Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008653.1 Hibiscus syriacus cultivar Beakdansim tig00111644_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: 1778368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1052313 original size:31 final size:32
Alignment explanation
Indices: 1052253--1052313 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1052243 TGACAAAATG
*
1052253 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
1052285 ACACAAACAAAAGAGAA-AAACAAGTTAGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGT
1052314 ACATGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.13
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
Found at i:1055834 original size:3 final size:3
Alignment explanation
Indices: 1055826--1055933 Score: 157
Period size: 3 Copynumber: 36.0 Consensus size: 3
1055816 AATATGTAAT
*
1055826 TAA TAA TAA TAA TAA TAA TTAA TAA -ACA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
1055872 TAA CAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1055920 TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA
1055934 CTAGAAAAGA
Statistics
Matches: 96, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 3 0.03
3 89 0.93
4 4 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1058478 original size:32 final size:32
Alignment explanation
Indices: 1058426--1058557 Score: 124
Period size: 32 Copynumber: 4.2 Consensus size: 32
1058416 ATAGGGGCCA
*
1058426 ACCCAAGGAAA-ACCTTGGGGCCTCAAAGCCT
1 ACCCAAGGAAATACCTTGGGGCCTGAAAGCCT
* *
1058457 ACCCAAGGAAACACCTTGGGGCCTGAGAGCCT
1 ACCCAAGGAAATACCTTGGGGCCTGAAAGCCT
* * * * ** * *
1058489 GCCAAAAGAAGTATTTTGGGGCTTGAGAGCCT
1 ACCCAAGGAAATACCTTGGGGCCTGAAAGCCT
* *
1058521 ACCCAAGGGAATATCTTGGGGCCT-AAGAGCCT
1 ACCCAAGGAAATACCTTGGGGCCTGAA-AGCCT
1058553 ACCCA
1 ACCCA
1058558 TGGGTCACCT
Statistics
Matches: 81, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
31 12 0.15
32 69 0.85
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (32 bp):
ACCCAAGGAAATACCTTGGGGCCTGAAAGCCT
Found at i:1061840 original size:18 final size:18
Alignment explanation
Indices: 1061801--1061841 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1061791 CTGGTCTCGG
* *
1061801 GTCAAAATCAACAATTAG
1 GTCAAAATCAACAATCAA
*
1061819 GTCAAAATCAACACTCAA
1 GTCAAAATCAACAATCAA
1061837 GTCAA
1 GTCAA
1061842 CTATTGGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (18 bp):
GTCAAAATCAACAATCAA
Found at i:1070888 original size:20 final size:21
Alignment explanation
Indices: 1070860--1070901 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1070850 TAAATTTATG
1070860 TAATGAATT-TATAATAA-TAT
1 TAATGAATTAT-TAATAACTAT
*
1070880 TAATTAATTATTAATAACTAT
1 TAATGAATTATTAATAACTAT
1070901 T
1 T
1070902 TATTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATGAATTATTAATAACTAT
Found at i:1073968 original size:12 final size:12
Alignment explanation
Indices: 1073953--1074002 Score: 91
Period size: 12 Copynumber: 4.2 Consensus size: 12
1073943 ATCACCATCA
1073953 TCATCGTCGTCG
1 TCATCGTCGTCG
*
1073965 TCATCGTCGTCA
1 TCATCGTCGTCG
1073977 TCATCGTCGTCG
1 TCATCGTCGTCG
1073989 TCATCGTCGTCG
1 TCATCGTCGTCG
1074001 TC
1 TC
1074003 TTGAGCAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.10, C:0.34, G:0.22, T:0.34
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:1073968 original size:24 final size:24
Alignment explanation
Indices: 1073941--1073993 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1073931 GTTGTCATCA
1073941 TCATCACCATCATCATCGTCGTCG
1 TCATCACCATCATCATCGTCGTCG
** *
1073965 TCATCGTCGTCATCATCGTCGTCG
1 TCATCACCATCATCATCGTCGTCG
1073989 TCATC
1 TCATC
1073994 GTCGTCGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.17, C:0.36, G:0.15, T:0.32
Consensus pattern (24 bp):
TCATCACCATCATCATCGTCGTCG
Found at i:1073986 original size:3 final size:3
Alignment explanation
Indices: 1073956--1074002 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
1073946 ACCATCATCA
* * * *
1073956 TCG TCG TCG TCA TCG TCG TCA TCA TCG TCG TCG TCA TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1074003 TTGAGCAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.09, C:0.34, G:0.23, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:1078656 original size:3 final size:3
Alignment explanation
Indices: 1078648--1078709 Score: 97
Period size: 3 Copynumber: 20.0 Consensus size: 3
1078638 AGATGCTTTG
1078648 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
1078697 ATTT AAT ATT ATT
1 A-TT ATT ATT ATT
1078710 TTTCTTTATG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 50 0.91
4 4 0.07
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1087975 original size:41 final size:41
Alignment explanation
Indices: 1087877--1087975 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
1087867 AGTAAGTCTC
* *
1087877 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCT
1 TCGGGCCATCTGTAAGTCTTTCGAGCAAGATGC-TAAATCCT
** * *
1087919 TCGGG-TTTTTCGTAAGTCTTTCGAGCAAGATGAC-AAGTCCT
1 TCGGGCCATCT-GTAAGTCTTTCGAGCAAGATG-CTAAATCCT
1087960 TCGGGCCATCTGTAAG
1 TCGGGCCATCTGTAAG
1087976 ACCTTTGGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
41 17 0.38
42 27 0.60
43 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
TCGGGCCATCTGTAAGTCTTTCGAGCAAGATGCTAAATCCT
Found at i:1088386 original size:42 final size:41
Alignment explanation
Indices: 1088339--1088441 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 41
1088329 GATTGGTAAG
* *
1088339 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG-ATAAA
* ** *
1088381 TCCTTCAGATCATCCA-TAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCAAGATGATAAA
*
1088422 TCCTTCGGGCCATCCGTAAG
1 TCCTTCGGGCCATCAGTAAG
1088442 ACCTTCGGGC
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
40 1 0.02
41 17 0.35
42 29 0.59
43 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:1088582 original size:234 final size:233
Alignment explanation
Indices: 1087868--1088899 Score: 1291
Period size: 233 Copynumber: 4.4 Consensus size: 233
1087858 TTCTTACTTA
** * *
1087868 GTAAGT-CTCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTTTTCGT
1 GTAAGTCCT-TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCAT
* * * *
1087932 AAGTCTTTCGAGCAAGATGACAAGTCCTTCGGGCCATCTGTAAGACCTTTGGGCAAGATGTTTTG
65 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGCAAGATGTTTTC
*
1087997 A-ATTATTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAG
130 ACA-TGTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAG
*
1088061 AAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
194 TAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * *** *
1088101 GTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGTGTCATATGTG
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCATA
* * ** * *
1088166 AGTCTTTCGAGAAAGATAATAAGTCCTTCGGGCCATCTATAAGAACTTCGGGCAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGCAAGATGTTTTCA
* * * * * * *
1088231 CACGTTGTTCGAAAAATGAGAAACGTTTCTCATTCAAATATGAAAATTGAAATTTTTTAAAAGTA
131 CATGTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTA
*
1088296 AGAAAAGTTTCTTACCTAGTAAACTATTTCCAAGATTG
196 AGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* *
1088334 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGATCATCCATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCATA
* * *
1088399 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGCAGGACGTTGTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGCAAGATGTTTTCA
*
1088464 CATGCTTTTTCGAAAAATGATAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGT
131 CATG-TTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGT
1088529 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
195 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * * *
1088568 GTAAGTCATTCGGGCCATCAGTAAGTCTTTTGAGTATGATGTTTAAATCCTTCGGGTCACCCATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCATA
* *
1088633 ATTCTTTCGAGCAATATGGTAAGTCCTCAGGCAATCCGTAAAACCTTCGGGCCATCCGTAAGACC
66 AGTCTTTCGAGCAAGAT-G--A----T-----AA---GT----CCTTCGGGCCATCCGTAAGACC
* * *
1088698 TTCGGGCAAGAAGTTTTCACATGTTTTTTGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAA
112 TTCGGGCAAGATGTTTTCACATGTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAA
*
1088763 TT-AAATTTTTTGAAAAGTAAG-AAAGTTTCTTACCTAGTAAACTATTTCCAAATTTG
177 TTGAAA-TTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * ** * * * *
1088819 GTAAGTCCTTCGAGCAATCAGTAAGTCTTTCGAGCAAGAT-AATAAGTCATTCGGGCCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCATA
* *
1088883 AGACCTTCGAGCAAGAT
66 AGTCTTTCGAGCAAGAT
1088900 ATTTTCACAT
Statistics
Matches: 692, Mismatches: 84, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
233 319 0.46
234 167 0.24
235 1 0.00
237 1 0.00
241 1 0.00
246 2 0.00
249 2 0.00
250 30 0.04
251 71 0.10
252 56 0.08
253 42 0.06
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (233 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCATA
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGCAAGATGTTTTCA
CATGTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTA
AGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
Found at i:1088691 original size:20 final size:20
Alignment explanation
Indices: 1088666--1088704 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1088656 TCCTCAGGCA
1088666 ATCCGTAAAACCTTCGGGCC
1 ATCCGTAAAACCTTCGGGCC
*
1088686 ATCCGTAAGACCTTCGGGC
1 ATCCGTAAAACCTTCGGGC
1088705 AAGAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (20 bp):
ATCCGTAAAACCTTCGGGCC
Found at i:1088865 original size:41 final size:41
Alignment explanation
Indices: 1088820--1088900 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
1088810 CCAAATTTGG
* * *
1088820 TAAGTCCTTCGAGCAATC-AGTAAGTCTTTCGAGCAAGATAA
1 TAAGTCATTCGAGCAATCTA-TAAGACCTTCGAGCAAGATAA
* *
1088861 TAAGTCATTCGGGCCATCTATAAGACCTTCGAGCAAGATA
1 TAAGTCATTCGAGCAATCTATAAGACCTTCGAGCAAGATA
1088901 TTTTCACATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
TAAGTCATTCGAGCAATCTATAAGACCTTCGAGCAAGATAA
Found at i:1089602 original size:233 final size:231
Alignment explanation
Indices: 1088839--1089588 Score: 1065
Period size: 233 Copynumber: 3.2 Consensus size: 231
1088829 CGAGCAATCA
* * * * *
1088839 GTAAGTCTTTCGAGCAAGATAATAAGTCATTCGGGCCATCTATAAGACCTTCGAGCAAGATATTT
1 GTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTTCGAGCATGATGTTT
1088904 TCACATGTTTTTCAAAAAATGAGAAATATTTCTCATTTAAATATAAAATTTGAAATTTTTGAAAA
66 TCACATGTTTTTCAAAAAATGAGAAA-ATTTCTCATTTAAATATAAAATTT-AAATTTTTGAAAA
* * *
1088969 GTAAGAAAAGTTTCTTACCTAGTAAAATATTTCCAAAATTGGCAAGTCATTTGGGCCATCAATAA
129 GTAAGAAAAGTTTCTTACCTAGTAAAATATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTAA
* *
1089034 GTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCC
194 GTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCC
* * * *
1089072 GTAAGTCTTTCGAGCAAGATGATAAGTAATT-TGGAGCATCCATAAGACCTTCGAGCATTATGTT
1 GTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGG-CCATCCATAAGACCTTCGAGCATGATGTT
* * * * *
1089136 TTCACTTGTTTTTCGAGAAATGAGAAAATTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAA
65 TTCACATGTTTTTCAAAAAATGAGAAAA-TTTCTCATTTAAATAT-AAAATTTAAATTTTTGAAA
* * * *
1089201 AGTAAGAAAAATTTCTTACCTAGTAAATTATTTCCAAAATTAGTAAGTCTTTCGGGCCATCAGTA
128 AGTAAGAAAAGTTTCTTACCTAGTAAAATATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTA
*
1089266 AGTCTTTCAAGCATGATGCTTAAATCATAT-GGGTCATCC
193 AGTCTTTCAAGCATGATGCTTAAATCCT-TCGGGTCATCC
* * * *
1089305 GCAAGTCTTTCGAGCAAGATGATAAATCCTTCAAGCCATCCATAAGACCTTC-AGGCATGATGTT
1 GTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTTCGA-GCATGATGTT
*
1089369 TTCACATGTTTTTCAAAAAATGAGAAAAGTTTCTCATTTAAATTTGAAAATTTAAATTTTTGAAA
65 TTCACATGTTTTTCAAAAAATGAGAAAA-TTTCTCATTTAAATAT-AAAATTTAAATTTTTGAAA
* * * *
1089434 AGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCAGACCATCAGTA
128 AGTAAGAAAAGTTTCTTACCTAGTAAAATATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTA
* *
1089499 AGTCTTTCAAGCATGATTCTTAAATCCTTCGTGTCATCC
193 AGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCC
* *
1089538 GTAAGTCTTTTGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTT
1 GTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTT
1089589 TGTCCAGGAT
Statistics
Matches: 459, Mismatches: 51, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
232 5 0.01
233 446 0.97
234 8 0.02
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (231 bp):
GTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTTCGAGCATGATGTTT
TCACATGTTTTTCAAAAAATGAGAAAATTTCTCATTTAAATATAAAATTTAAATTTTTGAAAAGT
AAGAAAAGTTTCTTACCTAGTAAAATATTTCCAAAATTGGTAAGTCATTCGGGCCATCAGTAAGT
CTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCC
Found at i:1090447 original size:3 final size:3
Alignment explanation
Indices: 1090439--1090480 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1090429 AATGTTTTGA
1090439 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1090481 TATGCAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1091324 original size:18 final size:19
Alignment explanation
Indices: 1091289--1091326 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1091279 CATGGAATGT
1091289 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1091309 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
1091327 GAATACTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1092760 original size:2 final size:2
Alignment explanation
Indices: 1092753--1092780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1092743 TGGATACTTA
1092753 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
1092781 GTCCCGTGTG
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:1093515 original size:15 final size:16
Alignment explanation
Indices: 1093495--1093527 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1093485 ACTTTTTATC
*
1093495 TTTTAAAA-TTATTTT
1 TTTTAAAAGATATTTT
1093510 TTTTAAAAGATATTTT
1 TTTTAAAAGATATTTT
1093526 TT
1 TT
1093528 AGGTATTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTAAAAGATATTTT
Found at i:1096094 original size:132 final size:131
Alignment explanation
Indices: 1095833--1096100 Score: 394
Period size: 132 Copynumber: 2.0 Consensus size: 131
1095823 ATAAATAGAA
* *
1095833 TGCTAACCTTCTAGGTTAAACACAACTAAAAATTCGAGAACTTCAAATTTCTTGAAAAAATATTT
1 TGCTAACCTTCTAGGTTAAACACAACTAAAAATTCAAGAACTTCAAATTTATTGAAAAAATATTT
* * * * *
1095898 CCTCTCCTTCTCTAGTTTTCCGGTATTAGGCAAAGGAAAAAAATAGTTCGTGGTCTAGAGAGTTT
66 CCTCTCATTCTCTAGTTTTCCGGTATTAGGCAAAAGAAAAAAATAGTTCATGATCTAGAAAGTTT
1095963 G
131 G
* * * *
1095964 TGCTAACCTTCTAGGTTAAACACAACTGAGAATTCAAGAACTTCTAATTTATTGAAAAAAATGTT
1 TGCTAACCTTCTAGGTTAAACACAACTAAAAATTCAAGAACTTCAAATTTATTG-AAAAAATATT
* *
1096029 TCCTCTCATTCTCTAGTTTTCCGGTGTTAGG-AAAAGACAATAAATAGTTCATGATCTAGAAAGT
65 TCCTCTCATTCTCTAGTTTTCCGGTATTAGGCAAAAGA-AAAAAATAGTTCATGATCTAGAAAGT
1096093 TTG
129 TTG
1096096 TGCTA
1 TGCTA
1096101 CTTTTCGTGG
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
131 54 0.44
132 68 0.56
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (131 bp):
TGCTAACCTTCTAGGTTAAACACAACTAAAAATTCAAGAACTTCAAATTTATTGAAAAAATATTT
CCTCTCATTCTCTAGTTTTCCGGTATTAGGCAAAAGAAAAAAATAGTTCATGATCTAGAAAGTTT
G
Found at i:1103247 original size:24 final size:24
Alignment explanation
Indices: 1103220--1103326 Score: 70
Period size: 24 Copynumber: 4.5 Consensus size: 24
1103210 AAATGGAGAT
1103220 ATCAGAAATCAAAACAAAATTCAA
1 ATCAGAAATCAAAACAAAATTCAA
* * * * *
1103244 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAA
* * * * * * *
1103268 GTTAGGAATCAGAACAAATTTTAG
1 ATCAGAAATCAAAACAAAATTCAA
** * *
1103292 ATCAGATGTCAAAACAGAATTTAA
1 ATCAGAAATCAAAACAAAATTCAA
1103316 ATCAGAAATCA
1 ATCAGAAATCA
1103327 GATAAAATAT
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAAAATTCAA
Found at i:1103326 original size:48 final size:48
Alignment explanation
Indices: 1103220--1103328 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1103210 AAATGGAGAT
* * *
1103220 ATCAGAAATCAAAACAAAATTCAAATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAAAATTCAAATCAGATATCAAAACAGAATCCAA
* * * * * * * **
1103268 GTTAGGAATCAGAACAAATTTTAGATCAGATGTCAAAACAGAATTTAA
1 ATCAGAAATCAGAACAAAATTCAAATCAGATATCAAAACAGAATCCAA
1103316 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1103329 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAAAATTCAAATCAGATATCAAAACAGAATCCAA
Found at i:1108117 original size:24 final size:24
Alignment explanation
Indices: 1108090--1108196 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1108080 AAACGGAGAT
*
1108090 ATCAGAAATCAAAACAAAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1108114 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1108138 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * * *
1108162 ATCAGATGTCAAAATAGAATTTAA
1 ATCAGAAATCAAAACAGAATTCAG
1108186 ATCAGAAATCA
1 ATCAGAAATCA
1108197 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1108196 original size:48 final size:48
Alignment explanation
Indices: 1108090--1108198 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1108080 AAACGGAGAT
* * *
1108090 ATCAGAAATCAAAACAAAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAAAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * * **
1108138 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAATAGAATTTAA
1 ATCAGAAATCAGAACAAAATTCAGATCAGATATCAAAACAGAATCCAA
1108186 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1108199 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAAAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1118072 original size:17 final size:18
Alignment explanation
Indices: 1118050--1118089 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1118040 TAATAGCGAG
1118050 TTATTATAA-AATATATT
1 TTATTATAATAATATATT
*
1118067 TTATTATAATTATATATT
1 TTATTATAATAATATATT
1118085 TTATT
1 TTATT
1118090 TCTATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATAATAATATATT
Found at i:1118103 original size:19 final size:18
Alignment explanation
Indices: 1118050--1118112 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1118040 TAATAGCGAG
*
1118050 TTATTATAA-AATATATT
1 TTATTATAATTATATATT
1118067 TTATTATAATTATATATT
1 TTATTATAATTATATATT
* * *
1118085 TTATTTCTATTTTTATATTT
1 TTA-TTATAATTATATA-TT
1118105 TTATTATA
1 TTATTATA
1118113 GTTTAAATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 9 0.24
18 10 0.26
19 14 0.37
20 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATAATTATATATT
Found at i:1122590 original size:5 final size:6
Alignment explanation
Indices: 1122512--1122592 Score: 56
Period size: 6 Copynumber: 12.8 Consensus size: 6
1122502 AAATTCTAAG
* * * * *
1122512 AAAATA AAAA-C AAAATA AATTAGA AAAATA AAATTG AAAATA AAAATA
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA AAAATA
*
1122560 AAATTTGA ACAAATGA AAAATA AAAATA AAAAT
1 AAA-AT-A A-AAAT-A AAAATA AAAATA AAAAT
1122593 GGGTTGTCTC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
5 4 0.07
6 37 0.64
7 9 0.16
8 6 0.10
9 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:1125778 original size:26 final size:27
Alignment explanation
Indices: 1125720--1125780 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
1125710 AAAAGACAAA
1125720 TATAAAATTTTATACTAGAGGATGAAAT
1 TATAAAATTTTATACTA-AGGATGAAAT
* *
1125748 AATAAAATTTTATAGT-AGGAT-AAATT
1 TATAAAATTTTATACTAAGGATGAAA-T
1125774 TATAAAA
1 TATAAAA
1125781 AATTTAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 12 0.41
28 14 0.48
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (27 bp):
TATAAAATTTTATACTAAGGATGAAAT
Found at i:1125916 original size:27 final size:27
Alignment explanation
Indices: 1125860--1125921 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
1125850 GGTCTAATTG
* *
1125860 ACCCGACTAAAAAATTATAAATCTTCC
1 ACCCGACTAAAAAATTATAAACCTTAC
* *
1125887 ACCCGACCTGAAAAA-TATACACCTTAC
1 ACCCGA-CTAAAAAATTATAAACCTTAC
*
1125914 ACCTGACT
1 ACCCGACT
1125922 CGAATTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 20 0.69
28 7 0.24
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (27 bp):
ACCCGACTAAAAAATTATAAACCTTAC
Found at i:1126287 original size:5 final size:5
Alignment explanation
Indices: 1126277--1126308 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1126267 TTGCCAGGCC
1126277 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CC
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT CC
1126309 TTTTCTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCCT
Found at i:1126902 original size:120 final size:120
Alignment explanation
Indices: 1126768--1127091 Score: 429
Period size: 120 Copynumber: 2.7 Consensus size: 120
1126758 TAAACGATAC
* * * * ** *
1126768 CTCTATTCAGATCTA-TCAATGAGTTGAATGAGGTAAGGAAAGTAATCATCTATTTAGAA-TTTG
1 CTCTATTTAAATCTATTC-ATGAGTTGAATGAGATAAAGAAAACAATCATCTATTTA-AAGTTTA
* *
1126831 GTATGATTTGATGGATTTTAAAAGAATCCTCGTAAAATTTAAGTTAATGGGCGTTGT
64 ATATGATTTGATAGATTTTAAAAGAATCCTCGTAAAATTTAAGTTAATGGGCGTTGT
* * * *
1126888 CTCTATTTAAATCTATTCATGAGTTTAATTAGATAAATAAAACAATCGTCTATTTAAAGTTTAAT
1 CTCTATTTAAATCTATTCATGAGTTGAATGAGATAAAGAAAACAATCATCTATTTAAAGTTTAAT
* *
1126953 ATGATTTGATAGATTTTAAAAGAATTCTCGTAAAATTTAAGTTAATGGGTGTTGT
66 ATGATTTGATAGATTTTAAAAGAATCCTCGTAAAATTTAAGTTAATGGGCGTTGT
* * * *
1127008 CTCTATTTAAATCTATTCATGAGTTTAATCAGATAAATAAAACAATCGTCTATTTAAAGTTTAAT
1 CTCTATTTAAATCTATTCATGAGTTGAATGAGATAAAGAAAACAATCATCTATTTAAAGTTTAAT
1127073 ATGATTTGATCA-ATTTTAA
66 ATGATTTGAT-AGATTTTAA
1127092 CAATTTATCT
Statistics
Matches: 185, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
119 2 0.01
120 180 0.97
121 3 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (120 bp):
CTCTATTTAAATCTATTCATGAGTTGAATGAGATAAAGAAAACAATCATCTATTTAAAGTTTAAT
ATGATTTGATAGATTTTAAAAGAATCCTCGTAAAATTTAAGTTAATGGGCGTTGT
Found at i:1127369 original size:117 final size:117
Alignment explanation
Indices: 1126919--1127369 Score: 378
Period size: 117 Copynumber: 3.8 Consensus size: 117
1126909 AGTTTAATTA
* * * * * *
1126919 GATAAATAAAACAATCGTCTATTTAAAGTTTAATATGATTTGAT-AGATTTTAAAAGAATTCTCG
1 GATAAATAAAATAATCATCTATTTAAAGTTTAGTATGATTTGATCA-ATTTT-AAA-ATTTATTG
* * ** * * * * ** * *
1126983 TAAAATTTAAGTTAATGGGTGTTGTCTCTATTTAAATCTAT-TCATGAGTTTAATCA
63 TAAAATTTAAATTAGTGAATGTTATC-CTATTTAGATTTATCT-ATAAGTTGGACCT
* * *
1127039 GATAAATAAAACAATCGTCTATTTAAAGTTTAATATGATTTGATCAATTTTAACAATTTATCT-T
1 GATAAATAAAATAATCATCTATTTAAAGTTTAGTATGATTTGATCAATTTTAA-AATTTAT-TGT
* * ** * * * *
1127103 AAAATTTAACTTAATGAATGACAT-CTTTTTAGATTTGTCTATAAGTTGTATCT
64 AAAATTTAAATTAGTGAATGTTATCCTATTTAGATTTATCTATAAGTTGGACCT
* * * * * *
1127156 GGTAAATAAAGTAATCATCTATTTAAAGTTTGGTATAATTTGATCAATTTTAAAAGTTTCTCGTA
1 GATAAATAAAATAATCATCTATTTAAAGTTTAGTATGATTTGATCAATTTTAAAA-TTTATTGTA
* * * *
1127221 AAATTTAAGTTAGTGAACGTTGTCCTGTTTAGATTTATCTA-AAGGTTGGACC-
65 AAATTTAAATTAGTGAATGTTATCCTATTTAGATTTATCTATAA-GTTGGACCT
*
1127273 GTATAAATAAAATAATC-TCTATTTAAAGTTTAGTATGATTT-AACTAATTTTAAAATTTATTGT
1 G-ATAAATAAAATAATCATCTATTTAAAGTTTAGTATGATTTGATC-AATTTTAAAATTTATTGT
1127336 AAAATTTAAATTAGTGAATGTTATCCCTATTTAG
64 AAAATTTAAATTAGTGAATGTTAT-CCTATTTAG
1127370 GTCTTTTTAT
Statistics
Matches: 273, Mismatches: 47, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
116 31 0.11
117 131 0.48
118 35 0.13
119 25 0.09
120 50 0.18
121 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.42
Consensus pattern (117 bp):
GATAAATAAAATAATCATCTATTTAAAGTTTAGTATGATTTGATCAATTTTAAAATTTATTGTAA
AATTTAAATTAGTGAATGTTATCCTATTTAGATTTATCTATAAGTTGGACCT
Found at i:1128409 original size:62 final size:62
Alignment explanation
Indices: 1128311--1128434 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
1128301 GAAAGTTGAG
1128311 AAGATCTAGAGAGTCAAAGGGCCTGATCAAGCTGCTTCTGAGGGTGAGACTTTAAATGCTTT
1 AAGATCTAGAGAGTCAAAGGGCCTGATCAAGCTGCTTCTGAGGGTGAGACTTTAAATGCTTT
* * * *
1128373 AAGATCTGGAGAGTCAAAGGGTCTGATCAAGTTGCTTCTGAGGGTGAGACTTTGAATGCTTT
1 AAGATCTAGAGAGTCAAAGGGCCTGATCAAGCTGCTTCTGAGGGTGAGACTTTAAATGCTTT
1128435 TGGGATCTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (62 bp):
AAGATCTAGAGAGTCAAAGGGCCTGATCAAGCTGCTTCTGAGGGTGAGACTTTAAATGCTTT
Found at i:1131709 original size:22 final size:22
Alignment explanation
Indices: 1131681--1131723 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1131671 GGCCTAGATG
1131681 CGTGCCTATGTGATCGGGGATA
1 CGTGCCTATGTGATCGGGGATA
1131703 CGTGCCTATGTGATCGGGGAT
1 CGTGCCTATGTGATCGGGGAT
1131724 GCAGACTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.19, G:0.37, T:0.28
Consensus pattern (22 bp):
CGTGCCTATGTGATCGGGGATA
Found at i:1132666 original size:2 final size:2
Alignment explanation
Indices: 1132661--1132702 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1132651 ATTTTTTGAG
1132661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1132703 AGCCGATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1133502 original size:18 final size:18
Alignment explanation
Indices: 1133479--1133521 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1133469 TGCATGGGAG
1133479 AATTGTTGCAAATAGTAT
1 AATTGTTGCAAATAGTAT
1133497 AATTGTTGCAAATAGTAT
1 AATTGTTGCAAATAGTAT
1133515 AATTGTT
1 AATTGTT
1133522 TGAGAAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
AATTGTTGCAAATAGTAT
Found at i:1134639 original size:17 final size:17
Alignment explanation
Indices: 1134619--1134651 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1134609 GAAAATACAA
1134619 AGAAAATACTAATAATC
1 AGAAAATACTAATAATC
1134636 AGAAAATACTAATAAT
1 AGAAAATACTAATAAT
1134652 AAGTTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
AGAAAATACTAATAATC
Found at i:1137993 original size:21 final size:23
Alignment explanation
Indices: 1137968--1138010 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
1137958 TTTTGAATTT
1137968 TTAAAAAAT-AGATAAA-AATAA
1 TTAAAAAATAAGATAAATAATAA
1137989 TTAAAAAATAAGATAAATAATA
1 TTAAAAAATAAGATAAATAATA
1138011 TTACTCTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (23 bp):
TTAAAAAATAAGATAAATAATAA
Found at i:1140474 original size:32 final size:32
Alignment explanation
Indices: 1140398--1140482 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
1140388 CTAGTAAGGT
*
1140398 TTGCATTCAGATAATGCACAATACAGTCAGGA
1 TTGCATTCAGATAATACACAATACAGTCAGGA
** * *
1140430 TTATAGTT-AGATAATACATAATACAGTCAGGG
1 TTGCA-TTCAGATAATACACAATACAGTCAGGA
*
1140462 TTGCATTCAGATAATGCACAA
1 TTGCATTCAGATAATACACAA
1140483 GAGTATTAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
31 2 0.05
32 38 0.90
33 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (32 bp):
TTGCATTCAGATAATACACAATACAGTCAGGA
Found at i:1145030 original size:72 final size:72
Alignment explanation
Indices: 1144938--1145086 Score: 246
Period size: 72 Copynumber: 2.1 Consensus size: 72
1144928 GTGGTGGAGG
*
1144938 AAGACATAGAGATGAAATAGATTGAAGTGGATTTGAAGGAATGATGGAGGATGAAGGTAGTAATG
1 AAGACATAGAGATAAAATAGATTGAAGTGGATTTGAAGGAATGATGGAGGATGAAGGTAGTAATG
* *
1145003 GAGGGTA
66 AAGGGGA
*
1145010 AAGACAT-GAGGATAAAATAGATTGAAGTGGATTTGAAGGAATGATGGTGGATGAAGGTAGTAAT
1 AAGACATAGA-GATAAAATAGATTGAAGTGGATTTGAAGGAATGATGGAGGATGAAGGTAGTAAT
1145074 GAAGGGGA
65 GAAGGGGA
1145082 AAGAC
1 AAGAC
1145087 GTGGAGATGA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 2 0.03
72 70 0.97
ACGTcount: A:0.41, C:0.02, G:0.36, T:0.21
Consensus pattern (72 bp):
AAGACATAGAGATAAAATAGATTGAAGTGGATTTGAAGGAATGATGGAGGATGAAGGTAGTAATG
AAGGGGA
Found at i:1151282 original size:45 final size:46
Alignment explanation
Indices: 1151202--1151292 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
1151192 CCCCATGACC
*
1151202 TAGTAGTCTAGATCGTGGAAAATGTATTATTTAGCTAATAATGTTA
1 TAGTAGTCTAGATCATGGAAAATGTATTATTTAGCTAATAATGTTA
* * *
1151248 TAGTAGTGTAGATCAT-GAAAGTGTATTCTTTAGCTAATAATGTTA
1 TAGTAGTCTAGATCATGGAAAATGTATTATTTAGCTAATAATGTTA
1151293 GTTGTTAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 27 0.66
46 14 0.34
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.40
Consensus pattern (46 bp):
TAGTAGTCTAGATCATGGAAAATGTATTATTTAGCTAATAATGTTA
Found at i:1154817 original size:26 final size:26
Alignment explanation
Indices: 1154781--1154833 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1154771 CTACAATGAG
* * *
1154781 TGATATTCATTTAATTGCACCACTAA
1 TGATATACATTAAAATGCACCACTAA
*
1154807 TGATATACATTAAAATGTACCACTAA
1 TGATATACATTAAAATGCACCACTAA
1154833 T
1 T
1154834 ATAAAAAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (26 bp):
TGATATACATTAAAATGCACCACTAA
Found at i:1161083 original size:20 final size:21
Alignment explanation
Indices: 1161032--1161083 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1161022 AACTCAGGGT
1161032 GGTATTGATACCCTAATACAA
1 GGTATTGATACCCTAATACAA
*
1161053 GAGTATCGATACTCC-AATA-AA
1 G-GTATTGATAC-CCTAATACAA
1161074 GGTATTGATA
1 GGTATTGATA
1161084 TTGTTAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.30
21 4 0.15
22 13 0.48
23 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (21 bp):
GGTATTGATACCCTAATACAA
Found at i:1163063 original size:18 final size:18
Alignment explanation
Indices: 1163040--1163096 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
1163030 TTTGAAAAAT
1163040 ACCCTTAGTATCGATACC
1 ACCCTTAGTATCGATACC
*
1163058 ACCCTTGTAGTATTGATACC
1 ACCC-T-TAGTATCGATACC
* *
1163078 CCTACCTTGGTATCGATAC
1 AC--CCTTAGTATCGATAC
1163097 TTTATGTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 4 0.13
19 1 0.03
20 23 0.74
21 1 0.03
22 2 0.06
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (18 bp):
ACCCTTAGTATCGATACC
Found at i:1163580 original size:29 final size:29
Alignment explanation
Indices: 1163547--1163604 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1163537 GCTGTTGAAA
1163547 ATGTTCAAGACTCAACCCAAGGTGAGTTT
1 ATGTTCAAGACTCAACCCAAGGTGAGTTT
* *
1163576 ATGTTCAAGACTCAACCTAATGTGAGTTT
1 ATGTTCAAGACTCAACCCAAGGTGAGTTT
1163605 TCCTTTCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (29 bp):
ATGTTCAAGACTCAACCCAAGGTGAGTTT
Found at i:1164970 original size:113 final size:114
Alignment explanation
Indices: 1164829--1165060 Score: 439
Period size: 113 Copynumber: 2.0 Consensus size: 114
1164819 GGTTGATTTT
*
1164829 TTTAGCAATTTCCTTGTATAGTCCTTCTACAATCTCAAATGGTTATTTCTTTTGTCAGTGATTAT
1 TTTATCAATTTCCTTGTATAGTCCTTCTACAATCTCAAATGGTTATTTCTTTTGTCAGTGATTAT
1164894 AGAAAAAAGTTCTAGGTATATATTTAGTTTAC-ATTATAATTGTAAACA
66 AGAAAAAAGTTCTAGGTATATATTTAGTTTACAATTATAATTGTAAACA
1164942 TTTATCAATTTCCTTGTATAGTCCTTCTACAATCTCAAATGGTTATTTCTTTTGTCAGTGATTAT
1 TTTATCAATTTCCTTGTATAGTCCTTCTACAATCTCAAATGGTTATTTCTTTTGTCAGTGATTAT
*
1165007 AGAAAAATGTTCTAGGTATATATTTAGTTTACAATTATAATTGTAAACA
66 AGAAAAAAGTTCTAGGTATATATTTAGTTTACAATTATAATTGTAAACA
1165056 TTTAT
1 TTTAT
1165061 TGTAATTCTG
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
113 95 0.82
114 21 0.18
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (114 bp):
TTTATCAATTTCCTTGTATAGTCCTTCTACAATCTCAAATGGTTATTTCTTTTGTCAGTGATTAT
AGAAAAAAGTTCTAGGTATATATTTAGTTTACAATTATAATTGTAAACA
Found at i:1165681 original size:14 final size:14
Alignment explanation
Indices: 1165662--1165695 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1165652 AGTTGTATAC
1165662 TTTCTCATCTCTCT
1 TTTCTCATCTCTCT
1165676 TTTCTCATCTCTCT
1 TTTCTCATCTCTCT
*
1165690 CTTCTC
1 TTTCTC
1165696 CAGCGTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTCTCATCTCTCT
Found at i:1165943 original size:21 final size:22
Alignment explanation
Indices: 1165917--1165957 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1165907 ATCACAAAAG
1165917 AAATTATGA-GGAAATTAAGAA
1 AAATTATGAGGGAAATTAAGAA
1165938 AAATTATGAGGGAAATTAAG
1 AAATTATGAGGGAAATTAAG
1165958 GAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (22 bp):
AAATTATGAGGGAAATTAAGAA
Found at i:1166192 original size:2 final size:2
Alignment explanation
Indices: 1166185--1166235 Score: 86
Period size: 2 Copynumber: 25.5 Consensus size: 2
1166175 TTTCCAGAAT
1166185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1166227 TA TA TA TA T
1 TA TA TA TA T
1166236 CTTAAAGTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1170062 original size:20 final size:21
Alignment explanation
Indices: 1170008--1170070 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1169998 GATTCTCCTG
1170008 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1170032 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1170052 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1170071 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1175911 original size:16 final size:18
Alignment explanation
Indices: 1175886--1175918 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1175876 ATTCTTTTTA
1175886 TAAATATATTTT-TTCCC
1 TAAATATATTTTCTTCCC
1175903 TAAAT-TATTTTCTTCC
1 TAAATATATTTTCTTCC
1175919 ACTCATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATATATTTTCTTCCC
Found at i:1182130 original size:36 final size:36
Alignment explanation
Indices: 1182087--1182156 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
1182077 CATCATACCA
1182087 CACCCTGAGATCTTACGGCACTTGCCAACACTATAC
1 CACCCTGAGATCTTACGGCACTTGCCAACACTATAC
1182123 CACCCTGAGATCTTACGGCACTTGCCAACACTAT
1 CACCCTGAGATCTTACGGCACTTGCCAACACTAT
1182157 CTAAATATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (36 bp):
CACCCTGAGATCTTACGGCACTTGCCAACACTATAC
Found at i:1189159 original size:2 final size:2
Alignment explanation
Indices: 1189152--1189182 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1189142 GAAAAGGAAA
1189152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1189183 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1189187 original size:4 final size:4
Alignment explanation
Indices: 1189180--1189274 Score: 52
Period size: 4 Copynumber: 22.2 Consensus size: 4
1189170 ATATATATAT
*
1189180 ATAA ATAAA AAAA ATAA A-ATA AT-A AT-A ATAA AGTAA GAATAA TATATA
1 ATAA AT-AA ATAA ATAA ATA-A ATAA ATAA ATAA A-TAA --ATAA -ATA-A
* * *
1189228 ATAA ATAA ATAA ATAA ATAA TAGTAA ATAT ATAT ATAA ATTA ATAA A
1 ATAA ATAA ATAA ATAA ATAA -A-TAA ATAA ATAA ATAA ATAA ATAA A
1189275 ACTGATAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
3 7 0.09
4 45 0.61
5 14 0.19
6 7 0.09
7 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:1189231 original size:35 final size:34
Alignment explanation
Indices: 1189192--1189273 Score: 82
Period size: 35 Copynumber: 2.4 Consensus size: 34
1189182 AAATAAAAAA
1189192 AATAAAATAATAAT-AATAA-AGTAAGAATAATATAT
1 AATAAAATAATAATAAATAATAGT-A-AAT-ATATAT
1189227 AAT-AAATAAATAAATAAATAATAGTAAATATATAT
1 AATAAAAT-AAT-AATAAATAATAGTAAATATATAT
*
1189262 -ATAAATTAATAA
1 AATAAAATAATAA
1189274 AACTGATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
33 2 0.05
34 9 0.22
35 15 0.37
36 6 0.15
37 6 0.15
38 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (34 bp):
AATAAAATAATAATAAATAATAGTAAATATATAT
Found at i:1189256 original size:26 final size:26
Alignment explanation
Indices: 1189164--1189325 Score: 84
Period size: 26 Copynumber: 6.0 Consensus size: 26
1189154 ATATATATAT
* * *
1189164 ATATATATATATATATATAAATAAAAA
1 ATATATA-ATAAATAAATAAATAAATA
* *
1189191 AAATAAAAT-AATAATAATAAAGTAAGAATA
1 ATATATAATAAAT-A-AATAAA-T-A-AATA
1189221 ATATATAATAAATAAATAAATAAATA
1 ATATATAATAAATAAATAAATAAATA
* * *
1189247 ATAGTA-AATATATATATAAATTAATA
1 ATA-TATAATAAATAAATAAATAAATA
* *
1189273 AAACTGATAATAAA-AAAT-AATATATA
1 ATA-T-ATAATAAATAAATAAATAAATA
1189299 TATATATAATCTAAA-AAATAAA-AAATA
1 -ATATATAA--TAAATAAATAAATAAATA
1189326 TACTAAAGTA
Statistics
Matches: 104, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
25 6 0.06
26 37 0.36
27 31 0.30
28 9 0.09
29 7 0.07
30 11 0.11
31 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (26 bp):
ATATATAATAAATAAATAAATAAATA
Found at i:1189272 original size:42 final size:41
Alignment explanation
Indices: 1189160--1189306 Score: 120
Period size: 43 Copynumber: 3.4 Consensus size: 41
1189150 AAATATATAT
* * *
1189160 ATATATATATATATATATATATAAATAAAAAAAATAAAATAATA
1 ATATAAATATATATATAAATAT-AAT-AAATAAATAAAA-AATA
*
1189204 ATAATAAAGTA-AGA-ATAATATATAATAAATAAATAAATAAATA
1 AT-ATAAA-TATATATATAA-ATATAATAAATAAATAAA-AAATA
1189247 ATAGTAAATATATATATAAAT-TAATAAAACTGATAATAAAAAATA
1 ATA-TAAATATATATATAAATATAAT-AAA-T-A-AATAAAAAATA
*
1189292 ATATATATATATATA
1 ATATAAATATATATA
1189307 ATCTAAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
42 7 0.08
43 27 0.31
44 25 0.29
45 19 0.22
46 8 0.09
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (41 bp):
ATATAAATATATATATAAATATAATAAATAAATAAAAAATA
Found at i:1189285 original size:38 final size:35
Alignment explanation
Indices: 1189160--1189325 Score: 99
Period size: 38 Copynumber: 5.0 Consensus size: 35
1189150 AAATATATAT
* * *
1189160 ATATATATATATATATATATATAAAT-AAAAA-AA
1 ATATATATATAAATAAATAAATAAATAAAAAATAA
*
1189193 ATA-A-A-AT-AAT-AAT-AATAAAGT-AAGAAT-A
1 ATATATATATAAATAAATAAATAAA-TAAAAAATAA
* *
1189221 ATATATA-ATAAATAAATAAATAAAT-AATAGTAA
1 ATATATATATAAATAAATAAATAAATAAAAAATAA
*
1189254 ATATATATATAAATTAATAAAACTGATAATAAAAAAT-A
1 ATATATATATAAATAAAT-AAA-T-A-AATAAAAAATAA
* *
1189292 ATATATATATATATAATCTAAA-AAATAAAAAATA
1 ATATATATATAAATAA-ATAAATAAATAAAAAATA
1189326 TACTAAAGTA
Statistics
Matches: 105, Mismatches: 12, Indels: 30
0.71 0.08 0.20
Matches are distributed among these distances:
27 5 0.05
28 11 0.10
29 3 0.03
30 5 0.05
31 4 0.04
32 9 0.09
33 17 0.16
34 19 0.18
35 4 0.04
36 1 0.01
37 1 0.01
38 21 0.20
39 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (35 bp):
ATATATATATAAATAAATAAATAAATAAAAAATAA
Found at i:1190519 original size:39 final size:36
Alignment explanation
Indices: 1190447--1190541 Score: 95
Period size: 39 Copynumber: 2.6 Consensus size: 36
1190437 AACTCGAGGG
*
1190447 TTTG-GTGTTTTAAGAGAAACATTTTCAAAGGTTTT
1 TTTGTGTGTTTCAAGAGAAACATTTTCAAAGGTTTT
* *
1190482 GTGTGTGTGTGTTTCAAGAGAAA-ATATTTCGAGGGTTTT
1 -T-T-TGTGTGTTTCAAGAGAAACAT-TTTCAAAGGTTTT
* *
1190521 TTTTTGTGTTTCAGGAGAAAC
1 TTTGTGTGTTTCAAGAGAAAC
1190542 TGTCTCAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
36 17 0.35
37 2 0.04
38 5 0.10
39 25 0.51
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.43
Consensus pattern (36 bp):
TTTGTGTGTTTCAAGAGAAACATTTTCAAAGGTTTT
Found at i:1190567 original size:36 final size:36
Alignment explanation
Indices: 1190527--1190758 Score: 214
Period size: 36 Copynumber: 6.6 Consensus size: 36
1190517 TTTTTTTTTG
* *
1190527 TGTTTCAGGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1190563 TGTTTCAAAAGAAACTGTCTCAAGAGAAACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
1190600 AG-TTCTAAAAAAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1190636 TGTTTCAAGA-AAAATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1190663 TGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1190699 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
1190736 TGTTTCAAGAGAAATTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
1190759 AACTCGTTTT
Statistics
Matches: 160, Mismatches: 23, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
27 12 0.08
28 5 0.03
29 2 0.01
30 1 0.01
31 3 0.02
32 2 0.01
33 1 0.01
34 2 0.01
35 5 0.03
36 73 0.46
37 54 0.34
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1190738 original size:100 final size:100
Alignment explanation
Indices: 1190561--1190750 Score: 242
Period size: 100 Copynumber: 1.9 Consensus size: 100
1190551 AGGGACAAAA
* *
1190561 TTTGTTTCAAAAGAAACTGTCTCAAGAGAAACAAAACTTAGTTCTAAAAAAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTGTCTCAAAAGAAACAAAACTTAGTTCTAAAAAAAACTGTCTCAAGAG
1190626 AGACGAAATTTGTTTCAAGAAAAATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGAAAAATATTCAAAGAT
** * * ***
1190661 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAAAGAAACAAAACTTAGTTCT-AAAAAAAACTGTCTCAAGA
*
1190724 GAGAC-AAGATTTTGTTTCAAGAGAAAT
65 GAGACGAA-A-TTTGTTTCAAGAAAAAT
1190751 TGTCTCAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
98 3 0.04
99 26 0.34
100 48 0.62
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (100 bp):
TTTGTTTCAAAAGAAACTGTCTCAAAAGAAACAAAACTTAGTTCTAAAAAAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGAAAAATATTCAAAGAT
Found at i:1190872 original size:36 final size:36
Alignment explanation
Indices: 1190822--1190890 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1190812 TCAAGGTTTA
* *
1190822 TGTTTCAAGAGAAACTATTTCAAGGGAGACAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTT
*
1190858 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAA
1190891 ATTAATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTT
Found at i:1190900 original size:36 final size:36
Alignment explanation
Indices: 1190824--1190907 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
1190814 AAGGTTTATG
* * * * **
1190824 TTTCAAGAGAAACTATTTCAAGGGAGACAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
1190860 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
*
1190896 TTTCAAAGGAAA
1 TTTCAAGGGAAA
1190908 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
Found at i:1190913 original size:101 final size:102
Alignment explanation
Indices: 1190795--1191033 Score: 363
Period size: 102 Copynumber: 2.4 Consensus size: 102
1190785 ATATTTTGTG
* * *
1190795 TTTCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATTTCAAGGGAGAC-AAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
1190859 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
* *
1190896 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * * *
1190961 GTTTTAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
*
1190998 TTTCAAGGGAAATGTTTTTAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1191034 GGAGACAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 52 0.42
102 72 0.58
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:1191060 original size:87 final size:87
Alignment explanation
Indices: 1190942--1191117 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
1190932 AGAAACTGTC
* * *
1190942 TCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
*
1191007 AAATGTTTTTAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * * *
1191029 TCAAGGGAGACAAAATTTCGTTTCAATGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
1191094 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
1191116 TC
1 TC
1191118 TAGAGAAACT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:1191556 original size:106 final size:106
Alignment explanation
Indices: 1191426--1191700 Score: 417
Period size: 106 Copynumber: 2.6 Consensus size: 106
1191416 CTGGAACTAA
* * * * *
1191426 GAAATTGTTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGTTGTCTAGAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGTCC
1191491 AATATCCTTCGCTGTAAAGTTGAAATTGGCTCCAAAATTGG
66 AATATCCTTCGCTGTAAAGTTGAAATTGGCTCCAAAATTGG
1191532 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCA-AGTC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-AGAGTC
* **
1191596 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
65 CAATATCCTTCGCTGTAAAGTTGAAATTGGCTCCAAAATTGG
* * * * *
1191638 GAAATTGTTTGTTGATAATCAGTCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCTCGAGT
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGT
1191701 GGCACGATAT
Statistics
Matches: 154, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
106 153 0.99
107 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGTCC
AATATCCTTCGCTGTAAAGTTGAAATTGGCTCCAAAATTGG
Found at i:1192333 original size:32 final size:32
Alignment explanation
Indices: 1192279--1192391 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
1192269 TTTGCATCAG
* * * *
1192279 GATGTTGAAT-TCCCAAATATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTT
*
1192311 GATGTTGAATCTCAAAAAATGCCTCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
* * *
1192343 GATGTTAAATCTAAAAAAATGCCCAAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1192375 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
1192392 GATGCCCTCA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
32 63 0.93
33 5 0.07
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTT
Found at i:1193439 original size:69 final size:69
Alignment explanation
Indices: 1193324--1193458 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
1193314 TGTCTCTCTC
* *
1193324 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAAAAATAAT-TGTGCTTGATCAAT
1 TTGATGCTCCATGATCTTCAAGTGAAGTGATTCAGTAATTCAAAAATAATAT-TGCTTGATCAAT
1193388 CTCAT
65 CTCAT
* * * * *
1193393 TTGATGCTCTATGATCTTCAAGTGAAGTGGTTCAGTGATTCGAAAATGATATTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCAAGTGAAGTGATTCAGTAATTCAAAAATAATATTGCTTGATCAATC
1193458 T
66 T
1193459 AATAGTTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 57 0.98
70 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCAAGTGAAGTGATTCAGTAATTCAAAAATAATATTGCTTGATCAATC
TCAT
Found at i:1193560 original size:13 final size:12
Alignment explanation
Indices: 1193533--1193581 Score: 73
Period size: 13 Copynumber: 4.0 Consensus size: 12
1193523 TATTCTTCAA
1193533 TTTTC-CTTTTT
1 TTTTCTCTTTTT
1193544 TTTTCTCTTTTT
1 TTTTCTCTTTTT
1193556 ATTTTCTCTTTGTT
1 -TTTTCTCTTT-TT
1193570 TTTTCTCTTTTT
1 TTTTCTCTTTTT
1193582 CTCTTTTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.14
12 8 0.23
13 20 0.57
14 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:1193577 original size:26 final size:24
Alignment explanation
Indices: 1193532--1193581 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
1193522 TTATTCTTCA
1193532 ATTTTCCTTTTTTTTTCTCTTTTT
1 ATTTTCCTTTTTTTTTCTCTTTTT
1193556 ATTTTCTCTTTGTTTTTTCTCTTTTT
1 ATTTTC-CTTT-TTTTTTCTCTTTTT
1193582 CTCTTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.25
25 4 0.17
26 14 0.58
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (24 bp):
ATTTTCCTTTTTTTTTCTCTTTTT
Found at i:1196907 original size:47 final size:42
Alignment explanation
Indices: 1196785--1196933 Score: 146
Period size: 47 Copynumber: 3.5 Consensus size: 42
1196775 ATAAAATAAT
*
1196785 AATAAAAAGT-AAAAATA-ATATATATATATATATAT-AATA
1 AATAAAAAATAAAAAATATATATATATATATATATATAAATA
*
1196824 AATAAAAAATAAAAAATAGTA-A-ATAGTATATATATATAAATT
1 AATAAAAAATAAAAAATA-TATATATA-TATATATATATAAATA
*
1196866 AATAAACTGATAATAAAAAAATATATATATATATATATATATATATA
1 AATAAA---A-AAT-AAAAAATATATATATATATATATATATAAATA
* *
1196913 ATCTAAAAAATAAAATATATA
1 A-ATAAAAAATAAAAAATATA
1196934 CTAAAGTAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 22
0.76 0.05 0.18
Matches are distributed among these distances:
39 9 0.10
40 10 0.11
41 12 0.13
42 10 0.11
43 9 0.10
44 3 0.03
45 2 0.02
46 5 0.05
47 24 0.26
48 7 0.08
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (42 bp):
AATAAAAAATAAAAAATATATATATATATATATATATAAATA
Found at i:1196932 original size:2 final size:2
Alignment explanation
Indices: 1196886--1196912 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1196876 TAATAAAAAA
1196886 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 A
1196913 ATCTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1196932 original size:23 final size:25
Alignment explanation
Indices: 1196904--1196952 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1196894 ATATATATAT
*
1196904 ATATATA-TAATCTAAAAAA-TAAA
1 ATATATACTAAACTAAAAAAGTAAA
*
1196927 ATATATACTAAAGTAAAAAAGTAAA
1 ATATATACTAAACTAAAAAAGTAAA
1196952 A
1 A
1196953 AAGAAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (25 bp):
ATATATACTAAACTAAAAAAGTAAA
Found at i:1197919 original size:38 final size:39
Alignment explanation
Indices: 1197877--1197993 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 39
1197867 TGAAAGAAAT
* *
1197877 AATTTAGAATATTAGTGTGAAATAATTTAA-AACTTTAG
1 AATTTAGAATATTAGTGTGAAATAATTTAAGAAATTAAG
* *
1197915 AATTTAGAATTTTA-TAGTG-AATTATTTAAGAAATTAAG
1 AATTTAGAATATTAGT-GTGAAATAATTTAAGAAATTAAG
* * *
1197953 AATTTATAATGTTAG-GATGAAATAATTTGAG-AATTAAG
1 AATTTAGAATATTAGTG-TGAAATAATTTAAGAAATTAAG
1197991 AAT
1 AAT
1197994 AAAAACTCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
37 11 0.17
38 46 0.70
39 9 0.14
ACGTcount: A:0.45, C:0.01, G:0.15, T:0.39
Consensus pattern (39 bp):
AATTTAGAATATTAGTGTGAAATAATTTAAGAAATTAAG
Found at i:1198176 original size:16 final size:17
Alignment explanation
Indices: 1198139--1198183 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
1198129 GTTTATGAGA
1198139 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
1198157 GAATTGGAATCTGT-AG
1 GAATTGGAATCTGTAAG
1198173 GAATTGGAATC
1 GAATTGGAATC
1198184 CAATTCGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:1198833 original size:37 final size:38
Alignment explanation
Indices: 1198763--1198835 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
1198753 AACTCGAACC
*
1198763 CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
1 CGACCCAAATATCACACTTAAAAAAACCCGACCCGACT
1198801 CGACCCAAATATCACACTT-AAAAAACCCGACCCGA
1 CGACCCAAATATCACACTTAAAAAAACCCGACCCGA
1198836 ATATATGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 16 0.47
38 18 0.53
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.12
Consensus pattern (38 bp):
CGACCCAAATATCACACTTAAAAAAACCCGACCCGACT
Found at i:1199054 original size:33 final size:33
Alignment explanation
Indices: 1198975--1199056 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1198965 CCCTAAACCC
*
1198975 AAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCAAATATCACACTTAAAA
* *
1199008 AACCCCAACCCGACCCAAATATCACACTTAAAA
1 AAACCCGACCCGACCCAAATATCACACTTAAAA
* *
1199041 AAATCCGATCCGACCC
1 AAACCCGACCCGACCC
1199057 GAACAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.41, C:0.39, G:0.07, T:0.12
Consensus pattern (33 bp):
AAACCCGACCCGACCCAAATATCACACTTAAAA
Found at i:1201295 original size:17 final size:17
Alignment explanation
Indices: 1201261--1201312 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1201251 ACCGGACAAA
* *
1201261 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
1201278 TTTATTAATTTACTGAG
1 TTTATTAATTTACAGAG
*
1201295 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
1201310 TTT
1 TTT
1201313 CTACTGTAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:1202410 original size:36 final size:35
Alignment explanation
Indices: 1202351--1202423 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
1202341 GTTAGAAAAT
*
1202351 ATTTATATATTTTTCTTAAAAAAT-TAAATTCATAAA
1 ATTTATATACTTTTCTTAAAAAATATAAA-T-ATAAA
*
1202387 ATTTATATAACTTTT-TTACAAAATATAAATATAAA
1 ATTTATAT-ACTTTTCTTAAAAAATATAAATATAAA
1202422 AT
1 AT
1202424 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 7 0.21
36 17 0.52
37 9 0.27
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATTTATATACTTTTCTTAAAAAATATAAATATAAA
Found at i:1209704 original size:15 final size:15
Alignment explanation
Indices: 1209684--1209713 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1209674 TTTTAGTAGT
*
1209684 GAGCTAACTTTACAA
1 GAGCTAACCTTACAA
1209699 GAGCTAACCTTACAA
1 GAGCTAACCTTACAA
1209714 AAAAAATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
GAGCTAACCTTACAA
Found at i:1211736 original size:67 final size:67
Alignment explanation
Indices: 1211660--1211794 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
1211650 ACTGAATCAT
1211660 TCAGCACTGTTTTGTTGAATCAGTCAACACTGAATCATTTAGATGTGAGAAACAAACGTACTGAA
1 TCAGCACTGTTTTGTTGAATCAGTCAACACTGAATCATTTAGATGTGAGAAACAAACGTACTGAA
1211725 TG
66 TG
1211727 TCAGCACTGTTTTGTTGAATCAGTCAACACTGAATCATTTAGATGTGAGAAACAAACGTACTGAA
1 TCAGCACTGTTTTGTTGAATCAGTCAACACTGAATCATTTAGATGTGAGAAACAAACGTACTGAA
1211792 TG
66 TG
1211794 T
1 T
1211795 TGAACGGTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (67 bp):
TCAGCACTGTTTTGTTGAATCAGTCAACACTGAATCATTTAGATGTGAGAAACAAACGTACTGAA
TG
Found at i:1221079 original size:37 final size:37
Alignment explanation
Indices: 1221045--1221114 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1221035 TACAAATTGT
1221045 AAAATATTTATAT-ATTTTGTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTTGTTTAAAAAATTAAATTC
* * *
1221081 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTGTTTAAAAAATTAAA
1221115 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTGTTTAAAAAATTAAATTC
Found at i:1221887 original size:91 final size:91
Alignment explanation
Indices: 1221792--1221974 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
1221782 TGTCGAGAGT
1221792 ACACTGATTTTTAAAATCTATTCATTTTCTTTTTGAAACATACATCATGGTATCAAATGGACATA
1 ACACTGATTTTTAAAATCTATTCATTTTCTTTTTGAAACATACATCATGGTATCAAATGGACATA
1221857 CAAGACAATTATAAAAACTTTTATAA
66 CAAGACAATTATAAAAACTTTTATAA
1221883 ACACTGATTTTTAAAATCTATTCATTTTCTTTTTGAAACATACATCATGGTATCAAATGGACATA
1 ACACTGATTTTTAAAATCTATTCATTTTCTTTTTGAAACATACATCATGGTATCAAATGGACATA
1221948 CAAGACAATTATAAAAACTTTTATAA
66 CAAGACAATTATAAAAACTTTTATAA
1221974 A
1 A
1221975 GTGGAGCTAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (91 bp):
ACACTGATTTTTAAAATCTATTCATTTTCTTTTTGAAACATACATCATGGTATCAAATGGACATA
CAAGACAATTATAAAAACTTTTATAA
Found at i:1223967 original size:12 final size:12
Alignment explanation
Indices: 1223934--1223967 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1223924 CATATATACT
1223934 ATCATTATCAAC
1 ATCATTATCAAC
**
1223946 ATCAACATCAAC
1 ATCATTATCAAC
1223958 ATCATTATCA
1 ATCATTATCA
1223968 TTATCATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (12 bp):
ATCATTATCAAC
Found at i:1224221 original size:22 final size:22
Alignment explanation
Indices: 1224193--1224298 Score: 185
Period size: 22 Copynumber: 4.8 Consensus size: 22
1224183 GGCATGTGAA
*
1224193 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGC
*
1224215 ATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
1224237 ATTTGTCCCGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
*
1224259 ATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
1224281 ATTTGTCCCGAAGGACCT
1 ATTTGTCCCGAAGGACCT
1224299 CTGTATACTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 79 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGC
Found at i:1224243 original size:44 final size:44
Alignment explanation
Indices: 1224193--1224304 Score: 206
Period size: 44 Copynumber: 2.5 Consensus size: 44
1224183 GGCATGTGAA
1224193 ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
*
1224237 ATTTGTCCCGAAGGACCTATGCATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
*
1224281 ATTTGTCCCGAAGGACCTCTGTAT
1 ATTTGTCCCGAAGGACCTATGTAT
1224305 ACTGTATATG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
Found at i:1227871 original size:44 final size:44
Alignment explanation
Indices: 1227780--1227871 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
1227770 TTTATTTCAA
* *
1227780 TTTAGTTATTTATTTTTTCCTTTTTAATTTTAGCATTTTTTTAT
1 TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
**
1227824 TTTAGTTATTCATTTTTGT-CTCTTTTAATTTTAGTGTATTTTT-T
1 TTTAGTTATTCATTTTT-TCCT-TTTTAATTTTAGCATATTTTTAT
1227868 TTTA
1 TTTA
1227872 TTTTTCTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 23 0.55
45 19 0.45
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (44 bp):
TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
Found at i:1227884 original size:45 final size:46
Alignment explanation
Indices: 1227780--1227885 Score: 109
Period size: 45 Copynumber: 2.4 Consensus size: 46
1227770 TTTATTTCAA
*
1227780 TTTAGTTA-T-TTATTTTTTCCTTTTTAATTTTAGCATTTTTTTAT
1 TTTAGTTATTCTTATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
**
1227824 TTTAGTTATTC--ATTTTTGT-CTCTTTTAATTTTAGTGTATTTTT-T
1 TTTAGTTATTCTTATTTTT-TCCT-TTTTAATTTTAGCATATTTTTAT
*
1227868 TTTA-TTTTTCTTATTTTT
1 TTTAGTTATTCTTATTTTT
1227886 ATTTTACCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
43 5 0.10
44 21 0.40
45 26 0.50
ACGTcount: A:0.16, C:0.07, G:0.06, T:0.72
Consensus pattern (46 bp):
TTTAGTTATTCTTATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
Found at i:1230956 original size:25 final size:27
Alignment explanation
Indices: 1230907--1230958 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1230897 AAAAAAAGAA
*
1230907 AAAAAGAGAGAAAATCAAAGAGAAAAT
1 AAAAAGAGAGAAAAACAAAGAGAAAAT
1230934 AAAAAGAGA-AAAAACAAAG-GAAAAT
1 AAAAAGAGAGAAAAACAAAGAGAAAAT
1230959 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.25
26 9 0.38
27 9 0.38
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAAAGAGAGAAAAACAAAGAGAAAAT
Found at i:1230974 original size:11 final size:11
Alignment explanation
Indices: 1230891--1230975 Score: 50
Period size: 11 Copynumber: 7.4 Consensus size: 11
1230881 AGATTCAATC
1230891 AAGAACAAAAA-
1 AAGAA-AAAAAG
1230902 AAGAAAAAAAG
1 AAGAAAAAAAG
1230913 AGAGAAAATCAAAG
1 A-AGAAAA--AAAG
1230927 -AGAAAATAAA-
1 AAGAAAA-AAAG
*
1230937 AAGAGAAAAAACA
1 AAGA-AAAAAA-G
* **
1230950 AAGGAAAATTG
1 AAGAAAAAAAG
1230961 AAGAAAAAAAG
1 AAGAAAAAAAG
1230972 AAGA
1 AAGA
1230976 CAAGATGCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
10 5 0.09
11 27 0.47
12 19 0.33
13 3 0.05
14 4 0.07
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.05
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:1232106 original size:32 final size:31
Alignment explanation
Indices: 1232070--1232184 Score: 122
Period size: 31 Copynumber: 3.6 Consensus size: 31
1232060 GGAACAATGA
* *
1232070 GGGCATCTTTGAAGATTCAGCATCAAATACTG
1 GGGCATCTTTG-AGATTCAACATCAAATATTG
* * *
1232102 GGGCATTTTTTGAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTCAACATCAAATATTG
* * *
1232134 GGGCATTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTGAGATTCAACATCAAATATTG
*
1232165 GGGCATCTTTGGGAATTCAA
1 GGGCATCTTTGAG-ATTCAA
1232185 TATCCTAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 32 0.46
32 32 0.46
33 5 0.07
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATATTG
Found at i:1232149 original size:31 final size:32
Alignment explanation
Indices: 1232077--1232170 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
1232067 TGAGGGCATC
* *
1232077 TTTGAAGATTCAGCATCAAATACTGGGGCATTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTT
* *
1232110 TTTGAGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATATTGGGGCATTT
*
1232142 TTT-AGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATATTGGGGCAT
1232171 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.43
32 27 0.50
33 4 0.07
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTT
Found at i:1233604 original size:21 final size:21
Alignment explanation
Indices: 1233578--1233624 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1233568 CAAAAACATT
* *
1233578 TTATTATATTTAT-TATTATTA
1 TTATTA-ATTTATATACTATAA
1233599 TTATTAATTTATATACTATAA
1 TTATTAATTTATATACTATAA
1233620 TTATT
1 TTATT
1233625 TTGTAGGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTAATTTATATACTATAA
Found at i:1234819 original size:43 final size:42
Alignment explanation
Indices: 1234771--1234863 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 42
1234761 TTAATCTATC
*
1234771 AATTTTA-ATTTATTTCAATTTAGTTATTCATTTTTTC-CTTTTT
1 AATTTTACATTT-TTT-AATTTAGTTATTCATTTTGTCTC-TTTT
*
1234814 AATTTTAGCATTTTTTTATTTAGTTATTCATTTTGTCTCTTTT
1 AATTTTA-CATTTTTTAATTTAGTTATTCATTTTGTCTCTTTT
1234857 AATTTTA
1 AATTTTA
1234864 GTGTATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 37 0.82
44 4 0.09
45 4 0.09
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.65
Consensus pattern (42 bp):
AATTTTACATTTTTTAATTTAGTTATTCATTTTGTCTCTTTT
Found at i:1234864 original size:43 final size:44
Alignment explanation
Indices: 1234788--1234879 Score: 134
Period size: 43 Copynumber: 2.1 Consensus size: 44
1234778 ATTTATTTCA
*
1234788 ATTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCAT-TTTTTT
1 ATTTAGTTATTCATTTTGTCCTTTTTAATTTTAGCATATTTTTT
**
1234831 ATTTAGTTATTCATTTTGT-CTCTTTTAATTTTAGTGTATTTTTT
1 ATTTAGTTATTCATTTTGTCCT-TTTTAATTTTAGCATATTTTTT
1234875 ATTTA
1 ATTTA
1234880 TTTTTCTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 2 0.05
43 31 0.70
44 11 0.25
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.66
Consensus pattern (44 bp):
ATTTAGTTATTCATTTTGTCCTTTTTAATTTTAGCATATTTTTT
Found at i:1235607 original size:30 final size:30
Alignment explanation
Indices: 1235573--1235630 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1235563 TTATTTTCAA
1235573 AATAAATAAATAAATAAATTAGGGGTAATT
1 AATAAATAAATAAATAAATTAGGGGTAATT
*
1235603 AATAAGTAAATAAATAAATTAGGGGTAA
1 AATAAATAAATAAATAAATTAGGGGTAA
1235631 ACATTTGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.28
Consensus pattern (30 bp):
AATAAATAAATAAATAAATTAGGGGTAATT
Found at i:1237292 original size:3 final size:3
Alignment explanation
Indices: 1237269--1237315 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
1237259 TTTTGGGTTT
1237269 TTA TT- TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1237314 TT
1 TT
1237316 TTTTGCAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1242570 original size:19 final size:18
Alignment explanation
Indices: 1242530--1242566 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1242520 TGATCAGGTC
1242530 TCTTTCTATGCACCTTTT
1 TCTTTCTATGCACCTTTT
*
1242548 TCTTTCTATGTACCTTTT
1 TCTTTCTATGCACCTTTT
1242566 T
1 T
1242567 TCTTCCTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.05, T:0.59
Consensus pattern (18 bp):
TCTTTCTATGCACCTTTT
Found at i:1243961 original size:3 final size:3
Alignment explanation
Indices: 1243955--1243993 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1243945 AGGCAGTTGT
*
1243955 ACC ACC ATC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
1243994 GGTGCTTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.64, G:0.00, T:0.03
Consensus pattern (3 bp):
ACC
Found at i:1252219 original size:64 final size:63
Alignment explanation
Indices: 1252103--1252243 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
1252093 CACATTGAAT
*
1252103 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAAGA
1 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAAGA
* * * * * * **
1252166 GTGCATCGATGCATTCTTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGTAT-GGGT
1 GTGCATCGATGCACTC-TTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAAAG-
1252229 A
63 A
1252230 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1252244 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
63 18 0.28
64 47 0.72
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAAGA
Found at i:1252280 original size:20 final size:20
Alignment explanation
Indices: 1252251--1252288 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1252241 CACATGTTAA
*
1252251 AGAATACATCGGTGCACTGT
1 AGAATACATCGATGCACTGT
*
1252271 AGAATGCATCGATGCACT
1 AGAATACATCGATGCACT
1252289 TCAAGGGGAA
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:0.24, T:0.24
Consensus pattern (20 bp):
AGAATACATCGATGCACTGT
Found at i:1253835 original size:19 final size:19
Alignment explanation
Indices: 1253811--1253850 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1253801 AATAAGTTAT
1253811 ATGTTATAAAAGTTTTTAA
1 ATGTTATAAAAGTTTTTAA
1253830 ATGTTATAAAAGTTTTTAA
1 ATGTTATAAAAGTTTTTAA
1253849 AT
1 AT
1253851 TACTCACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
ATGTTATAAAAGTTTTTAA
Found at i:1256375 original size:64 final size:63
Alignment explanation
Indices: 1256282--1256421 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 63
1256272 ACATTGAATA
* *
1256282 TGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-AG
1 TGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTAG
* * * * *
1256345 TGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTAG
1 TGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTAG
1256409 TGCATCGATGCAC
1 TGCATCGATGCAC
1256422 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
63 17 0.25
64 50 0.75
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTAG
Found at i:1256454 original size:20 final size:22
Alignment explanation
Indices: 1256409--1256466 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1256399 GCATGGGTAG
1256409 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1256433 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1256453 TGCATCGATGCACT
1 TGCATCGATGCACT
1256467 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1269980 original size:19 final size:19
Alignment explanation
Indices: 1269955--1270030 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
1269945 TGAAAAAAAC
1269955 CTATGAATATGAAATTAAG
1 CTATGAATATGAAATTAAG
* * * *
1269974 CTGTGAATCTAAAAATAAG
1 CTATGAATATGAAATTAAG
* * *
1269993 TTATAAATATGGAAA-TAGG
1 CTATGAATAT-GAAATTAAG
*
1270012 CTTTGAATATGAGAATTAA
1 CTATGAATATGA-AATTAA
1270031 TTATGAAATG
Statistics
Matches: 40, Mismatches: 14, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
18 2 0.05
19 33 0.82
20 5 0.12
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (19 bp):
CTATGAATATGAAATTAAG
Found at i:1270075 original size:13 final size:13
Alignment explanation
Indices: 1270054--1270123 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
1270044 AAGTACTTGT
*
1270054 TATGGAAATGAAA
1 TATGAAAATGAAA
1270067 TATGAAAATG-AA
1 TATGAAAATGAAA
*
1270079 TCT-ATAAATG-AA
1 TATGA-AAATGAAA
*
1270091 TATGAAAGTGAAA
1 TATGAAAATGAAA
* *
1270104 GATGAGAATGAAA
1 TATGAAAATGAAA
1270117 TATGAAA
1 TATGAAA
1270124 GTTCTGAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 1 0.02
12 17 0.38
13 27 0.60
ACGTcount: A:0.54, C:0.01, G:0.20, T:0.24
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:1273258 original size:18 final size:17
Alignment explanation
Indices: 1273231--1273264 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1273221 TGACAGAAGA
1273231 GAAAGAACAAATGATAT
1 GAAAGAACAAATGATAT
1273248 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
1273265 ATGCACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:1273364 original size:22 final size:22
Alignment explanation
Indices: 1273333--1273383 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1273323 GTCTACGCGA
1273333 TCCTTCGGGACAAATACATAAG
1 TCCTTCGGGACAAATACATAAG
* *
1273355 TCCTTGGGGACAAATACATAGG
1 TCCTTCGGGACAAATACATAAG
*
1273377 TCATTCG
1 TCCTTCG
1273384 AGAGAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (22 bp):
TCCTTCGGGACAAATACATAAG
Found at i:1274637 original size:24 final size:25
Alignment explanation
Indices: 1274610--1274656 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1274600 TTCACACATG
1274610 TTCC-AAAGAATACATA-ACATATCA
1 TTCCTAAAGAAT-CATATACATATCA
*
1274634 TTCCTTAAGAATCATATACATAT
1 TTCCTAAAGAATCATATACATAT
1274657 GCCAAGGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (25 bp):
TTCCTAAAGAATCATATACATATCA
Found at i:1274685 original size:87 final size:87
Alignment explanation
Indices: 1274539--1274708 Score: 295
Period size: 87 Copynumber: 2.0 Consensus size: 87
1274529 CATAAGAACC
* * *
1274539 ACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGGCTCACCAGACTTCA
1274604 CACATGTTCCAAAGAATACATA
66 CACATGTTCCAAAGAATACATA
*
1274626 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGGCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGGCTCACCAGACTTCA
*
1274691 CATATGTTCCAAAGAATA
66 CACATGTTCCAAAGAATA
1274709 TATATATGTC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (87 bp):
ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGGCTCACCAGACTTCA
CACATGTTCCAAAGAATACATA
Found at i:1282378 original size:24 final size:23
Alignment explanation
Indices: 1282336--1282384 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1282326 AATAACCTCA
*
1282336 TTTTGAGAGTTTAAGATTGAGAG
1 TTTTGAGAGTTTAAGATTGAAAG
1282359 TTTTGA-AGTTTAAAAGATTGAAAG
1 TTTTGAGAGTTT--AAGATTGAAAG
1282383 TT
1 TT
1282385 AGAAGGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 6 0.26
24 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (23 bp):
TTTTGAGAGTTTAAGATTGAAAG
Found at i:1282816 original size:170 final size:169
Alignment explanation
Indices: 1282500--1283032 Score: 710
Period size: 170 Copynumber: 3.1 Consensus size: 169
1282490 CCTTTTTTAT
* * *
1282500 CAGAGATTCTCTGAGAAAAAGAAAAATG-TTTCCCTGGAACGCGCCTTTCTTTTTCGTCAGATTT
1 CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGCGCCTTTCTTTTT-GTCAGATTT
* * * *
1282564 TATCTGGAAGTCTCAGTCCATTATATTGAGATTTATGTAGTCATTA-GGGAACTATTCCTGTCAG
65 TATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCAG
* * * * *
1282628 ACGGATATCATGTTTGATGGGGTGAGACATTATAACATGG
130 ACCGATATAATGTTTGATGGGATGAGACACTATGACATGG
* * * * *
1282668 CAGAGATTCTTTGAGAAAAGGAAAAACGCTTCCCCTGGGACACACTTTTTCTTTTTGTCAGATTT
1 CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGCGC-CTTTCTTTTTGTCAGATTT
* * *
1282733 TATCTGGAAGTCTCAGTCCAATATGTTGAGATTTCTATAGGCAGTAGGGGAACTATTCCCGTCAG
65 TATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCAG
*
1282798 ACCGATATAATGTTTGATGGGATGAGACACTATGACATTG
130 ACCGATATAATGTTTGATGGGATGAGACACTATGACATGG
* * * * * *
1282838 CAGAAAATCTCTAAGAAAAGGACAAACGCTTCCCCTGGAATGCGCCTTTCATTTTTCTCAGATTT
1 CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGCGCCTTTC-TTTTTGTCAGATTT
* * * * *
1282903 TATCTAGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGAAGTAGGAGAACTATTCCTATCAT
65 TATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCAG
*
1282968 ACCGATATAATGTTTAATGGGATGAGACACTATGACATGG
130 ACCGATATAATGTTTGATGGGATGAGACACTATGACATGG
* *
1283008 AAAAGATTCTCTGAGAAAAGGAAAA
1 CAGAGATTCTCTGAGAAAAGGAAAA
1283033 GTGTTTCCCA
Statistics
Matches: 313, Mismatches: 48, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
168 25 0.08
169 65 0.21
170 223 0.71
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (169 bp):
CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGCGCCTTTCTTTTTGTCAGATTTT
ATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCAGA
CCGATATAATGTTTGATGGGATGAGACACTATGACATGG
Found at i:1285770 original size:17 final size:18
Alignment explanation
Indices: 1285750--1285797 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1285740 TTTTATTTTA
1285750 ATTTTAATTTCATTAAT-
1 ATTTTAATTTCATTAATG
*
1285767 ATTTTAAATTGTTTATTAATG
1 ATTTT-AA-T-TTCATTAATG
1285788 ATTTTAATTT
1 ATTTTAATTT
1285798 TAATTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 2 0.08
20 10 0.38
21 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
ATTTTAATTTCATTAATG
Found at i:1286426 original size:55 final size:55
Alignment explanation
Indices: 1286338--1286452 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 55
1286328 GCAATTGTGT
* * * * *
1286338 GTCATAAATCTATGACGCGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCTC
1 GTCATAAATCTATGACACACATGTATGACGCTCATTGCGCGTCATTGAAGCACAC
* ** *
1286393 GTCATAAATTTATGACACACATGTATGTTGCTCATTGCGTGTCATTGAAGCACAC
1 GTCATAAATCTATGACACACATGTATGACGCTCATTGCGCGTCATTGAAGCACAC
1286448 GTCAT
1 GTCAT
1286453 TAAAAAAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (55 bp):
GTCATAAATCTATGACACACATGTATGACGCTCATTGCGCGTCATTGAAGCACAC
Found at i:1290964 original size:16 final size:17
Alignment explanation
Indices: 1290933--1290965 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1290923 ACTTTTGTTA
*
1290933 ATGTTATTATAAATTTT
1 ATGTTATTACAAATTTT
1290950 ATGTTATT-CAAATTTT
1 ATGTTATTACAAATTTT
1290966 CAATCGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (17 bp):
ATGTTATTACAAATTTT
Found at i:1291021 original size:12 final size:12
Alignment explanation
Indices: 1291004--1291028 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1290994 TCAATTAAAT
1291004 TTATCTTTTATA
1 TTATCTTTTATA
1291016 TTATCTTTTATA
1 TTATCTTTTATA
1291028 T
1 T
1291029 ATATGTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATCTTTTATA
Found at i:1298600 original size:60 final size:60
Alignment explanation
Indices: 1298527--1298652 Score: 252
Period size: 60 Copynumber: 2.1 Consensus size: 60
1298517 TTCTGATATA
1298527 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
1 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
1298587 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
1 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
1298647 TTTGAT
1 TTTGAT
1298653 CCTGATTTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.21, C:0.06, G:0.20, T:0.52
Consensus pattern (60 bp):
TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
Found at i:1300180 original size:11 final size:11
Alignment explanation
Indices: 1300164--1300195 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1300154 GGGATGGCAA
1300164 CGGGCCGGGTT
1 CGGGCCGGGTT
1300175 CGGGCCGGGTT
1 CGGGCCGGGTT
1300186 CGGGCCGGGT
1 CGGGCCGGGT
1300196 ATTGGTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.56, T:0.16
Consensus pattern (11 bp):
CGGGCCGGGTT
Found at i:1300380 original size:12 final size:12
Alignment explanation
Indices: 1300345--1300399 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
1300335 ATTATTTAAA
1300345 CGGGTATTGGGC
1 CGGGTATTGGGC
* *
1300357 CAGGTATTGGGT
1 CGGGTATTGGGC
*
1300369 CGGGTATTGGGT
1 CGGGTATTGGGC
* * *
1300381 TGGGAATCGGGC
1 CGGGTATTGGGC
1300393 CGGGTAT
1 CGGGTAT
1300400 ATATATATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.13, C:0.13, G:0.47, T:0.27
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:1300459 original size:24 final size:25
Alignment explanation
Indices: 1300397--1300459 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
1300387 TCGGGCCGGG
1300397 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
1300422 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
1300446 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
1300460 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Done.