTTTCTTTTTAAAAATGCATTTGAAAACACCAT
1400973 GTCAAGAAACCTCTGAAAATCAGACATAGTTTCTTT
1 GTCAAGAAACCTCTGAAAATCAGACATAGTTTCTTT
1401009 AAAGATATCA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 51 0.64
61 29 0.36
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (61 bp):
GTCAAGAAACCTCTGAAAATCAGACATAGTTTCTTTTTAAAAATGCATTTGAAAACACCAT
Found at i:1402847 original size:83 final size:79
Alignment explanation
Indices: 1402716--1402885 Score: 175
Period size: 83 Copynumber: 2.1 Consensus size: 79
1402706 AATTATCCTG
* * * *
1402716 AATATATTACGTAAGCATTAAAAGAATGTAATTTATATTACAACTCTTTTAATTGATATATATAT
1 AATATTTTAAGTAAACATTAAAAGAATGTAATTTAGATTACAACTC-TTTAA-TG-TATAT-T-T
1402781 AA-TTCGAAATAATTAAATA
61 AAGTTC-AAATAATTAAATA
* * *
1402800 AATATTTTAAGTAAACATT-AAAGATTGTAATTCT-GATTATAAGTCTTTAATGTATATTTAAGT
1 AATATTTTAAGTAAACATTAAAAGAATGTAATT-TAGATTACAACTCTTTAATGTATATTTAAGT
*
1402863 TCAATTAATTAAATA
65 TCAAATAATTAAATA
1402878 ATATATTT
1 A-ATATTT
1402886 ATTTATTAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
78 16 0.21
79 10 0.13
80 5 0.07
81 2 0.03
82 5 0.07
83 20 0.27
84 17 0.23
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (79 bp):
AATATTTTAAGTAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTAATGTATATTTAAGTT
CAAATAATTAAATA
Found at i:1410163 original size:28 final size:28
Alignment explanation
Indices: 1410130--1410197 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1410120 GAAAAGTAGA
* * * *
1410130 GTGTTTCTGGTTAATTTGGGGAAGTAAT
1 GTGTTTCAGGTTAATTTAGAGAAGCAAT
* *
1410158 GTGTTTCAGGTCAATTTAGAGAGGCAAT
1 GTGTTTCAGGTTAATTTAGAGAAGCAAT
1410186 GTGTTTCAGGTT
1 GTGTTTCAGGTT
1410198 GGCTTTTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.07, G:0.31, T:0.40
Consensus pattern (28 bp):
GTGTTTCAGGTTAATTTAGAGAAGCAAT
Found at i:1410963 original size:21 final size:21
Alignment explanation
Indices: 1410939--1411008 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
1410929 TCTTTTTTTC
1410939 CTTTTTTGT-TTTCTTTTCTCT
1 CTTTTTT-TCTTTCTTTTCTCT
1410960 CTTTTTTTACTTTCTTTTCT-T
1 CTTTTTTT-CTTTCTTTTCTCT
* *
1410981 TTTATTTTTCTTTATTTTCTCT
1 CTT-TTTTTCTTTCTTTTCTCT
1411003 CTTTTT
1 CTTTTT
1411009 ATATTTTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.02
21 23 0.55
22 18 0.43
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.77
Consensus pattern (21 bp):
CTTTTTTTCTTTCTTTTCTCT
Found at i:1410990 original size:17 final size:17
Alignment explanation
Indices: 1410916--1410993 Score: 54
Period size: 16 Copynumber: 4.6 Consensus size: 17
1410906 CATCTTGAAG
* *
1410916 TATTTTTCTTTCCTCTT
1 TATTTTTCTTTTCTTTT
* *
1410933 T-TTTTCCTTTTTTGTTT
1 TATTTTTCTTTTCT-TTT
* *
1410950 TCTTTTCTCTCTT-TTTT
1 TATTTT-TCTTTTCTTTT
*
1410967 TA-CTTTCTTTTCTTTT
1 TATTTTTCTTTTCTTTT
1410983 TATTTTTCTTT
1 TATTTTTCTTT
1410994 ATTTTCTCTC
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
15 5 0.11
16 17 0.37
17 15 0.33
18 5 0.11
19 4 0.09
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.77
Consensus pattern (17 bp):
TATTTTTCTTTTCTTTT
Found at i:1411015 original size:17 final size:18
Alignment explanation
Indices: 1410993--1411026 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1410983 TATTTTTCTT
1410993 TATTTTCTC-TCTTTTTA
1 TATTTTCTCTTCTTTTTA
*
1411010 TATTTTTTCTTCTTTTT
1 TATTTTCTCTTCTTTTT
1411027 GTTATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTCTCTTCTTTTTA
Found at i:1411288 original size:2 final size:2
Alignment explanation
Indices: 1411281--1411308 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1411271 AAAACAAGGG
1411281 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
1411309 TGAAAGGATA
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:1416571 original size:153 final size:154
Alignment explanation
Indices: 1416288--1416572 Score: 545
Period size: 153 Copynumber: 1.9 Consensus size: 154
1416278 CCCCCCCCCC
1416288 CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAAATAATAATAAAATGTTGCTG
1 CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAAATAATAATAAAATGTTGCTG
*
1416353 ATCTCTTTTGCTTACTATTTTGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTTAC
66 ATCTCTTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTTAC
1416418 TGGCTCTTACAATTTTTTTCTTCT
131 TGGCTCTTACAATTTTTTTCTTCT
*
1416442 CCCC-CCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAAATAATAATAAAATGTTGTTG
1 CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAAATAATAATAAAATGTTGCTG
1416506 ATCTCTTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTTAC
66 ATCTCTTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTTAC
1416571 TG
131 TG
1416573 ATGGCAGCAA
Statistics
Matches: 129, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
153 125 0.97
154 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (154 bp):
CCCCGCCGAGAGGATCCCCTTCCCCCTTTTGATGGGTTCTCCCAAATAATAATAAAATGTTGCTG
ATCTCTTTTGCTTACTATTTAGGTTTTACTGGAACAAGGATGGCATGGTAGCAGGGAGATCTTAC
TGGCTCTTACAATTTTTTTCTTCT
Found at i:1418717 original size:3 final size:3
Alignment explanation
Indices: 1418697--1418741 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1418687 TTATTGTATC
* * *
1418697 ATA ATA AGA ATA ACA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1418742 GAGATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1418951 original size:2 final size:2
Alignment explanation
Indices: 1418946--1419010 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
1418936 TGTGTGTGTG
1418946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1418987 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1419011 CCTAAAAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1420923 original size:3 final size:3
Alignment explanation
Indices: 1420917--1420989 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
1420907 TATAATAATA
* *
1420917 ATT ATT ATT ATT A-T ATT ATT A-A ATT ATT ATT ATTT ATT A-A ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* *
1420960 ATT ATT ATT ATT AAT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1420990 TTACAGTTAC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1420925 original size:18 final size:18
Alignment explanation
Indices: 1420904--1420988 Score: 55
Period size: 18 Copynumber: 4.5 Consensus size: 18
1420894 TTATAAAAAA
* *
1420904 TATTATAATAATAATTAT
1 TATTATTATAATAATAAT
* *
1420922 TATTATTATATTATTAAAT
1 TATTATTATAATAAT-AAT
* *
1420941 TATTATTATTTATTAAATTAT
1 TATTATTA--TAAT-AATAAT
*
1420962 TATTATTATTAATATTAA-
1 TATTATTA-TAATAATAAT
1420980 TATTATTAT
1 TATTATTAT
1420989 TTTACAGTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.02
18 20 0.37
19 13 0.24
20 4 0.07
21 14 0.26
22 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTATAATAATAAT
Found at i:1420962 original size:12 final size:11
Alignment explanation
Indices: 1420916--1420989 Score: 59
Period size: 11 Copynumber: 6.9 Consensus size: 11
1420906 TTATAATAAT
1420916 AATTATTATT-
1 AATTATTATTA
*
1420926 ATTATATTATTA
1 AAT-TATTATTA
1420938 AATTATTATT-
1 AATTATTATTA
1420948 -A-T-TTATTA
1 AATTATTATTA
1420956 AATTATTATTA
1 AATTATTATTA
* *
1420967 TTATTAATATTA
1 -AATTATTATTA
1420979 ATATTATTATT
1 A-ATTATTATT
1420990 TTACAGTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 2 0.04
10 3 0.06
11 20 0.40
12 19 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
AATTATTATTA
Found at i:1420989 original size:18 final size:17
Alignment explanation
Indices: 1420923--1420989 Score: 100
Period size: 18 Copynumber: 3.9 Consensus size: 17
1420913 AATAATTATT
1420923 ATTATTA-TATTATTAA
1 ATTATTATTATTATTAA
1420939 ATTATTATTATTTATTAA
1 ATTATTATTA-TTATTAA
1420957 ATTATTATTATTATTAA
1 ATTATTATTATTATTAA
*
1420974 TATTAATATTATTATT
1 -ATTATTATTATTATT
1420990 TTACAGTTAC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
16 7 0.15
17 9 0.19
18 31 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTATTATTATTAA
Found at i:1421181 original size:19 final size:19
Alignment explanation
Indices: 1421157--1421195 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1421147 ACAGCCCTCT
*
1421157 ATCCCACCGACGCCGAGCC
1 ATCCCACCAACGCCGAGCC
1421176 ATCCCACCAACGCCGAGCC
1 ATCCCACCAACGCCGAGCC
1421195 A
1 A
1421196 CTGAATGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.51, G:0.18, T:0.05
Consensus pattern (19 bp):
ATCCCACCAACGCCGAGCC
Found at i:1422487 original size:50 final size:47
Alignment explanation
Indices: 1422398--1422490 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 47
1422388 TATATACATG
* * *
1422398 TTATATTATATACCTATATATAAATTTATTAAATTATTATTACCCTT
1 TTATATTATATACATATATATAAATATATTAAATGATTATTACCCTT
* *
1422445 TTATATTCATATATATATATATATATATATTACAAATGATTATTAC
1 TTATATT-ATATACATATATATAAATATATT--AAATGATTATTAC
1422491 ATATTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 7 0.18
48 19 0.50
50 12 0.32
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (47 bp):
TTATATTATATACATATATATAAATATATTAAATGATTATTACCCTT
Found at i:1425651 original size:2 final size:2
Alignment explanation
Indices: 1425641--1425672 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1425631 CAACAAAAAA
1425641 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1425673 CAATAAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1427523 original size:18 final size:18
Alignment explanation
Indices: 1427500--1427582 Score: 123
Period size: 18 Copynumber: 4.6 Consensus size: 18
1427490 TTCAGTTTTA
*
1427500 AACCTAAAATATGGTTAT
1 AACCTAAAATATGGTTAC
1427518 AACCTAAAATATGGTTAC
1 AACCTAAAATATGGTTAC
*
1427536 AACCTAAAAACAT-GTTAC
1 AACCT-AAAATATGGTTAC
*
1427554 AACCCAAAATATGGTTAC
1 AACCTAAAATATGGTTAC
1427572 AACCTAAAATA
1 AACCTAAAATA
1427583 AGTTAAGTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
17 6 0.10
18 46 0.79
19 6 0.10
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.25
Consensus pattern (18 bp):
AACCTAAAATATGGTTAC
Found at i:1438456 original size:24 final size:24
Alignment explanation
Indices: 1438400--1438457 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1438390 CACCGAAGTG
* *
1438400 CCACGTAAAATTTGTCCTGAAGGA
1 CCACGTAGAATTTATCCTGAAGGA
*
1438424 CCACATAGAATTTATCCTGAAGGA
1 CCACGTAGAATTTATCCTGAAGGA
**
1438448 GTACGTAGAA
1 CCACGTAGAA
1438458 ATGTCTCGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (24 bp):
CCACGTAGAATTTATCCTGAAGGA
Found at i:1441414 original size:18 final size:17
Alignment explanation
Indices: 1441357--1441585 Score: 181
Period size: 18 Copynumber: 12.6 Consensus size: 17
1441347 AATCTGGTTC
*
1441357 ACAACCTAAAATTCAGTTT
1 ACAACCTAAAAAT-AG-TT
*
1441376 ACAACCTAAAAACAGGTTT
1 ACAACCTAAAAATA-G-TT
*
1441395 ACAAACTAAAAACTAGTT
1 ACAACCTAAAAA-TAGTT
*
1441413 ACAACCTAAAATATGGTT
1 ACAACCTAAAA-ATAGTT
*
1441431 ACAACCTAAAATATGGTT
1 ACAACCTAAAA-ATAGTT
* *
1441449 ACAACATAAAAAAATGTT
1 ACAACCTAAAAATA-GTT
* *
1441467 AAAACCTAAAATATGGTT
1 ACAACCTAAAA-ATAGTT
*
1441485 ACAACCTAAAAACATGTT
1 ACAACCTAAAAATA-GTT
* *
1441503 ACAATCTAAAATATTGTT
1 ACAACCTAAAA-ATAGTT
1441521 ACAACCTTAAAACAT-GTT
1 ACAACC-TAAAA-ATAGTT
* *
1441539 ACAACCTAAAATATGGTA
1 ACAACCTAAAA-ATAGTT
*
1441557 ACAACCTAAAAACAAGTT
1 ACAACCTAAAAA-TAGTT
1441575 ACAACCTAAAA
1 ACAACCTAAAA
1441586 TATGATTATT
Statistics
Matches: 174, Mismatches: 26, Indels: 21
0.79 0.12 0.10
Matches are distributed among these distances:
17 10 0.06
18 126 0.72
19 37 0.21
20 1 0.01
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (17 bp):
ACAACCTAAAAATAGTT
Found at i:1441440 original size:36 final size:34
Alignment explanation
Indices: 1441357--1441589 Score: 218
Period size: 36 Copynumber: 6.4 Consensus size: 34
1441347 AATCTGGTTC
* *
1441357 ACAACCTAAAAT-TCAGTTTACAACCTAAAAACAGGTTT
1 ACAACCTAAAATAT--GGTTACAACCT-AAAA-ATG-TT
* *
1441395 ACAAACTAAAA-ACTAGTTACAACCTAAAATATGGTT
1 ACAACCTAAAATA-TGGTTACAACCTAAAA-AT-GTT
*
1441431 ACAACCTAAAATATGGTTACAACATAAAAAAATGTT
1 ACAACCTAAAATATGGTTACAACCT--AAAAATGTT
*
1441467 AAAACCTAAAATATGGTTACAACCTAAAAACATGTT
1 ACAACCTAAAATATGGTTACAACCT-AAAA-ATGTT
* *
1441503 ACAATCTAAAATATTGTTACAACCTTAAAACATGTT
1 ACAACCTAAAATATGGTTACAACC-TAAAA-ATGTT
* *
1441539 ACAACCTAAAATATGGTAACAACCTAAAAACAAGTT
1 ACAACCTAAAATATGGTTACAACCT-AAAA-ATGTT
1441575 ACAACCTAAAATATG
1 ACAACCTAAAATATG
1441590 ATTATTAACA
Statistics
Matches: 169, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
35 6 0.04
36 134 0.79
37 14 0.08
38 14 0.08
39 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (34 bp):
ACAACCTAAAATATGGTTACAACCTAAAAATGTT
Found at i:1441492 original size:72 final size:72
Alignment explanation
Indices: 1441343--1441589 Score: 261
Period size: 72 Copynumber: 3.4 Consensus size: 72
1441333 GGTTTTCAAT
* * *
1441343 CTAAAATCTGGTTCACAACCTAAAAT-TCAGTTTACAACCTAAAAACAGGTTTACAAA-CTAAAA
1 CTAAAATATGGTT-ACAACCTAAAATAT--GGTTACAACCTAAAAACATG-TTA-AAACCTAAAA
*
1441406 -ACTAGTTACAAC
61 TA-TGGTTACAAC
* *
1441418 CTAAAATATGGTTACAACCTAAAATATGGTTACAACATAAAAAAATGTTAAAACCTAAAATATGG
1 CTAAAATATGGTTACAACCTAAAATATGGTTACAACCTAAAAACATGTTAAAACCTAAAATATGG
1441483 TTACAAC
66 TTACAAC
* * * * *
1441490 CTAAAAACAT-GTTACAATCTAAAATATTGTTACAACCTTAAAACATGTTACAACCTAAAATATG
1 CT-AAAATATGGTTACAACCTAAAATATGGTTACAACCTAAAAACATGTTAAAACCTAAAATATG
*
1441554 GTAACAAC
65 GTTACAAC
**
1441562 CTAAAA-ACAAGTTACAACCTAAAATATG
1 CTAAAATA-TGGTTACAACCTAAAATATG
1441590 ATTATTAACA
Statistics
Matches: 149, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
70 1 0.01
71 7 0.05
72 93 0.62
73 23 0.15
74 12 0.08
75 13 0.09
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (72 bp):
CTAAAATATGGTTACAACCTAAAATATGGTTACAACCTAAAAACATGTTAAAACCTAAAATATGG
TTACAAC
Found at i:1448069 original size:20 final size:20
Alignment explanation
Indices: 1448031--1448070 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1448021 TTTTTTAGTA
*
1448031 TTATTACATTATATCTTATT
1 TTATTACATTATATATTATT
1448051 TTATTATCATTA-ATATTATT
1 TTATTA-CATTATATATTATT
1448071 AATATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTACATTATATATTATT
Found at i:1449501 original size:20 final size:21
Alignment explanation
Indices: 1449469--1449508 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1449459 AAAGATTTTT
1449469 ATTTTATAATGTTA-AAATAG
1 ATTTTATAATGTTACAAATAG
1449489 ATTTT-TAATTGTTACAAATA
1 ATTTTATAA-TGTTACAAATA
1449509 TAGTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 10 0.56
21 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTTTATAATGTTACAAATAG
Found at i:1449551 original size:43 final size:44
Alignment explanation
Indices: 1449504--1449605 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 44
1449494 TAATTGTTAC
* *
1449504 AAATATAGTATATTATTATAAAATATATTGTTTTAACCGTTT-A
1 AAATATAGTATATTATTATAAAATATATTATTTTAACCATTTAA
* * * **
1449547 AAATATAATAAATAATTATAAAATATATTATTTTAATTATTTAA
1 AAATATAGTATATTATTATAAAATATATTATTTTAACCATTTAA
1449591 AAATATTAGTATATT
1 AAATA-TAGTATATT
1449606 CAAATTGAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 35 0.74
44 6 0.13
45 6 0.13
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (44 bp):
AAATATAGTATATTATTATAAAATATATTATTTTAACCATTTAA
Found at i:1454854 original size:28 final size:28
Alignment explanation
Indices: 1454776--1454930 Score: 150
Period size: 29 Copynumber: 5.4 Consensus size: 28
1454766 CATTTTACAG
** * *
1454776 AAATAGCACCATTTTTAAAATAATTACCA
1 AAATAGCACC-TTTTCGAATTAATTCCCA
** *
1454805 AAATAATACCTTTTCAAATTAAATTCCCA
1 AAATAGCACCTTTTCGAATT-AATTCCCA
1454834 AAATAGCA-CTTTTCGAATTAAATTCCCA
1 AAATAGCACCTTTTCGAATT-AATTCCCA
1454862 AAATAGCACCCCTTTTCGAATTAATTCCCA
1 AAATAGCA--CCTTTTCGAATTAATTCCCA
* * *
1454892 AAATAACACCCATTTCGAAATAATTCCCA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
*
1454921 AAATATCACC
1 AAATAGCACC
1454931 CGGTCAACTG
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
28 37 0.34
29 47 0.43
30 15 0.14
31 11 0.10
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.30
Consensus pattern (28 bp):
AAATAGCACCTTTTCGAATTAATTCCCA
Found at i:1454884 original size:59 final size:58
Alignment explanation
Indices: 1454813--1454931 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 58
1454803 CAAAATAATA
* * *
1454813 CCTTTTCAAATTAAATTCCCAAAATAGCA-CTTTTCGAATTAAATTCCCAAAATAGCACC
1 CCTTTTCAAATT-AATTCCCAAAATAACACCATTTCGAAAT-AATTCCCAAAATAGCACC
* *
1454872 CCTTTTCGAATTAATTCCCAAAATAACACCCATTTCGAAATAATTCCCAAAATATCACC
1 CCTTTTCAAATTAATTCCCAAAATAACA-CCATTTCGAAATAATTCCCAAAATAGCACC
1454931 C
1 C
1454932 GGTCAACTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
58 15 0.28
59 29 0.55
60 9 0.17
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.29
Consensus pattern (58 bp):
CCTTTTCAAATTAATTCCCAAAATAACACCATTTCGAAATAATTCCCAAAATAGCACC
Found at i:1454954 original size:17 final size:17
Alignment explanation
Indices: 1454932--1454969 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1454922 AATATCACCC
* *
1454932 GGTCAACTGTCGGGTCG
1 GGTCAACAGTCGGATCG
1454949 GGTCAACAGTCGGATCG
1 GGTCAACAGTCGGATCG
1454966 GGTC
1 GGTC
1454970 GGGTCGGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.39, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGATCG
Found at i:1459539 original size:8 final size:8
Alignment explanation
Indices: 1459526--1459598 Score: 56
Period size: 8 Copynumber: 10.1 Consensus size: 8
1459516 AACTTAGTTG
1459526 TAATTTTA
1 TAATTTTA
1459534 TAATTTTA
1 TAATTTTA
1459542 T--TTTTA
1 TAATTTTA
1459548 T-ATCTTTA
1 TAAT-TTTA
1459556 T-ATTTTA
1 TAATTTTA
1459563 T--TTTTA
1 TAATTTTA
*
1459569 -GATTTTA
1 TAATTTTA
1459576 TAA-TTT-
1 TAATTTTA
1459582 TAATTTTA
1 TAATTTTA
*
1459590 TAAATTTA
1 TAATTTTA
1459598 T
1 T
1459599 GTTATGTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
6 14 0.25
7 17 0.30
8 25 0.45
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (8 bp):
TAATTTTA
Found at i:1459548 original size:6 final size:7
Alignment explanation
Indices: 1459528--1459591 Score: 71
Period size: 8 Copynumber: 9.1 Consensus size: 7
1459518 CTTAGTTGTA
1459528 ATTTTAT
1 ATTTTAT
1459535 AATTTTAT
1 -ATTTTAT
1459543 -TTTTAT
1 ATTTTAT
1459549 ATCTTTAT
1 AT-TTTAT
1459557 ATTTTAT
1 ATTTTAT
*
1459564 -TTTTAG
1 ATTTTAT
1459570 ATTTTAT
1 ATTTTAT
1459577 AATTTTA-
1 -ATTTTAT
1459584 ATTTTAT
1 ATTTTAT
1459591 A
1 A
1459592 AATTTATGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 17 0.35
7 12 0.24
8 20 0.41
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:1459562 original size:21 final size:21
Alignment explanation
Indices: 1459528--1459591 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
1459518 CTTAGTTGTA
1459528 ATTTTATAATTTTATTTTTAT
1 ATTTTATAATTTTATTTTTAT
*
1459549 ATCTTTAT-ATTTTATTTTTAG
1 AT-TTTATAATTTTATTTTTAT
*
1459570 ATTTTATAATTTTAATTTTAT
1 ATTTTATAATTTTATTTTTAT
1459591 A
1 A
1459592 AATTTATGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 5 0.13
21 28 0.74
22 5 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTATAATTTTATTTTTAT
Found at i:1459637 original size:14 final size:14
Alignment explanation
Indices: 1459527--1459639 Score: 65
Period size: 14 Copynumber: 8.1 Consensus size: 14
1459517 ACTTAGTTGT
1459527 AATTTTATAATTTT-
1 AATTTTAT-ATTTTA
*
1459541 ATTTTTATATCTTTA
1 AATTTTATAT-TTTA
*
1459556 TATTTTAT-TTTTA
1 AATTTTATATTTTA
*
1459569 GATTTTATAATTTT-
1 AATTTTAT-ATTTTA
*
1459583 AATTTTATAAATTTA
1 AATTTTAT-ATTTTA
** * * *
1459598 TGTTATGTATTATA
1 AATTTTATATTTTA
1459612 AA-TTTA-AGTTTTA
1 AATTTTATA-TTTTA
1459625 AATTTTATATTTTA
1 AATTTTATATTTTA
1459639 A
1 A
1459640 TGTATTTTTA
Statistics
Matches: 74, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
12 1 0.01
13 21 0.28
14 37 0.50
15 15 0.20
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.62
Consensus pattern (14 bp):
AATTTTATATTTTA
Found at i:1461271 original size:55 final size:55
Alignment explanation
Indices: 1461133--1461274 Score: 205
Period size: 55 Copynumber: 2.6 Consensus size: 55
1461123 AGAAATGGAA
* * * * * *
1461133 AGGGTATTGATAAACTCATCAGTGTATCAATACACAAATAACATTCGATGTTTTG
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTTG
1461188 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAGA-ATTCGATATTTTG
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATA-ACATTCGATATTTTG
*
1461243 CGGGTATCGATACACTCCTCAGTGTACCGATA
1 AGGGTATCGATACACTCCTCAGTGTACCGATA
1461275 AACACTCATA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 78 0.99
56 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (55 bp):
AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGATATTTTG
Found at i:1467425 original size:21 final size:21
Alignment explanation
Indices: 1467400--1467506 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 21
1467390 GTAATTTGCA
1467400 CTGAAGTGCCACATAATTATC
1 CTGAAGTGCCACATAATTATC
1467421 CTGAA-TGACCACA-AAGTT-TGC
1 CTGAAGTG-CCACATAA-TTAT-C
*
1467442 ATCGAAGTGCCACATAGGATTGCA-C
1 CT-GAAGTGCCACATA--ATT--ATC
*
1467467 C-GAAGTGCCACATATTTATC
1 CTGAAGTGCCACATAATTATC
* *
1467487 CCGGAG-GACCACATAATTAT
1 CTGAAGTG-CCACATAATTAT
1467507 ACCAAAGAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 28
0.67 0.05 0.28
Matches are distributed among these distances:
19 1 0.01
20 8 0.12
21 30 0.45
22 8 0.12
23 16 0.24
24 2 0.03
25 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
CTGAAGTGCCACATAATTATC
Found at i:1468116 original size:55 final size:55
Alignment explanation
Indices: 1468021--1468216 Score: 159
Period size: 55 Copynumber: 3.6 Consensus size: 55
1468011 ATACTTAGGT
* * **
1468021 GTATCGATAC-CTACAC-ATGTACCGATAC-CTAAATTGCATTCGAAATGGCAAGG
1 GTATCGATACACTCCTCAATGTACCGATACAC-AAATAACATTCGAAATGGCAAGG
* * ** ****
1468074 GTATCGATATACTCCTCAATGTATCGATACACAAATAACATTCGATGTTTTGAGG
1 GTATCGATACACTCCTCAATGTACCGATACACAAATAACATTCGAAATGGCAAGG
* * ** *
1468129 GTATCGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATGTTTTGC--GG
1 GTATCGATACACTCCTCAATGTACCGATACACAAATAACATTCGA--AATGGCAAGG
* *
1468184 GTATCGATACACTCGTCAGTGTACCGATACACA
1 GTATCGATACACTCCTCAATGTACCGATACACA
1468217 CTCATACAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
53 9 0.08
54 4 0.03
55 101 0.86
56 1 0.01
57 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (55 bp):
GTATCGATACACTCCTCAATGTACCGATACACAAATAACATTCGAAATGGCAAGG
Found at i:1472301 original size:13 final size:13
Alignment explanation
Indices: 1472283--1472313 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1472273 TACTACCATC
1472283 GTTTTGTCAAAGA
1 GTTTTGTCAAAGA
1472296 GTTTTGTCAAAGA
1 GTTTTGTCAAAGA
1472309 GTTTT
1 GTTTT
1472314 CAATGATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (13 bp):
GTTTTGTCAAAGA
Found at i:1475860 original size:20 final size:20
Alignment explanation
Indices: 1475837--1475876 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1475827 AGTTTTATAT
*
1475837 TTAATACAGATGGAACAATA
1 TTAATACAGAAGGAACAATA
1475857 TTAATACAGAAGGAACAATA
1 TTAATACAGAAGGAACAATA
1475877 CCTGCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
TTAATACAGAAGGAACAATA
Found at i:1485860 original size:38 final size:38
Alignment explanation
Indices: 1485781--1485860 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1485771 ACCCGACCCG
* * * *
1485781 AATATCACACTTAAAAAAACCCGACCAGACTCGACTCA
1 AATACCACACTTAAAAAAAACCGACCAGACCCGACTAA
*
1485819 AATACCACACTTAAAAAAAACCGACCCGACCCGAAC-AA
1 AATACCACACTTAAAAAAAACCGACCAGACCCG-ACTAA
1485857 AATA
1 AATA
1485861 AAGTTTCATC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 34 0.94
39 2 0.06
ACGTcount: A:0.49, C:0.31, G:0.07, T:0.12
Consensus pattern (38 bp):
AATACCACACTTAAAAAAAACCGACCAGACCCGACTAA
Found at i:1486235 original size:27 final size:24
Alignment explanation
Indices: 1486205--1486271 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
1486195 ATCCAACAAG
1486205 GGAATTGAATTCCATCCATTTTTTGAT
1 GGAATTGAATTCCATCCA---TTTGAT
* * *
1486232 GGAATTCACTTTCCCT-CATTTGAT
1 GGAATTGA-ATTCCATCCATTTGAT
1486256 GGAATTGAATTCCATC
1 GGAATTGAATTCCATC
1486272 AGGGATTCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
23 5 0.16
24 13 0.41
27 9 0.28
28 5 0.16
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
GGAATTGAATTCCATCCATTTGAT
Found at i:1489442 original size:9 final size:9
Alignment explanation
Indices: 1489416--1489461 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1489406 CATTTGTACC
1489416 AATTTAATA
1 AATTTAATA
1489425 AA-TTAATA
1 AATTTAATA
*
1489433 AATTTTAT-
1 AATTTAATA
1489441 AATGTTCAATA
1 AAT-TT-AATA
1489452 AATTTAATA
1 AATTTAATA
1489461 A
1 A
1489462 CTATTTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 11 0.35
9 13 0.42
10 4 0.13
11 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
AATTTAATA
Found at i:1492339 original size:38 final size:38
Alignment explanation
Indices: 1492288--1492364 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1492278 AGACCCCACT
1492288 TTGAATGGTGTGATTGTAGTTAGAATAGGTGGGGAACC
1 TTGAATGGTGTGATTGTAGTTAGAATAGGTGGGGAACC
1492326 TTGAATGGTGTGATTGTAGTTAGAATAGGTGGGGAACC
1 TTGAATGGTGTGATTGTAGTTAGAATAGGTGGGGAACC
1492364 T
1 T
1492365 ACTCTTCCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (38 bp):
TTGAATGGTGTGATTGTAGTTAGAATAGGTGGGGAACC
Found at i:1494597 original size:12 final size:12
Alignment explanation
Indices: 1494567--1494610 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1494557 CATTTGCCAC
1494567 TTTCATATTCAT
1 TTTCATATTCAT
**
1494579 TCACATATTCAT
1 TTTCATATTCAT
1494591 TTTCATATTTCAT
1 TTTCATA-TTCAT
*
1494604 GTTCATA
1 TTTCATA
1494611 ATAAATACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:1494688 original size:19 final size:19
Alignment explanation
Indices: 1494666--1494718 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1494656 ATTTCCAAAT
*
1494666 TCATAACTTATTTTTAGAC
1 TCATAGCTTATTTTTAGAC
* * * *
1494685 TCATAGCTTACTGTCAGAT
1 TCATAGCTTATTTTTAGAC
1494704 TCATAGCTTATTTTT
1 TCATAGCTTATTTTT
1494719 CAAATTCATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (19 bp):
TCATAGCTTATTTTTAGAC
Found at i:1495045 original size:16 final size:18
Alignment explanation
Indices: 1495024--1495058 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1495014 CCAACTCTTC
1495024 ATATCATAA-CAT-TTAT
1 ATATCATAATCATATTAT
1495040 ATATCATAATCATATTAT
1 ATATCATAATCATATTAT
1495058 A
1 A
1495059 ATTATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATCATAATCATATTAT
Found at i:1503323 original size:21 final size:21
Alignment explanation
Indices: 1503299--1503342 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1503289 AAAGACAAGG
1503299 AAAAT-AACAAGTAAAACTAAA
1 AAAATGAACAAGTAAAAC-AAA
*
1503320 AAAATGAAGAAGTAAAACAAA
1 AAAATGAACAAGTAAAACAAA
1503341 AA
1 AA
1503343 TGCTATGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAATGAACAAGTAAAACAAA
Found at i:1505076 original size:25 final size:25
Alignment explanation
Indices: 1505000--1505079 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
1504990 GATTTTTCCT
* *
1505000 GAAGGACCGCTTAG-AATTTGTCTC
1 GAAGGAGCACTTAGAAATTTGTCTC
* * ** *
1505024 GATGGAGCACGTAGAAATTCATCCC
1 GAAGGAGCACTTAGAAATTTGTCTC
1505049 GAAGGAGCACTTAGAAATTTGTCTC
1 GAAGGAGCACTTAGAAATTTGTCTC
1505074 GAAGGA
1 GAAGGA
1505080 CCGCATAGAA
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
24 10 0.23
25 33 0.77
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (25 bp):
GAAGGAGCACTTAGAAATTTGTCTC
Found at i:1505229 original size:15 final size:15
Alignment explanation
Indices: 1505209--1505255 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1505199 CAAACACATC
*
1505209 CACATAGTACATATT
1 CACATAGAACATATT
* *
1505224 CACATAAAACATTTT
1 CACATAGAACATATT
*
1505239 CACGTAGAACATATT
1 CACATAGAACATATT
1505254 CA
1 CA
1505256 TATCCAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (15 bp):
CACATAGAACATATT
Found at i:1505320 original size:17 final size:17
Alignment explanation
Indices: 1505298--1505336 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1505288 TACCATTTAT
*
1505298 ATAAAACATTATATAAA
1 ATAAAACATTACATAAA
* *
1505315 ATAAAATATTCCATAAA
1 ATAAAACATTACATAAA
1505332 ATAAA
1 ATAAA
1505337 TAAAATTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAACATTACATAAA
Found at i:1508777 original size:28 final size:28
Alignment explanation
Indices: 1508737--1508790 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1508727 GATAGCCTTA
1508737 ATCTTCTAAGGATCCACCCGAATCCCAT
1 ATCTTCTAAGGATCCACCCGAATCCCAT
*
1508765 ATCTTCTGAGGATCCACCCGAATCCC
1 ATCTTCTAAGGATCCACCCGAATCCC
1508791 CTCTGCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (28 bp):
ATCTTCTAAGGATCCACCCGAATCCCAT
Found at i:1511985 original size:24 final size:24
Alignment explanation
Indices: 1511944--1511990 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1511934 CCACTGCTCA
* ** *
1511944 TATAATTTGCACTGAAGTGCCACG
1 TATAATATGCACCAAAGTACCACG
1511968 TATAATATGCACCAAAGTACCAC
1 TATAATATGCACCAAAGTACCAC
1511991 ATAGATTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (24 bp):
TATAATATGCACCAAAGTACCACG
Found at i:1512093 original size:26 final size:25
Alignment explanation
Indices: 1512013--1512094 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
1512003 CAAAAGAGAG
*
1512013 CGTAG-AATTTGTCCCGAAGTACCA
1 CGTAGAAATTTGTCCCGAAGGACCA
* *
1512037 CGTAGAAATTTGTCCTGAATGACCA
1 CGTAGAAATTTGTCCCGAAGGACCA
* *
1512062 TGTAGAAATTTGTCCCCGAAGGACCG
1 CGTAGAAATTTGT-CCCGAAGGACCA
1512088 CGTAGAA
1 CGTAGAA
1512095 TCCTCGACTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.10
25 28 0.58
26 15 0.31
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (25 bp):
CGTAGAAATTTGTCCCGAAGGACCA
Found at i:1512249 original size:30 final size:30
Alignment explanation
Indices: 1512196--1512265 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1512186 AAGTATCATT
*
1512196 TATTCACATCAAACACATCCACGTAGTAA-A
1 TATTCACATAAAACACATCCACGTAG-AACA
** *
1512226 TATTCACATAAAACATTTTCACGTAGAACA
1 TATTCACATAAAACACATCCACGTAGAACA
*
1512256 TATTCGCATA
1 TATTCACATA
1512266 CAACTAACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (30 bp):
TATTCACATAAAACACATCCACGTAGAACA
Found at i:1516167 original size:46 final size:46
Alignment explanation
Indices: 1516016--1516177 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
1516006 ATCAATTTCA
* * *
1516016 CATTTATGGTATCCTTTCATG-CTTTTATGCACCATTATACA-TTT
1 CATTTATGGCATCCTTTCATGCCTTTTATGCACCGTTATGCATTTT
* * *
1516060 CATTTGTGGC-TAC-TTCATGCCTTTAATGCA-CGTTATGCATTTT
1 CATTTATGGCATCCTTTCATGCCTTTTATGCACCGTTATGCATTTT
1516103 CA-TTATGGCATCCTTTCATGCCTTTTATGCACCGTTATGCATTTT
1 CATTTATGGCATCCTTTCATGCCTTTTATGCACCGTTATGCATTTT
*
1516148 CATTTATGGCATCCTTTCATGTCTTTTATG
1 CATTTATGGCATCCTTTCATGCCTTTTATG
1516178 TCAATTAATG
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
42 19 0.19
43 18 0.18
44 24 0.24
45 15 0.15
46 26 0.25
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (46 bp):
CATTTATGGCATCCTTTCATGCCTTTTATGCACCGTTATGCATTTT
Found at i:1516529 original size:52 final size:51
Alignment explanation
Indices: 1516446--1516758 Score: 211
Period size: 52 Copynumber: 6.0 Consensus size: 51
1516436 TTTATTAAGA
* * *
1516446 TGCACACGTAGTACCTATACGGTCGTTCATCAACCTATGATGAATGTCGTGAGT
1 TGCACACATAGTGCC-ATACGGT-GTTCATCAACATATGATGAAT-TCGTGAGT
* *
1516500 TGCACACATAGTGCCATACGGTATTCATCAACATATGATGAATTCCATGAGT
1 TGCACACATAGTGCCATACGGTGTTCATCAACATATGATGAATT-CGTGAGT
* * *
1516552 TGCACACATAGTGTCGTAACGGTGTTCATCATA-AT-TGATGAATTTCGTGGGT
1 TGCACACATAGTGCCAT-ACGGTGTTCATCA-ACATATGATGAA-TTCGTGAGT
* * * * *
1516604 TGC-CACTTAGTGCTGAAACGGTTGTTCATCAACCTATGATGAATTCCGTGA-A
1 TGCACACATAGTGC-CATACGG-TGTTCATCAACATATGATGAATT-CGTGAGT
** * ** * * * *
1516656 AACACACTTAGTGTTGAAACGAATGTTCATCAACATATGATAAATTCGTGGGT
1 TGCACACATAGTG-CCATACG-GTGTTCATCAACATATGATGAATTCGTGAGT
* * * ** * * *
1516709 TGCACACTTAGTGCTGAAACATTGTTCATTAACCTATGATGAATCCGTGA
1 TGCACACATAGTGC-CATACGGTGTTCATCAACATATGATGAATTCGTGA
1516759 AATCACACTT
Statistics
Matches: 209, Mismatches: 36, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
51 14 0.07
52 95 0.45
53 86 0.41
54 14 0.07
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (51 bp):
TGCACACATAGTGCCATACGGTGTTCATCAACATATGATGAATTCGTGAGT
Found at i:1516643 original size:105 final size:107
Alignment explanation
Indices: 1516470--1517047 Score: 333
Period size: 105 Copynumber: 5.6 Consensus size: 107
1516460 CTATACGGTC
* * * * * * * *
1516470 GTTCATCAACCTATGATGAATGTCGTGAGTTGCACACATAGTGC-CATACGG-TATTCATCAACA
1 GTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCTGAAACGGTTGTTCATCAACC
*** * *
1516533 TATGATGAATTCCATGAGTTGCACACATAGTGTCGTAACG-GT
66 TATGATGAATTCCATGA-AAACACACATAGTGTCGAAACGAAT
1516575 GTTCATCATA-AT-TGATGAATTTCGTGGGTTGC-CACTTAGTGCTGAAACGGTTGTTCATCAAC
1 GTTCATCA-ACATATGATGAATTTCGTGGGTTGCACACTTAGTGCTGAAACGGTTGTTCATCAAC
* * *
1516637 CTATGATGAATTCCGTGAAAACACACTTAGTGTTGAAACGAAT
65 CTATGATGAATTCCATGAAAACACACATAGTGTCGAAACGAAT
* * *
1516680 GTTCATCAACATATGAT-AAATTCGTGGGTTGCACACTTAGTGCTGAAAC-ATTGTTCATTAACC
1 GTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCTGAAACGGTTGTTCATCAACC
* * * * * **
1516743 TATGATGAA-TCCGTGAAATCACACTTAGTG-CAAAATGGTT
66 TATGATGAATTCCATGAAAACACACATAGTGTCGAAACGAAT
* * *** *
1516783 GTTCATCATC--ATGATGAATTCCGTGAAATGCA-A-TTAGTG-TCAAAACGGTTGTTCATCAAC
1 GTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCT-GAAACGGTTGTTCATCAAC
* * * **
1516843 ATATGGA-GAATTCCGT-AAAATGCACACTTAG-GTCGAAACGGTT
65 CTAT-GATGAATTCCATGAAAA--CACACATAGTGTCGAAACGAAT
* * * * * ** * * * *
1516886 ATT-GTCCACATAGGA--AATTCCGT-GAATGCACAGTTAGTGCT-AAAC-GTTATTCATCCACA
1 GTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCTGAAACGGTTGTTCATCAACC
* * * * * *
1516945 AAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG-AT
66 TATGATGAATTCCATGAAA-ACACACATAGTGTCGAAACGAAT
* * * * * *** * *
1516987 CATTCATCCATATAGGATGAATTCCGTGAAATGCATACTTAGTGCTGAAACGGTTATTCAT
1 -GTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCTGAAACGGTTGTTCAT
1517048 GCGCATAGAA
Statistics
Matches: 386, Mismatches: 56, Indels: 59
0.77 0.11 0.12
Matches are distributed among these distances:
99 1 0.00
100 12 0.03
101 64 0.17
102 49 0.13
103 58 0.15
104 64 0.17
105 89 0.23
106 36 0.09
107 4 0.01
108 9 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (107 bp):
GTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGCTGAAACGGTTGTTCATCAACC
TATGATGAATTCCATGAAAACACACATAGTGTCGAAACGAAT
Found at i:1517005 original size:54 final size:54
Alignment explanation
Indices: 1516500--1517451 Score: 756
Period size: 53 Copynumber: 18.3 Consensus size: 54
1516490 TGTCGTGAGT
* * * * * **
1516500 TGCACACATAGTGCC-ATACGG-TATTCATCAACATATGATGAATTCCATGAGT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * * * ***
1516552 TGCACACATAGTGTCGTAACGG-TGTTCAT-CATA-ATTGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATA-GGATGAATTCCGTGAAA
* * * * *
1516604 TGC-CACTTAGTGCTGAAACGGTTGTTCATCAACCTATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* ** ** * * * * ***
1516657 -ACACACTTAGTGTTGAAACGAATGTTCATCAACATATGATAAATT-CGTGGGT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * ** * *
1516709 TGCACACTTAGTGCTGAAAC-ATTGTTCATTAACCTATGATGAA-TCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
1516761 T-CACACTTAGTG-CAAAATGGTTGTTCAT-CATCAT--GATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCA-CATAGGATGAATTCCGTGAAA
* * * * *
1516811 TGCA-A-TTAGTGTCAAAACGGTTGTTCATCAACATATGGA-GAATTCCGTAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATA-GGATGAATTCCGTGAAA
* *
1516863 TGCACACTTAG-GTCGAAACGGTTATT-GTCCACATAGGA--AATTCCGTG-AA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
1516912 TGCACAGTTAGTG-CTAAAC-GTTATTCATCCACAAAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
1516964 TGCACACTTAGTGCCGAAACGATCATTCATCCATATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * ***
1517018 TGCATACTTAGTGCTGAAACGGTTATTCATGCGCATAGAATGAATTATATG-AA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * **
1517071 TCCATACTTAGT--CGAAAC-ATTATTCATCCACAAAGGATGAATTATGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
*
1517122 TGCACACTTAGTGCCG-AACGGTTATTCATCCACATAGGATGAATTCCTTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
1517175 TGTACACTTAGTGCTGAAAC-ATTATTCATCC-TATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* ** * * *
1517227 TGCACACTTAGTGTCGAAACAATTATTCGTCTACACAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* ** * *
1517281 TGCACACTTAGTGCTGAAACGGTTATTCCCCCACATAGGATGAATTCTGTAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* **
1517335 TGCACACTTAGTGTCGAAACGGTT-TTCATCCACATAGGATGAATTCTATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * ** *
1517388 TGTACA-GTAGTATCG-AA-GGTTATTCATCCAC--AGGATGAATTCAGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1517437 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
1517452 TATTTGGTAA
Statistics
Matches: 740, Mismatches: 125, Indels: 72
0.79 0.13 0.08
Matches are distributed among these distances:
48 6 0.01
49 60 0.08
50 75 0.10
51 80 0.11
52 152 0.21
53 205 0.28
54 162 0.22
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:1517224 original size:263 final size:265
Alignment explanation
Indices: 1516860--1517450 Score: 749
Period size: 263 Copynumber: 2.3 Consensus size: 265
1516850 GAATTCCGTA
* *
1516860 AAATGCACACTTAG-GTCGAAACGGTTATT-GTCCACATAGGA--AATTCCGTG-AATGCACAGT
1 AAATGCACACTTAGTGTCG-AACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACT
* *
1516920 TAGTGCTAAACGTTATTCATCCACAAAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
65 TAGTGCTAAACATTATTCATCCACAAAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACA
* * * **
1516985 ATCATTCATCCATATAGGATGAATTCCGTGAAATGCATACTTAGTGCTGAAACGGTTATTCATGC
130 ATCATTCATCCACACAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAACGGTTATTCACCC
* * *
1517050 GCATAGAATGAATTATAT-GAATCCATACTTA-GTCGAAAC-ATTATTCATCCACAAAGGATGAA
195 ACATAGAATGAATTATATAAAATCCACACTTAGGTCGAAACGATT-TTCATCCACAAAGGATGAA
*
1517112 TTATGTG
259 TTATATG
* * *
1517119 AAATGCACACTTAGTGCCGAACGGTTATTCATCCACATAGGATGAATTCCTTGAAATGTACACTT
1 AAATGCACACTTAGTGTCGAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* * *
1517184 AGTGCTGAAACATTATTCATCC-TATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACA
66 AGTGCT-AAACATTATTCATCCACAAAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACA
* * * *
1517248 ATTATTCGTCTACACAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAACGGTTATTCCCCC
130 ATCATTCATCCACACAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAACGGTTATTCACCC
* * * * * *
1517313 ACATAGGATGAATTCTGTAAAATGCACACTTAGTGTCGAAACGGTTTTCATCCACATAGGATGAA
195 ACATAGAATGAATTATATAAAATCCACACTTAG-GTCGAAACGATTTTCATCCACAAAGGATGAA
*
1517378 TTCTATG
259 TTATATG
* * * *
1517385 AAATGTACA-GTAGTATCGAA-GGTTATTCATCCAC--AGGATGAATTCAGTGAAATGCACACTT
1 AAATGCACACTTAGTGTCGAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
1517446 AGTGC
66 AGTGC
1517451 CTATTTGGTA
Statistics
Matches: 285, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
259 24 0.08
260 14 0.05
262 37 0.13
263 123 0.43
264 38 0.13
265 8 0.03
266 39 0.14
267 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (265 bp):
AAATGCACACTTAGTGTCGAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
AGTGCTAAACATTATTCATCCACAAAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAA
TCATTCATCCACACAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAACGGTTATTCACCCA
CATAGAATGAATTATATAAAATCCACACTTAGGTCGAAACGATTTTCATCCACAAAGGATGAATT
ATATG
Found at i:1520425 original size:2 final size:2
Alignment explanation
Indices: 1520418--1520452 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1520408 CCAGAAAAGC
1520418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1520453 TTCTGACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1522234 original size:46 final size:45
Alignment explanation
Indices: 1522112--1522278 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 45
1522102 ATCAATTTCA
*
1522112 CATTTATGACATCCTTTCATACCTGTTATGCACCATTATGCATTTT
1 CATTTATGACATCCTTTCATACCTTTTATGCA-CATTATGCATTTT
* * * *
1522158 -ATTTATTACATCCTTTCATGCCTATAATGCATCATTATGCATTTT
1 CATTTATGACATCCTTTCATACCTTTTATGCA-CATTATGCATTTT
* *
1522203 CATTTATGGCATCATTTCATACCTTTTATGCACAGTTATGCATTTT
1 CATTTATGACATCCTTTCATACCTTTTATGCACA-TTATGCATTTT
* *
1522249 CATTTATGGCATCCTTTCATGCCTTTTATG
1 CATTTATGACATCCTTTCATACCTTTTATG
1522279 TCAATTAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
45 42 0.40
46 64 0.60
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.46
Consensus pattern (45 bp):
CATTTATGACATCCTTTCATACCTTTTATGCACATTATGCATTTT
Found at i:1522963 original size:54 final size:54
Alignment explanation
Indices: 1522531--1523571 Score: 1116
Period size: 54 Copynumber: 19.3 Consensus size: 54
1522521 TTTTATTAAG
* * * ** * * *
1522531 ATGCACACGTAGTGCCTATACGGTCGTTCATCAACCTATGATGAATTCCCT-AA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * * * * *
1522584 GTTGCACACATAGTGCCTG-TACGGTTATTAATTAACATATGATGAATTCCGTGAG
1 -ATGCACACTTAGTGCC-GAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * * * * * **
1522639 TTTCACACTTAGTGCCGAAATGGTTGTTCATCAATATATGATGAATTTCGTGGG
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * * * *
1522693 TTGCACAATTAGTGCCAAAACGTTTATTCATCAACATATGATGAATTTCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* ** * **
1522747 ATGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATAATGAATTCTGTGGG
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* ** * * * *
1522801 TTGCACACTTAGTGCCGAAATAGTTGTTCATCAACGTATGATAAATTCCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * *
1522855 ATGCACACTTAGTGCCGAAACGGTTTTTCATCAACGTATGATGAATTCCATGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * *
1522909 ATGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGACGAATTCCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * * *
1522963 ATGCACACTTAGTGCCAAAATGGTTATTCGTCTACATAGGATGAATTCTGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* *** *
1523017 ATGCACAC-TAGTGCTGAAATATTTATTCGTCAACATAGGATGAATTCCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * *
1523070 ATGCACACTTAGTGTCGAAACGGTCATTCATCCACATAGGATGAATTCCATGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * *
1523124 ATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGTATGAATTCTGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * *
1523178 ATGCACACTTAGTGTCGAAATGGTTATTCATCCACATAGGATGAATTCCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * *
1523232 ATGCACACTTAGTGCCGAAACGGTTATTCGTCCACATAGGATGGATTCCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * ** ** * * *
1523286 GTGAACACTTAGTGTTGAAACAATTATTCGTCCACATAGGATGAATTCTGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * ** *
1523340 ATGAACACTTAGTGCCGAAACGGTTATTCATCCACATAATATGAATTCCATGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * *
1523394 ATGCACACTTTGTGCTGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* * * * * ***
1523448 ATGTACACTTAGTGTCGAAACGTTTATTCATCAATATAGGATGAATTCTGTTTT
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* *
1523502 ATGCACACTTAGTGCCGAAACGGTTATTCATCCATATAGGATGAATTCCGTGAA
1 ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
* *
1523556 ATGCATACTTATTGCC
1 ATGCACACTTAGTGCC
1523572 TATTTGGTAA
Statistics
Matches: 842, Mismatches: 141, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
53 48 0.06
54 793 0.94
55 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (54 bp):
ATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCGTGAA
Found at i:1523938 original size:22 final size:23
Alignment explanation
Indices: 1523903--1523949 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1523893 TCAGTATCGA
1523903 TACCTATACCATGGTAACGATAC
1 TACCTATACCATGGTAACGATAC
* *
1523926 TACC-ATACTATGGTACCGATAC
1 TACCTATACCATGGTAACGATAC
1523948 TA
1 TA
1523950 TTTTATGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (23 bp):
TACCTATACCATGGTAACGATAC
Found at i:1523958 original size:19 final size:19
Alignment explanation
Indices: 1523934--1523997 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
1523924 ACTACCATAC
1523934 TATGGTACCGATACTATTT
1 TATGGTACCGATACTATTT
1523953 TATGGTACCGATACTATTT
1 TATGGTACCGATACTATTT
*
1523972 TATGGTACCGATACCATTT
1 TATGGTACCGATACTATTT
1523991 TATGGTA
1 TATGGTA
1523998 TGGTACCATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (19 bp):
TATGGTACCGATACTATTT
Found at i:1523959 original size:41 final size:38
Alignment explanation
Indices: 1523913--1523997 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
1523903 TACCTATACC
*
1523913 ATGGTAACGATACTACCATACTATGGTACCGATACTATTTT
1 ATGGTAACGATACT---ATACTATGGTACCGATACCATTTT
* **
1523954 ATGGTACCGATACTATTTTATGGTACCGATACCATTTT
1 ATGGTAACGATACTATACTATGGTACCGATACCATTTT
1523992 ATGGTA
1 ATGGTA
1523998 TGGTACCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 27 0.68
41 13 0.32
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (38 bp):
ATGGTAACGATACTATACTATGGTACCGATACCATTTT
Found at i:1524065 original size:20 final size:20
Alignment explanation
Indices: 1524040--1524077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1524030 TCGATTCCTT
1524040 CCCTTCGGCATCAATACTCC
1 CCCTTCGGCATCAATACTCC
* *
1524060 CCCTTCGGTATCGATACT
1 CCCTTCGGCATCAATACT
1524078 GATTCAATCA
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:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (20 bp):
CCCTTCGGCATCAATACTCC
Found at i:1532678 original size:78 final size:78
Alignment explanation
Indices: 1532549--1532859 Score: 390
Period size: 78 Copynumber: 4.1 Consensus size: 78
1532539 ATAAAGTGTA
* * * * * * * *
1532549 CTTTTATGCTGATAATGCACCCATATGCATTTCAGCGAGGGTATCCTTTCATACTAATAATGCA-
1 CTTTTATGCTGACAATGTA-CCATATACATTTCAACTATGGCATCCTTTCATACCAATAATGCAC
* *
1532613 CCGTATCCATTATT
65 CCATATGCATTATT
* * *
1532627 CTTTTATGCTGACAATGTACCCATATACATTTTATCTATGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTA-CCATATACATTTCAACTATGGCATCCTTTCATACCAATAATGCAC
*
1532692 CCATATGCTTTATT
65 CCATATGCATTATT
1532706 CTTTTATGCTGACAATGTACCATATACATTTCAACTATGGCATCCTTTCATACCAATAATGCACC
1 CTTTTATGCTGACAATGTACCATATACATTTCAACTATGGCATCCTTTCATACCAATAATGCACC
1532771 CATATGCATTATT
66 CATATGCATTATT
* *
1532784 C-TTTATGCTGACAATGTACCATATACATTT---C-A--GC-T-GTTTCATGCCAATAATGCACC
1 CTTTTATGCTGACAATGTACCATATACATTTCAACTATGGCATCCTTTCATACCAATAATGCACC
1532840 CATATGCATTATT
66 CATATGCATTATT
1532853 CTTTTAT
1 CTTTTAT
1532860 TTCATTCGTT
Statistics
Matches: 212, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
69 33 0.16
70 6 0.03
71 2 0.01
73 1 0.00
74 1 0.00
77 29 0.14
78 110 0.52
79 30 0.14
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (78 bp):
CTTTTATGCTGACAATGTACCATATACATTTCAACTATGGCATCCTTTCATACCAATAATGCACC
CATATGCATTATT
Found at i:1533409 original size:91 final size:91
Alignment explanation
Indices: 1533295--1533467 Score: 228
Period size: 92 Copynumber: 1.9 Consensus size: 91
1533285 TTCTATATAG
*
1533295 GGTACCGATACCCCTTCTGGTATCG-TACCAAAATTAG-TTCGATGTTCATGGTATCGATACCCT
1 GGTACCGATACCCCTTC-GGTATCGATA-CAAAATTAGATTCGATGTTCATAGTATCGATACCCT
*
1533358 TT-ACTTGGTATCGATACTACCCTTCTAT
64 TTCA-ATGGTATCGATACTACCCTTCTAT
* **
1533386 GGTACCGATACTCCCTTAC-GTATCGATACGAAATTAGATTCGATGTTTTTAGTATCGATACCCT
1 GGTACCGATAC-CCCTT-CGGTATCGATACAAAATTAGATTCGATGTTCATAGTATCGATACCCT
1533450 TTCAATGGTATCGATACT
64 TTCAATGGTATCGATACT
1533468 GCATCAACGG
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
91 25 0.35
92 45 0.62
93 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (91 bp):
GGTACCGATACCCCTTCGGTATCGATACAAAATTAGATTCGATGTTCATAGTATCGATACCCTTT
CAATGGTATCGATACTACCCTTCTAT
Found at i:1533474 original size:20 final size:20
Alignment explanation
Indices: 1533451--1533488 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1533441 CGATACCCTT
* *
1533451 TCAATGGTATCGATACTGCA
1 TCAACGGTATCAATACTGCA
1533471 TCAACGGTATCAATACTG
1 TCAACGGTATCAATACTG
1533489 ATTGAATCAA
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:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (20 bp):
TCAACGGTATCAATACTGCA
Found at i:1538938 original size:37 final size:39
Alignment explanation
Indices: 1538888--1538964 Score: 131
Period size: 37 Copynumber: 2.0 Consensus size: 39
1538878 TCAAGCATTA
1538888 ACATCACATCATTTAACCATA-T-ACCTCTATAGGACCT
1 ACATCACATCATTTAACCATATTGACCTCTATAGGACCT
1538925 ACATCACATCATTTAACCATATTTGACCTCTATAGGACCT
1 ACATCACATCATTTAACCATA-TTGACCTCTATAGGACCT
1538965 TCACCATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
37 21 0.57
39 1 0.03
40 15 0.41
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (39 bp):
ACATCACATCATTTAACCATATTGACCTCTATAGGACCT
Found at i:1540026 original size:79 final size:79
Alignment explanation
Indices: 1539891--1540219 Score: 435
Period size: 79 Copynumber: 4.2 Consensus size: 79
1539881 TTCCAAATAA
* * * * * * * * * *
1539891 ATTATACTTTTATGCTCATAATGCACCCATATGCATTTCAGCGAGGGCATCATTTCATGCCAATA
1 ATTATTCTTTTATGCTGACAATGTAACCATATACATTTCAGCTATGACATCCTTTCATGCCAATA
1539956 ATGCACCCATATGC
66 ATGCACCCATATGC
*
1539970 ATTATTCTTTTATGCTGACAATGTAACCAAATACATTTCAGCTATGACATCCTTTCATGCCAATA
1 ATTATTCTTTTATGCTGACAATGTAACCATATACATTTCAGCTATGACATCCTTTCATGCCAATA
1540035 ATGCACCCATATGC
66 ATGCACCCATATGC
* * * *
1540049 ATTATTCTTTTATGCTGACAATGTATCCATGTACATTTCAGCTATGGCATCTTTTCATGCCAATA
1 ATTATTCTTTTATGCTGACAATGTAACCATATACATTTCAGCTATGACATCCTTTCATGCCAATA
* *
1540114 ATACATCCATATGC
66 ATGCACCCATATGC
* **
1540128 ATTATTCTTTTATGCTGACAATAT-ACTCATATACATTTCAGCTATGACATCCTTTCATGTAAAT
1 ATTATTCTTTTATGCTGACAATGTAAC-CATATACATTTCAGCTATGACATCCTTTCATGCCAAT
* * *
1540192 AAAGCACTCGTATGC
65 AATGCACCCATATGC
1540207 ATTATTCTTTTAT
1 ATTATTCTTTTAT
1540220 TTCATTCATT
Statistics
Matches: 219, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
78 1 0.00
79 218 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (79 bp):
ATTATTCTTTTATGCTGACAATGTAACCATATACATTTCAGCTATGACATCCTTTCATGCCAATA
ATGCACCCATATGC
Found at i:1542663 original size:20 final size:20
Alignment explanation
Indices: 1542625--1542663 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1542615 TAAATTTAGA
* *
1542625 TTTTTTTTATCATTTTTTAC
1 TTTTATTTATCATTATTTAC
*
1542645 TTTTATTTATTATTATTTA
1 TTTTATTTATCATTATTTA
1542664 GATGGTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTATCATTATTTAC
Found at i:1545689 original size:28 final size:27
Alignment explanation
Indices: 1545639--1545691 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1545629 GAATAAGTTG
*
1545639 TTATGATAAGGAAACGATTATAATAAC
1 TTATGATAAGGAAACGATCATAATAAC
* *
1545666 TTATGAATAAGTAAATGATCATAATA
1 TTATG-ATAAGGAAACGATCATAATA
1545692 CCCTATTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (27 bp):
TTATGATAAGGAAACGATCATAATAAC
Found at i:1551322 original size:31 final size:30
Alignment explanation
Indices: 1551285--1551354 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 30
1551275 TTCAAAGCCT
1551285 GAGAGCAAAGGATCCAAGAGCTGGAAGAAAA
1 GAGAGCAAAGGATCCAAGAGCTGGAAG-AAA
1551316 GAGAGCAAAGGATCCAAGAGCTGGAAGAAA
1 GAGAGCAAAGGATCCAAGAGCTGGAAGAAA
1551346 GAGAGCAAA
1 GAGAGCAAA
1551355 AGAATGATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
30 12 0.31
31 27 0.69
ACGTcount: A:0.49, C:0.13, G:0.33, T:0.06
Consensus pattern (30 bp):
GAGAGCAAAGGATCCAAGAGCTGGAAGAAA
Found at i:1557453 original size:22 final size:22
Alignment explanation
Indices: 1557419--1557504 Score: 81
Period size: 22 Copynumber: 3.9 Consensus size: 22
1557409 TTCTTGTATC
1557419 CTAAAATTCAAATAAAAAAAAGA
1 CTAAAATT-AAATAAAAAAAAGA
1557442 -TAAATATTAAATAACAAGAAAA-A
1 CTAAA-ATTAAATAA-AA-AAAAGA
*
1557465 CT-AAATTAAAT-AAATAAAGA
1 CTAAAATTAAATAAAAAAAAGA
* *
1557485 CTAAAATAAAATGAAAAAAA
1 CTAAAATTAAATAAAAAAAA
1557505 TTCAACAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
19 3 0.06
20 5 0.09
21 9 0.17
22 23 0.43
23 8 0.15
24 5 0.09
ACGTcount: A:0.70, C:0.06, G:0.05, T:0.20
Consensus pattern (22 bp):
CTAAAATTAAATAAAAAAAAGA
Found at i:1561369 original size:26 final size:24
Alignment explanation
Indices: 1561337--1561395 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1561327 TTAATTGGAC
*
1561337 TAAAAGAGATAATAAATTTCTTCTAA
1 TAAAAGAGA-AA-AAATATCTTCTAA
* *
1561363 TAAAAGAGGAAACAATATCTTTTAA
1 TAAAAGA-GAAAAAATATCTTCTAA
1561388 TAAAAGAG
1 TAAAAGAG
1561396 GAATTAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 17 0.59
26 9 0.31
27 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.29
Consensus pattern (24 bp):
TAAAAGAGAAAAAATATCTTCTAA
Found at i:1561940 original size:80 final size:80
Alignment explanation
Indices: 1561802--1562052 Score: 362
Period size: 80 Copynumber: 3.1 Consensus size: 80
1561792 AGAACTTATT
* * *
1561802 GGAGTTGGATCAACATTCTCAATAAAAGAAGTTCATAATGATAAT-AACTTGTTCAACCTTTGCT
1 GGAGTTGGATCAGCATTCTCAATAGAAGAAGTTCATAATGA-GATGAACTTGTTCAACCTTTGCT
*
1561866 CGATTCCATCACAGAA
65 CGATTCCATCACAAAA
* * *
1561882 GGAGTTGGATCAGCATTCCCAAGAGAAGAAGTTCATAATGAGATGAACTTGTTAAACCTTTGCTC
1 GGAGTTGGATCAGCATTCTCAATAGAAGAAGTTCATAATGAGATGAACTTGTTCAACCTTTGCTC
1561947 GATTCCATCACAAAA
66 GATTCCATCACAAAA
* * * *
1561962 GGAGTTGGGTTAGCATTTTC-ATAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTC
1 GGAGTTGGATCAGCATTCTCAATAGAAGAAGTTCATAATGAGATGAACTTGTTCAACCTTTGCTC
*
1562026 GGTTCCATCACAAAA
66 GATTCCATCACAAAA
*
1562041 GGAATTGGATCA
1 GGAGTTGGATCA
1562053 ATATTTCCAT
Statistics
Matches: 152, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 66 0.43
80 86 0.57
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (80 bp):
GGAGTTGGATCAGCATTCTCAATAGAAGAAGTTCATAATGAGATGAACTTGTTCAACCTTTGCTC
GATTCCATCACAAAA
Found at i:1562206 original size:3 final size:3
Alignment explanation
Indices: 1562200--1562234 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1562190 ATCATCATCA
1562200 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1562235 CAATAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1564581 original size:17 final size:16
Alignment explanation
Indices: 1564532--1564582 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
1564522 AACTGAATCG
* * *
1564532 AAAACAACCCGAACTA
1 AAAATAACCCAAACAA
1564548 AAAATAACCCAAACAA
1 AAAATAACCCAAACAA
1564564 AAAATAACCCAAACCAA
1 AAAATAACCCAAA-CAA
1564581 AA
1 AA
1564583 CCAACTCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.65, C:0.27, G:0.02, T:0.06
Consensus pattern (16 bp):
AAAATAACCCAAACAA
Found at i:1565946 original size:3 final size:3
Alignment explanation
Indices: 1565938--1565995 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
1565928 GTTTTCAAAT
1565938 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC
1565987 TTC TTC TTC
1 TTC TTC TTC
1565996 CGTTTATATG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1568133 original size:11 final size:11
Alignment explanation
Indices: 1568117--1568146 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1568107 CCCGGGTTAG
1568117 TAAAAAAATTT
1 TAAAAAAATTT
1568128 T-AAAAAATTT
1 TAAAAAAATTT
1568138 TAAAAAAAT
1 TAAAAAAAT
1568147 AGAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:1568493 original size:14 final size:15
Alignment explanation
Indices: 1568474--1568502 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1568464 TGAGTGATTG
1568474 GTGAGGTT-TTTTTT
1 GTGAGGTTATTTTTT
1568488 GTGAGGTTATTTTTT
1 GTGAGGTTATTTTTT
1568503 ACTAATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (15 bp):
GTGAGGTTATTTTTT
Found at i:1578567 original size:3 final size:3
Alignment explanation
Indices: 1578561--1578609 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
1578551 TTTAAAAAAA
* *
1578561 TAT TAT TAAT TAT TAT TAT TAA TAT TAT TAT TAT TAAT AAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
1578608 TA
1 TA
1578610 CCTAACCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1585344 original size:18 final size:18
Alignment explanation
Indices: 1585321--1585359 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1585311 CTCAAGGCGA
1585321 GAAGGGTTATCTGTCAAT
1 GAAGGGTTATCTGTCAAT
*
1585339 GAAGGGTTATCTGTTAAT
1 GAAGGGTTATCTGTCAAT
1585357 GAA
1 GAA
1585360 AACTTTCGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (18 bp):
GAAGGGTTATCTGTCAAT
Found at i:1586098 original size:128 final size:127
Alignment explanation
Indices: 1585689--1586940 Score: 1250
Period size: 128 Copynumber: 9.7 Consensus size: 127
1585679 CACAACAATT
** * * * *
1585689 TGTCATCCACCGACCAG-TCGTCCTCATCGTGTAGGAACCGTGTCACCCCAGATAACCAACCGTC
1 TGTCAT-CACCGACCAGATC-TCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTC
* * **
1585753 CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTACCGTCCTCATCGCGTAGGAATTG
64 CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
* * * **
1585817 TGTCATCACCTAACCATATTTCCTCATTATGTAGGAAATGTGTCAACCCTAGATAACCAGCCGTC
1 TGTCATCACC-GACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCC-AGATAACCAGCCGTC
* * * * * *
1585882 CTCATCACGTAGAAACCGTGTTATCA-CCTTAAGATGGCCAGAAC-TCTTCATCACGTATGAGCC
64 CTCATCACGTAGGAACCGTGTTATCACCCTT-AGATGGCCTG-CCGTCCTCATCACGTAGGAACC
1585945 G
127 G
* * * * * *
1585946 GGTCATCAACTGACCATATCTCCTCATTATGTAGGA-CATGTGTCAACCCAGGTAACTAGCTGTC
1 TGTCATC-ACCGACCAGATCTCCTCATTATGTAGGAGC-TGTGTCAACCCAGATAACCAGCCGTC
*
1586010 CTCATCACGTAGGAACCGTGTTATTACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
64 CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
* * * * * * * *
1586074 TTTCATAATCCAACCAGATTTCCTCATTATGTAGGATCTGTGTCAATCCATATAACCAGTC-TCC
1 TGTCATCA-CCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCC
** * * * * * *
1586138 TCATCACGTAGGAACTATGTTATCACCTTTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCG
65 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTG-CCGTCCTCATCACGTAGGAACCG
* * * * * * *
1586201 TGTCATCAACTGACCAGATCTCTTCATTATGTAGGAGCCGTGTCAACCCAGATAATCAACCATCT
1 TGTCATC-ACCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCC
* *
1586266 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGTCGTCCTCATCACATAGGAACCG
65 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
* * * *
1586329 TGTCATCACCCGACCAGATCTTCTCATTATGTAAGAGCTGTGTCAACCCAGATAACCAGGCATCC
1 TGTCATCA-CCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCC
* * * * *
1586394 TAATCACATAGGAACTGTGTTATCACCCTTAGATGGCATGTCGTCCTCATCACGTAGGAACCG
65 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
* *
1586457 TGTCATCACCCGACCAGATCTCCTCATTATGTATGAGCTATGTCAACCCAGATAACCAGCCGTCC
1 TGTCATCA-CCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCC
* *
1586522 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCATGCCGTCCTCATCACGTAGGAACTG
65 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
* * * * *
1586585 TATCATCACCCGACCAGATCTCCTCATTATGTAGGAGTTGTGTCAACCCAAATAACTAGCAGTCC
1 TGTCATCA-CCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCC
* * * * * * *
1586650 TCATCGCGTAGGAATCGTGTTATCACATTCCCTAAAGATGG-CTAGAAC-TCTTTATCACGTATG
65 TCATCACGTAGGAACCGTGTTAT--CA--CCCT-TAGATGGCCT-G-CCGTCCTCATCACGTAGG
**
1586713 AGTCG
123 AACCG
* * * *** * * * *
1586718 TGTCATTCCCCAACCAG-CCATCCTCATCGCGTAGGAACCGTGTC-ACCCTTGATAACCAGTCGT
1 TGTCA-TCACCGACCAGATC-TCCTCATTATGTAGGAGCTGTGTCAACCC-AGATAACCAGCCGT
* * * * * *
1586781 CGTCATCACGTAGGAACCGTGTTATCA-ACTATAGATGGCATGTCATCCTCATCGCGTAGGAACC
63 CCTCATCACGTAGGAACCGTGTTATCACCCT-TAGATGGCCTGCCGTCCTCATCACGTAGGAACC
1586845 G
127 G
* * * **
1586846 TGTCATCAACCGACCAGATCTCCTCATCACGTTGGAGCTGTGTC-ACCTCAGATAACCAGCATTC
1 TGTCATC-ACCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACC-CAGATAACCAGCCGTC
* *
1586910 CTCATCGCGTAGGAACCGAGTTATCACCCTT
64 CTCATCACGTAGGAACCGTGTTATCACCCTT
1586941 CCTAAAGATG
Statistics
Matches: 928, Mismatches: 164, Indels: 64
0.80 0.14 0.06
Matches are distributed among these distances:
127 112 0.12
128 603 0.65
129 112 0.12
130 5 0.01
131 2 0.00
132 10 0.01
133 81 0.09
134 3 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (127 bp):
TGTCATCACCGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCCT
CATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCG
Found at i:1586452 original size:46 final size:43
Alignment explanation
Indices: 1585702--1586595 Score: 211
Period size: 46 Copynumber: 20.9 Consensus size: 43
1585692 CATCCACCGA
** *
1585702 CCAGTCGTCCTCATCGTGTAGGAACCGTGTCA-C-CCCAGATAA
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGAT-G
** *
1585744 CCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCC--AGAT-G
* * ** *
1585790 CCTA-CCGTCCTCATCGCGTAGGAATTGTGTCATCACCTA-A--
1 CC-AGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
** * * ** *
1585830 CCA-TATTTCCTCATTATGTAGGAAATGTGTCA--ACCCTAGATAA
1 CCAGT-CGTCCTCATCACGTAGGAACCGTGTCATCACCC-AGAT-G
* * * *
1585873 CCAGCCGTCCTCATCACGTAGAAACCGTGTTATCACCTTAAGATGG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACC--CAGAT-G
* * * * * * *
1585919 CCAGAAC-TCTTCATCACGTATGAGCCGGGTCATCA-ACTGA--
1 CCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
* * * * * *
1585959 CCATATC-TCCTCATTATGTAGG-ACATGTGTCA--ACCCAGGTAA
1 CCA-GTCGTCCTCATCACGTAGGAAC-CGTGTCATCACCCAGAT-G
* * *
1586001 CTAG-CTGTCCTCATCACGTAGGAACCGTGTTATTACCCTTAGATGG
1 CCAGTC-GTCCTCATCACGTAGGAACCGTGTCATCACCC--AGAT-G
* * * * *
1586047 CCTGCCGTCCTCATCACGTAGGAACCGTTTCATAATCCA-A--
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
* * * * * * * *
1586087 CCAGAT-TTCCTCATTATGTAGGATCTGTGTCA--ATCCATATAA
1 CCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGAT-G
** * *
1586129 CCAGTC-TCCTCATCACGTAGGAACTATGTTATCACCTTTAGATGG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACC--CAGAT-G
* * * * * *
1586174 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCA-ACTGA--
1 CCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
* * * * *
1586214 CCAGATC-TCTTCATTATGTAGGAGCCGTGTCA--ACCCAGATAA
1 CCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGAT-G
* ** * * *
1586256 TCAACCATCTTCATCACGTAGGAACCGTGTTATCACCCTTAGATGG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCC--AGAT-G
* *
1586302 CCTGTCGTCCTCATCACATAGGAACCGTGTCATCACCC-GA--
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
* * * * * * *
1586342 CCAGATC-TTCTCATTATGTAAGAGCTGTGTCA--ACCCAGATAA
1 CCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGAT-G
* * * * * *
1586384 CCAGGCATCCTAATCACATAGGAACTGTGTTATCACCCTTAGATG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCC--AGATG
*
1586429 GCATGTCGTCCTCATCACGTAGGAACCGTGTCATCACCC-GA--
1 CCA-GTCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
* * * * ** *
1586470 CCAGATC-TCCTCATTATGTATGAGCTATGTCA--ACCCAGATAA
1 CCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGAT-G
* *
1586512 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCC--AGATG
* * * *
1586557 GCATGCCGTCCTCATCACGTAGGAACTGTATCATCACCC
1 CCA-GTCGTCCTCATCACGTAGGAACCGTGTCATCACCC
1586596 GACCAGATCT
Statistics
Matches: 614, Mismatches: 165, Indels: 142
0.67 0.18 0.15
Matches are distributed among these distances:
38 18 0.03
39 13 0.02
40 137 0.22
41 30 0.05
42 117 0.19
43 37 0.06
44 21 0.03
45 14 0.02
46 224 0.36
47 3 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (43 bp):
CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCAGATG
Found at i:1586533 original size:256 final size:256
Alignment explanation
Indices: 1585689--1587017 Score: 1396
Period size: 256 Copynumber: 5.1 Consensus size: 256
1585679 CACAACAATT
* ** * * *
1585689 TGTCATCCACCGACCAG-TCGTCCTCATCGTGTAGGAACCGTGTCACCCCAGATAACCAACCGTC
1 TGTCATCAACCGACCAGATC-TCCTCATTATGTAGGAGCCGTGTCAACCCAGATAACCAGCCGTC
* * **
1585753 CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTACCGTCCTCATCGCGTAGGAATTGT
65 CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCGT
** * ** * *
1585818 GTCATCACCTAACCATAT-TTCCTCATTATGTAGGAAATGTGTCAACCCTAGATAACCAGCCGTC
130 GTCATCACCCGACCAGATCTT-CTCATTATGTAGGAGCTGTGTCAACCC-AGATAACCAGGCATC
* *
1585882 CTCATCACGTAGAAACCGTGTTATCA-CCTTAAGATGGCCAGAACTCTTCATCACGTATGAGCCG
193 CTCATCACGTAGGAACTGTGTTATCACCCTT-AGATGGCCAGAACTCTTCATCACGTATGAGCCG
* * * * * * *
1585946 GGTCATCAACTGACCATATCTCCTCATTATGTAGGA-CATGTGTCAACCCAGGTAACTAGCTGTC
1 TGTCATCAACCGACCAGATCTCCTCATTATGTAGGAGC-CGTGTCAACCCAGATAACCAGCCGTC
*
1586010 CTCATCACGTAGGAACCGTGTTATTACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCGT
65 CTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCGT
* * * * * * * *
1586075 TTCATAATCCAACCAGAT-TTCCTCATTATGTAGGATCTGTGTCAATCCATATAACCAGTC-TCC
130 GTCATCACCCGACCAGATCTT-CTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGGCATCC
* *
1586138 TCATCACGTAGGAACTATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
194 TCATCACGTAGGAACTGTGTTATCACCCTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
* * * * * *
1586201 TGTCATCAACTGACCAGATCTCTTCATTATGTAGGAGCCGTGTCAACCCAGATAATCAACCATCT
1 TGTCATCAACCGACCAGATCTCCTCATTATGTAGGAGCCGTGTCAACCCAGATAACCAGCCGTCC
* *
1586266 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGTCGTCCTCATCACATAGGAACCGTG
66 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCGTG
* *
1586331 TCATCACCCGACCAGATCTTCTCATTATGTAAGAGCTGTGTCAACCCAGATAACCAGGCATCCTA
131 TCATCACCCGACCAGATCTTCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGGCATCCTC
* * * * *
1586396 ATCACATAGGAACTGTGTTATCACCCTTAGATGG-CATG-TCGTCCTCATCACGTAGGAACCG
196 ATCACGTAGGAACTGTGTTATCACCCTTAGATGGCCA-GAAC-TCTTCATCACGTATGAGCCG
* * **
1586457 TGTCATCACCCGACCAGATCTCCTCATTATGTATGAGCTATGTCAACCCAGATAACCAGCCGTCC
1 TGTCATCAACCGACCAGATCTCCTCATTATGTAGGAGCCGTGTCAACCCAGATAACCAGCCGTCC
* * *
1586522 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCATGCCGTCCTCATCACGTAGGAACTGTA
66 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCGTG
* * * *
1586587 TCATCACCCGACCAGATCTCCTCATTATGTAGGAGTTGTGTCAACCCAAATAACTA-GCAGTCCT
131 TCATCACCCGACCAGATCTTCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGGCA-TCCT
* * * *
1586651 CATCGCGTAGGAA-TCGTGTTATCACATTCCCTAAAGATGGCTAGAACTCTTTATCACGTATGAG
195 CATCACGTAGGAACT-GTGTTAT--CA--CCCT-TAGATGGCCAGAACTCTTCATCACGTATGAG
*
1586715 TCG
254 CCG
* * * *** * * *
1586718 TGTCATTC-CCCAACCAG-CCATCCTCATCGCGTAGGAACCGTGTC-ACCCTTGATAACCAGTCG
1 TGTCA-TCAACCGACCAGATC-TCCTCATTATGTAGGAGCCGTGTCAACCC-AGATAACCAGCCG
* * * * * *
1586780 TCGTCATCACGTAGGAACCGTGTTATCA-ACTATAGATGGCATGTCATCCTCATCGCGTAGGAAC
63 TCCTCATCACGTAGGAACCGTGTTATCACCCT-TAGATGGCCTGCCGTCCTCATCACGTAGGAAC
* * * * *
1586844 CGTGTCATCAACCGACCAGATCTCCTCATCACGTTGGAGCTGTGTC-ACCTCAGATAACCA-GCA
127 CGTGTCATCACCCGACCAGATCTTCTCATTATGTAGGAGCTGTGTCAACC-CAGATAACCAGGCA
* * * *
1586907 TTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATTACGT
191 -TCCTCATCACGTAGGAACTGTGTTATCACCC-T--T--AGATGGCC-AGAACTCTTCATCACGT
**
1586972 ATGAGCAT
249 ATGAGCCG
* * * * *
1586980 TATTATC-CCCTGACCAGATCTCCTCATCACGTAGGAGC
1 TGTCATCAACC-GACCAGATCTCCTCATTATGTAGGAGC
1587018 TGTATAAACC
Statistics
Matches: 907, Mismatches: 135, Indels: 55
0.83 0.12 0.05
Matches are distributed among these distances:
255 226 0.25
256 257 0.28
257 150 0.17
258 5 0.01
259 2 0.00
260 14 0.02
261 204 0.22
262 48 0.05
263 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (256 bp):
TGTCATCAACCGACCAGATCTCCTCATTATGTAGGAGCCGTGTCAACCCAGATAACCAGCCGTCC
TCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTGCCGTCCTCATCACGTAGGAACCGTG
TCATCACCCGACCAGATCTTCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGGCATCCTC
ATCACGTAGGAACTGTGTTATCACCCTTAGATGGCCAGAACTCTTCATCACGTATGAGCCG
Found at i:1587237 original size:3 final size:3
Alignment explanation
Indices: 1587223--1587274 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
1587213 TTTTAAAAAA
* *
1587223 TAT TAT TAAT TAT TAT TAT TAA TAT TAA TAT TAT TAT TAT TAAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
1587270 TAT TA
1 TAT TA
1587275 CCTAACCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1587860 original size:29 final size:28
Alignment explanation
Indices: 1587788--1587941 Score: 107
Period size: 29 Copynumber: 5.2 Consensus size: 28
1587778 TGAATCTCTG
* * *
1587788 TGTTTTTCTGATTTTGACACTTTAGTTTC
1 TGTTTTTCT-ATTTAGTCACTTAAGTTTC
1587817 TGTTATTT-TATTTTAGTCACTTAAGTTTC
1 TGTT-TTTCTA-TTTAGTCACTTAAGTTTC
*
1587846 TGTTTTTGCTATTTATGTC-CATTAAATTTC
1 TGTTTTT-CTATTTA-GTCAC-TTAAGTTTC
* ** *
1587876 TGTTTTAACTATTTTAGTCTTTTAAGTTTA
1 TGTTTT-TCTA-TTTAGTCACTTAAGTTTC
* *
1587906 TGTTCTTACCATTTAGTCACTTAAG-TTC
1 TGTT-TTTCTATTTAGTCACTTAAGTTTC
1587934 ATGTTTTT
1 -TGTTTTT
1587942 TTTTCTCTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
28 8 0.08
29 45 0.45
30 42 0.42
31 6 0.06
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.57
Consensus pattern (28 bp):
TGTTTTTCTATTTAGTCACTTAAGTTTC
Found at i:1592025 original size:26 final size:28
Alignment explanation
Indices: 1591946--1592036 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
1591936 AAATTAAAAA
* * *
1591946 TTCAT-ATATTTAATTTATAATTCTTTCTT
1 TTCATAATATTT-ATATATAATT-ATTATT
* *
1591975 TTCAAAATTTTTATATATAATTATTATT
1 TTCATAATATTTATATATAATTATTATT
*
1592003 TTCATAATATTTATATGT-A-TATTATT
1 TTCATAATATTTATATATAATTATTATT
*
1592029 TTAATAAT
1 TTCATAAT
1592037 GTTTCATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
26 14 0.27
27 1 0.02
28 19 0.37
29 13 0.25
30 5 0.10
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.58
Consensus pattern (28 bp):
TTCATAATATTTATATATAATTATTATT
Found at i:1595326 original size:15 final size:15
Alignment explanation
Indices: 1595306--1595337 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1595296 GATCAATACC
1595306 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1595321 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1595336 TT
1 TT
1595338 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1599134 original size:9 final size:9
Alignment explanation
Indices: 1599120--1599151 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1599110 AAATGGAAAT
1599120 CATTCTTTA
1 CATTCTTTA
1599129 CATTCTTTA
1 CATTCTTTA
*
1599138 CATTTTTTA
1 CATTCTTTA
1599147 CATTC
1 CATTC
1599152 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (9 bp):
CATTCTTTA
Found at i:1601923 original size:3 final size:3
Alignment explanation
Indices: 1601915--1601979 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
1601905 TCCATTTTTG
** *
1601915 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
1601961 TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1601980 TACAAACAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1601941 original size:21 final size:22
Alignment explanation
Indices: 1601915--1601974 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
1601905 TCCATTTTTG
1601915 TTATTATTATTATTATTAAA-A
1 TTATTATTATTATTATTAAATA
1601936 TTATTATTATTATTATTAAATA
1 TTATTATTATTATTATTAAATA
*
1601958 TTATTA-TATTATAATTA
1 TTATTATTATTATTATTA
1601975 TTATTTACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
21 30 0.81
22 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTATTATTATTATTAAATA
Found at i:1602022 original size:26 final size:26
Alignment explanation
Indices: 1601986--1602040 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1601976 TATTTACAAA
*
1601986 CAGTTACAAACAAAACT-GGACCGGCC
1 CAGTTACAAACAAAA-TAGAACCGGCC
*
1602012 CAGTTATAAACAAAATAGAACCGGCC
1 CAGTTACAAACAAAATAGAACCGGCC
1602038 CAG
1 CAG
1602041 ACCAACCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.13
Consensus pattern (26 bp):
CAGTTACAAACAAAATAGAACCGGCC
Found at i:1603297 original size:15 final size:15
Alignment explanation
Indices: 1603250--1603308 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
1603240 ATCCATTAGT
1603250 TTTTAA-TATTATTA
1 TTTTAATTATTATTA
1603264 CTTTTAATT-TCT-TTCA
1 -TTTTAATTAT-TATT-A
1603280 TTTTAATTATTATTA
1 TTTTAATTATTATTA
*
1603295 -TTTATTTATTATTA
1 TTTTAATTATTATTA
1603309 CGTTTGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 13 0.34
15 19 0.50
16 6 0.16
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATTATTATTA
Found at i:1604067 original size:13 final size:12
Alignment explanation
Indices: 1604051--1604095 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
1604041 TCTTTCAAAT
1604051 TTTTTATTACTTA
1 TTTTTATTA-TTA
1604064 TTTTTA-TATTA
1 TTTTTATTATTA
*
1604075 -TTTTATTAATA
1 TTTTTATTATTA
1604086 TTTTT-TTATT
1 TTTTTATTATT
1604096 TTATTCAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 5 0.18
11 11 0.39
12 6 0.21
13 6 0.21
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:1604078 original size:23 final size:22
Alignment explanation
Indices: 1604052--1604095 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1604042 CTTTCAAATT
*
1604052 TTTTATTACTTATTTTTATATTA
1 TTTTATTA-ATATTTTTATATTA
*
1604075 TTTTATTAATATTTTTTTATT
1 TTTTATTAATATTTTTATATT
1604096 TTATTCAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTAATATTTTTATATTA
Found at i:1604096 original size:19 final size:20
Alignment explanation
Indices: 1604072--1604120 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1604062 TATTTTTATA
1604072 TTATTTTATT-A-ATATTTTT
1 TTATTTTATTCAGATA-TTTT
*
1604091 TTATTTTATTCAGGTATTTT
1 TTATTTTATTCAGATATTTT
1604111 TTATTTTATT
1 TTATTTTATT
1604121 TGTCTGCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.37
20 15 0.56
21 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (20 bp):
TTATTTTATTCAGATATTTT
Found at i:1604539 original size:29 final size:30
Alignment explanation
Indices: 1604506--1604567 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
1604496 AAATTTTGTC
* *
1604506 TAGTGATTAAAGTGTAAGTTTTG-AAAGTT
1 TAGTGATTAAAGTATAAATTTTGAAAAGTT
*
1604535 TAGTGGTTAAAGTATAAATTTTGAAAAGTT
1 TAGTGATTAAAGTATAAATTTTGAAAAGTT
1604565 TAG
1 TAG
1604568 GGATCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (30 bp):
TAGTGATTAAAGTATAAATTTTGAAAAGTT
Found at i:1608026 original size:29 final size:30
Alignment explanation
Indices: 1607973--1608032 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1607963 TTTTCATCCT
*
1607973 TTGTTTTTATTATATTATAAAAGTTAATAA
1 TTGTTTTTATTATATTACAAAAGTTAATAA
* * *
1608003 TTGTTTTTATTAT-TTCCAGAAGTTCATAA
1 TTGTTTTTATTATATTACAAAAGTTAATAA
1608032 T
1 T
1608033 GAGAGAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (30 bp):
TTGTTTTTATTATATTACAAAAGTTAATAA
Found at i:1608192 original size:98 final size:98
Alignment explanation
Indices: 1608014--1608281 Score: 418
Period size: 99 Copynumber: 2.7 Consensus size: 98
1608004 TGTTTTTATT
1608014 ATTTCCAGAAGTTCATAATGAGAGAACTTATCT-AAGAGGAAAA-AAGTTCA-AATGAGAAATTG
1 ATTTCCAGAAGTTCATAATGA-AGAACTTATCTGAAGAGGAAAAGAAGTT-ATAATGAGAAATTG
1608076 TTCAACCTTTGTTTGATTCATCACTAGATGCATCA
64 TTCAACCTTTGTTTGATTCATCACTAGATGCATCA
* *
1608111 ATTTCCAGAAGTTCATAATGAAGAACTCATCTGAAGAGGAAAAGAAATTATAATGAGAAATTGTT
1 ATTTCCAGAAGTTCATAATGAAGAACTTATCTGAAGAGGAAAAGAAGTTATAATGAGAAATTGTT
* *
1608176 CAACCTTTGTTTGATTCATCACTCGATGGATCA
66 CAACCTTTGTTTGATTCATCACTAGATGCATCA
* *
1608209 ATTTTCCAGAAGTTCATAATTAAGAACTTATCTG-AGAGGAAGAAGAAGTTATAATGAGAACTTG
1 A-TTTCCAGAAGTTCATAATGAAGAACTTATCTGAAGAGGAA-AAGAAGTTATAATGAGAAATTG
1608273 TTCAACCTT
64 TTCAACCTT
1608282 GTTATTTTAT
Statistics
Matches: 158, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
96 10 0.06
97 32 0.20
98 57 0.36
99 59 0.37
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (98 bp):
ATTTCCAGAAGTTCATAATGAAGAACTTATCTGAAGAGGAAAAGAAGTTATAATGAGAAATTGTT
CAACCTTTGTTTGATTCATCACTAGATGCATCA
Found at i:1608615 original size:3 final size:3
Alignment explanation
Indices: 1608603--1608673 Score: 81
Period size: 3 Copynumber: 23.0 Consensus size: 3
1608593 TTTTATCCAT
*
1608603 TTA TTT TTA TTA TTA TTA TATA TTA TTA TTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA
* *
1608650 TTA TTGA -TA TTA ATA ATA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA
1608674 ATAAATAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 1 0.02
3 52 0.87
4 7 0.12
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1608628 original size:16 final size:16
Alignment explanation
Indices: 1608609--1608675 Score: 82
Period size: 16 Copynumber: 4.1 Consensus size: 16
1608599 CCATTTATTT
1608609 TTATTATTATTA-TATA
1 TTATTATTATTATTA-A
1608625 TTATTATTATTATTAA
1 TTATTATTATTATTAA
1608641 TTATTATTATTATTGATA
1 TTATTATTATTATT-A-A
* *
1608659 TTAATAATATTATTAA
1 TTATTATTATTATTAA
1608675 T
1 T
1608676 AAATAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
16 29 0.63
17 4 0.09
18 13 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
TTATTATTATTATTAA
Found at i:1608631 original size:19 final size:19
Alignment explanation
Indices: 1608603--1608654 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
1608593 TTTTATCCAT
*
1608603 TTATTTTTATTATTATT-A
1 TTATTATTATTATTATTAA
1608621 TATATTATTATTATTATTAA
1 T-TATTATTATTATTATTAA
1608641 TTATTATTATTATT
1 TTATTATTATTATT
1608655 GATATTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 28 0.90
20 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATTATTATTATTAA
Found at i:1609807 original size:17 final size:17
Alignment explanation
Indices: 1609776--1609822 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
1609766 TAAACGTTTG
1609776 ATATTTT-CA-TTTAAT
1 ATATTTTGCATTTTAAT
1609791 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
1609808 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
1609823 TTCTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.48
16 7 0.24
17 8 0.28
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:1609854 original size:20 final size:21
Alignment explanation
Indices: 1609826--1609870 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1609816 TTTTAATTTC
1609826 TTTTATTTTGATT-ATTAGTA
1 TTTTATTTTGATTGATTAGTA
* * *
1609846 TTTTGTTTTGTTTGATTATTA
1 TTTTATTTTGATTGATTAGTA
1609867 TTTT
1 TTTT
1609871 TTATATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (21 bp):
TTTTATTTTGATTGATTAGTA
Found at i:1609881 original size:24 final size:23
Alignment explanation
Indices: 1609828--1609913 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
1609818 TTAATTTCTT
* *
1609828 TTAT-TTTGATTATTAGTATTTTG
1 TTATGTTTGATTATTA-TTTTTTA
*
1609851 TTTTGTTTGATTATTATTTTTTA
1 TTATGTTTGATTATTATTTTTTA
*
1609874 TATATGTTTAAATTATTATTTTCATTA
1 T-TATGTTT-GATTATTATTTT--TTA
1609901 TTAT-TTT-ATTATT
1 TTATGTTTGATTATT
1609914 CTTAAGTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
23 15 0.28
24 17 0.32
25 14 0.26
26 3 0.06
27 4 0.08
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.67
Consensus pattern (23 bp):
TTATGTTTGATTATTATTTTTTA
Found at i:1609902 original size:12 final size:11
Alignment explanation
Indices: 1609837--1609913 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
1609827 TTTATTTTGA
*
1609837 TTATTAGTATT
1 TTATTATTATT
* *
1609848 TTGTT-TTGTT
1 TTATTATTATT
*
1609858 TGATTATTATT
1 TTATTATTATT
1609869 TT-TTATATATGT
1 TTATTAT-TAT-T
1609881 TTAAATTATTATT
1 TT--ATTATTATT
1609894 TTCATTATTATT
1 TT-ATTATTATT
1609906 TTATTATT
1 TTATTATT
1609914 CTTAAGTCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
10 10 0.19
11 18 0.35
12 14 0.27
13 3 0.06
14 3 0.06
15 4 0.08
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (11 bp):
TTATTATTATT
Done.