Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 336 of 349
Found at i:111282503 original size:14 final size:14
Alignment explanation
Indices: 111282486--111282519 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
111282476 ATAATAACAG
*
111282486 TAATAAAATAAGTA
1 TAATAAAATAAATA
*
111282500 TAATATAATAAATA
1 TAATAAAATAAATA
111282514 TAATAA
1 TAATAA
111282520 TATTATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
TAATAAAATAAATA
Found at i:111283304 original size:16 final size:17
Alignment explanation
Indices: 111283272--111283304 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
111283262 TTTATAAGTA
*
111283272 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
111283289 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
111283305 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:111283747 original size:92 final size:92
Alignment explanation
Indices: 111283590--111283862 Score: 402
Period size: 92 Copynumber: 3.0 Consensus size: 92
111283580 TTTGACATGA
* * * *
111283590 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
* *
111283655 CATGGTCTTATTCTTTTCATGTCACGT
66 CATGGTCTTATTCGTTTCATATCACGT
* * *
111283682 TGCCATGGTATCTTTCAACCATGGTATTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
111283747 CATGGTCTTATTCGTTTCATATCACGT
66 CATGGTCTTATTCGTTTCATATCACGT
* * * *
111283774 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
** *
111283839 CATGGTCTTACACATTTCATATCA
66 CATGGTCTTATTCGTTTCATATCA
111283863 GAGAGCACAC
Statistics
Matches: 162, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 162 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCGTTTCATATCACGT
Found at i:111283863 original size:46 final size:46
Alignment explanation
Indices: 111283590--111283862 Score: 359
Period size: 46 Copynumber: 5.9 Consensus size: 46
111283580 TTTGACATGA
* * * * *
111283590 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * *
111283636 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * *** *
111283682 TGCCATGGTATCTTTCAACCATGGTATTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
111283728 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
111283774 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
111283820 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
111283863 GAGAGCACAC
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 201 0.98
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:111285953 original size:11 final size:11
Alignment explanation
Indices: 111285937--111285967 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
111285927 ATATATACTA
111285937 AATAAAATAAT
1 AATAAAATAAT
111285948 AATAAAATAAT
1 AATAAAATAAT
111285959 AATAAAATA
1 AATAAAATA
111285968 TCATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:111285999 original size:11 final size:11
Alignment explanation
Indices: 111285937--111286005 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
111285927 ATATATACTA
*
111285937 AATAAAATAAT
1 AATAAAATATT
*
111285948 AATAAAATAAT
1 AATAAAATATT
*
111285959 AATAAAATATC
1 AATAAAATATT
*
111285970 ATTTAAAA-ATT
1 A-ATAAAATATT
111285981 AAATTAAAATATT
1 -AA-TAAAATATT
*
111285994 AATAAACTATT
1 AATAAAATATT
111286005 A
1 A
111286006 TTTATTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 32 0.67
12 13 0.27
13 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:111286633 original size:24 final size:24
Alignment explanation
Indices: 111286601--111286650 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
111286591 TCTTTTTGTA
*
111286601 GGCAAGTGGGGTGATGGAGTTAGT
1 GGCAAGTGGGGTAATGGAGTTAGT
111286625 GGCAAGTGGGGTAATGGAGTTAGT
1 GGCAAGTGGGGTAATGGAGTTAGT
111286649 GG
1 GG
111286651 GATGGTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.50, T:0.24
Consensus pattern (24 bp):
GGCAAGTGGGGTAATGGAGTTAGT
Found at i:111286651 original size:17 final size:16
Alignment explanation
Indices: 111286629--111286683 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
111286619 GTTAGTGGCA
111286629 AGTGGGGTAATGGAGTT
1 AGTGGGGT-ATGGAGTT
*
111286646 AGT-GGG-ATGG-TTT
1 AGTGGGGTATGGAGTT
*
111286659 AGTGGGGTGATTGAGTT
1 AGTGGGGT-ATGGAGTT
111286676 AGTGGGGT
1 AGTGGGGT
111286684 GATTTAGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
16 6 0.19
17 13 0.42
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (16 bp):
AGTGGGGTATGGAGTT
Found at i:111286665 original size:30 final size:30
Alignment explanation
Indices: 111286629--111286696 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
111286619 GTTAGTGGCA
*
111286629 AGTGGGGTAATGGAGTTAGTGGGATGGTTT
1 AGTGGGGTAATGGAGTTAGTGGGATGATTT
* * *
111286659 AGTGGGGTGATTGAGTTAGTGGGGTGATTT
1 AGTGGGGTAATGGAGTTAGTGGGATGATTT
*
111286689 AGTAGGGT
1 AGTGGGGT
111286697 GTGGGGGTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.34
Consensus pattern (30 bp):
AGTGGGGTAATGGAGTTAGTGGGATGATTT
Found at i:111287271 original size:133 final size:133
Alignment explanation
Indices: 111287012--111287292 Score: 379
Period size: 133 Copynumber: 2.1 Consensus size: 133
111287002 CTGCTCAATA
* *
111287012 AAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGG
1 AAGATAAGATCTGGTA-GTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGA
* * *
111287077 AATCTACTCCATTGCCGATACATGGAGATAAGATTCATCAAAATTTGATCTGCTCTGCTCCTACT
65 AATCTACTCCATTGCCGATACATGGAGATAAGATTCA-CAAAATCTAATCTGCTCTACTCCTACT
111287142 CAGCG
129 CAGCG
* *
111287147 AAGATAAGATCTGGTA-TTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAA
1 AAGATAAGATCTGGTAGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAA
* * * *
111287211 ATCTGCTCCATTGCCGTTACATGGAGATAAGACTTGC-CAAAATCTAATTTGCT-TCACTCCTGC
66 ATCTACTCCATTGCCGATACATGGAGATAAGA-TT-CACAAAATCTAATCTGCTCT-ACTCCTAC
* *
111287274 TTAGTG
128 TCAGCG
111287280 AAGATAAGATCTG
1 AAGATAAGATCTG
111287293 TCAAAATTTG
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
132 1 0.01
133 110 0.85
134 2 0.02
135 17 0.13
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (133 bp):
AAGATAAGATCTGGTAGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGACTGAA
ATCTACTCCATTGCCGATACATGGAGATAAGATTCACAAAATCTAATCTGCTCTACTCCTACTCA
GCG
Found at i:111287435 original size:85 final size:85
Alignment explanation
Indices: 111287330--111287963 Score: 832
Period size: 85 Copynumber: 7.5 Consensus size: 85
111287320 CAGTGGGATG
* * * * *
111287330 AGATCTG-CAATTTTAGCCTGTTACCCTACTGCTTAGGGGATTAAGACGAGTCTTCGACCTACTT
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
111287394 CACCACTGCTTGGAGAG-CC
66 CACCACTGCTTGGAGAGCCC
* *
111287413 AGGATTTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG-TAGATCTTCGACCTGC
1 A-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAG-TCTTCGACCTGC
* * *
111287477 TCCATCACTGCTCGGCGAGCCC
64 TCCACCACTGCTTGGAGAGCCC
* *
111287499 AAATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAATGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
* * *
111287564 CGCCATTGC-TCGACGAGCCC
66 CACCACTGCTTGGA-GAGCCC
* * * *
111287584 AGATCTGTAAATTTTAGTCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTATATCTTTGATCTGC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG-A-GTCTTCGACCTGC
** *
111287649 TCTGCCACTGC-TCGACGAGCCC
64 TCCACCACTGCTTGGA-GAGCCC
* *
111287671 AGATCTGTAAATTTTAGCCTGTTGCCCTACTGCTTAGGAGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
* *
111287736 CACCATTG-TTCGGGGAGCCC
66 CACCACTGCTT-GGAGAGCCC
* *
111287756 AGATCTATAAATTTTAGCCTGTTACCCTACTGCTTA-GGGGTTAAGGCGAGTCTTCGACCTACTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
* * *
111287820 CACCACTGCTCGGCGAGTCC
66 CACCACTGCTTGGAGAGCCC
* *
111287840 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCAACCTACTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
* *
111287905 CACCACTGCTCGGCGAGCCC
66 CACCACTGCTTGGAGAGCCC
*
111287925 AGATCTGTAAATTTTAGCCTGTTAACCTACTGCTTAGGG
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGG
111287964 AGATAAGATC
Statistics
Matches: 488, Mismatches: 51, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
83 1 0.00
84 83 0.17
85 320 0.66
86 8 0.02
87 76 0.16
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
CACCACTGCTTGGAGAGCCC
Found at i:111287956 original size:341 final size:341
Alignment explanation
Indices: 111287330--111287963 Score: 990
Period size: 341 Copynumber: 1.9 Consensus size: 341
111287320 CAGTGGGATG
* *
111287330 AGATCTGCAATTTTAGCCTGTTACCCTACTGCTTAGGGGATTAAGACGAGTCTTCGACCTACTTC
1 AGATCTGAAATTTTAGCCTGTTACCCTACTGCTTAGGGGATTAAGACGAGTCTTCGACCTACTCC
* *
111287395 ACCACTGCTTGGAGAGCCAGGATTTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
66 ACCACTGCTTGGAGAGCCAGGATCTATAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
* * *
111287460 GTAGATCTTCGACCTGCTCCATCACTGCTCGGCGAGCCCAAATCTGTAAATTTTAGCCTGTTACC
131 GGAGATCTTCGACCTACTCCACCACTGCTCGGCGAGCCCAAATCTGTAAATTTTAGCCTGTTACC
* * * * *
111287525 CTACTGCTTAGGGGGTTAATGCGAGTCTTCGACCTGCTCCGCCATTGCTCGACGAGCCCAGATCT
196 CTACTGCTTAGGGGGTTAAGGCGAGTCTTCAACCTACTCCACCACTGCTCGACGAGCCCAGATCT
* *
111287590 GTAAATTTTAGTCTGTTACCCTACTGCTTAGGGGGTTAAGGCGTATATCTTTGATCTGCTCTGCC
261 GTAAATTTTAGCCTGTTAACCTACTGCTTAGGGGGTTAAGGCGTATATCTTTGATCTGCTCTGCC
111287655 ACTGCTCGACGAGCCC
326 ACTGCTCGACGAGCCC
* * *
111287671 AGATCTGTAAATTTTAGCCTGTTGCCCTACTGCTTAGGAGG-TTAAGGCGAGTCTTCGACCTGCT
1 AGATCTG-AAATTTTAGCCTGTTACCCTACTGCTTAGG-GGATTAAGACGAGTCTTCGACCTACT
* *
111287735 CCACCATTG-TTCGGGGAGCCCA-GATCTATAAATTTTAGCCTGTTACCCTACTGCTTA-GGGGT
64 CCACCACTGCTT-GGAGAG-CCAGGATCTATAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGT
* *
111287797 TAAGGCGAG-TCTTCGACCTACTCCACCACTGCTCGGCGAGTCCAGATCTGTAAATTTTAGCCTG
127 TAAGG-GAGATCTTCGACCTACTCCACCACTGCTCGGCGAGCCCAAATCTGTAAATTTTAGCCTG
*
111287861 TTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCAACCTACTCCACCACTGCTCGGCGAGCCCA
191 TTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCAACCTACTCCACCACTGCTCGACGAGCCCA
111287926 GATCTGTAAATTTTAGCCTGTTAACCTACTGCTTAGGG
256 GATCTGTAAATTTTAGCCTGTTAACCTACTGCTTAGGG
111287964 AGATAAGATC
Statistics
Matches: 266, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
341 165 0.62
342 96 0.36
343 5 0.02
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (341 bp):
AGATCTGAAATTTTAGCCTGTTACCCTACTGCTTAGGGGATTAAGACGAGTCTTCGACCTACTCC
ACCACTGCTTGGAGAGCCAGGATCTATAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
GGAGATCTTCGACCTACTCCACCACTGCTCGGCGAGCCCAAATCTGTAAATTTTAGCCTGTTACC
CTACTGCTTAGGGGGTTAAGGCGAGTCTTCAACCTACTCCACCACTGCTCGACGAGCCCAGATCT
GTAAATTTTAGCCTGTTAACCTACTGCTTAGGGGGTTAAGGCGTATATCTTTGATCTGCTCTGCC
ACTGCTCGACGAGCCC
Found at i:111288084 original size:40 final size:40
Alignment explanation
Indices: 111288039--111288175 Score: 104
Period size: 40 Copynumber: 3.3 Consensus size: 40
111288029 ATCTGCTCCG
111288039 CTACTGTTTAGGGGAGATCTGTATTTTTTAGCCTGTTACC
1 CTACTGTTTAGGGGAGATCTGTATTTTTTAGCCTGTTACC
* * * *
111288079 CTACTGATTAGGGG-GTTACGGCTTGCTA-TCTTT-G-AT-TTACTCC
1 CTACTGTTTAGGGGAG--A--TC-TG-TATTTTTTAGCCTGTTA--CC
*
111288122 GCTACTGTTTAGGGGAGATCTGTATTTTTCAGCCTGTTACC
1 -CTACTGTTTAGGGGAGATCTGTATTTTTTAGCCTGTTACC
*
111288163 CTACTGCTTAGGG
1 CTACTGTTTAGGG
111288176 TTTTAAGGCC
Statistics
Matches: 73, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
39 3 0.04
40 30 0.41
41 8 0.11
42 2 0.03
43 8 0.11
44 19 0.26
45 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (40 bp):
CTACTGTTTAGGGGAGATCTGTATTTTTTAGCCTGTTACC
Found at i:111288103 original size:84 final size:84
Alignment explanation
Indices: 111287981--111288175 Score: 266
Period size: 84 Copynumber: 2.3 Consensus size: 84
111287971 ATCTATAATC
* * * *
111287981 TTCAGCTTGTTACCCTA-TTACTTAGGGAGTTAAAGCTTGCTGTCTCCGATCTGCTCCGCTACTG
1 TTCAGCCTGTTACCCTACTGA-TTAGGGAGTTAAAGCTTGCTATCTCCGATCTACTCCGCTACTG
111288045 TTTAGGGGAGATCTGTATTT
65 TTTAGGGGAGATCTGTATTT
* * ** ** *
111288065 TTTAGCCTGTTACCCTACTGATTAGGGGGTTACGGCTTGCTATCTTTGATTTACTCCGCTACTGT
1 TTCAGCCTGTTACCCTACTGATTAGGGAGTTAAAGCTTGCTATCTCCGATCTACTCCGCTACTGT
111288130 TTAGGGGAGATCTGTATTT
66 TTAGGGGAGATCTGTATTT
*
111288149 TTCAGCCTGTTACCCTACTGCTTAGGG
1 TTCAGCCTGTTACCCTACTGATTAGGG
111288176 TTTTAAGGCC
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
84 95 0.98
85 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (84 bp):
TTCAGCCTGTTACCCTACTGATTAGGGAGTTAAAGCTTGCTATCTCCGATCTACTCCGCTACTGT
TTAGGGGAGATCTGTATTT
Found at i:111290080 original size:9 final size:9
Alignment explanation
Indices: 111290066--111290099 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
111290056 TTTCTTCTTC
111290066 TTTTTTTAT
1 TTTTTTTAT
111290075 TTTTTTTAT
1 TTTTTTTAT
**
111290084 TTTTTTCCT
1 TTTTTTTAT
111290093 TTTTTTT
1 TTTTTTT
111290100 TTGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:111294562 original size:18 final size:18
Alignment explanation
Indices: 111294539--111294580 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
111294529 ATAATGCTAC
*
111294539 AATAACCA-TAAACATAGT
1 AATAACCATTAAA-ATAAT
*
111294557 AATAACGATTAAAATAAT
1 AATAACCATTAAAATAAT
111294575 AATAAC
1 AATAAC
111294581 AACAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.24
Consensus pattern (18 bp):
AATAACCATTAAAATAAT
Found at i:111294577 original size:3 final size:3
Alignment explanation
Indices: 111294569--111294749 Score: 74
Period size: 3 Copynumber: 60.3 Consensus size: 3
111294559 TAACGATTAA
* * * *
111294569 AAT AAT AAT AAC AAC AAT AA- AAT AGA- AGAC AAT AAT AAT -AT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT
* * * * ** **
111294613 AAT AAA AAT AAT AAT -AT AAA AAT AAT AAA AAT AAA AAT -AT GTT TCT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
111294659 AAT AAT AAT AAT AAAT CAAT GAT AAT AAAT ATAT ACAA AAT AAT AAT
1 AAT AAT AAT AAT -AAT -AAT AAT AAT -AAT A-AT A-AT AAT AAT AAT
* *
111294706 AAC AGT AAT AA- AAT AAGT -AT AAT -AT AAT AA- ATAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT
111294749 A
1 A
111294750 TTATTAAAAA
Statistics
Matches: 135, Mismatches: 28, Indels: 30
0.70 0.15 0.16
Matches are distributed among these distances:
2 14 0.10
3 103 0.76
4 18 0.13
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:111294622 original size:14 final size:14
Alignment explanation
Indices: 111294599--111294652 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
111294589 AATAGAAGAC
* *
111294599 AATAATAATATATT
1 AATAAAAATATATA
111294613 AATAAAAATA-ATA
1 AATAAAAATATATA
*
111294626 ATATAAAAATAATAAA
1 A-ATAAAAAT-ATATA
111294642 AATAAAAATAT
1 AATAAAAATAT
111294653 GTTTCTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.09
14 19 0.56
15 9 0.26
16 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAAATATATA
Found at i:111294728 original size:14 final size:14
Alignment explanation
Indices: 111294711--111294749 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
111294701 ATAATAACAG
*
111294711 TAATAAAATAAGTA
1 TAATAAAATAAATA
*
111294725 TAATATAATAAATA
1 TAATAAAATAAATA
111294739 TAATAATAATA
1 TAATAA-AATA
111294750 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
TAATAAAATAAATA
Found at i:111298169 original size:21 final size:21
Alignment explanation
Indices: 111298139--111298178 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
111298129 TAATTGAGTT
111298139 TTTCTATTATTTCAATATGTG
1 TTTCTATTATTTCAATATGTG
*
111298160 TTTCTTTTATTTCAATATG
1 TTTCTATTATTTCAATATG
111298179 GTCAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTCTATTATTTCAATATGTG
Found at i:111300204 original size:13 final size:13
Alignment explanation
Indices: 111300186--111300210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111300176 CCCAATGGGT
111300186 AATTGGACTTGAA
1 AATTGGACTTGAA
111300199 AATTGGACTTGA
1 AATTGGACTTGA
111300211 GATCGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
AATTGGACTTGAA
Found at i:111314769 original size:37 final size:37
Alignment explanation
Indices: 111314713--111314787 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
111314703 CTGAAAAAAG
*
111314713 TACAAACAATAGAATAGAATATAGGCATTTTTGCTGC
1 TACAAACAATAGAAAAGAATATAGGCATTTTTGCTGC
* *
111314750 TACAAACAATCGAAAAGAATATAGGCATTTTTTCTGC
1 TACAAACAATAGAAAAGAATATAGGCATTTTTGCTGC
111314787 T
1 T
111314788 CATAATCTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (37 bp):
TACAAACAATAGAAAAGAATATAGGCATTTTTGCTGC
Found at i:111316256 original size:18 final size:18
Alignment explanation
Indices: 111316235--111316517 Score: 119
Period size: 18 Copynumber: 15.3 Consensus size: 18
111316225 GAACAATTAT
111316235 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
111316253 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * *
111316271 TTATTCAATAATA-ACTAG
1 TTATTCAGTAACAGTC-AG
*
111316289 TTATTCAGTATC-GATCAATTG
1 TTATTCAGTAACAG-TC-A--G
*
111316310 ATTGATTATCCAGTAACAGTCAA
1 -TT-A-T-T-CAGTAACAGTCAG
* *
111316333 TTATTCAATAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
111316350 ATATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
111316369 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* * *
111316386 TTCATTCAGTGACAATCAA
1 TT-ATTCAGTAACAGTCAG
* * *
111316405 TTATTCAGTAATAATCAA
1 TTATTCAGTAACAGTCAG
* * *
111316423 TTATTTAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
111316441 TTATTCAGTAACAGTC--
1 TTATTCAGTAACAGTCAG
* * *
111316457 TAATATCTAGTAGCAGTCAA
1 TTAT-TC-AGTAACAGTCAG
* * *
111316477 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
111316495 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
111316513 TTATT
1 TTATT
111316518 TTATAACTTT
Statistics
Matches: 198, Mismatches: 48, Indels: 38
0.70 0.17 0.13
Matches are distributed among these distances:
16 3 0.02
17 18 0.09
18 134 0.68
19 20 0.10
20 4 0.02
21 2 0.01
22 4 0.02
23 1 0.01
24 1 0.01
25 2 0.01
26 8 0.04
27 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:111316275 original size:36 final size:36
Alignment explanation
Indices: 111316226--111316517 Score: 155
Period size: 36 Copynumber: 7.9 Consensus size: 36
111316216 TAACTCTCCG
* * *
111316226 AACAATTATTTATTCAGTAACAGTCAGTTATTCGGT
1 AACAATCAATTATTCAGTAACAGTCAGTTATTCAGT
* * *
111316262 AACAATCAATTATTCAATAATA-ACTAGTTATTCAGT
1 AACAATCAATTATTCAGTAACAGTC-AGTTATTCAGT
* * * *
111316298 ATCGATCAATTGATTGATTATCCAGTAACAGTCAATTATTCAAT
1 A---A-CAA-TCA---ATTATTCAGTAACAGTCAGTTATTCAGT
* *
111316342 AA-AATCAGA-TATTCAGTAACAATTAAGTTATTCAGT
1 AACAATCA-ATTATTCAGTAAC-AGTCAGTTATTCAGT
* * * * *
111316378 AGCAGTC-ATTCATTCAGTGACAATCAATTATTCAGT
1 AACAATCAATT-ATTCAGTAACAGTCAGTTATTCAGT
* * * *
111316414 AATAATCAATTATTTAGTAATATTCAGTTATTCAGT
1 AACAATCAATTATTCAGTAACAGTCAGTTATTCAGT
* * * * *
111316450 AACAGTCTAA-TA-TCTAGTAGCAGTCAATTATCCGGT
1 AACAATC-AATTATTC-AGTAACAGTCAGTTATTCAGT
* * *
111316486 AACAGTCAATTATTCAGTAATAATCAGTTATT
1 AACAATCAATTATTCAGTAACAGTCAGTTATT
111316518 TTATAACTTT
Statistics
Matches: 190, Mismatches: 47, Indels: 38
0.69 0.17 0.14
Matches are distributed among these distances:
35 15 0.08
36 123 0.65
37 19 0.10
38 2 0.01
39 3 0.02
40 3 0.02
41 3 0.02
44 21 0.11
45 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (36 bp):
AACAATCAATTATTCAGTAACAGTCAGTTATTCAGT
Found at i:111316378 original size:54 final size:55
Alignment explanation
Indices: 111316236--111316517 Score: 159
Period size: 54 Copynumber: 5.1 Consensus size: 55
111316226 AACAATTATT
* * * * * *
111316236 TATTCAGTAAC-AGTCAGTTATTCGGTAACAATCAATTATTCAATAATAA-CTAGT
1 TATTCAGTAACAATTAAGTTATTCAGTAACAGTCAATTATTCAGTAATAATC-AGA
* * *
111316290 TATTCAGTATCGATCAATTGATTGATTATCCAGTAACAGTCAATTATTCAATAA-AATCAGA
1 TATTCAGTA---A-CAATT-A-AG-TTATTCAGTAACAGTCAATTATTCAGTAATAATCAGA
* * *
111316351 TATTCAGTAACAATTAAGTTATTCAGTAGCAGTC-ATTCATTCAGTGACAATCA-A
1 TATTCAGTAACAATTAAGTTATTCAGTAACAGTCAATT-ATTCAGTAATAATCAGA
* * * * * * * *
111316405 TTATTCAGTAATAATCAA-TTATTTAGTAATATTCAGTTATTCAGTAACAGTCTA-A
1 -TATTCAGTAACAATTAAGTTATTCAGTAACAGTCAATTATTCAGTAATAATC-AGA
* * * * * *
111316460 TA-TCTAGTAGCAGTCAA-TTATCCGGTAACAGTCAATTATTCAGTAATAATCAGT
1 TATTC-AGTAACAATTAAGTTATTCAGTAACAGTCAATTATTCAGTAATAATCAGA
111316514 TATT
1 TATT
111316518 TTATAACTTT
Statistics
Matches: 178, Mismatches: 33, Indels: 33
0.73 0.14 0.14
Matches are distributed among these distances:
53 6 0.03
54 94 0.53
55 26 0.15
56 1 0.01
57 6 0.03
58 2 0.01
59 2 0.01
61 14 0.08
62 27 0.15
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (55 bp):
TATTCAGTAACAATTAAGTTATTCAGTAACAGTCAATTATTCAGTAATAATCAGA
Found at i:111316446 original size:72 final size:69
Alignment explanation
Indices: 111316320--111316517 Score: 193
Period size: 72 Copynumber: 2.8 Consensus size: 69
111316310 ATTGATTATC
* * * *
111316320 CAGTAACAGTCAATTATTCAATAAAATCAGA-TATTCAGTAACAATTAAGTTATTCAGTAGCAGT
1 CAGT-ACAGTCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAACAGT
*
111316384 C-ATTCATT
63 CTAAT-A-T
* *
111316392 CAGTGACAATCAATTATTCAGTAATAATCAATTATTTAGTAATATTCAGTTATTCAGTAACAGTC
1 CAGT-ACAGTCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAACAGTC
111316457 TAATAT
64 TAATAT
* * * *
111316463 CTAGTAGCAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 C-AGTA-CAGTCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
111316518 TTATAACTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
71 3 0.03
72 87 0.82
73 16 0.15
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (69 bp):
CAGTACAGTCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA
ATAT
Found at i:111316696 original size:47 final size:47
Alignment explanation
Indices: 111316634--111316750 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 47
111316624 CAGTAACAGT
* * * * *
111316634 AACAGTAGCAGTACGGTACACGGAGTACCTTATTGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* *
111316681 AGCAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
111316728 AACAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAGT-ACGGTACACAG
111316751 TAACAATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
47 54 0.90
48 6 0.10
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:111319065 original size:13 final size:13
Alignment explanation
Indices: 111319047--111319072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
111319037 TATATACAAA
111319047 TATATATGTATGT
1 TATATATGTATGT
111319060 TATATATGTATGT
1 TATATATGTATGT
111319073 GTAATGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TATATATGTATGT
Found at i:111319548 original size:24 final size:23
Alignment explanation
Indices: 111319521--111319596 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 23
111319511 TTACTGGATA
111319521 TGCGAATTTGAGTGGCACTATGTG
1 TGCGAATTTGA-TGGCACTATGTG
*
111319545 TGCGTATTTGTATGGCACTATGTG
1 TGCGAATTTG-ATGGCACTATGTG
*
111319569 TGCGTAATTAT-TTGGCACTATGTG
1 TGCG-AATT-TGATGGCACTATGTG
111319593 TGCG
1 TGCG
111319597 GAGTTGAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 41 0.89
25 4 0.09
26 1 0.02
ACGTcount: A:0.18, C:0.13, G:0.30, T:0.38
Consensus pattern (23 bp):
TGCGAATTTGATGGCACTATGTG
Found at i:111321795 original size:41 final size:41
Alignment explanation
Indices: 111321510--111321789 Score: 390
Period size: 41 Copynumber: 6.8 Consensus size: 41
111321500 TTAAACAGAT
** * * *
111321510 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
111321552 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
111321592 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
111321633 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
111321674 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
111321715 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
*
111321754 CTTCACCGGCATTAAGCCTGCTAGACTTAACGTCTG
1 --TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
111321790 TATTACATTC
Statistics
Matches: 223, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
39 2 0.01
40 8 0.04
41 209 0.94
42 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:111328156 original size:29 final size:30
Alignment explanation
Indices: 111328104--111328167 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
111328094 TATGGCATCG
* *
111328104 TTTTTAATAGTTCAATGATTTAAATGA-AA
1 TTTTTAATAATTCAATGATCTAAATGATAA
*
111328133 TTTTTGAATAATTCAATGA-CTAAATTATAA
1 TTTTT-AATAATTCAATGATCTAAATGATAA
111328163 TTTTT
1 TTTTT
111328168 TTAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTTTAATAATTCAATGATCTAAATGATAA
Found at i:111331497 original size:22 final size:22
Alignment explanation
Indices: 111331449--111331490 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
111331439 AAAATATGTT
111331449 AAAATAATTAATTAAAAATAAA
1 AAAATAATTAATTAAAAATAAA
*
111331471 AAAATAATT-TTTAAAAATAA
1 AAAATAATTAATTAAAAATAA
111331491 TACAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAATTAATTAAAAATAAA
Found at i:111338462 original size:14 final size:14
Alignment explanation
Indices: 111338443--111338470 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
111338433 ATTAATAATT
111338443 TTATTGTATTTTTA
1 TTATTGTATTTTTA
111338457 TTATTGTATTTTTA
1 TTATTGTATTTTTA
111338471 ATTAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
TTATTGTATTTTTA
Found at i:111342869 original size:11 final size:10
Alignment explanation
Indices: 111342839--111342884 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
111342829 ATACATTTTG
111342839 AAATTATAAA
1 AAATTATAAA
*
111342849 AAA-TAAAAA
1 AAATTATAAA
111342858 AAATTATTAAA
1 AAATTA-TAAA
*
111342869 AAATTATTAA
1 AAATTATAAA
111342879 AAATTA
1 AAATTA
111342885 ATTCAAAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 8 0.26
10 14 0.45
11 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATTATAAA
Found at i:111342887 original size:14 final size:11
Alignment explanation
Indices: 111342839--111342881 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
111342829 ATACATTTTG
111342839 AAATTA-TAAA
1 AAATTATTAAA
*
111342849 AAA-TA-AAAA
1 AAATTATTAAA
111342858 AAATTATTAAA
1 AAATTATTAAA
111342869 AAATTATTAAA
1 AAATTATTAAA
111342880 AA
1 AA
111342882 TTAATTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
10 5 0.17
11 16 0.55
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATTATTAAA
Found at i:111343196 original size:18 final size:19
Alignment explanation
Indices: 111343173--111343208 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
111343163 ATATTTTTTA
111343173 TATTTTTTATA-AATTCTT
1 TATTTTTTATATAATTCTT
*
111343191 TATTTTTTTTATAATTCT
1 TATTTTTTATATAATTCT
111343209 AAAATGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTTATATAATTCTT
Found at i:111343198 original size:20 final size:19
Alignment explanation
Indices: 111343169--111343208 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
111343159 ATGAATATTT
111343169 TTTATATTTTTTATAAATTC
1 TTTATATTTTTTAT-AATTC
*
111343189 TTTATTTTTTTTATAATTC
1 TTTATATTTTTTATAATTC
111343208 T
1 T
111343209 AAAATGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATATTTTTTATAATTC
Found at i:111356453 original size:12 final size:11
Alignment explanation
Indices: 111356385--111356466 Score: 69
Period size: 11 Copynumber: 7.4 Consensus size: 11
111356375 TTGTTGCAAC
111356385 TTTATTATTAT
1 TTTATTATTAT
* *
111356396 ATTATTACTAT
1 TTTATTATTAT
111356407 TTTATTATTAT
1 TTTATTATTAT
111356418 TATT-TATATT-T
1 T-TTAT-TATTAT
* * *
111356429 TTAACTCTTAT
1 TTTATTATTAT
*
111356440 TTTATTGTTAAT
1 TTTATTATT-AT
111356452 TTTATTATTAT
1 TTTATTATTAT
111356463 TTTA
1 TTTA
111356467 ACAATATTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
10 4 0.07
11 35 0.64
12 16 0.29
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:111358928 original size:31 final size:32
Alignment explanation
Indices: 111358893--111358958 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
111358883 TAAAACCTTA
* * *
111358893 AATATAATAATAAATGACATTTAAA-TAATTT
1 AATATAATAATAAATAAAATATAAATTAATTT
* *
111358924 AATATAATGATACATAAAATATAAATTAATTT
1 AATATAATAATAAATAAAATATAAATTAATTT
111358956 AAT
1 AAT
111358959 TTTTATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (32 bp):
AATATAATAATAAATAAAATATAAATTAATTT
Found at i:111359036 original size:7 final size:7
Alignment explanation
Indices: 111359020--111359051 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
111359010 TCCAAACACA
*
111359020 AAAAGGC
1 AAAAGCC
111359027 AAAAGCC
1 AAAAGCC
111359034 AAAAGCC
1 AAAAGCC
111359041 AAAAGCC
1 AAAAGCC
111359048 AAAA
1 AAAA
111359052 ACACCTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.22, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGCC
Found at i:111363810 original size:21 final size:20
Alignment explanation
Indices: 111363773--111363814 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
111363763 GAGAACTACG
111363773 AAAAATTAAAATAAAATGTT
1 AAAAATTAAAATAAAATGTT
*
111363793 AAAAATTAAAGATTAAATGTT
1 AAAAATTAAA-ATAAAATGTT
111363814 A
1 A
111363815 TTTTATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAATTAAAATAAAATGTT
Found at i:111373282 original size:102 final size:102
Alignment explanation
Indices: 111373106--111373303 Score: 351
Period size: 102 Copynumber: 1.9 Consensus size: 102
111373096 TCTCCTCTAA
* * *
111373106 GGGCTTTAGACAATATAATAGCTCTTATATGAGTTTTTTGCTCATTGTAATTCCATAAATTATAG
1 GGGCTTTAGACAATATAATAGCTCTCATATGAGTTTCTTGCTCATTGTAATTCCATAAACTATAG
111373171 GAATGTTTAGATTACCAACCACAGAAAGTTGTCTACG
66 GAATGTTTAGATTACCAACCACAGAAAGTTGTCTACG
111373208 GGGCTTTAGACAATATAATAGCTCTCATATGAGTTTCTTGCTCATTGTAATTCCATAAACTATAG
1 GGGCTTTAGACAATATAATAGCTCTCATATGAGTTTCTTGCTCATTGTAATTCCATAAACTATAG
**
111373273 GAATGTTTAGATTACCAACCATGGAAAGTTG
66 GAATGTTTAGATTACCAACCACAGAAAGTTG
111373304 CCTTTCGCAT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (102 bp):
GGGCTTTAGACAATATAATAGCTCTCATATGAGTTTCTTGCTCATTGTAATTCCATAAACTATAG
GAATGTTTAGATTACCAACCACAGAAAGTTGTCTACG
Found at i:111378495 original size:25 final size:25
Alignment explanation
Indices: 111378467--111378545 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
111378457 CGAATGACCA
111378467 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* *
111378492 ATGTGAT-AAGGCCG-A-ATGGCCA-AT
1 ATGTGATGAATG-TGAACAT-G-CATAT
111378516 A--TGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
111378539 ATGTGAT
1 ATGTGAT
111378546 AAGGTAGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 7 0.17
23 10 0.24
24 10 0.24
25 14 0.34
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:111378590 original size:47 final size:47
Alignment explanation
Indices: 111378283--111378570 Score: 486
Period size: 47 Copynumber: 6.1 Consensus size: 47
111378273 GATTTTATGA
*
111378283 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGACCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
111378330 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATTT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
111378377 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* * * *
111378424 GATGAATGTGAACTTGCATATGTATGATAAGGCCGAATGACCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
111378471 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATAT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
111378518 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
111378565 GATGAA
1 GATGAA
111378571 CGTGGAAGTG
Statistics
Matches: 224, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 224 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:111378649 original size:46 final size:46
Alignment explanation
Indices: 111378594--111378720 Score: 209
Period size: 46 Copynumber: 2.8 Consensus size: 46
111378584 ATATGTGGCG
*
111378594 AAGCTGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
111378640 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
* * **
111378686 AAGCCGAATGGCTAATGTGAGATATGTATGAGATG
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATG
111378721 TGTGTATATA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (46 bp):
AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
Found at i:111388136 original size:52 final size:52
Alignment explanation
Indices: 111388078--111388176 Score: 198
Period size: 52 Copynumber: 1.9 Consensus size: 52
111388068 TTAAAATAAA
111388078 TATTTCTTAATAATTTAAAAATAACATTAAAACAATAAGAAAATAATGTGTC
1 TATTTCTTAATAATTTAAAAATAACATTAAAACAATAAGAAAATAATGTGTC
111388130 TATTTCTTAATAATTTAAAAATAACATTAAAACAATAAGAAAATAAT
1 TATTTCTTAATAATTTAAAAATAACATTAAAACAATAAGAAAATAAT
111388177 ATTGACACGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (52 bp):
TATTTCTTAATAATTTAAAAATAACATTAAAACAATAAGAAAATAATGTGTC
Found at i:111390731 original size:19 final size:19
Alignment explanation
Indices: 111390707--111390748 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
111390697 CCACATTTAC
*
111390707 ACTGCTAATGTGGCTGTTG
1 ACTGCTAATGTGGCCGTTG
*
111390726 ACTGCTGATGTGGCCGTTG
1 ACTGCTAATGTGGCCGTTG
111390745 ACTG
1 ACTG
111390749 TGCGTTCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (19 bp):
ACTGCTAATGTGGCCGTTG
Found at i:111390933 original size:28 final size:29
Alignment explanation
Indices: 111390887--111390947 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
111390877 AAAAGTACAG
* *
111390887 AAAAAATTGTAAAATTTATTAAACATTAT
1 AAAAAATTGTAAAATTTATTAAAAATCAT
111390916 AAAAAATTG-AACAA-TTATTAAAAATCAT
1 AAAAAATTGTAA-AATTTATTAAAAATCAT
111390944 AAAA
1 AAAA
111390948 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAAAATTGTAAAATTTATTAAAAATCAT
Found at i:111390957 original size:18 final size:16
Alignment explanation
Indices: 111390904--111391038 Score: 73
Period size: 18 Copynumber: 8.0 Consensus size: 16
111390894 TGTAAAATTT
111390904 ATTAAACATTATAAAAA
1 ATTAAA-ATTATAAAAA
*
111390921 ATTGAACAATTATTAAAA
1 ATT-AA-AATTATAAAAA
111390939 ATCATAAAATTAT-AAAA
1 AT--TAAAATTATAAAAA
* *
111390956 A--AAACTGTA-AAAAT
1 ATTAAAAT-TATAAAAA
*
111390970 ATTAAACATTATGAAAA
1 ATTAAA-ATTATAAAAA
111390987 ATTGAACAATTATAAAAAA
1 ATT-AA-AATTAT-AAAAA
*
111391006 ATTAAAAAGTAGTAAAAA
1 ATT-AAAATTA-TAAAAA
*
111391024 TTTAAAATT-TAAAAA
1 ATTAAAATTATAAAAA
111391039 CTAAAAACTA
Statistics
Matches: 93, Mismatches: 11, Indels: 30
0.69 0.08 0.22
Matches are distributed among these distances:
13 4 0.04
14 6 0.06
15 6 0.06
16 5 0.05
17 20 0.22
18 37 0.40
19 14 0.15
20 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (16 bp):
ATTAAAATTATAAAAA
Found at i:111390981 original size:48 final size:48
Alignment explanation
Indices: 111390915--111391006 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
111390905 TTAAACATTA
* *
111390915 TAAAAAATTGAACAATTATTAAAAATCAT-AA-AATTATAAAAAAAACTG
1 TAAAAAATTAAACAATTATGAAAAAT--TGAACAATTATAAAAAAAACTG
111390963 TAAAAATATTAAAC-ATTATGAAAAATTGAACAATTATAAAAAAA
1 TAAAAA-ATTAAACAATTATGAAAAATTGAACAATTATAAAAAAA
111391007 TTAAAAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
46 1 0.03
47 2 0.05
48 30 0.77
49 6 0.15
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.27
Consensus pattern (48 bp):
TAAAAAATTAAACAATTATGAAAAATTGAACAATTATAAAAAAAACTG
Found at i:111391023 original size:66 final size:67
Alignment explanation
Indices: 111390877--111391023 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 67
111390867 AAAAGAGAGC
* * * * *
111390877 AAAAGTACAGAAAAAATTGTAAAATTTATTAAACATTATAAAAAATTGAACAATTATTAAAAATC
1 AAAAGTATAAAAAAAACTGTAAAATATATTAAACATTATAAAAAATTGAACAATTATAAAAAATC
111390942 AT
66 AT
* *
111390944 AAAATTATAAAAAAAACTGTAAAA-ATATTAAACATTATGAAAAATTGAACAATTATAAAAAAAT
1 AAAAGTATAAAAAAAACTGTAAAATATATTAAACATTATAAAAAATTGAACAATTAT-AAAAAAT
*
111391008 TA-
65 CAT
111391010 AAAAGTAGTAAAAA
1 AAAAGTA-TAAAAA
111391024 TTTAAAATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
66 36 0.52
67 33 0.48
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (67 bp):
AAAAGTATAAAAAAAACTGTAAAATATATTAAACATTATAAAAAATTGAACAATTATAAAAAATC
AT
Found at i:111399957 original size:245 final size:245
Alignment explanation
Indices: 111399527--111400016 Score: 813
Period size: 245 Copynumber: 2.0 Consensus size: 245
111399517 TAAAACAAGA
111399527 AAGTTAGCACATAAGTTAATCCTACCAGATAAGCAACACCACAAGCATGGCAATGTAGCATCATA
1 AAGTTAGCACATAAGTTAATCCTACCAGATAAGCAACACCACAAGCATGGCAATGTAGCATCATA
** * *
111399592 AAGGTGGTTTAAGGATCAATATTAAAGATGCAATAACAATTTCTTTGTTTTTATTTCTTGCATAG
66 AAGGTAATTTAAGGACCAATATTAAAGATGCAATAACAATTTCTCTGTTTTTATTTCTTGCATAG
* * * *
111399657 CTTCGATTTGGCCTCCATCAGTTTCACCAAAGACATTTAATTATTAAGTAGTTGCCTTGACGTTC
131 CTTCGATTCGGCCTCCATCAGTTTCACCAAAGACATTTAATTATCAACTAGTTGCCTCGACGTTC
*
111399722 TATGATAAGTTCTCAAGCACAACACCAAAAACAGAAGTCAGTGACAAGTC
196 TATGATAAGTTCTCAAGCACAACACCAAAAACAAAAGTCAGTGACAAGTC
*
111399772 AAGTTAGCACATAAGTTAATCCTACCAGATAAGCAACACCAGAAGCATGGCAATGTAGCATCATA
1 AAGTTAGCACATAAGTTAATCCTACCAGATAAGCAACACCACAAGCATGGCAATGTAGCATCATA
* *
111399837 AAGGTAATTTAAGGACCCATATTAAAGATGCAATAACAGTTTCTCTGTTTTTATTTCTTGCATAG
66 AAGGTAATTTAAGGACCAATATTAAAGATGCAATAACAATTTCTCTGTTTTTATTTCTTGCATAG
**
111399902 C-TCTGATTCGGCCTCCATCAGTTTTC-GTAAAGACATTTAATTATCAACTAGTTGCCTCGACGT
131 CTTC-GATTCGGCCTCCATCAG-TTTCACCAAAGACATTTAATTATCAACTAGTTGCCTCGACGT
*
111399965 TCTATGATAAGTTCTCAAGCACAATACCAAAAACAAAAGTCAGTGACAAGTC
194 TCTATGATAAGTTCTCAAGCACAACACCAAAAACAAAAGTCAGTGACAAGTC
111400017 TGTTTCAGCT
Statistics
Matches: 228, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
244 2 0.01
245 222 0.97
246 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (245 bp):
AAGTTAGCACATAAGTTAATCCTACCAGATAAGCAACACCACAAGCATGGCAATGTAGCATCATA
AAGGTAATTTAAGGACCAATATTAAAGATGCAATAACAATTTCTCTGTTTTTATTTCTTGCATAG
CTTCGATTCGGCCTCCATCAGTTTCACCAAAGACATTTAATTATCAACTAGTTGCCTCGACGTTC
TATGATAAGTTCTCAAGCACAACACCAAAAACAAAAGTCAGTGACAAGTC
Found at i:111409195 original size:27 final size:27
Alignment explanation
Indices: 111409165--111409228 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 27
111409155 ATTATAAAAA
*
111409165 TAAAAATTATTTAAATA-TTTAAGAATT
1 TAAAAAATATTTAAATATTTTAAG-ATT
111409192 TAAAAAATATTTAAATATTTTAAGATT
1 TAAAAAATATTTAAATATTTTAAGATT
111409219 TAATAAAATA
1 TAA-AAAATA
111409229 AAAATATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
TAAAAAATATTTAAATATTTTAAGATT
Found at i:111409711 original size:24 final size:24
Alignment explanation
Indices: 111409668--111409733 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
111409658 TAAAAGTTTA
*
111409668 ACTAAAATCTTAAGAGTAATTTTATT-
1 ACTAAAATCTT-A-ACTAATTTT-TTC
* *
111409694 TCTAAAATTTTAACTAATTTTTTC
1 ACTAAAATCTTAACTAATTTTTTC
111409718 ACTAAAATCTTAACTA
1 ACTAAAATCTTAACTA
111409734 CTAAGTCGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.06
24 22 0.65
25 1 0.03
26 9 0.26
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (24 bp):
ACTAAAATCTTAACTAATTTTTTC
Found at i:111413079 original size:13 final size:13
Alignment explanation
Indices: 111413061--111413085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111413051 AATTTACTCC
111413061 TTATTTTATTTAT
1 TTATTTTATTTAT
111413074 TTATTTTATTTA
1 TTATTTTATTTA
111413086 AAAATCTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:111414855 original size:17 final size:18
Alignment explanation
Indices: 111414822--111414855 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
111414812 TTTTCCTCAT
*
111414822 TTTAATTTCTGCAATTTA
1 TTTAATTTCTACAATTTA
111414840 TTTAATTTC-ACAATTT
1 TTTAATTTCTACAATTT
111414856 CAATTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTACAATTTA
Found at i:111418000 original size:51 final size:51
Alignment explanation
Indices: 111417935--111418035 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
111417925 ACATTTATCA
111417935 CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCG
1 CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCG
* *
111417986 CTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTGTC
1 CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTC
111418036 ACTGATCAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (51 bp):
CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCG
Found at i:111422846 original size:14 final size:13
Alignment explanation
Indices: 111422809--111422846 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
111422799 TTTTATGAGA
111422809 TATTTATTATTAT
1 TATTTATTATTAT
111422822 TATTATATTATTATT
1 TATT-TATTATTA-T
111422837 TATTTATTAT
1 TATTTATTAT
111422847 AAAAGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTATTATTAT
Found at i:111424733 original size:46 final size:46
Alignment explanation
Indices: 111424681--111425082 Score: 554
Period size: 46 Copynumber: 8.7 Consensus size: 46
111424671 AGTGTGCTCT
*
111424681 CTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
*
111424727 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
111424773 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
*
111424819 TTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
* *
111424865 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
* ** * *
111424911 GTGATATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
* *** **
111424957 ATGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
* * * ** *
111425003 GTAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
* * * *
111425049 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA
111425083 CACTATGGCA
Statistics
Matches: 328, Mismatches: 27, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 327 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
Found at i:111425319 original size:25 final size:25
Alignment explanation
Indices: 111425256--111425322 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
111425246 AAATAGTTGT
** *
111425256 ATGAAATAATTATGAAGATAGATAA
1 ATGAAATAAGAATTAAGATAGATAA
*
111425281 ACGAAATAAGAATTAAGATAGATAA
1 ATGAAATAAGAATTAAGATAGATAA
111425306 ATGAAATAAGAATTAAG
1 ATGAAATAAGAATTAAG
111425323 TACATTGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.58, C:0.01, G:0.16, T:0.24
Consensus pattern (25 bp):
ATGAAATAAGAATTAAGATAGATAA
Found at i:111425425 original size:16 final size:17
Alignment explanation
Indices: 111425404--111425436 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111425394 ATGATGGAGC
111425404 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
111425420 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
111425437 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:111432716 original size:10 final size:10
Alignment explanation
Indices: 111432701--111432750 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
111432691 TAATTTTAGG
111432701 ATTTAT-TTT
1 ATTTATCTTT
111432710 CATTTATCTTT
1 -ATTTATCTTT
*
111432721 AATTATCTTT
1 ATTTATCTTT
111432731 ATTTAT-TTGT
1 ATTTATCTT-T
111432741 ATTTATCTTT
1 ATTTATCTTT
111432751 TAGAATTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:111433499 original size:17 final size:18
Alignment explanation
Indices: 111433467--111433500 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
111433457 TTTTCCTCAT
111433467 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
111433485 TTTAATTTC-GCAATTT
1 TTTAATTTCTGCAATTT
111433501 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:111434806 original size:18 final size:18
Alignment explanation
Indices: 111434779--111434814 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
111434769 GCTTGGAAGC
111434779 CTCCTCCGCTAGGTTGTT
1 CTCCTCCGCTAGGTTGTT
*
111434797 CTCCTTCGCTAGGTTGTT
1 CTCCTCCGCTAGGTTGTT
111434815 TTTTGTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.22, T:0.42
Consensus pattern (18 bp):
CTCCTCCGCTAGGTTGTT
Found at i:111435349 original size:2 final size:2
Alignment explanation
Indices: 111435337--111435367 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
111435327 AGAATCATAG
*
111435337 TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
111435368 GCTTACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:111443298 original size:183 final size:183
Alignment explanation
Indices: 111442959--111443484 Score: 754
Period size: 183 Copynumber: 2.9 Consensus size: 183
111442949 CTGTCATACC
* * * *
111442959 CTCAGTTGTAGCTGGTTTCAGAGTCAATTCTAAACTCGGATTTAGTCTAGGCCCTTT-TGTCTTG
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCCTTTCT-TCTTG
* * *
111443023 TGTCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATATGCTCCTTGTTGATGCTGGGGGT
65 TATCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTGGTGATGCTGGGGGT
* **
111443088 TGTAGTTGCAGTGATTTGATTTAGTTCATGGTTCAGGACATCTGCCAAAAGATA
130 TGTAGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAAAGATA
* * * * *
111443142 CTCAGCTGTAGTTGGTTTTAGAGTCAATTCTAAACTTGTACTCAATCTAGGCCCTTTCTTCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCCTTTCTTCTTGT
*
111443207 ATCTTGCTATATCTTGGGAAGTGCTGCGGTTGGTTGGTATGTGCTCCTTGGTGATGCTGGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTGGTGATGCTGGGGGTT
* * * * *
111443272 CTAGCTGCAGTGGTTCGACCTAGTTCATGTTTCAGGACATCTGCCAAATGATA
131 GTAGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAAAGATA
* *
111443325 CTCAGTTGTGGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGG-CCTCTTCATCTTG
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCCT-TTCTTCTTG
* *
111443389 TATCTTGCTATATCTTGGGAAGTGCTGTTGG-TGGTTGGTATGCGCTCCTT-GTAGATGCCGGGG
65 TATCTTGCTATATCTTGGGAAGTGCTG-TGGTTGGTTGGTATGTGCTCCTTGGT-GATGCTGGGG
*
111443452 GTTGTAGTTGCAGTGGTTTGGCCTAGTTCATGG
128 GTTGTAGTTGCAGTGGTTTGACCTAGTTCATGG
111443485 CTTAAGACCT
Statistics
Matches: 304, Mismatches: 35, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
182 5 0.02
183 296 0.97
184 3 0.01
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.38
Consensus pattern (183 bp):
CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCCTTTCTTCTTGT
ATCTTGCTATATCTTGGGAAGTGCTGTGGTTGGTTGGTATGTGCTCCTTGGTGATGCTGGGGGTT
GTAGTTGCAGTGGTTTGACCTAGTTCATGGTTCAGGACATCTGCCAAAAGATA
Found at i:111450160 original size:11 final size:10
Alignment explanation
Indices: 111450144--111450202 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
111450134 ACTACTACAA
111450144 ACCATACAACC
1 ACCATAC-ACC
111450155 ACCATATCACC
1 ACCATA-CACC
*
111450166 ACCATTCAACC
1 ACCATAC-ACC
*
111450177 ACCTTAGCACC
1 ACCATA-CACC
111450188 ACCATACCACC
1 ACCATA-CACC
111450199 ACCA
1 ACCA
111450203 CATTACAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 1 0.03
11 37 0.93
12 2 0.05
ACGTcount: A:0.37, C:0.47, G:0.02, T:0.14
Consensus pattern (10 bp):
ACCATACACC
Found at i:111450169 original size:22 final size:22
Alignment explanation
Indices: 111450144--111450202 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
111450134 ACTACTACAA
*
111450144 ACCATACAACCACCATATCACC
1 ACCATACAACCACCATAGCACC
* *
111450166 ACCATTCAACCACCTTAGCACC
1 ACCATACAACCACCATAGCACC
*
111450188 ACCATACCACCACCA
1 ACCATACAACCACCA
111450203 CATTACAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.37, C:0.47, G:0.02, T:0.14
Consensus pattern (22 bp):
ACCATACAACCACCATAGCACC
Found at i:111454836 original size:12 final size:13
Alignment explanation
Indices: 111454812--111454841 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
111454802 ATAAGAACAA
111454812 AAAACCTTAATCT
1 AAAACCTTAATCT
111454825 AAAACC-TAATCT
1 AAAACCTTAATCT
111454837 AAAAC
1 AAAAC
111454842 GAAAAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAACCTTAATCT
Found at i:111456512 original size:48 final size:51
Alignment explanation
Indices: 111456440--111456565 Score: 204
Period size: 48 Copynumber: 2.5 Consensus size: 51
111456430 GCGGGATTAC
111456440 CAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGTC-GG-G
1 CAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGTCGGGTG
111456489 -AGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGTCGGGATTG
1 CAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGTCGGG--TG
111456541 CCAGTCCAGGCTAAATCCCCTGCAA
1 -CAGTCCAGGCTAAATCCCCTGCAA
111456566 CGACAATTAC
Statistics
Matches: 71, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
48 45 0.63
49 2 0.03
52 1 0.01
54 23 0.32
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (51 bp):
CAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGTCGGGTG
Found at i:111458821 original size:24 final size:24
Alignment explanation
Indices: 111458775--111458846 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 24
111458765 AGATTACAAA
111458775 ATCATATCTTCAAGATTGCATATCAT
1 ATCATATC-T-AAGATTGCATATCAT
*
111458801 ATCATATCTAATATTGCATATC--
1 ATCATATCTAAGATTGCATATCAT
111458823 A-C--ATCTAAGATTGCATATCAT
1 ATCATATCTAAGATTGCATATCAT
111458844 ATC
1 ATC
111458847 TAAGATTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 16 0.39
21 2 0.05
22 2 0.05
24 12 0.29
25 1 0.02
26 8 0.20
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (24 bp):
ATCATATCTAAGATTGCATATCAT
Found at i:111458822 original size:19 final size:19
Alignment explanation
Indices: 111458798--111458860 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
111458788 GATTGCATAT
*
111458798 CATATCATATCTAATATTG
1 CATATCATATCTAAGATTG
*
111458817 CATATCACATCTAAGATTG
1 CATATCATATCTAAGATTG
111458836 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
111458855 CATATC
1 CATATC
111458861 CTTAAAGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (19 bp):
CATATCATATCTAAGATTG
Found at i:111463960 original size:22 final size:22
Alignment explanation
Indices: 111463932--111463989 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
111463922 CGTCTAGATT
111463932 TGGTGTCATGACATCACATGGC
1 TGGTGTCATGACATCACATGGC
** *
111463954 TGGTGTCGCGACAACACATGGC
1 TGGTGTCATGACATCACATGGC
*
111463976 TGGTATCATGACAT
1 TGGTGTCATGACAT
111463990 TGATGGTAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (22 bp):
TGGTGTCATGACATCACATGGC
Found at i:111466053 original size:29 final size:27
Alignment explanation
Indices: 111466035--111466104 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
111466025 ATATTAAGTC
111466035 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
111466062 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
111466090 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
111466105 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:111466098 original size:28 final size:28
Alignment explanation
Indices: 111466035--111466132 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
111466025 ATATTAAGTC
*
111466035 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
111466062 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
111466090 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
111466119 CGCACACTTAGTGC
1 CGCACACTTAGTGC
111466133 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:111477358 original size:15 final size:15
Alignment explanation
Indices: 111477334--111477368 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
111477324 AAATATATTT
*
111477334 TAGATTAAGATCCTG
1 TAGATCAAGATCCTG
111477349 TAGATCAAGATCCTG
1 TAGATCAAGATCCTG
111477364 TAGAT
1 TAGAT
111477369 TTATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (15 bp):
TAGATCAAGATCCTG
Found at i:111478468 original size:22 final size:22
Alignment explanation
Indices: 111478420--111478468 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
111478410 TTTGGTGTTG
* * *
111478420 TGACATCACATGGCTGGTGTCA
1 TGACAACACATGGCTAGTATCA
*
111478442 CGACAACACATGGCTAGTATCA
1 TGACAACACATGGCTAGTATCA
111478464 TGACA
1 TGACA
111478469 TTGATGGTCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (22 bp):
TGACAACACATGGCTAGTATCA
Found at i:111489308 original size:49 final size:50
Alignment explanation
Indices: 111489235--111489411 Score: 176
Period size: 49 Copynumber: 3.7 Consensus size: 50
111489225 TAGGGTGTAA
*
111489235 TGCCGATGTCATGTCCCAGACATGGTCTTACACTGACTATCAAAATC-AAG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATC-AAATCTAAG
* * * **
111489285 -GCCGACT-CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCTCTG
1 TGCCGA-TGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATCTAAG
* *
111489334 TGCCGATGCCATGTCTCAGACATGGTCTTACACTGAC-A-C--ATCTCA-
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATCTAAG
*
111489379 TAGCCGGTG-CATGTCCCAGACAT-GTCTTACACT
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACT
111489412 CGCTTACATC
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
44 10 0.09
45 14 0.13
46 11 0.10
48 5 0.05
49 37 0.34
50 33 0.30
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (50 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATCTAAG
Found at i:111496362 original size:14 final size:15
Alignment explanation
Indices: 111496343--111496375 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
111496333 TCTCTCCTTG
111496343 CTTTCCTTCTC-TTT
1 CTTTCCTTCTCTTTT
111496357 CTTTCCTTCTCTTTT
1 CTTTCCTTCTCTTTT
111496372 CTTT
1 CTTT
111496376 ATTTCTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTCCTTCTCTTTT
Found at i:111496380 original size:19 final size:19
Alignment explanation
Indices: 111496352--111496394 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
111496342 GCTTTCCTTC
*
111496352 TCTTTCTTTCCTT-CTCTTT
1 TCTTTATTTCCTTCCTC-TT
*
111496371 TCTTTATTTCTTTCCTCTT
1 TCTTTATTTCCTTCCTCTT
111496390 TCTTT
1 TCTTT
111496395 CACTTTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTATTTCCTTCCTCTT
Found at i:111496629 original size:16 final size:15
Alignment explanation
Indices: 111496608--111496638 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
111496598 CTTCATTTAC
111496608 TTCTTTATTACTTATT
1 TTCTTTATTA-TTATT
111496624 TTCTTTATTATTATT
1 TTCTTTATTATTATT
111496639 ATTACTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTTATTATTATT
Found at i:111506821 original size:45 final size:44
Alignment explanation
Indices: 111506652--111506808 Score: 168
Period size: 41 Copynumber: 3.7 Consensus size: 44
111506642 ATATCGTACA
* * * *
111506652 ATGCCAACGTCCCAAAC-GTGGTCTTACATGCTATCAC-ATATCG
1 ATGCCAACGTCCCAGACAGTGGTCTTACACG-AATCACAATATTG
111506695 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAATCA-AATA-TG
1 ATGCCAAC-GTCCCAGACAGTGGTCTTACACGAATCACAATATTG
* *
111506736 ATGCCAAAGTCCCAGACA-TGGTCTTACACGTAACCACATATATTG
1 ATGCCAACGTCCCAGACAGTGGTCTTACACG-AATCACA-ATATTG
111506781 ATGCCAACGTCCCAGA-AGTGGTCTTACA
1 ATGCCAACGTCCCAGACAGTGGTCTTACA
111506809 TGAGAACACA
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
41 27 0.28
42 14 0.14
43 24 0.25
44 5 0.05
45 27 0.28
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACAGTGGTCTTACACGAATCACAATATTG
Found at i:111520859 original size:89 final size:88
Alignment explanation
Indices: 111520749--111520946 Score: 281
Period size: 89 Copynumber: 2.2 Consensus size: 88
111520739 CTTGGTTTAC
* * * *
111520749 CGCATTACATAGTACAGCTTATACGCTAGCCTTGCTGCATAATATATATGATTTGGCAGTTCATA
1 CGCATTGCACAGTACAGCTTATACGCTAGCCTTGCTACATAATATATATGATCTGGCAGTTCATA
* *
111520814 CTACATGTTTGTATCGCGGTC-TT
66 CTACATGTCTGTACCGC-GTCTTT
*
111520837 CTGCATTGCACAGTACAGCTTATACGCTAGCCTTGCTACATAATATATCTGATCTGGCAGTTCAT
1 C-GCATTGCACAGTACAGCTTATACGCTAGCCTTGCTACATAATATATATGATCTGGCAGTTCAT
111520902 ACTACATGTCTGTACCGCGTCTTT
65 ACTACATGTCTGTACCGCGTCTTT
* * *
111520926 CACATGGCACCGTACAGCTTA
1 CGCATTGCACAGTACAGCTTA
111520947 CTGATAGCCC
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
88 21 0.21
89 77 0.79
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (88 bp):
CGCATTGCACAGTACAGCTTATACGCTAGCCTTGCTACATAATATATATGATCTGGCAGTTCATA
CTACATGTCTGTACCGCGTCTTT
Found at i:111522061 original size:67 final size:67
Alignment explanation
Indices: 111521944--111522189 Score: 198
Period size: 67 Copynumber: 3.7 Consensus size: 67
111521934 GGTTTAAGGT
* *
111521944 GTAAGACCATAGCTC-ATCTAT-AGCAACCA-ATAGAGTCCGCCAAGACATTAAACAT-AGGATT
1 GTAAGACCATAACTCGA-CTATGA-CAA-CATATAGAGTCCGCCAGGACATTAAACATAAGG-TT
*
111522005 ACATGT
62 ACATGC
* * * * **
111522011 GTAAGACCATAACTCGACTATGATAACATGTAGAGTCCACCAGGATATTAATTATAAGGTTACAT
1 GTAAGACCATAACTCGACTATGACAACATATAGAGTCCGCCAGGACATTAAACATAAGGTTACAT
111522076 GC
66 GC
** * * * * * *
111522078 GTAAGACTGTAGCTCGGCTATGGCAACATATGGAGTTCGCCAGGACATTAAACATGAGGTTACAT
1 GTAAGACCATAACTCGACTATGACAACATATAGAGTCCGCCAGGACATTAAACATAAGGTTACAT
*
111522143 GG
66 GC
* * * *
111522145 GTAAGA-CATAGCTC-AGCTATGACAATAGATAAATGTCCGCCAGGA
1 GTAAGACCATAACTCGA-CTATGACAACATATAGA-GTCCGCCAGGA
111522190 TAGTGAACCA
Statistics
Matches: 140, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
66 20 0.14
67 115 0.82
68 5 0.04
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (67 bp):
GTAAGACCATAACTCGACTATGACAACATATAGAGTCCGCCAGGACATTAAACATAAGGTTACAT
GC
Found at i:111525780 original size:14 final size:14
Alignment explanation
Indices: 111525761--111525789 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
111525751 AAATATTAAA
111525761 TTATTTTTTAGTTT
1 TTATTTTTTAGTTT
111525775 TTATTTTTTAGTTT
1 TTATTTTTTAGTTT
111525789 T
1 T
111525790 GTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTATTTTTTAGTTT
Found at i:111527598 original size:14 final size:14
Alignment explanation
Indices: 111527581--111527610 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
111527571 TTCACTATTA
111527581 TACTATTATGTTAT
1 TACTATTATGTTAT
*
111527595 TACTATTTTGTTAT
1 TACTATTATGTTAT
111527609 TA
1 TA
111527611 TTGTTTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (14 bp):
TACTATTATGTTAT
Found at i:111528923 original size:19 final size:20
Alignment explanation
Indices: 111528894--111528935 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
111528884 AAAAAAAAAA
111528894 GTTAGTTTTCTCAATGTCTT
1 GTTAGTTTTCTCAATGTCTT
* *
111528914 GTTA-TTTTCTCATTGTTTT
1 GTTAGTTTTCTCAATGTCTT
111528933 GTT
1 GTT
111528936 GTCATTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (20 bp):
GTTAGTTTTCTCAATGTCTT
Found at i:111534746 original size:22 final size:23
Alignment explanation
Indices: 111534716--111534760 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
111534706 CTTGTTAAAT
* *
111534716 AAACAATAATATTTATGATATAA
1 AAACAATAATAATAATGATATAA
111534739 AAAC-ATAATAATAATGATATAA
1 AAACAATAATAATAATGATATAA
111534761 TATAATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
AAACAATAATAATAATGATATAA
Found at i:111535708 original size:6 final size:6
Alignment explanation
Indices: 111535699--111535736 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
111535689 CCTGACTATG
*
111535699 ACTGTT ACTGTT ACTGTT ATTGTT ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
111535737 CCTACGGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
ACTGTT
Found at i:111537631 original size:41 final size:40
Alignment explanation
Indices: 111537566--111537648 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 40
111537556 GGATGTCTAG
*
111537566 TTGTTAGGATGAAATAGATTTTTAATTAAATAAATTTCAT
1 TTGTTAGGATGAAATAGATTTTTAATTAAATAAATTTAAT
* *
111537606 TTGTTGGGATGAAAATAGGTTTTTAATTAAATAAATTTAAT
1 TTGTTAGGATG-AAATAGATTTTTAATTAAATAAATTTAAT
111537647 TT
1 TT
111537649 AGATTACCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (40 bp):
TTGTTAGGATGAAATAGATTTTTAATTAAATAAATTTAAT
Found at i:111537852 original size:31 final size:29
Alignment explanation
Indices: 111537780--111537853 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
111537770 ACAAAGCGAT
* **
111537780 AACATAAGTGACTAAAATGTAACATTTCA
1 AACAAAAGTGACTAAAATGTAACATGGCA
*
111537809 AACACAAA-TGACTAAAATGTAATATGAGGCA
1 AACA-AAAGTGACTAAAATGTAACAT--GGCA
111537840 AACAAAAGTGACTA
1 AACAAAAGTGACTA
111537854 TTTTTGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 20 0.54
30 5 0.14
31 12 0.32
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.22
Consensus pattern (29 bp):
AACAAAAGTGACTAAAATGTAACATGGCA
Found at i:111539150 original size:39 final size:40
Alignment explanation
Indices: 111539107--111539185 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 40
111539097 TATTCTTCTA
111539107 TAATCTAAAAAAATAAAGAGACCAAAATT-AAAATTTAAC
1 TAATCTAAAAAAATAAAGAGACCAAAATTAAAAATTTAAC
* *
111539146 TAATCTAAAAATATAAAGAGATCAAAATTAAAAATTTAAC
1 TAATCTAAAAAAATAAAGAGACCAAAATTAAAAATTTAAC
111539186 CATTTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 27 0.73
40 10 0.27
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (40 bp):
TAATCTAAAAAAATAAAGAGACCAAAATTAAAAATTTAAC
Found at i:111539557 original size:29 final size:30
Alignment explanation
Indices: 111539496--111539559 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
111539486 ATTAAATTCT
* *
111539496 AATTTTAAAATATAAATAATAGAAAAATTA
1 AATTTTAAAATATAAATAATAAAAAAATCA
111539526 AATTCTTAAAAT-TAAA-AATAAAAAAATCA
1 AATT-TTAAAATATAAATAATAAAAAAATCA
111539555 AATTT
1 AATTT
111539560 CAAATTCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 15 0.48
30 8 0.26
31 7 0.23
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
AATTTTAAAATATAAATAATAAAAAAATCA
Found at i:111540238 original size:20 final size:19
Alignment explanation
Indices: 111540208--111540257 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
111540198 TTATAAAAAT
111540208 TTTA-AATTTTTA-ACTTTC
1 TTTATAATTTTTAGA-TTTC
*
111540226 TTTATATATTTTTAGATTTT
1 TTTATA-ATTTTTAGATTTC
111540246 TTTATAATTTTT
1 TTTATAATTTTT
111540258 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 7 0.25
20 16 0.57
21 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATAATTTTTAGATTTC
Found at i:111540293 original size:19 final size:18
Alignment explanation
Indices: 111540271--111540332 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 18
111540261 AAAATATAAA
*
111540271 ATTTGGAATTTTTATAAAT
1 ATTT-GAATTTTTAAAAAT
111540290 ATTTTGAA-TTTTAAAAATT
1 A-TTTGAATTTTTAAAAA-T
111540309 AATTTGAATTTTTGAAAAAT
1 -ATTTGAATTTTT-AAAAAT
111540329 ATTT
1 ATTT
111540333 TTTTTTGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 8 0.22
19 15 0.41
20 9 0.24
21 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (18 bp):
ATTTGAATTTTTAAAAAT
Found at i:111543164 original size:26 final size:27
Alignment explanation
Indices: 111543113--111543166 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
111543103 ACATTAGCAA
*
111543113 CCAAAAGATTAGATTTTTTTTTTCATT
1 CCAAAAGATTAGATTTTTTTTCTCATT
111543140 CCAAAAGATTAGA-TTTTTTTCTCATT
1 CCAAAAGATTAGATTTTTTTTCTCATT
111543166 C
1 C
111543167 TCTTGATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (27 bp):
CCAAAAGATTAGATTTTTTTTCTCATT
Found at i:111544869 original size:35 final size:35
Alignment explanation
Indices: 111544823--111544895 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
111544813 TTACATATTA
111544823 ATAGGAAGATTTAACCTGCATTATGAATATAAAAT
1 ATAGGAAGATTTAACCTGCATTATGAATATAAAAT
111544858 ATAGGAAGATTTAACCTGCATTATGAATATAAAAT
1 ATAGGAAGATTTAACCTGCATTATGAATATAAAAT
111544893 ATA
1 ATA
111544896 TCCATCTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (35 bp):
ATAGGAAGATTTAACCTGCATTATGAATATAAAAT
Found at i:111544978 original size:3 final size:3
Alignment explanation
Indices: 111544970--111545007 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
111544960 TCTGAACTCT
111544970 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
111545008 TTCAATTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:111555506 original size:17 final size:17
Alignment explanation
Indices: 111555466--111555529 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
111555456 CAATGATATG
* *
111555466 CAATATTAGATATGATTG
1 CAATCTTAGATATGA-TA
111555484 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
111555501 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
111555520 CAATCTTAGA
1 CAATCTTAGA
111555530 AGATATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
17 15 0.36
18 14 0.33
19 13 0.31
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:111555517 original size:22 final size:20
Alignment explanation
Indices: 111555491--111555538 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
111555481 TTGCAATCTT
111555491 AGATATGATACAATCTTAG-
1 AGATATGATACAATCTTAGA
*
111555510 ATATGAT-ATACAATCTTAGA
1 AGAT-ATGATACAATCTTAGA
111555530 AGATATGAT
1 AGATATGAT
111555539 TTTGTAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (20 bp):
AGATATGATACAATCTTAGA
Found at i:111555522 original size:19 final size:19
Alignment explanation
Indices: 111555458--111555529 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
111555448 ATAATCTTCA
* *
111555458 ATGATATGCAATATTAGAT
1 ATGATATACAATCTTAGAT
*
111555477 ATGAT-TGCAATCTTAGAT
1 ATGATATACAATCTTAGAT
111555495 ATG--ATACAATCTTAGAT
1 ATGATATACAATCTTAGAT
111555512 ATGATATACAATCTTAGA
1 ATGATATACAATCTTAGA
111555530 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
17 15 0.31
18 15 0.31
19 18 0.38
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATACAATCTTAGAT
Found at i:111555534 original size:17 final size:17
Alignment explanation
Indices: 111555484--111555535 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
111555474 GATATGATTG
*
111555484 CAATCTTAG-ATATGATA
1 CAATCTTAGAAGAT-ATA
111555501 CAATCTTAGATATGATATA
1 CAATCTTAGA-A-GATATA
111555520 CAATCTTAGAAGATAT
1 CAATCTTAGAAGATAT
111555536 GATTTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 14 0.45
18 1 0.03
19 14 0.45
20 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
CAATCTTAGAAGATATA
Found at i:111562461 original size:84 final size:83
Alignment explanation
Indices: 111562211--111562662 Score: 608
Period size: 84 Copynumber: 5.4 Consensus size: 83
111562201 ACAAAATTCA
* *
111562211 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-TAAAATTACAGATCTTATCTCCCTAAGCAGT
*
111562276 AGTGGAGCAGATCAAAGAC
65 AGTAGAGCAGATCAAAGAC
* *
111562295 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT----TCACAGATCTTATCTTCCTAAGCAGTA
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTAAAATTACAGATCTTATCTCCCTAAGCAGTA
*
111562356 GTGGAGCAGATCAAAGAC
66 GTAGAGCAGATCAAAGAC
* *
111562374 TCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGT
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-TAAAATTACAGATCTTATCTCCCTAAGCAGT
* *
111562439 AGCAGAACAGATCAAAGAC
65 AGTAGAGCAGATCAAAGAC
* * *
111562458 TCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGT
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-TAAAATTACAGATCTTATCTCCCTAAGCAGT
* *
111562523 AGCAGAACAGATCAACGACGAC
65 AGTAGAGCAGATCAA--A-GAC
* * * *
111562545 TCTCCTTAATCCCCTAAGTAGTAGGGTAACAGGTCAAAATTGCAGATTTTATCTCCCTAAGCAGT
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT-AAAATTACAGATCTTATCTCCCTAAGCAGT
*
111562610 AGTAGAGCAGATCGAAGA-
65 AGTAGAGCAGATCAAAGAC
*
111562628 TGCGCCTTAAACCCCTAAGCAGTAGGGTAACAGGT
1 T-CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT
111562663 TAAAGTATAG
Statistics
Matches: 334, Mismatches: 24, Indels: 20
0.88 0.06 0.05
Matches are distributed among these distances:
79 74 0.22
80 1 0.00
83 2 0.01
84 183 0.55
85 1 0.00
86 2 0.01
87 71 0.21
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (83 bp):
TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTAAAATTACAGATCTTATCTCCCTAAGCAGTA
GTAGAGCAGATCAAAGAC
Found at i:111562610 original size:171 final size:166
Alignment explanation
Indices: 111562211--111562662 Score: 617
Period size: 163 Copynumber: 2.7 Consensus size: 166
111562201 ACAAAATTCA
* *
111562211 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTTATCTCCCTAAGCAGT
* * *
111562276 AGTGGAGCAGATCAAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT---TCACAGATC
66 AGTAGAGCAGATCAAAGACTCGCCTTAAACCCCTAAGCAGTAGGGTAACAGGTAAATCACAAATC
* ** *
111562338 TTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGAC
131 TTATCTCCCTAAGCAGTAGCAGAACAGATCAAAGAC
* * *
111562374 TCGCCTTAACCCCCTAAGCAGTAGGGTAACAGG-CTAAAATTACAAATCTTATCTCCCTAAGCAG
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTC-AAAATTGCAGATCTTATCTCCCTAAGCAG
* * * * *
111562438 TAGCAGAACAGATCAAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTACAA
65 TAGTAGAGCAGATCAAAGACTCGCCTTAAACCCCTAAGCAGTAGGGTAACAGG-T-AAATCACAA
111562503 ATCTTATCTCCCTAAGCAGTAGCAGAACAGATCAACGACGAC
128 ATCTTATCTCCCTAAGCAGTAGCAGAACAGATCAA--A-GAC
* * *
111562545 TCTCCTTAATCCCCTAAGTAGTAGGGTAACAGGTCAAAATTGCAGATTTTATCTCCCTAAGCAGT
1 TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTTATCTCCCTAAGCAGT
*
111562610 AGTAGAGCAGATCGAAGA-TGCGCCTTAAACCCCTAAGCAGTAGGGTAACAGGT
66 AGTAGAGCAGATCAAAGACT-CGCCTTAAACCCCTAAGCAGTAGGGTAACAGGT
111562663 TAAAGTATAG
Statistics
Matches: 251, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
163 106 0.42
164 1 0.00
168 35 0.14
170 3 0.01
171 105 0.42
172 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (166 bp):
TCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTTATCTCCCTAAGCAGT
AGTAGAGCAGATCAAAGACTCGCCTTAAACCCCTAAGCAGTAGGGTAACAGGTAAATCACAAATC
TTATCTCCCTAAGCAGTAGCAGAACAGATCAAAGAC
Found at i:111562797 original size:44 final size:43
Alignment explanation
Indices: 111562716--111562798 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
111562706 GATCCAAGAT
* * *
111562716 GATTTGGCGTCTCTGTATTGTCAGAGAACAAATCGAAGAAACA
1 GATTTGGCATCTCTATATTGACAGAGAACAAATCGAAGAAACA
* *
111562759 GATTTGGCATCTCTATATTCGACAGAGAGCAGATCGAAGA
1 GATTTGGCATCTCTATATT-GACAGAGAACAAATCGAAGA
111562799 CATAGCTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 17 0.50
44 17 0.50
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (43 bp):
GATTTGGCATCTCTATATTGACAGAGAACAAATCGAAGAAACA
Found at i:111563150 original size:207 final size:207
Alignment explanation
Indices: 111562795--111563711 Score: 1516
Period size: 207 Copynumber: 4.4 Consensus size: 207
111562785 GAGCAGATCG
* * * *
111562795 AAGACATAGCTGATTTGGCTTTCACATGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
111562860 TGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCA
66 TGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCA
*
111562925 GATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACA
131 GATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACA
111562990 AGGAACAAATCA
196 AGGAACAAATCA
111563002 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
* * * *
111563067 TGTATTGTCAGAGAACAAATAGAAGTTTGGCGTCTTCATATTCGACAGAGGGCAGACACATAGCA
66 TGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCA
* * * *
111563132 AATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGGTGGTTTGGCATCCTTGTGTTTACA
131 GATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACA
*
111563197 AGGAACAAATCG
196 AGGAACAAATCA
*
111563209 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGTATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
*
111563274 TGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGTAGACACATAGCA
66 TGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCA
*
111563339 GATCTGACCTTCAGATGTTTATACTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACA
131 GATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACA
*
111563404 AGGAACAAATCG
196 AGGAACAAATCA
*
111563416 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGAAAGTCTAAGATGATTTGGCATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
* * *
111563481 TGTATTGTCAGAGAACAAGTCGAAGTTTGG-AGTCTCCATATTCGACGGAGGACAGACATATAGC
66 TGTATTGTCAGAGAACAAATCGAAGTTTGGCA-TCTCCATATTCGACGGAGGGCAGACACATAGC
* * * *
111563545 AGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGTGCTTAC
130 AGATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTAC
*
111563609 AAGGAGCAAATCA
195 AAGGAACAAATCA
* * *
111563622 AAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
*
111563687 TGTATTGTCA-AGGAACAAATTGAAG
66 TGTATTGTCAGA-GAACAAATCGAAG
111563712 AAGCAGATTT
Statistics
Matches: 666, Mismatches: 42, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
205 1 0.00
206 126 0.19
207 539 0.81
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (207 bp):
AAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTC
TGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCA
GATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACA
AGGAACAAATCA
Found at i:111564091 original size:17 final size:18
Alignment explanation
Indices: 111564078--111564238 Score: 97
Period size: 17 Copynumber: 8.9 Consensus size: 18
111564068 TAATCTTCAA
111564078 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
111564097 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
111564114 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
*
111564133 TGAT-TGCAATCTTAGATA
1 TGATATGCAATCTTAGA-G
111564151 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
*
111564167 T-ATGATACAATCTTAGA-
1 TGAT-ATGCAATCTTAGAG
* *
111564184 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
* *
111564203 TGAT-TGCAATATTAGAATA
1 TGATATGCAATCTTAG-A-G
*
111564222 TGATATACAATCTTAGA
1 TGATATGCAATCTTAGA
111564239 AGATATGATT
Statistics
Matches: 124, Mismatches: 7, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.02
16 3 0.02
17 41 0.33
18 38 0.31
19 27 0.22
20 13 0.10
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Found at i:111564161 original size:53 final size:53
Alignment explanation
Indices: 111564077--111564238 Score: 245
Period size: 53 Copynumber: 3.0 Consensus size: 53
111564067 ATAATCTTCA
*
111564077 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
111564132 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
* *
111564185 ATGA-TACAATCTTAGATATGATTGCAATATTAGAATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATGATTGCAATCTTAG-ATATG--ATACAATCTTAGA
111564239 AGATATGATT
Statistics
Matches: 101, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
52 27 0.27
53 39 0.39
54 17 0.17
55 18 0.18
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (53 bp):
ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:111564191 original size:70 final size:73
Alignment explanation
Indices: 111564077--111564238 Score: 267
Period size: 70 Copynumber: 2.2 Consensus size: 73
111564067 ATAATCTTCA
*
111564077 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAA
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGATATGATACAATCTTAGATATGATTGCAA
*
111564142 TCTTAG-AT
65 TATTAGAAT
111564150 ATGAT-TGCAATCTTAGATATGATA-CAATCTTAGATATGATACAATCTTAGATATGATTGCAAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGATATGATACAATCTTAGATATGATTGCAAT
111564213 ATTAGAAT
66 ATTAGAAT
*
111564221 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
111564239 AGATATGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
70 43 0.51
71 7 0.08
72 29 0.35
73 5 0.06
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (73 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGATATGATACAATCTTAGATATGATTGCAAT
ATTAGAAT
Found at i:111565248 original size:24 final size:24
Alignment explanation
Indices: 111565212--111565291 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
111565202 TTACGAGAAT
* *
111565212 GTGAAAGGTTTAAGGAAGATTAAAA
1 GTGAAA-GATTAAGGAAGATGAAAA
* *
111565237 GTTAAATG-TTAAAGAAGATGAAAA
1 GTGAAA-GATTAAGGAAGATGAAAA
* *
111565261 GTGGAAGATTAAGGAAGATGAAAG
1 GTGAAAGATTAAGGAAGATGAAAA
111565285 GTGAAAG
1 GTGAAAG
111565292 GTTGAACATC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.02
24 38 0.84
25 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (24 bp):
GTGAAAGATTAAGGAAGATGAAAA
Found at i:111567567 original size:16 final size:17
Alignment explanation
Indices: 111567541--111567572 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
111567531 ATAATTCATG
111567541 CCAATCTATTTATTTTT
1 CCAATCTATTTATTTTT
111567558 CCAA-CTATTTATTTT
1 CCAATCTATTTATTTT
111567573 CTCCCCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (17 bp):
CCAATCTATTTATTTTT
Found at i:111567979 original size:30 final size:30
Alignment explanation
Indices: 111567945--111568005 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
111567935 ATTGGAGACG
111567945 TTTGATTAATGATTCAGCAAAATTTGTCAT
1 TTTGATTAATGATTCAGCAAAATTTGTCAT
111567975 TTTGATTAATGATTCAGCAAAATTTGTCAT
1 TTTGATTAATGATTCAGCAAAATTTGTCAT
111568005 T
1 T
111568006 ATCACAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTGATTAATGATTCAGCAAAATTTGTCAT
Found at i:111569280 original size:17 final size:18
Alignment explanation
Indices: 111569247--111569283 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
111569237 TGTGTTATAA
111569247 GAAGATGAAAAGTTTAAG
1 GAAGATGAAAAGTTTAAG
* *
111569265 GAAGATTAAAAGTTAAAG
1 GAAGATGAAAAGTTTAAG
111569283 G
1 G
111569284 TTAAAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
GAAGATGAAAAGTTTAAG
Found at i:111569282 original size:24 final size:24
Alignment explanation
Indices: 111569255--111569329 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
111569245 AAGAAGATGA
* * * *
111569255 AAAGTTTAAGGAAGATTAAAAGTT
1 AAAGGTTAAAGAAGATGAAAAGTG
111569279 AAAGGTTAAAGAAGATGAAAAGTG
1 AAAGGTTAAAGAAGATGAAAAGTG
* *
111569303 AAAGGTTAAAGGAGATGAAATGTG
1 AAAGGTTAAAGAAGATGAAAAGTG
111569327 AAA
1 AAA
111569330 TGTTGAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.21
Consensus pattern (24 bp):
AAAGGTTAAAGAAGATGAAAAGTG
Found at i:111577568 original size:28 final size:28
Alignment explanation
Indices: 111577536--111577589 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
111577526 TTTTTCGTCT
111577536 ATATTATTTCGATTATTAATTTGATAGG
1 ATATTATTTCGATTATTAATTTGATAGG
* * *
111577564 ATATTATTTTGGTTATTAGTTTGATA
1 ATATTATTTCGATTATTAATTTGATA
111577590 ATGCATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.54
Consensus pattern (28 bp):
ATATTATTTCGATTATTAATTTGATAGG
Found at i:111585103 original size:20 final size:19
Alignment explanation
Indices: 111585065--111585107 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
111585055 ACAATTTACA
111585065 AATTTAAAATAATATATAT
1 AATTTAAAATAATATATAT
111585084 AATTTAAACATAA-ATAATAT
1 AATTTAAA-ATAATAT-ATAT
111585104 AATT
1 AATT
111585108 GGTAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTAAAATAATATATAT
Found at i:111585210 original size:12 final size:13
Alignment explanation
Indices: 111585164--111585213 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
111585154 CAAGTAAAAC
111585164 ATAATAAATATTAT
1 ATAATAAATA-TAT
111585178 ATAATAAA-ATAT
1 ATAATAAATATAT
***
111585190 ATGGGAAATA-AT
1 ATAATAAATATAT
111585202 ATAATAAATATA
1 ATAATAAATATA
111585214 GCATGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
12 17 0.61
13 3 0.11
14 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (13 bp):
ATAATAAATATAT
Found at i:111585250 original size:13 final size:13
Alignment explanation
Indices: 111585234--111585277 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
111585224 ATGAAAATTT
111585234 ATATGTAAAAATA
1 ATATGTAAAAATA
111585247 ATATGTATATATAAT-
1 ATATGTA-A-A-AATA
111585262 ATATGTAAAAATA
1 ATATGTAAAAATA
111585275 ATA
1 ATA
111585278 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.11
13 11 0.41
14 2 0.07
15 8 0.30
16 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (13 bp):
ATATGTAAAAATA
Found at i:111585269 original size:28 final size:29
Alignment explanation
Indices: 111585233--111585289 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
111585223 AATGAAAATT
*
111585233 TATATGTAAAAATAAT-ATGTATATATAA
1 TATATGTAAAAATAATAATATATATATAA
111585261 TATATGTAAAAATAATAATATATATATAA
1 TATATGTAAAAATAATAATATATATATAA
111585290 AATAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (29 bp):
TATATGTAAAAATAATAATATATATATAA
Found at i:111585293 original size:19 final size:18
Alignment explanation
Indices: 111585257--111585344 Score: 74
Period size: 18 Copynumber: 4.9 Consensus size: 18
111585247 ATATGTATAT
*
111585257 ATAATATATGTAAAAATA
1 ATAATATATATAAAAATA
111585275 ATAATATATATATAAAATA
1 ATAATATATATA-AAAATA
* * *
111585294 ATAAT-TATGAGAGAATTA
1 ATAATATAT-ATAAAAATA
*
111585312 AT-ATATA-ATAAACAATC
1 ATAATATATATAAA-AATA
*
111585329 ATAATACATATAAAAA
1 ATAATATATATAAAAA
111585345 ATAACACTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 3 0.05
17 6 0.11
18 28 0.51
19 18 0.33
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (18 bp):
ATAATATATATAAAAATA
Done.