Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007711.1 Hibiscus syriacus cultivar Beakdansim tig00109926_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: 1768490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 8
Found at i:1010701 original size:30 final size:30
Alignment explanation
Indices: 1010639--1010743 Score: 147
Period size: 31 Copynumber: 3.4 Consensus size: 30
1010629 AGTAACGAGC
* *
1010639 TTAATGAGCAAGAGTTGAACAACAAGTTTTT
1 TTAACGAGCACGAGTTGAACAACAA-TTTTT
*
1010670 TTAACGAGCACGAGTTGAACAATAATTTTT
1 TTAACGAGCACGAGTTGAACAACAATTTTT
* *
1010700 TTAACGAGCACCAGTTGAGCAACAATTTTT
1 TTAACGAGCACGAGTTGAACAACAATTTTT
1010730 ATTAACGAGCACGA
1 -TTAACGAGCACGA
1010744 ATCGAACACT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 32 0.48
31 34 0.52
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (30 bp):
TTAACGAGCACGAGTTGAACAACAATTTTT
Found at i:1011505 original size:21 final size:20
Alignment explanation
Indices: 1011471--1011527 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1011461 CGTTACAATG
* *
1011471 TTGATTTGGTAGTTCACAGTA
1 TTGATGTGGCAGTTCAC-GTA
*
1011492 TTGATGTGGCAGTTCACGTG
1 TTGATGTGGCAGTTCACGTA
*
1011512 CTGATGTGGCAGTTCA
1 TTGATGTGGCAGTTCA
1011528 TGGTGCTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.37
Consensus pattern (20 bp):
TTGATGTGGCAGTTCACGTA
Found at i:1011965 original size:103 final size:104
Alignment explanation
Indices: 1011823--1012013 Score: 269
Period size: 105 Copynumber: 1.8 Consensus size: 104
1011813 TTTTGCCTTA
* * * * * *
1011823 ATTTTGTTAACCATCGCAACTGTAATTTTTATAAATAATGGTT-TGACCATTTTGTAACTTTTTA
1 ATTTTATTAACCATCGCAACAGTAATTTTTAAAAATAATGATTAGGACCATTTTGTAACTTTATA
1011887 GAACTTGAGTGACCAATTTATAAATTTGTTATTATGTTG
66 GAACTTGAGTGACCAATTTATAAATTTGTTATTATGTTG
* *
1011926 ATTTTATTTACCATCGCAACAGT-TTTTTTAAAAATTAATGATTAAGGACCATTTTGTAACTTTA
1 ATTTTATTAACCATCGCAACAGTAATTTTTAAAAA-TAATGATT-AGGACCATTTTGTAACTTTA
*
1011990 TATAACTTGAGTGACCAATTTATA
64 TAGAACTTGAGTGACCAATTTATA
1012014 CTTTTTATAG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
102 9 0.12
103 27 0.36
105 40 0.53
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (104 bp):
ATTTTATTAACCATCGCAACAGTAATTTTTAAAAATAATGATTAGGACCATTTTGTAACTTTATA
GAACTTGAGTGACCAATTTATAAATTTGTTATTATGTTG
Found at i:1012755 original size:21 final size:22
Alignment explanation
Indices: 1012715--1012755 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1012705 ATATTGTAAA
*
1012715 TTTTATTTTATAATTTATCTAT
1 TTTTATTTTATAATTAATCTAT
*
1012737 TTTTATTTT-TTATTAATCT
1 TTTTATTTTATAATTAATCT
1012756 GAAGTAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTTTATAATTAATCTAT
Found at i:1022635 original size:2 final size:2
Alignment explanation
Indices: 1022628--1022677 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
1022618 CAATTGTCGA
1022628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
1022670 AT AG AT AT
1 AT AT AT AT
1022678 TTATTAGTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1025801 original size:31 final size:30
Alignment explanation
Indices: 1025729--1025801 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 30
1025719 CCAACGTCTA
*
1025729 AGTGACCAAAACTTAATAAAACGATAACGT
1 AGTGACCAAAACTTAATAAAACGATAACAT
*
1025759 AGGTGATCAAAACTTAATAAAACGATAACAT
1 A-GTGACCAAAACTTAATAAAACGATAACAT
1025790 GAGTGACCAAAA
1 -AGTGACCAAAA
1025802 GTGTACAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (30 bp):
AGTGACCAAAACTTAATAAAACGATAACAT
Found at i:1026286 original size:26 final size:26
Alignment explanation
Indices: 1026256--1026313 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1026246 CTTTTGATAA
* *
1026256 ATTTTTTATTATAACTGAT-TTATTTT
1 ATTTTTGATTATAACTGATAATA-TTT
1026282 ATTTTTGATTATAACTGATAATATTT
1 ATTTTTGATTATAACTGATAATATTT
1026308 ATTTTT
1 ATTTTT
1026314 AACTTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (26 bp):
ATTTTTGATTATAACTGATAATATTT
Found at i:1026581 original size:44 final size:44
Alignment explanation
Indices: 1026495--1026582 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
1026485 ACTAACATGC
* * ** * **
1026495 CGTTAATTTATGCACTATTTTCTCGGATGTAACCTCTTATATAT
1 CGTTAATTTATGCACCATTTACTCACATATAACCTCCAATATAT
*
1026539 CGTTAATTTATGCACCATTTACTCACATATAAGCTCCAATATAT
1 CGTTAATTTATGCACCATTTACTCACATATAACCTCCAATATAT
1026583 TATAATCATG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (44 bp):
CGTTAATTTATGCACCATTTACTCACATATAACCTCCAATATAT
Found at i:1027179 original size:137 final size:138
Alignment explanation
Indices: 1026986--1027262 Score: 475
Period size: 137 Copynumber: 2.0 Consensus size: 138
1026976 TATAATCATG
1026986 GTATCTTATATTAATTTATTCGAGCATGATAATGTATTTTCTAGTCTCATTATCAATCAACCTAA
1 GTATCTTATATTAATTTATTCGAGCATGATAATGTATTTTCTAGTCTCATTATCAATCAACCTAA
* * *
1027051 GATATTACTCTCATTATATAGGA-GGGCAAACTTACGATGATCAATCATATCTCACTACATTGAT
66 GATATTACTCTCATTATATAGAAGGGGCAAACTTACGATGATCAACCACATCTCACTACATTGAT
1027115 CGTGACAT
131 CGTGACAT
**
1027123 GTATCTTATATTAATTTATTCGAGCATGATAATGTATTTTCTAGTCTCATTATCAATCGGCCTAA
1 GTATCTTATATTAATTTATTCGAGCATGATAATGTATTTTCTAGTCTCATTATCAATCAACCTAA
* * *
1027188 GATATTGCTCTCATTATGTAGAAGGGGCAAACTTACGATGATCAACCACATCTCACTATATTGAT
66 GATATTACTCTCATTATATAGAAGGGGCAAACTTACGATGATCAACCACATCTCACTACATTGAT
1027253 CGTGACAT
131 CGTGACAT
1027261 GT
1 GT
1027263 CCACATCAAT
Statistics
Matches: 131, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
137 83 0.63
138 48 0.37
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (138 bp):
GTATCTTATATTAATTTATTCGAGCATGATAATGTATTTTCTAGTCTCATTATCAATCAACCTAA
GATATTACTCTCATTATATAGAAGGGGCAAACTTACGATGATCAACCACATCTCACTACATTGAT
CGTGACAT
Found at i:1027745 original size:16 final size:17
Alignment explanation
Indices: 1027726--1027760 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1027716 ATAATTTATG
1027726 TTAAAATGAA-TTAAAT
1 TTAAAATGAATTTAAAT
*
1027742 TTAAAGTGAATTTAAAT
1 TTAAAATGAATTTAAAT
1027759 TT
1 TT
1027761 CAGAGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TTAAAATGAATTTAAAT
Found at i:1027807 original size:17 final size:17
Alignment explanation
Indices: 1027787--1027825 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1027777 TTTTTAATAA
1027787 AAAATACATAAAATTTT
1 AAAATACATAAAATTTT
* *
1027804 AAAATATATAAATTTTT
1 AAAATACATAAAATTTT
1027821 AAAAT
1 AAAAT
1027826 TTTCAGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATACATAAAATTTT
Found at i:1031253 original size:159 final size:157
Alignment explanation
Indices: 1031042--1031805 Score: 713
Period size: 159 Copynumber: 5.0 Consensus size: 157
1031032 TCTCAACTGA
* * * * *
1031042 AAATGTTGATCCACCACTTTCTGTGAT-GGA-CGAGC-TAAGGTCGAACAAGTTCTTCTCATTAT
1 AAATGTTGATCCACCTCTTTCTGTGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCTCATTAT
* * * * * ** * ** *
1031104 AAACTTGTTCTCTTGGGAATGCTGATATAACC-CCTTATGTGATGGAATCGAG-CAAATATTGAG
66 GAACTTATTCAC-TGGAAATGTTGAT-CCACCTCCTTCTGTGATGG-A-CGAGTC-AAGGTTGAA
1031167 CAAGTTCTTCTTCTTATGAACTTCTTCACTAG
126 CAAGTTCTTCTTCTTATGAACTTCTTCACTAG
* * * *
1031199 AGATGTTGATCCACCTCATT-TGTGATAGACTTGAGCAAAAGATTGAACAAGTTCTT-TCATTAT
1 AAATGTTGATCCACCTCTTTCTGTGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCTCATTAT
1031262 GAACTTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAA--
66 GAACTTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAGT
* * *
1031325 AC-TATTC---T---C--ATT-A-TGAG
131 TCTTCTTCTTATGAACTTCTTCACT-AG
* * *
1031342 AGATGTTGATCCACCTCCTTCTGTGATAGACTCGAGC-AAAGATTGAACAAGTTC-T-TCATTAT
1 AAATGTTGATCCACCTCTTTCTGTGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCTCATTAT
**
1031404 GAACTTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAAC
66 GAACTTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAGT
* * * *
1031469 TATTC-TCATTACGAACTTTTTCACTGG
131 TCTTCTTC-TTATGAACTTCTTCACTAG
* * *
1031496 AAATGTTGACCCACCTCTTTCTGTGAT-GAAATTGAGCAAAA-ATTAAACAAGTTCTTCTCATTA
1 AAATGTTGATCCACCTCTTTCTGTGATAG-AATCGAGCAAAAGATTGAACAAGTTCTTCTCATTA
* * ** * * * * *
1031559 TGAACGTTTTTCATTGGAAATGTTGATATACCTCTTTTTGTGATGAAATCGAG-CAAATGTTAAA
65 TGAAC-TTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATG-GA-CGAGTC-AAGGTTGAA
* *
1031623 CAAGTTCTTCTTATTATGAACTTCTTCACTGG
126 CAAGTTCTTCTTCTTATGAACTTCTTCACTAG
* * *
1031655 AAATGTTGATCCACCTCTTTCTGTAATGGAATCGAG-AAAATG-TTAAACAAGTTCTTCTCATTA
1 AAATGTTGATCCACCTCTTTCTGTGATAGAATCGAGCAAAA-GATTGAACAAGTTCTTCTCATTA
* * *
1031718 TGAACTTCTTCACTGGAAATGTTGATCCACCTCCTTTTGTGATGGATGAGTCAAGGTTGAACAAG
65 TGAACTTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAG
* * *
1031783 TCCTTCTTATTATAAACTTCTTC
130 TTCTTCTTCTTATGAACTTCTTC
1031806 TCCATCATCG
Statistics
Matches: 507, Mismatches: 66, Indels: 69
0.79 0.10 0.11
Matches are distributed among these distances:
142 72 0.14
143 39 0.08
144 19 0.04
145 1 0.00
146 1 0.00
149 1 0.00
151 1 0.00
152 4 0.01
153 4 0.01
154 44 0.09
155 18 0.04
156 57 0.11
157 76 0.15
158 60 0.12
159 108 0.21
160 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (157 bp):
AAATGTTGATCCACCTCTTTCTGTGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCTCATTAT
GAACTTATTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAGT
TCTTCTTCTTATGAACTTCTTCACTAG
Found at i:1031401 original size:65 final size:65
Alignment explanation
Indices: 1031279--1031479 Score: 197
Period size: 77 Copynumber: 2.9 Consensus size: 65
1031269 TTCACTGGAA
* *
1031279 ATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAACTATTCTCATTATGAGAG
1 ATGTTGATCCACCTCCTTCTGTGATAGACGAGTCAAGATTGAACAAACTATTCTCATTATGAGAG
* * *
1031344 ATGTTGATCCACCTCCTTCTGTGATAGACTCGAG-CAAAGATTGAACAAGTTCTTCATTATGAAC
1 ATGTTGATCCACCTCCTTCTGTGATAGA--CGAGTC-AAGATTGAACAA--AC-T-ATTCT-CA-
* *
1031408 TTATTCACTGGAA
57 TTA-TGA---GAG
* *
1031421 ATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGTTGAACAAACTATTCTCATTA
1 ATGTTGATCCACCTCCTTCTGTGATAGACGAGTCAAGATTGAACAAACTATTCTCATTA
1031480 CGAACTTTTT
Statistics
Matches: 110, Mismatches: 12, Indels: 24
0.75 0.08 0.16
Matches are distributed among these distances:
65 27 0.25
66 1 0.01
67 15 0.14
69 4 0.04
70 2 0.02
71 8 0.07
72 2 0.02
73 4 0.04
74 2 0.02
75 15 0.14
76 1 0.01
77 29 0.26
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (65 bp):
ATGTTGATCCACCTCCTTCTGTGATAGACGAGTCAAGATTGAACAAACTATTCTCATTATGAGAG
Found at i:1031478 original size:77 final size:78
Alignment explanation
Indices: 1031344--1031805 Score: 513
Period size: 79 Copynumber: 5.9 Consensus size: 78
1031334 ATTATGAGAG
* * *
1031344 ATGTTGATCCACCTCCTTCTGTGATAGACTCGAGCAAAGATTGAACAAGTTC-T-TCATTATGAA
1 ATGTTGATCCACCTCCTTCTGTGATGGA-TCGAGCAAAGGTTAAACAAGTTCTTCTCATTATGAA
*
1031407 CTTATTCACTGGAA
65 CTTCTTCACTGGAA
* ** * *
1031421 ATGTTGATCCACCTCCTTCTGTGATGGA-CGAGTC-AAGGTTGAACAAACTATTCTCATTACGAA
1 ATGTTGATCCACCTCCTTCTGTGATGGATCGAG-CAAAGGTTAAACAAGTTCTTCTCATTATGAA
*
1031484 CTTTTTCACTGGAA
65 CTTCTTCACTGGAA
* * * * **
1031498 ATGTTGACCCACCTCTTTCTGTGATGAAATTGAGCAAAAATTAAACAAGTTCTTCTCATTATGAA
1 ATGTTGATCCACCTCCTTCTGTGATG-GATCGAGCAAAGGTTAAACAAGTTCTTCTCATTATGAA
* *
1031563 CGTTTTTCATTGGAA
65 C-TTCTTCACTGGAA
** * * * * *
1031578 ATGTTGATATACCTCTTTTTGTGATGAAATCGAGCAAATGTTAAACAAGTTCTTCTTATTATGAA
1 ATGTTGATCCACCTCCTTCTGTGATG-GATCGAGCAAAGGTTAAACAAGTTCTTCTCATTATGAA
1031643 CTTCTTCACTGGAA
65 CTTCTTCACTGGAA
* * * *
1031657 ATGTTGATCCACCTCTTTCTGTAATGGAATCGAGAAAATGTTAAACAAGTTCTTCTCATTATGAA
1 ATGTTGATCCACCTCCTTCTGTGATGG-ATCGAGCAAAGGTTAAACAAGTTCTTCTCATTATGAA
1031722 CTTCTTCACTGGAA
65 CTTCTTCACTGGAA
* * * * *
1031736 ATGTTGATCCACCTCCTTTTGTGATGGAT-GAGTC-AAGGTTGAACAAGTCCTTCTTATTATAAA
1 ATGTTGATCCACCTCCTTCTGTGATGGATCGAG-CAAAGGTTAAACAAGTTCTTCTCATTATGAA
1031799 CTTCTTC
65 CTTCTTC
1031806 TCCATCATCG
Statistics
Matches: 331, Mismatches: 45, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
75 16 0.05
76 2 0.01
77 107 0.32
78 4 0.01
79 132 0.40
80 70 0.21
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (78 bp):
ATGTTGATCCACCTCCTTCTGTGATGGATCGAGCAAAGGTTAAACAAGTTCTTCTCATTATGAAC
TTCTTCACTGGAA
Found at i:1039768 original size:3 final size:3
Alignment explanation
Indices: 1039760--1039794 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1039750 TTTAGGTTTG
1039760 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1039795 GTAAAGGGGT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1044563 original size:51 final size:51
Alignment explanation
Indices: 1044488--1044620 Score: 189
Period size: 51 Copynumber: 2.6 Consensus size: 51
1044478 TTCATACTAC
* * * *
1044488 AAAAAA-TGTATA-ACTTAACACATACTTACACTGATGTAAGTGAATTAAAT
1 AAAAAAGTGTA-ACACTTAACACATACTTACACCGATGTAAATAAATAAAAT
1044538 AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAATAAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAATAAATAAAAT
**
1044589 AAAAAAGTACAACACTTAACACATACTTACAC
1 AAAAAAGTGTAACACTTAACACATACTTACAC
1044621 GAATAAAATA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 7 0.09
51 68 0.91
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.25
Consensus pattern (51 bp):
AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAATAAATAAAAT
Found at i:1044626 original size:41 final size:41
Alignment explanation
Indices: 1044581--1044661 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
1044571 GATGTAAATA
* *
1044581 AATAAAATAAAAAAGTACAACACTTAACACATACTTACACG
1 AATAAAATAAAAAAATACAACACTTAACACATACCTACACG
* *
1044622 AATAAAATAAAAAAATATAGCACTTAACACATACCTACAC
1 AATAAAATAAAAAAATACAACACTTAACACATACCTACAC
1044662 CAGTGTAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.57, C:0.20, G:0.04, T:0.20
Consensus pattern (41 bp):
AATAAAATAAAAAAATACAACACTTAACACATACCTACACG
Found at i:1044823 original size:20 final size:19
Alignment explanation
Indices: 1044790--1044833 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
1044780 AAGTTATTTG
1044790 TATATAAATTTTATTAAATATA
1 TATATAAA-TTTA-TAAATA-A
1044812 TATATAAA-TTATAAATAA
1 TATATAAATTTATAAATAA
1044830 TATA
1 TATA
1044834 GAAGTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.23
19 6 0.27
20 3 0.14
22 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATAAATTTATAAATAA
Found at i:1044841 original size:18 final size:19
Alignment explanation
Indices: 1044804--1044841 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1044794 TAAATTTTAT
*
1044804 TAAATATATATATAAATTA
1 TAAATATATATAGAAATTA
*
1044823 TAAATA-ATATAGAAGTTA
1 TAAATATATATAGAAATTA
1044841 T
1 T
1044842 TTGTGTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAATATATATAGAAATTA
Found at i:1046475 original size:31 final size:31
Alignment explanation
Indices: 1046437--1046505 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
1046427 AAAATTTGAA
*
1046437 AGTTTAGGTACTAGCATGGACCAAAACTGAT
1 AGTTTAGGTACTAACATGGACCAAAACTGAT
1046468 AGTTTAGGTACTAACATGGACCAAAACTGAT
1 AGTTTAGGTACTAACATGGACCAAAACTGAT
1046499 AGTTTAG
1 AGTTTAG
1046506 CTACCGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (31 bp):
AGTTTAGGTACTAACATGGACCAAAACTGAT
Found at i:1067418 original size:16 final size:16
Alignment explanation
Indices: 1067397--1067429 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1067387 TATCTCAAAT
1067397 TTAAATACT-ATGAAAA
1 TTAAATA-TAATGAAAA
1067413 TTAAATATAATGAAAA
1 TTAAATATAATGAAAA
1067429 T
1 T
1067430 GGTTTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (16 bp):
TTAAATATAATGAAAA
Found at i:1068007 original size:60 final size:60
Alignment explanation
Indices: 1067898--1068013 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1067888 AATGAGTGAC
* * *
1067898 TATTTTATAACTTTTAATAGTCGAGGGACCCAACAAAGCAACACTCTATAGTCGGATGAT
1 TATTTTATAACTTTTAATAGTCGAGAGACCCAACAAAACAACACCCTATAGTCGGATGAT
* * ** * * *
1067958 TATTTTGTAACTTTTAATAGTCGATAGACTTAATAAAACAATACCCTATATTCGGA
1 TATTTTATAACTTTTAATAGTCGAGAGACCCAACAAAACAACACCCTATAGTCGGA
1068014 GGACCATTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (60 bp):
TATTTTATAACTTTTAATAGTCGAGAGACCCAACAAAACAACACCCTATAGTCGGATGAT
Found at i:1070449 original size:23 final size:23
Alignment explanation
Indices: 1070421--1070466 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1070411 TTTATGATCC
*
1070421 TAATTTTATTTTTATAATTTTTA
1 TAATTTTATTTTCATAATTTTTA
1070444 TAATTTTATTTTCATAATTTTTA
1 TAATTTTATTTTCATAATTTTTA
1070467 GTGTTAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TAATTTTATTTTCATAATTTTTA
Found at i:1070933 original size:16 final size:16
Alignment explanation
Indices: 1070912--1070956 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1070902 GCATTTCTTA
*
1070912 TTAAATAATTATTTTT
1 TTAAATAATTATTATT
1070928 TTAAAT-ATATATTATT
1 TTAAATAAT-TATTATT
1070944 TT--ATAATTATTAT
1 TTAAATAATTATTAT
1070957 ATAAAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
16 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATAATTATTATT
Found at i:1071156 original size:41 final size:41
Alignment explanation
Indices: 1071100--1071218 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 41
1071090 AGGATCTCTA
* *
1071100 ATTTTTTATTTTTATATTTGAGTCCTTCAATTTTTTTAATT-T
1 ATTTTTTA-TCTTATAATTGAGTCCTT-AATTTTTTTAATTCT
* * *
1071142 ATTTTTTATCTTATAATTGA-TGCCCTAAATTTTATAATTCT
1 ATTTTTTATCTTATAATTGAGT-CCTTAATTTTTTTAATTCT
* *
1071183 ACTTTTTATCTTTATAATTGAGACCTTAATTTTTTT
1 ATTTTTTATC-TTATAATTGAGTCCTTAATTTTTTT
1071219 TTCCCAATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
40 12 0.19
41 23 0.37
42 28 0.44
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (41 bp):
ATTTTTTATCTTATAATTGAGTCCTTAATTTTTTTAATTCT
Found at i:1071345 original size:43 final size:42
Alignment explanation
Indices: 1071223--1071359 Score: 141
Period size: 42 Copynumber: 3.2 Consensus size: 42
1071213 TTTTTTTTCC
* * *
1071223 CAATCTCACTTCTTTACATTTATAATTGATGAACCTATTTTTTT
1 CAATCTCACAT-TTTACATTTATAATTGA-GCACCTAATTTTTT
* * ** * * *
1071267 CAATTTTACATTGCACCTTTATAATCGAGCTCCTAATTTTTT
1 CAATCTCACATTTTACATTTATAATTGAGCACCTAATTTTTT
*
1071309 CAACCTCACATTTTACATTTATAATTGAGGCACCTAATTTTTT
1 CAATCTCACATTTTACATTTATAATTGA-GCACCTAATTTTTT
1071352 -AATCTCAC
1 CAATCTCAC
1071360 TATAAGGATG
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
42 39 0.53
43 26 0.36
44 8 0.11
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (42 bp):
CAATCTCACATTTTACATTTATAATTGAGCACCTAATTTTTT
Found at i:1071566 original size:86 final size:83
Alignment explanation
Indices: 1071369--1071576 Score: 269
Period size: 86 Copynumber: 2.5 Consensus size: 83
1071359 CTATAAGGAT
* * * * *
1071369 GCCCATAA-TTTTTCAATCTCACTTTTTACTTAAATAATTTAGGCCCCTAATTTTTATTCTCATT
1 GCCCTTAATTTTTTCAATCTCACTTTTTACTTATATAATTTAGACCCCTAATTTTTAATATCATT
* *
1071433 TTTATCTTTATAATTGAG
66 TTTAGCTTTAAAATTGAG
1071451 GCCCTTAATTTTTTCAATCTCACTTTTTACTTATATAATTTAGACCCCTAATTTTTTTAATATCA
1 GCCCTTAATTTTTTCAATCTCACTTTTTACTTATATAATTTAGACCCCTAA--TTTTTAATATC-
1071516 ATTTTTAGCTTTAAAATTGAG
63 ATTTTTAGCTTTAAAATTGAG
* *
1071537 GTCCC-TAATTTTTTTAATCTTACTTTTTACCTT-TATAATT
1 G-CCCTTAATTTTTTCAATCTCACTTTTTA-CTTATATAATT
1071577 GAGGTTTCTT
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
82 7 0.06
83 40 0.36
85 9 0.08
86 49 0.44
87 6 0.05
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.50
Consensus pattern (83 bp):
GCCCTTAATTTTTTCAATCTCACTTTTTACTTATATAATTTAGACCCCTAATTTTTAATATCATT
TTTAGCTTTAAAATTGAG
Found at i:1071581 original size:43 final size:42
Alignment explanation
Indices: 1071369--1071580 Score: 225
Period size: 43 Copynumber: 5.0 Consensus size: 42
1071359 CTATAAGGAT
* * * *
1071369 GCCCATAA-TTTTTCAATCTCACTTTTTACTTAAATAATTTAG
1 GCCCCTAATTTTTTTAATCTCACTTTTTACTT-TATAATTGAG
*
1071411 GCCCCTAA--TTTTTATTCTCA-TTTTTATCTTTATAATTGAG
1 GCCCCTAATTTTTTTAATCTCACTTTTTA-CTTTATAATTGAG
* * *
1071451 GCCCTTAATTTTTTCAATCTCACTTTTTACTTATATAATTTAG
1 GCCCCTAATTTTTTTAATCTCACTTTTTACTT-TATAATTGAG
* * * *
1071494 ACCCCTAATTTTTTTAATATCAATTTTTAGCTTTAAAATTGAG
1 GCCCCTAATTTTTTTAATCTCACTTTTTA-CTTTATAATTGAG
* *
1071537 GTCCCTAATTTTTTTAATCTTACTTTTTACCTTTATAATTGAG
1 GCCCCTAATTTTTTTAATCTCACTTTTTA-CTTTATAATTGAG
1071580 G
1 G
1071581 TTTCTTTTAT
Statistics
Matches: 141, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
40 21 0.15
41 13 0.09
42 20 0.14
43 84 0.60
44 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (42 bp):
GCCCCTAATTTTTTTAATCTCACTTTTTACTTTATAATTGAG
Found at i:1073054 original size:46 final size:46
Alignment explanation
Indices: 1072999--1073088 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
1072989 TATTTTATCT
* *
1072999 GAACTTTAAGGATCAAATTAAAAATTAATCACTATTATTAATATAA
1 GAACTTTAAGAATAAAATTAAAAATTAATCACTATTATTAATATAA
* *
1073045 GAACTTTAAGAATAAAATTAAAAATTAATCATTATTATTTATAT
1 GAACTTTAAGAATAAAATTAAAAATTAATCACTATTATTAATAT
1073089 CTCATATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.38
Consensus pattern (46 bp):
GAACTTTAAGAATAAAATTAAAAATTAATCACTATTATTAATATAA
Found at i:1081587 original size:60 final size:59
Alignment explanation
Indices: 1081520--1081631 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
1081510 TGTAGGATAT
*
1081520 TATTTTATCGAGTCACTTAACTACTAAAAGTTATAAAATAGTCATCC-GACTATAGAGAGC
1 TATTTTATCGAGTCACTCAACTACTAAAAGTTAT-AAATAGTCA-CCTGACTATAGAGAGC
** * * *
1081580 TATTTTATTTATTCTCTCAACTATTAAAAGTTATAAATAGTCACCTGACTAT
1 TATTTTATCGAGTCACTCAACTACTAAAAGTTATAAATAGTCACCTGACTAT
1081632 TCATATGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.04
59 15 0.33
60 28 0.62
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (59 bp):
TATTTTATCGAGTCACTCAACTACTAAAAGTTATAAATAGTCACCTGACTATAGAGAGC
Found at i:1089129 original size:197 final size:197
Alignment explanation
Indices: 1088779--1089174 Score: 639
Period size: 197 Copynumber: 2.0 Consensus size: 197
1088769 CGAAGCACTC
* *
1088779 GGGAACTGTAAACGCTTCGCTTGTCAAAGAGTTATACACAAACATATTTGACCTGCTACAACACT
1 GGGAAATGTAAACGCTTCGCTTGTCAAAGAGTTATACACAAACATATTTGACATGCTACAACACT
*
1088844 TCGTCTTTGTAAGGGGTAAATTCATTCACTTACACCTTCTGCAATTAACTGATATTTTAAGCTGC
66 CCGTCTTTGTAAGGGGTAAATTCATTCACTTACACCTTCTGCAATTAACTGATATTTTAAGCTGC
* * * *
1088909 AGGATATTGTTGATCGTCATACAAACTTTGTGAATAAGGCAGACAATGAGTCATATTAATGTGTG
131 AGGATATTGTCGATCGCCATACAAACTTTGTGAAGAAGGCAGACAATGAGTCATATCAATGTGTG
1088974 TT
196 TT
* * * *
1088976 GGGAAATGTAAATGCTTCGCTTTTCAAAGAGTTCTACACAAACATCTTTGACATGCTACAACACT
1 GGGAAATGTAAACGCTTCGCTTGTCAAAGAGTTATACACAAACATATTTGACATGCTACAACACT
* * *
1089041 CCGTCTTTGTGAGGGGTAAATTCATTCGCTTACACCTTTTGCAATTAACTGATATTTTAAGCTGC
66 CCGTCTTTGTAAGGGGTAAATTCATTCACTTACACCTTCTGCAATTAACTGATATTTTAAGCTGC
* * *
1089106 ATGATATTGTCGATCGCCATACAAACTTTGTGAAGAATGCCGACAATGAGTCATATCAATGTGTG
131 AGGATATTGTCGATCGCCATACAAACTTTGTGAAGAAGGCAGACAATGAGTCATATCAATGTGTG
1089171 TT
196 TT
1089173 GG
1 GG
1089175 AGGGTCTATG
Statistics
Matches: 182, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
197 182 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (197 bp):
GGGAAATGTAAACGCTTCGCTTGTCAAAGAGTTATACACAAACATATTTGACATGCTACAACACT
CCGTCTTTGTAAGGGGTAAATTCATTCACTTACACCTTCTGCAATTAACTGATATTTTAAGCTGC
AGGATATTGTCGATCGCCATACAAACTTTGTGAAGAAGGCAGACAATGAGTCATATCAATGTGTG
TT
Found at i:1090526 original size:18 final size:18
Alignment explanation
Indices: 1090457--1090526 Score: 52
Period size: 20 Copynumber: 3.7 Consensus size: 18
1090447 ATACCTCTTG
1090457 ATATATTATTTTTCCAATTAA
1 ATATATTATTTTT--AA-TAA
* *
1090478 AT-TCTTATTTTTATTTAAA
1 ATATATTATTTTTA-AT-AA
* *
1090497 AAATAATATTTTTAATAA
1 ATATATTATTTTTAATAA
1090515 ATATATTATTTT
1 ATATATTATTTT
1090527 ATGTAGGGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
18 14 0.37
19 4 0.11
20 18 0.47
21 2 0.05
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATATTATTTTTAATAA
Found at i:1110532 original size:261 final size:260
Alignment explanation
Indices: 1110068--1110591 Score: 976
Period size: 261 Copynumber: 2.0 Consensus size: 260
1110058 AATGAATCAA
*
1110068 GCTTGAACGAATAAGGTTATGTTTGTGTTCGTTTATTTATTTTTGAAGGTGTTCATATTCTATTC
1 GCTTGAACGAATAAGGTTATGTTTGTGTTCGTTTATTTAATTTTGAAGGTGTTCATATTCTATTC
*
1110133 GTGTTCATTTAAATTTTTAGCATCGTGTTCGTGTTCGTTTATTTATTTTTGAAGGTGTTCATTTA
66 GTGTTCATTTAAATTTTTAGCATCGTGTTCGTGTTCATTTATTTATTTTTGAAGGTGTTCATTTA
1110198 TTTATTGTTCACAATCACGAACATGTTCGCTTAATGTTCACGAACGTGTTCATATAGCGTTCACA
131 TTTATTGTTCACAATCACGAACATGTTCGCTTAATGTTCACGAACGTGTTCATATAGCGTTCACA
* *
1110263 AATATGTTCGTTTTTTAGTTTTACCCTTTTAAGCTAAAGAAAAAATGGTAAAATTACGCCATTAG
196 AATATGTTCGTTTTCTAGTTTTACCCTTTTAAGCTAAAG-AAAAATGATAAAATTACGCCATTAG
1110328 T
260 T
*
1110329 GCTTGAACGAATAAGGTTATGTTTGTGTTCTTTTATTTAATTTTGAAGGTGTTCATATTCTATTC
1 GCTTGAACGAATAAGGTTATGTTTGTGTTCGTTTATTTAATTTTGAAGGTGTTCATATTCTATTC
*
1110394 GTGTTCATTTAAATTTTTAGCATCGTGTTCGTGTTCATTTATTTATTTTTGAAGGTGTTTATTTA
66 GTGTTCATTTAAATTTTTAGCATCGTGTTCGTGTTCATTTATTTATTTTTGAAGGTGTTCATTTA
*
1110459 TTTATTGTTCACAATCACGAACATGTTCGCTTAATGTTCACGAACGTGTTCATTTAGCGTTCACA
131 TTTATTGTTCACAATCACGAACATGTTCGCTTAATGTTCACGAACGTGTTCATATAGCGTTCACA
1110524 AATATGTTCGTTTTCTAGTTTTACCCTTTTAAGCTAAAGAAAAATGATAAAATTACGCCATTAGT
196 AATATGTTCGTTTTCTAGTTTTACCCTTTTAAGCTAAAGAAAAATGATAAAATTACGCCATTAGT
1110589 GCT
1 GCT
1110592 AAGACTCTTT
Statistics
Matches: 256, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
260 28 0.11
261 228 0.89
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (260 bp):
GCTTGAACGAATAAGGTTATGTTTGTGTTCGTTTATTTAATTTTGAAGGTGTTCATATTCTATTC
GTGTTCATTTAAATTTTTAGCATCGTGTTCGTGTTCATTTATTTATTTTTGAAGGTGTTCATTTA
TTTATTGTTCACAATCACGAACATGTTCGCTTAATGTTCACGAACGTGTTCATATAGCGTTCACA
AATATGTTCGTTTTCTAGTTTTACCCTTTTAAGCTAAAGAAAAATGATAAAATTACGCCATTAGT
Found at i:1115238 original size:2 final size:2
Alignment explanation
Indices: 1115233--1115265 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1115223 TATATCAATA
1115233 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1115266 TACAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1115250 original size:23 final size:23
Alignment explanation
Indices: 1115222--1115265 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1115212 AAAAAAATTA
1115222 ATATATCA-ATAATATATATATAT
1 ATATAT-ATATAATATATATATAT
1115245 ATATATATATAATATATATAT
1 ATATATATATAATATATATAT
1115266 TACAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATATATATAATATATATATAT
Found at i:1115931 original size:60 final size:60
Alignment explanation
Indices: 1115809--1115933 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
1115799 GTTGGTTGAT
* * * * *
1115809 CATTTTGTAACTTCTAATAATTGAGGGACTTAACAAAATAACATCTTATAGTTGTGATAC
1 CATTTTATAACTTCTAATAATCGAGGGACTCAACAAAATAACATCTTATAGTCGTGAGAC
* * * ** *
1115869 CATTTTATAACTTTTAATAGTCGAGGGACTCAATAAAATAGTATTTTATAGTCGATG-GAC
1 CATTTTATAACTTCTAATAATCGAGGGACTCAACAAAATAACATCTTATAGTCG-TGAGAC
1115929 CATTT
1 CATTT
1115934 ATGTAATTTG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 51 0.96
61 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (60 bp):
CATTTTATAACTTCTAATAATCGAGGGACTCAACAAAATAACATCTTATAGTCGTGAGAC
Found at i:1117671 original size:23 final size:23
Alignment explanation
Indices: 1117643--1117695 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1117633 GACTGAGGCC
1117643 ATCCGAACGAGCTATGCGAGGGCA
1 ATCCGAACGAGCTATGCGAGGG-A
*
1117667 A-CCGAGCGAGCTATGCGAGGGA
1 ATCCGAACGAGCTATGCGAGGGA
1117689 ATCCGAA
1 ATCCGAA
1117696 GGTAACCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 23 0.88
24 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.34, T:0.11
Consensus pattern (23 bp):
ATCCGAACGAGCTATGCGAGGGA
Found at i:1117755 original size:29 final size:29
Alignment explanation
Indices: 1117713--1117797 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
1117703 GAGCAAGGGT
1117713 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1117742 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
1117771 AGGTCGCCCGGAGGGCATTGCGACCTA
1 AGGTCGCCCGGAGTGCATGGCGACCTA
1117798 TGTGTTGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.20, C:0.31, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:1117902 original size:29 final size:29
Alignment explanation
Indices: 1117856--1117912 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1117846 GAGTAAGGGT
1117856 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1117885 AGGTCGCCCGGAAG-GCATGGCGACCTAC
1 AGGTCGCCCGG-AGTGCATGGCGACCTAC
1117913 GGCCAATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.21, C:0.32, G:0.35, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:1119062 original size:4 final size:4
Alignment explanation
Indices: 1119048--1119150 Score: 52
Period size: 4 Copynumber: 24.2 Consensus size: 4
1119038 TCTATTCATA
* * *
1119048 TTAT GTAT TTAT TTAT TTA- TT-T TTGT TTAG TTATT TTAT TTACT CTTATT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTA-T -TTA-T
*
1119098 TTAT TTAT TT-T AATAT TTCGA- TTATT TTAGT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT -TTAT TT--AT TTA-T TTA-T TTAT TTAT TTAT TTAT
1119145 TATAT T
1 T-TAT T
1119151 ATGTTGATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
3 6 0.08
4 46 0.59
5 21 0.27
6 5 0.06
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1119141 original size:27 final size:26
Alignment explanation
Indices: 1119048--1119147 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 26
1119038 TCTATTCATA
* *
1119048 TTATGTATTTATTT-ATTTATTTTTGT
1 TTATTTATTTATTTCA-TTATTTTAGT
* *
1119074 TTAGTTATTTTATTTACTCTTATTTTA-T
1 TTATTTA-TTTATTT-C-ATTATTTTAGT
*
1119102 TTATTT-TAATATTTCGATTATTTTAGT
1 TTATTTAT-TTATTTC-ATTATTTTAGT
1119129 TTATTTATTTATTT-ATTAT
1 TTATTTATTTATTTCATTAT
1119148 ATTATGTTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
25 5 0.09
26 15 0.26
27 24 0.41
28 7 0.12
29 7 0.12
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (26 bp):
TTATTTATTTATTTCATTATTTTAGT
Found at i:1121175 original size:12 final size:12
Alignment explanation
Indices: 1121147--1121183 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1121137 TTTGGTAATC
1121147 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
1121160 CCCGCCCCGATA
1 CCCGCCCCGATA
*
1121172 CCCGACCCGATA
1 CCCGCCCCGATA
1121184 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:1121201 original size:2 final size:2
Alignment explanation
Indices: 1121194--1121315 Score: 109
Period size: 2 Copynumber: 65.5 Consensus size: 2
1121184 AATATTAAAA
1121194 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1121235 AT AT AT AT AT -T AT AT -T AT AA AT TT A- AT TT AA AT -T A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1121272 AT A- AT AT AT AT AT AT AT AT A- AT AT TT A- AT TT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1121311 AT AT A
1 AT AT A
1121316 CCCGACCCGA
Statistics
Matches: 96, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
1 9 0.09
2 87 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1146480 original size:113 final size:113
Alignment explanation
Indices: 1146282--1146512 Score: 453
Period size: 113 Copynumber: 2.0 Consensus size: 113
1146272 TTCTGCGGTT
1146282 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
1 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
1146347 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
66 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
1146395 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
1 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
*
1146460 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACTCATCTTAC
66 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
1146508 TAGCC
1 TAGCC
1146513 TCGATAAATA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 117 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (113 bp):
TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
Found at i:1150121 original size:22 final size:22
Alignment explanation
Indices: 1150078--1150123 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1150068 TTATTATGAC
*
1150078 AATGTATATACATCTTGCAGAT
1 AATGTATATACATATTGCAGAT
*
1150100 AATGTATATATC-TATTGTAGAT
1 AATGTATATA-CATATTGCAGAT
1150122 AA
1 AA
1150124 AACTACTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (22 bp):
AATGTATATACATATTGCAGAT
Found at i:1152656 original size:18 final size:18
Alignment explanation
Indices: 1152627--1152670 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1152617 AAGTAAAGTT
*
1152627 GAAGACGAGGAAGAGGAA
1 GAAGAAGAGGAAGAGGAA
*
1152645 GAGGAAGAGGAAGAGGAA
1 GAAGAAGAGGAAGAGGAA
1152663 GAAGAAGA
1 GAAGAAGA
1152671 AGATTGTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.45, T:0.00
Consensus pattern (18 bp):
GAAGAAGAGGAAGAGGAA
Found at i:1152673 original size:6 final size:6
Alignment explanation
Indices: 1152633--1152670 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1152623 AGTTGAAGAC
*
1152633 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAAGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
1152671 AGATTGTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:1167510 original size:21 final size:20
Alignment explanation
Indices: 1167482--1167566 Score: 109
Period size: 21 Copynumber: 4.2 Consensus size: 20
1167472 TATATATATC
*
1167482 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
1167502 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
**
1167523 TAATAAGCACTATAAATATTA
1 TAAT-AGCACTATAAATAAAA
1167544 TAATAGCACTA-AGAATAAAA
1 TAATAGCACTATA-AATAAAA
1167564 TAA
1 TAA
1167567 AATGAAATGG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 1 0.02
20 19 0.33
21 38 0.66
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:1167552 original size:41 final size:41
Alignment explanation
Indices: 1167482--1167566 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
1167472 TATATATATC
*
1167482 TAATAGCACTATAGATAAAATAATAAGCACTATA-AATAAAA
1 TAATAGCACTATAAATAAAATAATAAGCACTA-AGAATAAAA
**
1167523 TAATAAGCACTATAAATATTATAAT-AGCACTAAGAATAAAA
1 TAAT-AGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
1167564 TAA
1 TAA
1167567 AATGAAATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 21 0.54
42 17 0.44
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (41 bp):
TAATAGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
Found at i:1168127 original size:29 final size:28
Alignment explanation
Indices: 1168094--1168324 Score: 196
Period size: 29 Copynumber: 8.0 Consensus size: 28
1168084 TTTCGGTTAT
* *
1168094 GGTGTTATTTTCGTAATTATTTTTAAAA
1 GGTGTTATTTTGGTAATTATTGTTAAAA
* *
1168122 GTGTGTTATTTTCGTATTTACTT-TTAAAAA
1 G-GTGTTATTTTGGTAATTA-TTGTT-AAAA
*
1168152 GGGTGTTATTTTCGTAATTAATT-TTAAAA
1 -GGTGTTATTTTGGTAATT-ATTGTTAAAA
* *
1168181 CGGTGATATTTTGGCAATTATTGTTAAAA
1 -GGTGTTATTTTGGTAATTATTGTTAAAA
** * *
1168210 CAATGATATTTTGGTAATTATTGTTAAAT
1 -GGTGTTATTTTGGTAATTATTGTTAAAA
**
1168239 GGTACTATTTTGGTAATTATTGTTAAAA
1 GGTGTTATTTTGGTAATTATTGTTAAAA
* *
1168267 CAGTGCTATTTTGGTAATTATTGTTAAAA
1 -GGTGTTATTTTGGTAATTATTGTTAAAA
** * *
1168296 CAATGATATTTTGATAATTATTGTTAAAA
1 -GGTGTTATTTTGGTAATTATTGTTAAAA
1168325 ACAGTAATAT
Statistics
Matches: 176, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
28 27 0.15
29 121 0.69
30 26 0.15
31 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.48
Consensus pattern (28 bp):
GGTGTTATTTTGGTAATTATTGTTAAAA
Found at i:1168256 original size:28 final size:28
Alignment explanation
Indices: 1168187--1168344 Score: 167
Period size: 29 Copynumber: 5.5 Consensus size: 28
1168177 AAAACGGTGA
* *
1168187 TATTTTGGCAATTATTGTTAAAACAATGA-
1 TATTTTGGTAATTATTGTT-AAACAGT-AC
**
1168216 TATTTTGGTAATTATTGTTAAATGGTAC
1 TATTTTGGTAATTATTGTTAAACAGTAC
*
1168244 TATTTTGGTAATTATTGTTAAAACAGTGC
1 TATTTTGGTAATTATTGTT-AAACAGTAC
*
1168273 TATTTTGGTAATTATTGTTAAAACAATGA-
1 TATTTTGGTAATTATTGTT-AAACAGT-AC
* *
1168302 TATTTTGATAATTATTGTTAAAAACAGTAA
1 TATTTTGGTAATTATTGTT--AAACAGTAC
1168332 TATTTTGGTAATT
1 TATTTTGGTAATT
1168345 GTTAAAAAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.01
28 23 0.21
29 69 0.62
30 19 0.17
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (28 bp):
TATTTTGGTAATTATTGTTAAACAGTAC
Found at i:1168262 original size:57 final size:58
Alignment explanation
Indices: 1168158--1168370 Score: 233
Period size: 57 Copynumber: 3.7 Consensus size: 58
1168148 AAAAGGGTGT
* ** * *
1168158 TATTTTCGTAATTAATT-TTAAAACGGTGATATTTTGGCAATTATTGTTAAAACAATGA
1 TATTTTGGTAATT-ATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAAACAGTGA
*** *
1168216 TATTTTGGTAATTATTGTT-AAATGGT-ACTATTTTGGTAATTATTGTTAAAACAGTGC
1 TATTTTGGTAATTATTGTTAAAACAATGA-TATTTTGGTAATTATTGTTAAAACAGTGA
* *
1168273 TATTTTGGTAATTATTGTTAAAACAATGATATTTTGATAATTATTGTTAAAAACAGTAA
1 TATTTTGGTAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTT-AAAACAGTGA
*
1168332 TATTTTGGT-A--ATTGTTAAAAAAATGATATTTCT-GTAATT
1 TATTTTGGTAATTATTGTTAAAACAATGATATTT-TGGTAATT
1168371 TTACTGTGGA
Statistics
Matches: 136, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
56 26 0.19
57 55 0.40
58 37 0.27
59 18 0.13
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (58 bp):
TATTTTGGTAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAAACAGTGA
Found at i:1168280 original size:86 final size:86
Alignment explanation
Indices: 1168158--1168323 Score: 271
Period size: 86 Copynumber: 1.9 Consensus size: 86
1168148 AAAAGGGTGT
*
1168158 TATTTTCGTAATTAATTTTAAAACGGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTTG
1 TATTTTCGTAATTAATTTTAAAACAGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTTG
*
1168223 GTAATTATTGTTAAATGGTAC
66 ATAATTATTGTTAAATGGTAC
* * *
1168244 TATTTTGGTAATT-ATTGTTAAAACAGTGCTATTTTGGTAATTATTGTTAAAACAATGATATTTT
1 TATTTTCGTAATTAATT-TTAAAACAGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTT
1168308 GATAATTATTGTTAAA
65 GATAATTATTGTTAAA
1168324 AACAGTAATA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 3 0.04
86 71 0.96
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (86 bp):
TATTTTCGTAATTAATTTTAAAACAGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTTG
ATAATTATTGTTAAATGGTAC
Found at i:1170954 original size:2 final size:2
Alignment explanation
Indices: 1170947--1170981 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1170937 TTGATATGTT
1170947 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
1170982 GTCTCCACAT
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:1173078 original size:27 final size:28
Alignment explanation
Indices: 1173047--1173111 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
1173037 GCTGGTAATT
*
1173047 TTAAAAATTTTATTTA-AAATTAAAAAA
1 TTAAAAATTTTATATATAAATTAAAAAA
* *
1173074 TT-AAAATTATATATATATATTAAAAAA
1 TTAAAAATTTTATATATAAATTAAAAAA
* *
1173101 ATAAACATTTT
1 TTAAAAATTTT
1173112 GAAATAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 11 0.37
27 13 0.43
28 6 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAAAATTTTATATATAAATTAAAAAA
Found at i:1177243 original size:184 final size:184
Alignment explanation
Indices: 1176955--1177324 Score: 636
Period size: 184 Copynumber: 2.0 Consensus size: 184
1176945 AAATTAAATG
* *
1176955 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1177020 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* *
1177085 GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTAATAT
131 GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
1177139 TTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTC
* *
1177203 ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
64 AGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
* *
1177267 TTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
129 TTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
1177323 TT
1 TT
1177325 AAAATTTAAT
Statistics
Matches: 176, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
184 128 0.73
185 40 0.23
186 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (184 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
Found at i:1177349 original size:9 final size:9
Alignment explanation
Indices: 1177330--1177363 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
1177320 TATTTAAAAT
1177330 TTAATTTCGG
1 TTAA-TTCGG
1177340 TTAATTCGG
1 TTAATTCGG
1177349 TTAATTCGG
1 TTAATTCGG
1177358 TTAATT
1 TTAATT
1177364 AACCGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:1181349 original size:217 final size:217
Alignment explanation
Indices: 1180974--1181539 Score: 1132
Period size: 217 Copynumber: 2.6 Consensus size: 217
1180964 CCTTTTCATT
1180974 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1181039 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
66 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
1181104 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
131 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
1181169 AGGGCAAGTTTCATCGCAGGCC
196 AGGGCAAGTTTCATCGCAGGCC
1181191 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1181256 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
66 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
1181321 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
131 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
1181386 AGGGCAAGTTTCATCGCAGGCC
196 AGGGCAAGTTTCATCGCAGGCC
1181408 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1181473 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
66 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
1181538 CA
131 CA
1181540 GCTCCCTCAG
Statistics
Matches: 349, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 349 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (217 bp):
CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
AGGGCAAGTTTCATCGCAGGCC
Found at i:1181533 original size:33 final size:33
Alignment explanation
Indices: 1181496--1181572 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
1181486 ACAGCAGCAG
1181496 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
1 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
1181529 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
1 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
1181562 CAGCAGCAGCA
1 CAGCAGCAGCA
1181573 AGCAACAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.31, C:0.39, G:0.19, T:0.10
Consensus pattern (33 bp):
CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
Found at i:1181547 original size:250 final size:250
Alignment explanation
Indices: 1181279--1181758 Score: 960
Period size: 250 Copynumber: 1.9 Consensus size: 250
1181269 ACAGCAGCAG
1181279 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAGCAAGCAACAATAATGTTTGGATC
1 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAGCAAGCAACAATAATGTTTGGATC
1181344 AGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCCC
66 AGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCCC
1181409 TATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGCA
131 TATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGCA
1181474 TTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
196 TTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
1181529 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAGCAAGCAACAATAATGTTTGGATC
1 CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAGCAAGCAACAATAATGTTTGGATC
1181594 AGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCCC
66 AGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCCC
1181659 TATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGCA
131 TATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGCA
1181724 TTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGC
196 TTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGC
1181759 AGCAGCAGCA
Statistics
Matches: 230, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 230 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (250 bp):
CAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAGCAAGCAACAATAATGTTTGGATC
AGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCCC
TATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGCA
TTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTA
Found at i:1181745 original size:3 final size:3
Alignment explanation
Indices: 1181737--1181770 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1181727 GCAGATCCTA
1181737 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1181771 TCCCTCAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1210242 original size:27 final size:25
Alignment explanation
Indices: 1210191--1210242 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
1210181 TATGATTTAT
* *
1210191 AAAAAAAAAATAAAAGTTGAGTGAC
1 AAAAAAAAAATAAAAGGTGAATGAC
*
1210216 AAAAAAAATAAGTAAGAGGTGAATGAC
1 AAAAAAAA-AA-TAAAAGGTGAATGAC
1210243 CAAATGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 2 0.09
27 12 0.55
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (25 bp):
AAAAAAAAAATAAAAGGTGAATGAC
Found at i:1210949 original size:24 final size:24
Alignment explanation
Indices: 1210903--1210952 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1210893 ATATTTAGTT
*
1210903 TTTGTTTATTTTAGTATCCCATCG
1 TTTGTTTATTTTAATATCCCATCG
*
1210927 TTTGTTTCATTTTAATA-CTCATCG
1 TTTGTTT-ATTTTAATATCCCATCG
1210951 TT
1 TT
1210953 AAAAATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (24 bp):
TTTGTTTATTTTAATATCCCATCG
Found at i:1214754 original size:26 final size:26
Alignment explanation
Indices: 1214704--1214754 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1214694 AAAAATATGG
*
1214704 GTTTTTAATTTAAAAAATATTTTTAT
1 GTTTTTAATTTAAAAAATAATTTTAT
1214730 GTTTTTAATTTAAATAAA-AATTTTA
1 GTTTTTAATTTAAA-AAATAATTTTA
1214755 AAATTATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
GTTTTTAATTTAAAAAATAATTTTAT
Found at i:1215435 original size:12 final size:12
Alignment explanation
Indices: 1215420--1215448 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1215410 GTACTTATAG
1215420 AAATATATTTAA
1 AAATATATTTAA
1215432 AAATA-ATTTAA
1 AAATATATTTAA
1215443 AAATAT
1 AAATAT
1215449 TTACCTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATTTAA
Found at i:1220160 original size:21 final size:21
Alignment explanation
Indices: 1220111--1220152 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1220101 CAGAATCGTG
*
1220111 ACTGCTATATCAGCACCGTAA
1 ACTGCAATATCAGCACCGTAA
1220132 ACTGCAATATCAGCACCGTAA
1 ACTGCAATATCAGCACCGTAA
1220153 TGATCAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (21 bp):
ACTGCAATATCAGCACCGTAA
Found at i:1221797 original size:24 final size:24
Alignment explanation
Indices: 1221682--1221800 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
1221672 AAACATAATT
*
1221682 CATGTCAAGTATCACATCAAAATC
1 CATGTCAAGTATCACATCAGAATC
*
1221706 CATGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCACATCAGAATC
* *
1221730 CAAGTCAAGTATCACATCAAAATC
1 CATGTCAAGTATCACATCAGAATC
*
1221754 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCACATCAGAATC
*
1221778 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCACATCAGAAT
1221801 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCACATCAGAATC
Found at i:1222881 original size:26 final size:28
Alignment explanation
Indices: 1222845--1222921 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
1222835 TGAGTTTGGT
* *
1222845 GATATTCTTGGTTATTTC-CA-TACCAGG
1 GATATT-TTGGTCATTTCACAGAACCAGG
* *
1222872 GGTATTTTGGTCATTTCACAGAACCATG
1 GATATTTTGGTCATTTCACAGAACCAGG
1222900 GATATTTTGGTCATTTCACAGA
1 GATATTTTGGTCATTTCACAGA
1222922 TCCATTGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 10 0.23
27 7 0.16
28 26 0.60
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (28 bp):
GATATTTTGGTCATTTCACAGAACCAGG
Found at i:1230872 original size:2 final size:2
Alignment explanation
Indices: 1230849--1230904 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
1230839 CACAAAAGCC
* * *
1230849 AT AT AC AT A- AT AT AT GT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1230890 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1230905 CCTGCCTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1236802 original size:2 final size:2
Alignment explanation
Indices: 1236795--1236824 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1236785 CCATACGCTC
1236795 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1236825 TCTTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1237002 original size:26 final size:26
Alignment explanation
Indices: 1236972--1237024 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1236962 GCTTTACCCT
1236972 ATTAATAACCTAAGTAGTGCTTAATC
1 ATTAATAACCTAAGTAGTGCTTAATC
1236998 ATTAATAACCTAAGTAGTGCTTAATC
1 ATTAATAACCTAAGTAGTGCTTAATC
1237024 A
1 A
1237025 ATGGGCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
ATTAATAACCTAAGTAGTGCTTAATC
Found at i:1237092 original size:17 final size:17
Alignment explanation
Indices: 1237067--1237123 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 17
1237057 TATACCCTAA
*
1237067 TTTAGATATTAGGTCTTTT
1 TTTATATATTAGGTC--TT
1237086 TATATATATATTAGGTCTT
1 T-T-TATATATTAGGTCTT
1237105 TTTATATATTAGGTCTT
1 TTTATATATTAGGTCTT
1237122 TT
1 TT
1237124 ATCTTGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
17 17 0.49
18 1 0.03
19 4 0.11
20 1 0.03
21 12 0.34
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTATATATTAGGTCTT
Found at i:1237096 original size:21 final size:21
Alignment explanation
Indices: 1237072--1237113 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1237062 CCTAATTTAG
1237072 ATATTAGGTCTTTTTATATAT
1 ATATTAGGTCTTTTTATATAT
1237093 ATATTAGGTCTTTTTATATAT
1 ATATTAGGTCTTTTTATATAT
1237114 TAGGTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (21 bp):
ATATTAGGTCTTTTTATATAT
Found at i:1240187 original size:22 final size:22
Alignment explanation
Indices: 1240159--1240204 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1240149 AGGGTCACAT
1240159 TGAGTTTGTTTTCTGAGTTAGA
1 TGAGTTTGTTTTCTGAGTTAGA
1240181 TGAGTTTGTTTTCTGAGTTAGA
1 TGAGTTTGTTTTCTGAGTTAGA
1240203 TG
1 TG
1240205 GTCATATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.28, T:0.50
Consensus pattern (22 bp):
TGAGTTTGTTTTCTGAGTTAGA
Found at i:1250355 original size:4 final size:4
Alignment explanation
Indices: 1250341--1250375 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1250331 CATCAATCAT
* *
1250341 ATAC ATGC ATAC ATAC ATAC ATAC ACAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1250376 GTTTCATCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:1252796 original size:10 final size:12
Alignment explanation
Indices: 1252763--1252809 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 12
1252753 GGACGAACTT
*
1252763 ATAAAAT-TTTA
1 ATAAAATATATA
1252774 ATAAAATA-A-A
1 ATAAAATATATA
1252784 ATAAAA-AT-TA
1 ATAAAATATATA
1252794 ATAAAATATATA
1 ATAAAATATATA
1252806 ATAA
1 ATAA
1252810 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
9 1 0.03
10 14 0.47
11 9 0.30
12 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAATATATA
Found at i:1254521 original size:23 final size:23
Alignment explanation
Indices: 1254495--1254553 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1254485 CTGCCACGCC
*
1254495 AGCTACCACGTCATCGCCACATT
1 AGCTACCACATCATCGCCACATT
*
1254518 AGCTAACACATCATCGCCACATT
1 AGCTACCACATCATCGCCACATT
*
1254541 AGCTACAACATCA
1 AGCTACCACATCA
1254554 GCCGCTGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.36, G:0.10, T:0.20
Consensus pattern (23 bp):
AGCTACCACATCATCGCCACATT
Found at i:1276931 original size:16 final size:17
Alignment explanation
Indices: 1276903--1276937 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1276893 ATTAAAATAA
1276903 TATTTATATAAA-TTAT
1 TATTTATATAAATTTAT
*
1276919 TATTTATTTAAATTTAT
1 TATTTATATAAATTTAT
1276936 TA
1 TA
1276938 ATTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTATATAAATTTAT
Found at i:1277582 original size:60 final size:60
Alignment explanation
Indices: 1277472--1277586 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
1277462 AACATACCAC
* *
1277472 CGTGTCACCTGAGTCAGCAAAACCCCATGAAGGCGCGTCCCTGGGTATGCGCCTTTCACA
1 CGTGTCACCTGAGTCAGCAAAACCCCATGAAAGCGCGTCCCCGGGTATGCGCCTTTCACA
* **
1277532 CGTGTCACCTGAGTCGGCATAAA-TTCATGGAAAGCGCGTCCCCGGG-ATGCGCCTT
1 CGTGTCACCTGAGTCAGCA-AAACCCCAT-GAAAGCGCGTCCCCGGGTATGCGCCTT
1277587 CCGCCACCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 30 0.62
61 18 0.38
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.21
Consensus pattern (60 bp):
CGTGTCACCTGAGTCAGCAAAACCCCATGAAAGCGCGTCCCCGGGTATGCGCCTTTCACA
Found at i:1285169 original size:31 final size:30
Alignment explanation
Indices: 1285125--1285189 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1285115 CCAGGAATGA
1285125 GATT-CCGATCAACTAAACATGGAAATGTAG
1 GATTCCCGATCAACTAAA-ATGGAAATGTAG
* * *
1285155 GATTCCCGGTCAACTAAAATGGGAATGTGG
1 GATTCCCGATCAACTAAAATGGAAATGTAG
1285185 GATTC
1 GATTC
1285190 TCATCCCATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (30 bp):
GATTCCCGATCAACTAAAATGGAAATGTAG
Found at i:1287791 original size:21 final size:21
Alignment explanation
Indices: 1287743--1287803 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1287733 ATATGCCTCG
**
1287743 ACGGGCTCGACATGTAACCTA
1 ACGGGCTCGACATGTAAATTA
* * *
1287764 ACAGGCTCGACATGCAAATTT
1 ACGGGCTCGACATGTAAATTA
*
1287785 ACGGGCTCAACATGTAAAT
1 ACGGGCTCGACATGTAAAT
1287804 CAGTGGGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
ACGGGCTCGACATGTAAATTA
Found at i:1289613 original size:20 final size:20
Alignment explanation
Indices: 1289569--1289614 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1289559 TTAGGGCTTT
* *
1289569 GGTTTAAGGTTTGATTTTAG
1 GGTTTAAGGTTTGAGTCTAG
* *
1289589 TGTTTAAGTTTTGAGTCTAG
1 GGTTTAAGGTTTGAGTCTAG
1289609 GGTTTA
1 GGTTTA
1289615 TAAAAATGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (20 bp):
GGTTTAAGGTTTGAGTCTAG
Found at i:1290674 original size:10 final size:10
Alignment explanation
Indices: 1290659--1290683 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1290649 TTTAGAAAAC
1290659 TATTTTTATT
1 TATTTTTATT
1290669 TATTTTTATT
1 TATTTTTATT
1290679 TATTT
1 TATTT
1290684 AAAGTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1291359 original size:14 final size:14
Alignment explanation
Indices: 1291318--1291362 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
1291308 GTTCATGAAC
*
1291318 GTTCGGTTATGTTC
1 GTTCGGTTATGTTT
1291332 GTTCGGTTATGTTT
1 GTTCGGTTATGTTT
1291346 GTTCGGTTATGTTT
1 GTTCGGTTATGTTT
1291360 GTT
1 GTT
1291363 TATGTTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.07, C:0.09, G:0.29, T:0.56
Consensus pattern (14 bp):
GTTCGGTTATGTTT
Found at i:1291374 original size:24 final size:24
Alignment explanation
Indices: 1291338--1291407 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1291328 GTTCGTTCGG
**
1291338 TTATGTTTGTTCGGTTATGTTTGT
1 TTATGTTCATTCGGTTATGTTTGT
* * *
1291362 TTATGTTCATTCGGTAATATTCGT
1 TTATGTTCATTCGGTTATGTTTGT
**
1291386 TTATGTTCATTCATTTATGTTT
1 TTATGTTCATTCGGTTATGTTT
1291408 AACCCAATCT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59
Consensus pattern (24 bp):
TTATGTTCATTCGGTTATGTTTGT
Found at i:1292150 original size:16 final size:16
Alignment explanation
Indices: 1292129--1292194 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
1292119 CGTTTGTTCG
1292129 TTATGTTCGTGTTCAT
1 TTATGTTCGTGTTCAT
*
1292145 TTATGTTCGTGTTCGT
1 TTATGTTCGTGTTCAT
**
1292161 TTATGTTCGTGTTTGT
1 TTATGTTCGTGTTCAT
1292177 TTATGTTCGT-TT-AT
1 TTATGTTCGTGTTCAT
1292191 TTAT
1 TTAT
1292195 TAATGAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (16 bp):
TTATGTTCGTGTTCAT
Found at i:1292168 original size:32 final size:31
Alignment explanation
Indices: 1292123--1292186 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
1292113 CTCCAACGTT
1292123 TGTTCGTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTATGTTCGTGTTCATTTATGTTCG
**
1292154 TGTTCGTTTATGTTCGTGTTTGTTTATGTTCG
1 TGTTCG-TTATGTTCGTGTTCATTTATGTTCG
1292186 T
1 T
1292187 TTATTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (31 bp):
TGTTCGTTATGTTCGTGTTCATTTATGTTCG
Found at i:1292220 original size:29 final size:29
Alignment explanation
Indices: 1292187--1292243 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1292177 TTATGTTCGT
* * *
1292187 TTATTTATTAATGAACAAACATGAACAAG
1 TTATTCATTAATAAACAAACATAAACAAG
* *
1292216 TTATTCCTTAATAAACGAACATAAACAA
1 TTATTCATTAATAAACAAACATAAACAA
1292244 AAAAAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (29 bp):
TTATTCATTAATAAACAAACATAAACAAG
Found at i:1292278 original size:16 final size:16
Alignment explanation
Indices: 1292253--1292293 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1292243 AAAAAAAATT
1292253 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
1292269 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
1292285 T-TT-ATTTAT
1 TGTTCATTTAT
1292294 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1292919 original size:18 final size:18
Alignment explanation
Indices: 1292884--1292938 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 18
1292874 GGTTCACAAA
*
1292884 ATAAGATTATTCGTGAGAAT
1 ATAAGATTATT--AGAGAAT
1292904 ATAAGATTATTAGAGAAT
1 ATAAGATTATTAGAGAAT
*
1292922 A-AA-ATTACTA-AGAAT
1 ATAAGATTATTAGAGAAT
1292937 AT
1 AT
1292939 TGTATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 2 0.06
18 7 0.22
20 11 0.34
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.33
Consensus pattern (18 bp):
ATAAGATTATTAGAGAAT
Found at i:1292928 original size:16 final size:18
Alignment explanation
Indices: 1292898--1292938 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1292888 GATTATTCGT
*
1292898 GAGAATATAAGATTATTA
1 GAGAATATAAGATTACTA
1292916 GAGAATA-AA-ATTACTA
1 GAGAATATAAGATTACTA
1292932 -AGAATAT
1 GAGAATAT
1292939 TGTATTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 2 0.10
18 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (18 bp):
GAGAATATAAGATTACTA
Found at i:1293791 original size:18 final size:19
Alignment explanation
Indices: 1293751--1293792 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1293741 TGGTTCATAA
*
1293751 AATATAAGATTATTCGTGAG
1 AATATAAGATTATTC-AGAG
1293771 AATATAAGATTATT-AGAG
1 AATATAAGATTATTCAGAG
1293789 AATA
1 AATA
1293793 AAATTACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (19 bp):
AATATAAGATTATTCAGAG
Found at i:1296326 original size:7 final size:7
Alignment explanation
Indices: 1296316--1296346 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1296306 CCATAACCTA
1296316 TAAACCC
1 TAAACCC
*
1296323 TAAATCC
1 TAAACCC
1296330 TAAACCC
1 TAAACCC
1296337 TAAACCC
1 TAAACCC
1296344 TAA
1 TAA
1296347 CTCAAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:1296332 original size:95 final size:94
Alignment explanation
Indices: 1296197--1296372 Score: 228
Period size: 95 Copynumber: 1.9 Consensus size: 94
1296187 AACCCTAAAC
* * * * * * *
1296197 TATAAATCATAACCCCATGATCTATAAACTATAAACCCTAAA-TATAAATCTTAACTAATAGTTT
1 TATAAACCATAACCCCATAACCTATAAACCATAAACCCTAAACCATAAACCCTAACTAA-AGTTT
1296261 ATAATTTAGGATTTTAAATTAGAGGTAGGG
65 ATAATTTAGGATTTTAAATTAGAGGTAGGG
* * * *
1296291 TATAAACCATAACCCCCATAACCTATAAACCCTAAATCCTAAACCCTAAACCCTAACTCAAGTTT
1 TATAAACCATAA-CCCCATAACCTATAAACCATAAACCCTAAACCATAAACCCTAACTAAAGTTT
1296356 ATAATTTAGGATTTTAA
65 ATAATTTAGGATTTTAA
1296373 GTTAAGGGTA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
94 11 0.16
95 47 0.68
96 11 0.16
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.31
Consensus pattern (94 bp):
TATAAACCATAACCCCATAACCTATAAACCATAAACCCTAAACCATAAACCCTAACTAAAGTTTA
TAATTTAGGATTTTAAATTAGAGGTAGGG
Found at i:1297472 original size:22 final size:22
Alignment explanation
Indices: 1297447--1297496 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1297437 TACAAAGTGC
1297447 ATAATTTTCTAGGGT-AAATTAA
1 ATAATTTT-TAGGGTGAAATTAA
*
1297469 ATAATATTTTAGGTTGAAATTAA
1 ATAAT-TTTTAGGGTGAAATTAA
1297492 A-AATT
1 ATAATT
1297497 GTATGTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 13 0.52
23 11 0.44
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (22 bp):
ATAATTTTTAGGGTGAAATTAA
Found at i:1298345 original size:21 final size:21
Alignment explanation
Indices: 1298321--1298364 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1298311 AATGATATAT
1298321 TATAAATTATTTTATTATTTG
1 TATAAATTATTTTATTATTTG
1298342 TATAAATTATTTTATTATTTG
1 TATAAATTATTTTATTATTTG
1298363 TA
1 TA
1298365 GGCACGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TATAAATTATTTTATTATTTG
Found at i:1309627 original size:43 final size:43
Alignment explanation
Indices: 1309579--1309675 Score: 194
Period size: 43 Copynumber: 2.3 Consensus size: 43
1309569 CTAAAATGGA
1309579 ACAAAAACTAAACATTAAATATGATTTTAAAAAAATTGAAAGT
1 ACAAAAACTAAACATTAAATATGATTTTAAAAAAATTGAAAGT
1309622 ACAAAAACTAAACATTAAATATGATTTTAAAAAAATTGAAAGT
1 ACAAAAACTAAACATTAAATATGATTTTAAAAAAATTGAAAGT
1309665 ACAAAAACTAA
1 ACAAAAACTAA
1309676 TAATTTAGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (43 bp):
ACAAAAACTAAACATTAAATATGATTTTAAAAAAATTGAAAGT
Found at i:1310006 original size:2 final size:2
Alignment explanation
Indices: 1309999--1310027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1309989 ATCCTCAACT
1309999 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 T
1310028 TATTTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1313994 original size:14 final size:14
Alignment explanation
Indices: 1313975--1314015 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
1313965 CCGAACCGAA
1313975 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
1313989 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
1314006 CCGAACCGAA
1 CCGAACCGAA
1314016 CCGAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:1314546 original size:162 final size:158
Alignment explanation
Indices: 1314227--1314547 Score: 416
Period size: 162 Copynumber: 2.0 Consensus size: 158
1314217 AAAACCAAAA
1314227 AAAAGAGACTAAATAAAAATAGATTTTTAATGAATTAAAATGATAAATCAAAATATTTAAATTAT
1 AAAAGAGACTAAATAAAAATAGATTTTTAATGAATTAAAATGATAAATCAAAATATTTAAATTAT
* * *
1314292 AGCATGAATTATTTTTAAAAAGGTGATTAATTTATTTTTAATATTTTATATACAATTGTTTTAAA
66 AACATGAATTATTTTAAAAAAAGTGATTAATTTATTTTTAATATTTTATATACAATTGTTTTAAA
* *
1314357 AACGGGTATCAAATTAATTCTTTTTAAG
131 AACGAGTATCAAATCAATTCTTTTTAAG
* * *
1314385 AAAAG-GACTAAATAAAAATAAGTTTTTTAATGTATTAAAAATGATAATATTTAAAAT-TTTAAA
1 AAAAGAGACTAAATAAAAAT-AGATTTTTAATGAATT-AAAATGATAA-A-TCAAAATATTTAAA
* * * *
1314448 TTCTAATATGAATTA-TTTAAAAAATATTATATTAATTTATTTTTAATAATTTTATATACAATTG
62 TTATAACATGAATTATTTTAAAAAA-AGT-GATTAATTTATTTTTAAT-ATTTTATATACAATTG
* *
1314512 TTTTAAAAAATGAGTATCAAATCGATTC-TTTTAAG
124 TTTT-AAAAACGAGTATCAAATCAATTCTTTTTAAG
1314547 A
1 A
1314548 GAAAATAACT
Statistics
Matches: 141, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
157 14 0.10
158 19 0.13
159 18 0.13
160 20 0.14
161 23 0.16
162 28 0.20
163 19 0.13
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (158 bp):
AAAAGAGACTAAATAAAAATAGATTTTTAATGAATTAAAATGATAAATCAAAATATTTAAATTAT
AACATGAATTATTTTAAAAAAAGTGATTAATTTATTTTTAATATTTTATATACAATTGTTTTAAA
AACGAGTATCAAATCAATTCTTTTTAAG
Found at i:1314776 original size:57 final size:57
Alignment explanation
Indices: 1314704--1314815 Score: 179
Period size: 57 Copynumber: 2.0 Consensus size: 57
1314694 GCAACGCGGT
* * *
1314704 TTTTCAAATTCGCAACGGTAATTACCGAAATAGGTAAACAGTACTATCGCAATGTGA
1 TTTTCAAATTCGCAACGCTAATTACCGAAATAGGTAAACAATACTATCACAATGTGA
* *
1314761 TTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAATACTATCACAATGT
1 TTTTCAAATTCGCAACGCTAATTACCGAAATAGGTAAACAATACTATCACAATGT
1314816 AAACAGTACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (57 bp):
TTTTCAAATTCGCAACGCTAATTACCGAAATAGGTAAACAATACTATCACAATGTGA
Found at i:1314819 original size:20 final size:20
Alignment explanation
Indices: 1314794--1314834 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1314784 ACCGATATAG
1314794 GTAAACAATACTATCACAAT
1 GTAAACAATACTATCACAAT
* *
1314814 GTAAACAGTACTATCGCAAT
1 GTAAACAATACTATCACAAT
1314834 G
1 G
1314835 CGATTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (20 bp):
GTAAACAATACTATCACAAT
Found at i:1314827 original size:77 final size:77
Alignment explanation
Indices: 1314737--1314912 Score: 280
Period size: 77 Copynumber: 2.3 Consensus size: 77
1314727 ACCGAAATAG
* *
1314737 GTAAACAGTACTATCGCAATGTGATTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAA
1 GTAAACAGTACTATCGCAATGTGATTTTCAAATTCGCAACGCTAATTACCAATATAGGTAAACAA
1314802 TACTATCACAAT
66 TACTATCACAAT
* * *
1314814 GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAATGCTAATTACCAATATAGGTAAACAG
1 GTAAACAGTACTATCGCAATGTGATTTTCAAATTCGCAACGCTAATTACCAATATAGGTAAACAA
* *
1314879 TACTATCGCAGT
66 TACTATCACAAT
*
1314891 GTAAACAATACTATCGCAATGT
1 GTAAACAGTACTATCGCAATGT
1314913 AAACAGTACT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 90 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (77 bp):
GTAAACAGTACTATCGCAATGTGATTTTCAAATTCGCAACGCTAATTACCAATATAGGTAAACAA
TACTATCACAAT
Found at i:1314896 original size:20 final size:20
Alignment explanation
Indices: 1314871--1314931 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
1314861 ACCAATATAG
*
1314871 GTAAACAGTACTATCGCAGT
1 GTAAACAGTACTATCGCAAT
*
1314891 GTAAACAATACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1314911 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1314931 G
1 G
1314932 CGATTTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:1314920 original size:97 final size:97
Alignment explanation
Indices: 1314794--1315105 Score: 552
Period size: 97 Copynumber: 3.2 Consensus size: 97
1314784 ACCGATATAG
* *
1314794 GTAAACAATACTATCACAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAATGCTAA
1 GTAAACAATACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
* *
1314859 TTACCAATATAGGTAAACAGTACTATCGCAGT
66 TTACCGATATAGGTAAACAGTACTATCGCAAT
1314891 GTAAACAATACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1 GTAAACAATACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1314956 TTACCGATATAGGTAAACAGTACTATCGCAAT
66 TTACCGATATAGGTAAACAGTACTATCGCAAT
*
1314988 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1 GTAAACAATACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
* *
1315053 TTATCGATATAGGTAAACAGTACTATCGTAAT
66 TTACCGATATAGGTAAACAGTACTATCGCAAT
*
1315085 GTAAACAGTACTATCGCAATG
1 GTAAACAATACTATCGCAATG
1315106 CGATTTTCAA
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 208 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (97 bp):
GTAAACAATACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
TTACCGATATAGGTAAACAGTACTATCGCAAT
Found at i:1314993 original size:20 final size:20
Alignment explanation
Indices: 1314968--1315028 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
1314958 ACCGATATAG
1314968 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1314988 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1315008 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1315028 G
1 G
1315029 CGATTTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:1315069 original size:77 final size:77
Alignment explanation
Indices: 1314988--1315182 Score: 363
Period size: 77 Copynumber: 2.5 Consensus size: 77
1314978 CTATCGCAAT
1314988 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
*
1315053 TTATCGATATAG
66 TTACCGATATAG
*
1315065 GTAAACAGTACTATCGTAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1315130 TTACCGATATAG
66 TTACCGATATAG
*
1315142 GTAAACAGTACTATCGCAATGTAAACAATACTATCGCAATG
1 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATG
1315183 TAAACAGTAT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 114 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (77 bp):
GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
TTACCGATATAG
Found at i:1315090 original size:20 final size:20
Alignment explanation
Indices: 1315065--1315105 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1315055 ATCGATATAG
*
1315065 GTAAACAGTACTATCGTAAT
1 GTAAACAGTACTATCGCAAT
1315085 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
1315105 G
1 G
1315106 CGATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:1315167 original size:20 final size:20
Alignment explanation
Indices: 1315142--1315200 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1315132 ACCGATATAG
1315142 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
1315162 GTAAACAATACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
1315182 GTAAACAGTATTATCGCAA
1 GTAAACAGTACTATCGCAA
1315201 CGCGATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:1315208 original size:174 final size:173
Alignment explanation
Indices: 1314737--1315209 Score: 627
Period size: 174 Copynumber: 2.7 Consensus size: 173
1314727 ACCGAAATAG
* * *
1314737 GTAAACAGTACTATCGCAATGTGATTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAA
1 GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
* *** * **
1314802 TACTATCACAATGTAAACAGTACTATCGCAATGCGATTTTCA--AAT-TCGCAATGCTAATTACC
66 TACTATCGCAATGTAAACAGTACTATCGCAAT--G-TAAACAGTAATATCGCAATGC-GATTTTC
*
1314864 AATATAGGTAAACAGTACTATCGCAGTGTAAACAATACTATCGCAAT
127 AATATACGTAAACAGTACTATCGCAGTGTAAACAATACTATCGCAAT
1314911 GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
1 GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
*
1314976 TACTATCGCAATGTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAA-A
66 TACTATCGCAATGTAAACAGTACTATCGCAATGTAAACAGTAATATCGCAATGCGATTTTCAATA
* * * * * *
1315040 TTCG-CAAC-GCTAATTATCG-ATATAGGTAAACAGTACTATCGTAAT
131 TACGTAAACAG-T-ACTATCGCA-GT--GTAAACAATACTATCGCAAT
1315085 GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
1 GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
* * *
1315150 TACTATCGCAATGTAAACAATACTATCGCAATGTAAACAGTATTATCGCAACGCGATTTT
66 TACTATCGCAATGTAAACAGTACTATCGCAATGTAAACAGTAATATCGCAATGCGATTTT
1315210 TTCTACCGTG
Statistics
Matches: 270, Mismatches: 21, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
170 1 0.00
171 8 0.03
172 11 0.04
173 8 0.03
174 242 0.90
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (173 bp):
GTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
TACTATCGCAATGTAAACAGTACTATCGCAATGTAAACAGTAATATCGCAATGCGATTTTCAATA
TACGTAAACAGTACTATCGCAGTGTAAACAATACTATCGCAAT
Found at i:1315273 original size:20 final size:20
Alignment explanation
Indices: 1315248--1315291 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1315238 TGAGTTGAGA
*
1315248 ATTTACCTATTCGCGTTGTG
1 ATTTACCTATTCGCGTTGCG
1315268 ATTTACCTATTCGCGTTGCG
1 ATTTACCTATTCGCGTTGCG
1315288 ATTT
1 ATTT
1315292 TGGAACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTTACCTATTCGCGTTGCG
Found at i:1319352 original size:33 final size:33
Alignment explanation
Indices: 1319315--1319380 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1319305 GAACTCCGAA
1319315 TCACCTTCGACGTCGTCGGCGTTTAAGTCTTCT
1 TCACCTTCGACGTCGTCGGCGTTTAAGTCTTCT
1319348 TCACCTTCGACGTCGTCGGCGTTTAAGTCTTCT
1 TCACCTTCGACGTCGTCGGCGTTTAAGTCTTCT
1319381 CCGGGCTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.36
Consensus pattern (33 bp):
TCACCTTCGACGTCGTCGGCGTTTAAGTCTTCT
Found at i:1321659 original size:67 final size:62
Alignment explanation
Indices: 1321542--1321665 Score: 162
Period size: 67 Copynumber: 1.9 Consensus size: 62
1321532 TTTAGTGAGC
1321542 TTAACGAGCAACGAGTCGAGTTGAGCAATAAATTTTTTAAATGAGCACGAGTCGAGCAATATT
1 TTAACGAGCAACGAGTCGAGTTGAGCAATAAATTTTTTAAA-GAGCACGAGTCGAGCAATATT
1321605 TTAACGAGCTTAACGAGTAACGAGTTGAGCAGCA-AAATTTTTTAACA-AGCACGAGTCGAGC
1 TTAACGAGC--AACGAGT--CGAGTTGAGCA--ATAAATTTTTTAA-AGAGCACGAGTCGAGC
1321666 GCTGCCCAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
63 9 0.17
65 7 0.13
67 25 0.46
68 11 0.20
69 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (62 bp):
TTAACGAGCAACGAGTCGAGTTGAGCAATAAATTTTTTAAAGAGCACGAGTCGAGCAATATT
Found at i:1330068 original size:2 final size:2
Alignment explanation
Indices: 1330063--1330094 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1330053 ATAAAGAGAG
1330063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1330095 TTCATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1330174 original size:21 final size:20
Alignment explanation
Indices: 1330125--1330174 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1330115 TAATGTTATT
*
1330125 TAATA-TATCAAATACAATC
1 TAATATTATAAAATACAATC
* *
1330144 TAAAATTATAAAATATAATC
1 TAATATTATAAAATACAATC
1330164 ATAATATTATA
1 -TAATATTATA
1330175 TTTTAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATATTATAAAATACAATC
Found at i:1340702 original size:14 final size:14
Alignment explanation
Indices: 1340683--1340713 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1340673 CAAGTTGGCA
*
1340683 ATGCCATGGTTTAC
1 ATGCCACGGTTTAC
1340697 ATGCCACGGTTTAC
1 ATGCCACGGTTTAC
1340711 ATG
1 ATG
1340714 GTTCTTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (14 bp):
ATGCCACGGTTTAC
Found at i:1342254 original size:2 final size:2
Alignment explanation
Indices: 1342249--1342274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1342239 CGAAAAAATA
1342249 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
1342275 TATTTAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351685 original size:29 final size:29
Alignment explanation
Indices: 1351643--1351705 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
1351633 GTGATCGCCA
*
1351643 TAGGTCGCCATGTAGTCCCGGCGACCTTG
1 TAGGTCGCCATGTAATCCCGGCGACCTTG
1351672 TAGGTCGCCATGTAATCCCGGCGACCTTG
1 TAGGTCGCCATGTAATCCCGGCGACCTTG
*
1351701 GAGGT
1 TAGGT
1351706 ATTTTGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTAATCCCGGCGACCTTG
Found at i:1352313 original size:21 final size:21
Alignment explanation
Indices: 1352288--1352331 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1352278 AATCTAGTTA
1352288 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1352309 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1352330 AT
1 AT
1352332 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1352341 original size:28 final size:30
Alignment explanation
Indices: 1352308--1352370 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1352298 TAGTATAAAT
*
1352308 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1352336 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1352366 TATTA
1 TATTA
1352371 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Done.