Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:3145296 original size:15 final size:15
Alignment explanation
Indices: 3145276--3145306 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3145266 ATAAAGCATC
3145276 TATCAAACCCTCATT
1 TATCAAACCCTCATT
3145291 TATCAAACCCTCATT
1 TATCAAACCCTCATT
3145306 T
1 T
3145307 TGATCATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (15 bp):
TATCAAACCCTCATT
Found at i:3157385 original size:29 final size:29
Alignment explanation
Indices: 3157348--3157406 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3157338 ATGGTGCACA
3157348 TTATCTACGAGGCACTTTCGAGTGCATAT
1 TTATCTACGAGGCACTTTCGAGTGCATAT
*
3157377 TTATTTACGAGGCACTTTCGAGTGCATAT
1 TTATCTACGAGGCACTTTCGAGTGCATAT
3157406 T
1 T
3157407 GCATACACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (29 bp):
TTATCTACGAGGCACTTTCGAGTGCATAT
Found at i:3161956 original size:33 final size:33
Alignment explanation
Indices: 3161910--3161985 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
3161900 TGGGACCAAA
* *
3161910 CGACCACCATCCACGGCAGTCAATGACGACATC
1 CGACCACCTTCCACGACAGTCAATGACGACATC
3161943 CGACCACCTTCCACGACAGTCAATGACGACATC
1 CGACCACCTTCCACGACAGTCAATGACGACATC
3161976 CGACCACCTT
1 CGACCACCTT
3161986 TTATTTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.29, C:0.41, G:0.16, T:0.14
Consensus pattern (33 bp):
CGACCACCTTCCACGACAGTCAATGACGACATC
Found at i:3166616 original size:18 final size:19
Alignment explanation
Indices: 3166580--3166619 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3166570 CCAAAAAATA
3166580 AAAGTGTATATTAACATGT
1 AAAGTGTATATTAACATGT
* *
3166599 AAAGTGTGT-TTAATATGT
1 AAAGTGTATATTAACATGT
3166617 AAA
1 AAA
3166620 TCATATCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (19 bp):
AAAGTGTATATTAACATGT
Found at i:3176695 original size:35 final size:35
Alignment explanation
Indices: 3176649--3176715 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
3176639 GCTAAGGAAA
3176649 AATGATTTATGCTAAGGAAACAATATATACAACCT
1 AATGATTTATGCTAAGGAAACAATATATACAACCT
3176684 AATGATTTATGCTAAGGAAACAATATATACAA
1 AATGATTTATGCTAAGGAAACAATATATACAA
3176716 ATCCCATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (35 bp):
AATGATTTATGCTAAGGAAACAATATATACAACCT
Found at i:3178587 original size:42 final size:42
Alignment explanation
Indices: 3178528--3178646 Score: 175
Period size: 43 Copynumber: 2.8 Consensus size: 42
3178518 CCGCCATAAA
* *
3178528 AGGTGTTGAGATTTAGCGGCGTTTGTCCACAAACGTCGCAAT
1 AGGTGTTGAGATTTAGCGGCGTTTTTCCACAAACGCCGCAAT
* *
3178570 AGGTGTTGAGATTTAGCGGTGTTTTTCTCAAAAACGCCGCAAT
1 AGGTGTTGAGATTTAGCGGCGTTTTTC-CACAAACGCCGCAAT
*
3178613 AGGTGTAGAGATTTAGCGGCGTTTTTCCCACAAA
1 AGGTGTTGAGATTTAGCGGCGTTTTT-CCACAAA
3178647 TTCCGTAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 25 0.37
43 42 0.62
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
AGGTGTTGAGATTTAGCGGCGTTTTTCCACAAACGCCGCAAT
Found at i:3181154 original size:17 final size:16
Alignment explanation
Indices: 3181134--3181169 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
3181124 TATCAAAATG
3181134 AAATAAGACAACAATAC
1 AAATAAGACAACAA-AC
3181151 AAATAAGACAACAAAC
1 AAATAAGACAACAAAC
3181167 AAA
1 AAA
3181170 CTAAACCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.08
Consensus pattern (16 bp):
AAATAAGACAACAAAC
Found at i:3189904 original size:20 final size:23
Alignment explanation
Indices: 3189852--3189910 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 23
3189842 CTATGCGCTA
*
3189852 GGTATCGATACCCCCTTTGAATG
1 GGTATCGATACCCCCTATGAATG
3189875 GGTA-CTGATACCCCC-ATG-A-G
1 GGTATC-GATACCCCCTATGAATG
3189895 GGTATCGATACCCCCT
1 GGTATCGATACCCCCT
3189911 TCGGGTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 3 0.09
23 13 0.41
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (23 bp):
GGTATCGATACCCCCTATGAATG
Found at i:3191825 original size:27 final size:27
Alignment explanation
Indices: 3191792--3191871 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
3191782 GGATTGATAT
3191792 GTTTGGATGTTTGAATGTTTAACTTTG
1 GTTTGGATGTTTGAATGTTTAACTTTG
3191819 GTTTGGATGTTTGAATGTTTAACTTTG
1 GTTTGGATGTTTGAATGTTTAACTTTG
* * *
3191846 TTTTGAATGTTTGGATGTTTGAACTT
1 GTTTGGATGTTTGAATGTTT-AACTT
3191872 AAATGCTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 44 0.90
28 5 0.10
ACGTcount: A:0.19, C:0.04, G:0.25, T:0.53
Consensus pattern (27 bp):
GTTTGGATGTTTGAATGTTTAACTTTG
Found at i:3193827 original size:22 final size:22
Alignment explanation
Indices: 3193776--3193828 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3193766 TGTTCACGTT
*
3193776 TTCAAAAGCTATTATTTTCCTA
1 TTCAAAACCTATTATTTTCCTA
* * *
3193798 TCCGAAACCTATTATTTTTCTA
1 TTCAAAACCTATTATTTTCCTA
3193820 TTCAAAACC
1 TTCAAAACC
3193829 GGAAAAACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (22 bp):
TTCAAAACCTATTATTTTCCTA
Found at i:3194557 original size:41 final size:42
Alignment explanation
Indices: 3194472--3194566 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 42
3194462 TTTTTTTTAT
* * * * *
3194472 AAAACACCACTAAATTACTATTATTTTTCTGCGTTTGTAT-A
1 AAAACGCCACTAAATTACTACTATTTTGCGGCGTTTATATAA
* *
3194513 AAAACGCCGCTAAATTACTACTCTTTTGCGGCGTTTAT-TGAA
1 AAAACGCCACTAAATTACTACTATTTTGCGGCGTTTATAT-AA
3194555 AAAACGCCACTA
1 AAAACGCCACTA
3194567 TAAAGAACTC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.02
41 31 0.70
42 12 0.27
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (42 bp):
AAAACGCCACTAAATTACTACTATTTTGCGGCGTTTATATAA
Found at i:3194643 original size:42 final size:40
Alignment explanation
Indices: 3194502--3194645 Score: 96
Period size: 42 Copynumber: 3.5 Consensus size: 40
3194492 TTATTTTTCT
* * * * *
3194502 GCGTTTGTATAAAAACGCCGCTAAATTACTACTCTTTTGCG
1 GCGTTTGTGTAAAAACGCCACAAAATTAC-ACTCTATTACG
* * *
3194543 GCGTTTATTGAAAAAACGCCACTATAAA-GA-ACTCTA-TACCG
1 GCGTTT-GTGTAAAAACGCCAC-A-AAATTACACTCTATTA-CG
* * *
3194584 ACGTTTGTGCCATAAACGCCACAAAATTACCACTCTATTACG
1 GCGTTTGTG-TAAAAACGCCACAAAATTA-CACTCTATTACG
3194626 GCGTTTGTTGTAAAAACGCC
1 GCGTTTG-TGTAAAAACGCC
3194646 GCTAAAGTAT
Statistics
Matches: 77, Mismatches: 16, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
39 3 0.04
40 5 0.06
41 28 0.36
42 33 0.43
43 5 0.06
44 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
GCGTTTGTGTAAAAACGCCACAAAATTACACTCTATTACG
Found at i:3206493 original size:48 final size:48
Alignment explanation
Indices: 3206441--3206549 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
3206431 AAATATTTTA
3206441 TCTGATTTCTGA-CTTGAATTCTGTTCTGATA-CATGACCTAAATTATGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATATC-TGACCTAAATTATGT
* * *
3206489 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTAAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTGATATCTGACCTAAATTATGT
* *
3206537 TTTGATTTATGAT
1 TCTGATTTCTGAT
3206550 ATCTCTGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATATCTGACCTAAATTATGT
Found at i:3206549 original size:24 final size:24
Alignment explanation
Indices: 3206457--3206549 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
3206447 TTCTGACTTG
* *
3206457 AATTCTGTTCTGATACATGACCTA
1 AATTCTGTTCTGATATATGATCTA
* * * *
3206481 AATTATGTTCTGATTTCTGATCTG
1 AATTCTGTTCTGATATATGATCTA
* *
3206505 GATTCTGTTCTGATATCTGATCTA
1 AATTCTGTTCTGATATATGATCTA
* *
3206529 AATTCTGTTTTGATTTATGAT
1 AATTCTGTTCTGATATATGAT
3206550 ATCTCTGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTCTGTTCTGATATATGATCTA
Found at i:3208744 original size:2 final size:2
Alignment explanation
Indices: 3208739--3208764 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3208729 AATTTTTTAA
3208739 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3208765 TAATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3211043 original size:4 final size:4
Alignment explanation
Indices: 3211026--3211071 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
3211016 TGCAATAACT
* * *
3211026 ATGC ATGT ATGC ATGC ATGT ATGC ATGC ATGT ATGC ATGC ATGC AT
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC AT
3211072 CTAAAGGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (4 bp):
ATGC
Found at i:3211043 original size:12 final size:12
Alignment explanation
Indices: 3211026--3211068 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
3211016 TGCAATAACT
3211026 ATGCATGTATGC
1 ATGCATGTATGC
3211038 ATGCATGTATGC
1 ATGCATGTATGC
3211050 ATGCATGTATGC
1 ATGCATGTATGC
3211062 ATGCATG
1 ATGCATG
3211069 CATCTAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (12 bp):
ATGCATGTATGC
Found at i:3212556 original size:39 final size:39
Alignment explanation
Indices: 3212513--3212590 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
3212503 GATAGATGGT
* *
3212513 TTATTATTGTTACTGATGAGTGGTGTG-GAGAAAGTGGAG
1 TTATTATTGTTACTGATAAGTAGTG-GAGAGAAAGTGGAG
*
3212552 TTATTATTGTTATTGATAAGTAGTGGAGAGAAAGTGGAG
1 TTATTATTGTTACTGATAAGTAGTGGAGAGAAAGTGGAG
3212591 AGAAAGTGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.29, C:0.01, G:0.33, T:0.36
Consensus pattern (39 bp):
TTATTATTGTTACTGATAAGTAGTGGAGAGAAAGTGGAG
Found at i:3212589 original size:11 final size:11
Alignment explanation
Indices: 3212573--3212601 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3212563 ATTGATAAGT
3212573 AGTGGAGAGAA
1 AGTGGAGAGAA
3212584 AGTGGAGAGAA
1 AGTGGAGAGAA
3212595 AGTGGAG
1 AGTGGAG
3212602 TATTAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.48, T:0.10
Consensus pattern (11 bp):
AGTGGAGAGAA
Found at i:3215674 original size:26 final size:26
Alignment explanation
Indices: 3215645--3215700 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3215635 AATCGATACC
* *
3215645 TTTTGCATTTGTATTTGCATTCACAT
1 TTTTACATTTGTATTTACATTCACAT
* **
3215671 TTTTACGTTTGTATTTACATTTTCAT
1 TTTTACATTTGTATTTACATTCACAT
3215697 TTTT
1 TTTT
3215701 TTTTTGCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (26 bp):
TTTTACATTTGTATTTACATTCACAT
Found at i:3218136 original size:11 final size:11
Alignment explanation
Indices: 3218120--3218234 Score: 102
Period size: 10 Copynumber: 10.7 Consensus size: 11
3218110 ATCAAAAAAG
3218120 AAAAAGAAGAA
1 AAAAAGAAGAA
3218131 AAAAAG-AGAA
1 AAAAAGAAGAA
3218141 AAAAA-AGAGAA
1 AAAAAGA-AGAA
*
3218152 AAAAAG-GGAA
1 AAAAAGAAGAA
3218162 AAAAAG-AGAA
1 AAAAAGAAGAA
3218172 AAAAA-AGAGAAA
1 AAAAAGA-AG-AA
3218184 AAAAAGAGAGAA
1 AAAAAGA-AGAA
3218196 AAAAAGAA-AA
1 AAAAAGAAGAA
*
3218206 GAAAA-AAGAA
1 AAAAAGAAGAA
3218216 AAGAAAGAA-AA
1 AA-AAAGAAGAA
*
3218227 GAAAAGAA
1 AAAAAGAA
3218235 ATGAAATTGA
Statistics
Matches: 89, Mismatches: 5, Indels: 21
0.77 0.04 0.18
Matches are distributed among these distances:
9 2 0.02
10 41 0.46
11 24 0.27
12 18 0.20
13 4 0.04
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:3218151 original size:21 final size:21
Alignment explanation
Indices: 3218120--3218233 Score: 135
Period size: 22 Copynumber: 5.3 Consensus size: 21
3218110 ATCAAAAAAG
3218120 AAAAAGAAGAAAAAAAGAGAAA
1 AAAAAG-AGAAAAAAAGAGAAA
*
3218142 AAAAAGAGAAAAAAAG-GGAA
1 AAAAAGAGAAAAAAAGAGAAA
3218162 AAAAAGAGAAAAAAAAGAGAAA
1 AAAAAGAG-AAAAAAAGAGAAA
3218184 AAAAAGAGAGAAAAAA-AGAAA
1 AAAAAGAGA-AAAAAAGAGAAA
*
3218205 AGAAAAAAGAAAAGAAAGA-AAA
1 A-AAAAGAGAAAA-AAAGAGAAA
*
3218227 GAAAAGA
1 AAAAAGA
3218234 AATGAAATTG
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.14
21 33 0.41
22 36 0.44
23 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAAAAAGAGAAA
Found at i:3218168 original size:42 final size:42
Alignment explanation
Indices: 3218113--3218233 Score: 144
Period size: 42 Copynumber: 2.9 Consensus size: 42
3218103 CTCATCCATC
3218113 AAAAAAG--AAAAAGAAGAAAAAAAGAGAAAAAAAAGAGA-A
1 AAAAAAGAAAAAAAGAAGAAAAAAAGAGAAAAAAAAGAGAGA
*
3218152 AAAAAGGGAAAAAAAG-AGAAAAAAAAGAGAAAAAAAAGAGAGA
1 AAAAA-AGAAAAAAAGAAG-AAAAAAAGAGAAAAAAAAGAGAGA
* *
3218195 AAAAAAGAAAAGAAAAAAGAAAAGAAAGA-AAAGAAAAGA
1 AAAAAAGAAAA-AAAGAAGAAAA-AAAGAGAAAAAAAAGA
3218234 AATGAAATTG
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
39 5 0.07
40 1 0.01
41 2 0.03
42 33 0.47
43 22 0.31
44 7 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (42 bp):
AAAAAAGAAAAAAAGAAGAAAAAAAGAGAAAAAAAAGAGAGA
Found at i:3218234 original size:10 final size:9
Alignment explanation
Indices: 3218113--3218235 Score: 108
Period size: 9 Copynumber: 13.1 Consensus size: 9
3218103 CTCATCCATC
3218113 AAAAAAGAA
1 AAAAAAGAA
*
3218122 AAAGAAGAA
1 AAAAAAGAA
3218131 AAAAAGAGAA
1 AAAAA-AGAA
3218141 AAAAAAGAGA
1 AAAAAAGA-A
3218151 AAAAAAGGGAA
1 AAAAAA--GAA
3218162 AAAAAGAGAAA
1 AAAAA-AG-AA
3218173 AAAAAGAGAA
1 AAAAA-AGAA
*
3218183 AAAAAAGAG
1 AAAAAAGAA
*
3218192 AGAAAA-AA
1 AAAAAAGAA
*
3218200 AGAAAAG--
1 AAAAAAGAA
3218207 AAAAAAGAA
1 AAAAAAGAA
*
3218216 AAGAAAGAA
1 AAAAAAGAA
3218225 AAGAAAAGAA
1 AA-AAAAGAA
3218235 A
1 A
3218236 TGAAATTGAA
Statistics
Matches: 96, Mismatches: 8, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.06
8 7 0.07
9 33 0.34
10 31 0.32
11 16 0.17
12 3 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:3218235 original size:31 final size:29
Alignment explanation
Indices: 3218113--3218235 Score: 131
Period size: 31 Copynumber: 4.0 Consensus size: 29
3218103 CTCATCCATC
3218113 AAAAAAGAAAAAGAAGAAAAAAAGAGAAAA
1 AAAAAAGAAAAA-AAGAAAAAAAGAGAAAA
*
3218143 AAAAGAGAAAAAAAGGGAAAAAAAGAGAAAA
1 AAAAAAGAAAAAAA--GAAAAAAAGAGAAAA
* *
3218174 AAAAGAGAAAAAAAAGAGAGAAAAAAAGAAAA
1 AAAAAAG-AAAAAAAGA-A-AAAAAGAGAAAA
3218206 GAAAAAAGAAAAGAAAGAAAAGAAA-AGAAA
1 -AAAAAAGAAAA-AAAGAAAA-AAAGAGAAA
3218236 TGAAATTGAA
Statistics
Matches: 82, Mismatches: 3, Indels: 15
0.82 0.03 0.15
Matches are distributed among these distances:
29 2 0.02
30 13 0.16
31 30 0.37
32 26 0.32
33 11 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAAAGAAAAAAAGAAAAAAAGAGAAAA
Found at i:3218241 original size:5 final size:5
Alignment explanation
Indices: 3218115--3218240 Score: 77
Period size: 5 Copynumber: 24.6 Consensus size: 5
3218105 CATCCATCAA
*
3218115 AAAAG AAAA- AGAAG AAAA- AAAGAG AAAA- AAAAG AGAAA- AAAAGGG
1 AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG A-AAAG AAAA--G
* *
3218160 AAAA- AAAGAG AAAA- AAAAG AGAAAA AAAAG AGAGAAA AAAAG AAAAG
1 AAAAG AAA-AG AAAAG AAAAG A-AAAG AAAAG A-A-AAG AAAAG AAAAG
*
3218207 AAAAAAG AAAAG -AAAG AAAAG AAAAG AAATG AAA
1 --AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
3218241 TTGAATCAAG
Statistics
Matches: 97, Mismatches: 7, Indels: 34
0.70 0.05 0.25
Matches are distributed among these distances:
4 24 0.25
5 46 0.47
6 15 0.15
7 12 0.12
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:3219810 original size:28 final size:28
Alignment explanation
Indices: 3219770--3219823 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
3219760 TCCAAGTGGG
3219770 GCATCTTGAAGGCTCACA-TCAGCATGGA
1 GCATCTTGAAGGCTCACACT-AGCATGGA
3219798 GCATCTTGAAGGCTCACACTAGCATG
1 GCATCTTGAAGGCTCACACTAGCATG
3219824 AAAAGGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (28 bp):
GCATCTTGAAGGCTCACACTAGCATGGA
Found at i:3221194 original size:23 final size:22
Alignment explanation
Indices: 3221168--3221357 Score: 71
Period size: 23 Copynumber: 9.3 Consensus size: 22
3221158 TATCTCATTC
3221168 AAGATTGTTTTTCCTTGAAACA
1 AAGATTGTTTTTCCTTGAAACA
*
3221190 GAAGATT-TTATTTCATT----C-
1 -AAGATTGTT-TTTCCTTGAAACA
3221208 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAAC-A
*
3221231 AAGATT-TTATTTCATT----C-
1 AAGATTGTT-TTTCCTTGAAACA
3221248 AAGATTGTTTTTCCTTGAAACAA
1 AAGATTGTTTTTCCTTGAAAC-A
* * **
3221271 AAGA-T-TTTAT-C-TCACTC-
1 AAGATTGTTTTTCCTTGAAACA
3221288 AAGATTGTTTTTCCTTGAAACA
1 AAGATTGTTTTTCCTTGAAACA
* * * **
3221310 AA-A-AGATTTTACC-TCACTC-
1 AAGATTG-TTTTTCCTTGAAACA
3221329 AAGATTGTTTTTCCTTGAAACA
1 AAGATTGTTTTTCCTTGAAACA
3221351 GAAGATT
1 -AAGATT
3221358 TTATCTCACT
Statistics
Matches: 118, Mismatches: 22, Indels: 54
0.61 0.11 0.28
Matches are distributed among these distances:
17 28 0.24
18 5 0.04
19 11 0.09
20 13 0.11
21 20 0.17
22 7 0.06
23 34 0.29
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (22 bp):
AAGATTGTTTTTCCTTGAAACA
Found at i:3221475 original size:23 final size:23
Alignment explanation
Indices: 3221449--3221517 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
3221439 TATCTCACTC
3221449 AAGATTGTTTTTCCTTGAAATAG
1 AAGATTGTTTTTCCTTGAAATAG
* * * *
3221472 AAGA-T-TTTGT-CTCG--CT-C
1 AAGATTGTTTTTCCTTGAAATAG
3221489 AAGATTGTTTTTCCTTGAAATAG
1 AAGATTGTTTTTCCTTGAAATAG
3221512 AAGATT
1 AAGATT
3221518 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 4 0.12
20 6 0.19
21 4 0.12
22 2 0.06
23 10 0.31
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAATAG
Found at i:3221538 original size:20 final size:20
Alignment explanation
Indices: 3221515--3221579 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
3221505 GAAATAGAAG
3221515 ATTTTATCTCGCTCAAGATT
1 ATTTTATCTCGCTCAAGATT
* ** *
3221535 ATTTT-TCCTTG-AAACAGAAT
1 ATTTTAT-CTCGCTCA-AGATT
3221555 ATTTTATCTCGCTCAAGATT
1 ATTTTATCTCGCTCAAGATT
*
3221575 GTTTT
1 ATTTT
3221580 TCGCTGAAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (20 bp):
ATTTTATCTCGCTCAAGATT
Found at i:3221687 original size:40 final size:40
Alignment explanation
Indices: 3221116--3221684 Score: 888
Period size: 40 Copynumber: 14.2 Consensus size: 40
3221106 ATATGGAGGA
** *
3221116 TTTATCTCACTGGAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
3221156 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
3221196 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
3221236 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
3221276 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAAC-AGAAGAT
*
3221317 TTTACCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
3221357 TTTATCTCACTCAAGATTGTTTTTTCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
3221397 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
3221437 TTTATCTCACTCAAGATTGTTTTTCCTTGAAATAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
3221477 TTTGTCTCGCTCAAGATTGTTTTTCCTTGAAATAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
3221517 TTTATCTCGCTCAAGATTATTTTTCCTTGAAACAGAATAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
3221557 TTTATCTCGCTCAAGATTGTTTTTCGC-TGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTC-CTTGAAACAGAAGAT
*
3221597 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
3221637 TTTATCTCGCTCAAGATTGTTTTTCCTTAAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
3221677 TTTATCTC
1 TTTATCTC
3221685 GCTTGATATA
Statistics
Matches: 502, Mismatches: 24, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.00
40 461 0.92
41 40 0.08
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (40 bp):
TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
Found at i:3221724 original size:39 final size:38
Alignment explanation
Indices: 3221116--3221819 Score: 272
Period size: 40 Copynumber: 17.8 Consensus size: 38
3221106 ATATGGAGGA
* * * *
3221116 TTTATCTCACTGGAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
* * * * *
3221156 TTTATCTC-ATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTT-GAGATAG-TTTCCCTTGAAA-AAAAGAT
* * * * *
3221196 TTTATTTC-ATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCGCTT-GAGATAG-TTTCCCTTGAAA-AAAAGAT
* * * * *
3221236 TTTATTTC-ATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCGCTT-GAGATAG-TTTCCCTTGAAA-AAAAGAT
* ** * *
3221276 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTG-AA-AAAAAGAT
* * ** * * *
3221317 TTTACCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
* ** * ** *
3221357 TTTATCTCACTCAAGATTGTTTTTTCTTGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
* ** * * *
3221397 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
* ** * * *
3221437 TTTATCTCACTCAAGATTGTTTTTCCTTGAAATAGAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
* ** * * *
3221477 TTTGTCTCGCTCAAGATTGTTTTTCCTTGAAATAGAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
** * * * *
3221517 TTTATCTCGCTCAAGATTATTTTTCCTTGAAACAGAATAT
1 TTTATCTCGCTTGAGA-TAGTTTCCCTTGAAA-AAAAGAT
** * * *
3221557 TTTATCTCGCTCAAGATTGTTTTTCGC-TGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAG--TTTCCCTTGAAA-AAAAGAT
** * * *
3221597 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
** * * *
3221637 TTTATCTCGCTCAAGATTGTTTTTCCTTAAAACAAAAGAT
1 TTTATCTCGCTTGAGATAG-TTTCCCTTGAAA-AAAAGAT
* *
3221677 TTTATCTCGCTTGATATAGTTTCCCTCGAAATAAAAGAT
1 TTTATCTCGCTTGAGATAGTTTCCCTTGAAA-AAAAGAT
*
3221716 TTTATCTCGCTTGAGATAGTTTCCCTTG-AAACAA-AT
1 TTTATCTCGCTTGAGATAGTTTCCCTTGAAAAAAAGAT
* *
3221752 TTTGTCTCGCTTGAGATAGTTTCCCTTG-AAACAAG-T
1 TTTATCTCGCTTGAGATAGTTTCCCTTGAAAAAAAGAT
* * * *
3221788 TTTGTCTCCCTTGAAATAGTTTCTCTTGAAAA
1 TTTATCTCGCTTGAGATAGTTTCCCTTGAAAA
3221820 TTTTGAGAAC
Statistics
Matches: 607, Mismatches: 46, Indels: 25
0.90 0.07 0.04
Matches are distributed among these distances:
36 61 0.10
37 6 0.01
38 2 0.00
39 50 0.08
40 444 0.73
41 43 0.07
42 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (38 bp):
TTTATCTCGCTTGAGATAGTTTCCCTTGAAAAAAAGAT
Found at i:3221876 original size:36 final size:36
Alignment explanation
Indices: 3221822--3221936 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
3221812 CTTGAAAATT
*
3221822 TTGAGAACA-TTTCCCTTGAAACGAATTTTGTCTCCC
1 TTGAG-ACAGTTTCTCTTGAAACGAATTTTGTCTCCC
*
3221858 TTGAGACAGTTTCTCTTGAAACAGAGTTTTGTCTCCC
1 TTGAGACAGTTTCTCTTGAAAC-GAATTTTGTCTCCC
** ** * * * * *
3221895 TAAAGATGGTTTTTCTTAAAACCAAATTTGTCTCAC
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCCC
3221931 TTGAGA
1 TTGAGA
3221937 TGGTTTTTCT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
35 3 0.05
36 31 0.49
37 29 0.46
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (36 bp):
TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCCC
Found at i:3222007 original size:28 final size:28
Alignment explanation
Indices: 3221957--3222066 Score: 143
Period size: 28 Copynumber: 3.9 Consensus size: 28
3221947 TAAAAAACCC
3221957 TTGAGACAGTTT-TCCTTTGAAACAAGTTT
1 TTGAGACAGTTTCT-C-TTGAAACAAGTTT
*
3221986 TTGAGATAGTTTCTCTTGAAACAAGTTT
1 TTGAGACAGTTTCTCTTGAAACAAGTTT
*
3222014 TTGAGACAGTTTTTCTTGAAACAAGTTT
1 TTGAGACAGTTTCTCTTGAAACAAGTTT
*
3222042 TTGAGACAATTT-TCCTTCGAAACAA
1 TTGAGACAGTTTCT-CTT-GAAACAA
3222067 AATTTATCTC
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
27 1 0.01
28 53 0.72
29 19 0.26
30 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (28 bp):
TTGAGACAGTTTCTCTTGAAACAAGTTT
Found at i:3222042 original size:15 final size:14
Alignment explanation
Indices: 3221972--3222043 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 14
3221962 ACAGTTTTCC
3221972 TTTGAAACAAG-TT
1 TTTGAAACAAGTTT
* *
3221985 TTTGAGA-TAGTTT
1 TTTGAAACAAGTTT
3221998 CTCTTGAAACAAG-TT
1 -T-TTGAAACAAGTTT
*
3222013 TTTGAGAC-AGTTTT
1 TTTGAAACAAG-TTT
3222027 TCTTGAAACAAGTTT
1 T-TTGAAACAAGTTT
3222042 TT
1 TT
3222044 GAGACAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
12 4 0.09
13 14 0.31
14 6 0.13
15 17 0.38
16 4 0.09
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (14 bp):
TTTGAAACAAGTTT
Found at i:3222042 original size:16 final size:16
Alignment explanation
Indices: 3221993--3222043 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3221983 TTTTTGAGAT
*
3221993 AGTTTCTCTTGAAACA
1 AGTTTTTCTTGAAACA
*
3222009 AG--TTT-TTGAGAC-
1 AGTTTTTCTTGAAACA
3222021 AGTTTTTCTTGAAACA
1 AGTTTTTCTTGAAACA
3222037 AGTTTTT
1 AGTTTTT
3222044 GAGACAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
12 2 0.07
13 6 0.21
14 5 0.18
15 6 0.21
16 9 0.32
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (16 bp):
AGTTTTTCTTGAAACA
Found at i:3222064 original size:57 final size:57
Alignment explanation
Indices: 3221957--3222066 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
3221947 TAAAAAACCC
*
3221957 TTGAGACAGTTTTCCTTTGAAACAAGTTTTTGAGATAGTTTCTCTTGAAACAAGTTT
1 TTGAGACAGTTTTCCTTTGAAACAAGTTTTTGAGAAAGTTTCTCTTGAAACAAGTTT
* *
3222014 TTGAGACAGTTTTTC-TTGAAACAAGTTTTTGAGACAATTTTC-CTTCGAAACAA
1 TTGAGACAGTTTTCCTTTGAAACAAGTTTTTGAGA-AAGTTTCTCTT-GAAACAA
3222067 AATTTATCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
56 22 0.46
57 26 0.54
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (57 bp):
TTGAGACAGTTTTCCTTTGAAACAAGTTTTTGAGAAAGTTTCTCTTGAAACAAGTTT
Found at i:3222176 original size:24 final size:24
Alignment explanation
Indices: 3222140--3222185 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3222130 TTTATCTCAA
* * *
3222140 TTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACGATTTTCCTTAAAACCC
*
3222164 TTGAGACGATTTTCCTTGAAAC
1 TTGAGACGATTTTCCTTAAAAC
3222186 AAAATTTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (24 bp):
TTGAGACGATTTTCCTTAAAACCC
Found at i:3222277 original size:120 final size:122
Alignment explanation
Indices: 3222042--3222281 Score: 378
Period size: 120 Copynumber: 2.0 Consensus size: 122
3222032 AAACAAGTTT
3222042 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGA
* * * *
3222107 GACAGTTTTCCTTTGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
66 GACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGCTTCTCTTAAAACCC
* *
3222164 TTGAGACGATTTTCCTT-GAAACAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CCTTGA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGA
* *
3222227 GACAATTTTCCTTCGAAGCAAAATTTATCTCACTTGAGA-GAGCTTCTCTTAAAAC
66 GACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATG-GCTTCTCTTAAAAC
3222282 AAGTTTCTTA
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
119 1 0.01
120 53 0.49
121 39 0.36
122 16 0.15
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (122 bp):
TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGA
GACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGCTTCTCTTAAAACCC
Found at i:3222281 original size:60 final size:61
Alignment explanation
Indices: 3222042--3222265 Score: 380
Period size: 61 Copynumber: 3.7 Consensus size: 61
3222032 AAACAAGTTT
3222042 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
* * *
3222103 TTGAGACAGTTTTCCTTTGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
* *
3222164 TTGAGACGATTTTCCTT-GAAACAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
*
3222223 TTGAGACAATTTTCCTTCGAAGCAAAATTTATCTCACTTGAGA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGA
3222266 GAGCTTCTCT
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
59 18 0.12
60 62 0.41
61 73 0.48
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (61 bp):
TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCC
Found at i:3222602 original size:20 final size:20
Alignment explanation
Indices: 3222538--3222602 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
3222528 TTCCAGTATA
*
3222538 TAGTTTATAATGAGAAGAAC
1 TAGTTCATAATGAGAAGAAC
* * *
3222558 TCG-TC-TAACGAGGAAGAAG
1 TAGTTCATAATGA-GAAGAAC
*
3222577 AAGTTCATAATGAGAAGAAC
1 TAGTTCATAATGAGAAGAAC
*
3222597 TTGTTC
1 TAGTTC
3222603 GACCTCGCAT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 14 0.44
21 5 0.16
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (20 bp):
TAGTTCATAATGAGAAGAAC
Found at i:3222875 original size:136 final size:136
Alignment explanation
Indices: 3222618--3223097 Score: 799
Period size: 136 Copynumber: 3.6 Consensus size: 136
3222608 CGCATTAGTG
*
3222618 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
**
3222683 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACATCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
3222748 TTAACA
131 TTAACA
*
3222754 TTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
3222819 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
3222884 TTAACA
131 TTAACA
3222890 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* * * *
3222955 AAGAGCTTGTTTGACTTATCACTCGATTCACGATATTTTGAATCAGTGACGCCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
*
3223020 TTGACA
131 TTAACA
* * * *
3223026 TTTCTAATTAAGAGTTCATAATGAGAAGAACTCGTCCTA-A-AGGG-G-A-AAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
*
3223086 AAGAACTTGTTC
66 AAGAGCTTGTTC
3223098 CTTTCAAGTC
Statistics
Matches: 328, Mismatches: 16, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
131 24 0.07
132 1 0.00
133 1 0.00
134 4 0.01
135 1 0.00
136 297 0.91
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (136 bp):
TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGA
TTAACA
Found at i:3223272 original size:117 final size:111
Alignment explanation
Indices: 3223035--3223327 Score: 371
Period size: 117 Copynumber: 2.6 Consensus size: 111
3223025 ATTTCTAATT
* *
3223035 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAGG--GGAAAGTTCATAATGAGAAGAACTTGTT-
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGGAAGAAAAGTTCATAATGAGAAGAACTTGTTC
3223097 --CCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
65 AACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
* *
3223142 GAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA--AGGAAGAA-AAGTTCATAATGAGAAGAACTTGT
* * * *
3223207 TCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTG
63 TCAACC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
* *
3223259 AAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAAAAGTTCATAATTAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGGA-AG-AAAAGTTCATAATGAGAAGAACTTGT
3223324 TCAA
63 TCAA
3223328 TCCAAAGCTT
Statistics
Matches: 160, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
106 2 0.01
107 25 0.16
108 3 0.02
110 2 0.01
111 25 0.16
114 2 0.01
115 1 0.01
116 3 0.02
117 95 0.59
118 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (111 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGGAAGAAAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
Found at i:3243917 original size:146 final size:150
Alignment explanation
Indices: 3243752--3244051 Score: 527
Period size: 152 Copynumber: 2.0 Consensus size: 150
3243742 AAAATTATAA
3243752 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTAAAGG-AAACA-T-ATAATA
1 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTAAAGGAAAACATTAATAATA
*
3243814 TTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAACACAC-TAT
66 TTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACACATAT
3243878 CTTATAAATTTTGAAGCACG
131 CTTATAAATTTTGAAGCACG
3243898 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTAAAGGAAAACATTGTCAATA
1 AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTAAAGGAAAACA-T-T-AATA
3243963 ATATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACACA
63 ATATTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACACA
*
3244028 TATCTTTTAAATTTTGAAGCACG
128 TATCTTATAAATTTTGAAGCACG
3244051 A
1 A
3244052 TTTTGAAATC
Statistics
Matches: 145, Mismatches: 2, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
146 50 0.34
147 5 0.03
150 1 0.01
152 66 0.46
153 23 0.16
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (150 bp):
AAAAATCAAATTAAAATTTGCTCATAGTTGTTTATATCATTTTTTAAAGGAAAACATTAATAATA
TTTTATTTATTGTTTTGGCTCAAAATTTAAACTTGAAATAATTTTAAAAACTCAAAAACACATAT
CTTATAAATTTTGAAGCACG
Found at i:3245965 original size:18 final size:18
Alignment explanation
Indices: 3245934--3245972 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3245924 TTGACCAACA
* *
3245934 CGACCCGTTGACCCGACC
1 CGACCAGTTAACCCGACC
3245952 CGACCAGTTAACCCGACC
1 CGACCAGTTAACCCGACC
3245970 CGA
1 CGA
3245973 TAATTTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.46, G:0.21, T:0.10
Consensus pattern (18 bp):
CGACCAGTTAACCCGACC
Found at i:3246013 original size:29 final size:29
Alignment explanation
Indices: 3245971--3246103 Score: 159
Period size: 29 Copynumber: 4.7 Consensus size: 29
3245961 AACCCGACCC
*
3245971 GATAATTTGGTAATTATTTTTAAAACGGT
1 GATATTTTGGTAATTATTTTTAAAACGGT
* *
3246000 GATATTTTGGTAATTATTGTTAAAACGAT
1 GATATTTTGGTAATTATTTTTAAAACGGT
* *
3246029 GAT-TTTTAGTAATTATTTTTAAAA-TGT
1 GATATTTTGGTAATTATTTTTAAAACGGT
*
3246056 GATA-TTTGAG-AATTA-TTTTAAAAAGGT
1 GATATTTTG-GTAATTATTTTTAAAACGGT
*
3246083 GATATTTTGGTAAATATTTTT
1 GATATTTTGGTAATTATTTTT
3246104 TTAAAAAATG
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.09
27 19 0.22
28 28 0.32
29 33 0.38
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.48
Consensus pattern (29 bp):
GATATTTTGGTAATTATTTTTAAAACGGT
Found at i:3246058 original size:27 final size:28
Alignment explanation
Indices: 3245971--3246103 Score: 144
Period size: 28 Copynumber: 4.8 Consensus size: 28
3245961 AACCCGACCC
* *
3245971 GATAATTTGGTAATTATTTTTAAAACGGT
1 GATATTTTAGTAATTATTTTTAAAA-GGT
* * *
3246000 GATATTTTGGTAATTATTGTTAAAACGAT
1 GATATTTTAGTAATTATTTTTAAAA-GGT
*
3246029 GAT-TTTTAGTAATTATTTTTAAAATGT
1 GATATTTTAGTAATTATTTTTAAAAGGT
* *
3246056 GATATTTGAG-AATTATTTTAAAAAGGT
1 GATATTTTAGTAATTATTTTTAAAAGGT
* *
3246083 GATATTTTGGTAAATATTTTT
1 GATATTTTAGTAATTATTTTT
3246104 TTAAAAAATG
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
27 27 0.31
28 32 0.36
29 29 0.33
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.48
Consensus pattern (28 bp):
GATATTTTAGTAATTATTTTTAAAAGGT
Found at i:3252727 original size:41 final size:41
Alignment explanation
Indices: 3252682--3252766 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
3252672 CTATTTTAGA
3252682 AGTAAAGGAAATTCAGGAACCAAGCCCTAATTTACCCAAGG
1 AGTAAAGGAAATTCAGGAACCAAGCCCTAATTTACCCAAGG
3252723 AGTAAAGGAAATTCAGGAACCAAGCCCTAATTTACCCAAGG
1 AGTAAAGGAAATTCAGGAACCAAGCCCTAATTTACCCAAGG
3252764 AGT
1 AGT
3252767 GTAAATTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (41 bp):
AGTAAAGGAAATTCAGGAACCAAGCCCTAATTTACCCAAGG
Found at i:3253326 original size:29 final size:29
Alignment explanation
Indices: 3253282--3253449 Score: 222
Period size: 29 Copynumber: 6.0 Consensus size: 29
3253272 GACCCGACCC
*
3253282 GGTGATATTTTGGTAATTATTGTTAAAAT
1 GGTGATATTTTAGTAATTATTGTTAAAAT
3253311 GGTGATATTTTAGTAATTATTGTTAAAAT
1 GGTGATATTTTAGTAATTATTGTTAAAAT
3253340 GGTGATATTTTAGTAATTATTGTTAAAAT
1 GGTGATATTTTAGTAATTATTGTTAAAAT
3253369 GGTGATATTTTAGTAATTATT-TTAAAA-
1 GGTGATATTTTAGTAATTATTGTTAAAAT
* * *
3253396 CGTGATA--TT-GGAATTATT-TATAAAAA
1 GGTGATATTTTAGTAATTATTGT-TAAAAT
* * *
3253422 GGTGATATTTTGGTAAATATTTTTAAAA
1 GGTGATATTTTAGTAATTATTGTTAAAA
3253450 ATAGTGCTAT
Statistics
Matches: 127, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.07
25 7 0.06
26 6 0.05
27 6 0.05
28 8 0.06
29 90 0.71
30 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTATTGTTAAAAT
Found at i:3253414 original size:24 final size:26
Alignment explanation
Indices: 3253383--3253430 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3253373 ATATTTTAGT
3253383 AATTATTT-T-AAAACGTGATATTGG
1 AATTATTTATAAAAACGTGATATTGG
*
3253407 AATTATTTATAAAAAGGTGATATT
1 AATTATTTATAAAAACGTGATATT
3253431 TTGGTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.42
Consensus pattern (26 bp):
AATTATTTATAAAAACGTGATATTGG
Found at i:3255162 original size:144 final size:144
Alignment explanation
Indices: 3254927--3255215 Score: 578
Period size: 144 Copynumber: 2.0 Consensus size: 144
3254917 AATTAACTTG
3254927 TTATTTTTCTCATATTTATGAGTTGGGTTTTTTTTTATAATATAATTTATTATAATTTCATAAAT
1 TTATTTTTCTCATATTTATGAGTTGGGTTTTTTTTTATAATATAATTTATTATAATTTCATAAAT
3254992 GACATTTACAAATATGATTTTACGTTAATAGAATAACGGTTTCGGAAAAATGTCTTTAAGAATCA
66 GACATTTACAAATATGATTTTACGTTAATAGAATAACGGTTTCGGAAAAATGTCTTTAAGAATCA
3255057 TGAATGTGATCCAC
131 TGAATGTGATCCAC
3255071 TTATTTTTCTCATATTTATGAGTTGGGTTTTTTTTTATAATATAATTTATTATAATTTCATAAAT
1 TTATTTTTCTCATATTTATGAGTTGGGTTTTTTTTTATAATATAATTTATTATAATTTCATAAAT
3255136 GACATTTACAAATATGATTTTACGTTAATAGAATAACGGTTTCGGAAAAATGTCTTTAAGAATCA
66 GACATTTACAAATATGATTTTACGTTAATAGAATAACGGTTTCGGAAAAATGTCTTTAAGAATCA
3255201 TGAATGTGATCCAC
131 TGAATGTGATCCAC
3255215 T
1 T
3255216 AGACTTAGTC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (144 bp):
TTATTTTTCTCATATTTATGAGTTGGGTTTTTTTTTATAATATAATTTATTATAATTTCATAAAT
GACATTTACAAATATGATTTTACGTTAATAGAATAACGGTTTCGGAAAAATGTCTTTAAGAATCA
TGAATGTGATCCAC
Found at i:3271995 original size:19 final size:19
Alignment explanation
Indices: 3271973--3272022 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3271963 GTTGTTTTCG
3271973 AAATAAAAAAATAAGAATT
1 AAATAAAAAAATAAGAATT
*
3271992 AAATAAAAGAAA-AATAATT
1 AAATAAAA-AAATAAGAATT
*
3272011 AAATAAACAAAT
1 AAATAAAAAAAT
3272023 TAAAGAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Found at i:3272685 original size:64 final size:64
Alignment explanation
Indices: 3272608--3272778 Score: 308
Period size: 64 Copynumber: 2.7 Consensus size: 64
3272598 TAAAACATCT
* *
3272608 TAAATCCTAATTAAAACATTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATAATATTA
1 TAAATCCTAATTAAAATA-CTAAAACCTATTTAAACTAAAATACCTAAAAAATAATATAATATTA
3272672 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAATATAATATTA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAATATAATATTA
3272736 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
3272779 AAAGATAAAA
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
63 5 0.05
64 99 0.95
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (64 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAATATAATATTA
Found at i:3272699 original size:19 final size:19
Alignment explanation
Indices: 3272672--3272769 Score: 54
Period size: 19 Copynumber: 4.8 Consensus size: 19
3272662 TATAATATTA
*
3272672 TAAATCCTAATTAAAATAC
1 TAAAACCTAATTAAAATAC
*
3272691 TAAAACCTATTTAAACTAAAATACC
1 TAAAACC----T-AATTAAAATA-C
** *
3272716 TAAAAAATAATATAATATTA-
1 TAAAACCTAAT-TAA-AATAC
*
3272736 TAAATCCTAATTAAAATAC
1 TAAAACCTAATTAAAATAC
*
3272755 TAAAACCTATTTAAA
1 TAAAACCTAATTAAA
3272770 CTAAAATACA
Statistics
Matches: 58, Mismatches: 12, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
18 3 0.05
19 22 0.38
20 10 0.17
21 4 0.07
22 3 0.05
23 1 0.02
24 9 0.16
25 6 0.10
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAACCTAATTAAAATAC
Found at i:3274441 original size:5 final size:5
Alignment explanation
Indices: 3274431--3274483 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
3274421 TGTTCAGAGA
**
3274431 AAAAT AAAAT AAAAT AAAAT -AAAT GGAAT AAAAT -AAAT AAAAT GAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
3274480 AAAA
1 AAAA
3274484 CGAAATAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 8 0.19
5 29 0.69
6 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:3274460 original size:14 final size:14
Alignment explanation
Indices: 3274431--3274482 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
3274421 TGTTCAGAGA
3274431 AAAATAAAATAAAAT
1 AAAAT-AAATAAAAT
**
3274446 AAAATAAATGGAAT
1 AAAATAAATAAAAT
3274460 AAAATAAATAAAAT
1 AAAATAAATAAAAT
3274474 GAAAATAAA
1 -AAAATAAA
3274483 ACGAAATAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:3280790 original size:80 final size:81
Alignment explanation
Indices: 3280612--3280884 Score: 342
Period size: 81 Copynumber: 3.4 Consensus size: 81
3280602 TCCTTAATAC
* * * * *
3280612 CATCTTTGACCTCTTTTGAATACTC-GACTTTCTTTTCTTTGGAGTTTTTTGAAGTCTCTTTTTC
1 CATCTTGGACCTCTTTTGAATGCTCTG-CTTTCTCTCCTTTGGAATTTTTTGAAGTCTCTTTTTC
3280676 ATCCTCCTTCTCATTAG
65 ATCCTCCTTCTCATTAG
* *
3280693 CATCTTGGCCCTCTTTTGAATGCTCTGCTTTCTCTCCTTTGGAATTTTTTGAAGTATCTTTTT-A
1 CATCTTGGACCTCTTTTGAATGCTCTGCTTTCTCTCCTTTGGAATTTTTTGAAGTCTCTTTTTCA
*
3280757 TCCTCCTTCTCGTTAG
66 TCCTCCTTCTCATTAG
* * * *
3280773 CATCTTGGACCTCTTTTGAATGCTCT-ATTTTTC-CCTTTGG-A-GTTTGGAAGTCTCTTTTTCA
1 CATCTTGGACCTCTTTTGAATGCTCTGCTTTCTCTCCTTTGGAATTTTTTGAAGTCTCTTTTTCA
* *
3280834 TCTTCCTTCTTATTAG
66 TCCTCCTTCTCATTAG
* * *
3280850 CATCTTGGACCTCTTTTAAACGCTATGCTTTCTCT
1 CATCTTGGACCTCTTTTGAATGCTCTGCTTTCTCT
3280885 TTTTGTTTAA
Statistics
Matches: 166, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
76 15 0.09
77 38 0.23
78 12 0.07
79 5 0.03
80 41 0.25
81 54 0.33
82 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.13, T:0.49
Consensus pattern (81 bp):
CATCTTGGACCTCTTTTGAATGCTCTGCTTTCTCTCCTTTGGAATTTTTTGAAGTCTCTTTTTCA
TCCTCCTTCTCATTAG
Found at i:3297323 original size:29 final size:29
Alignment explanation
Indices: 3297255--3297369 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 29
3297245 AAATAGAATG
* *
3297255 GGGATATAATCCTATGTAGAATCAGGACA
1 GGGATATAATCCCATGCAGAATCAGGACA
* * **
3297284 GTGATATAATCCCATGTAGAATCAGGAGG
1 GGGATATAATCCCATGCAGAATCAGGACA
* *
3297313 GGGA-ATAAATCTCATGCATAATCAGGACA
1 GGGATAT-AATCCCATGCAGAATCAGGACA
* * * *
3297342 GAGAAAAAATCTCATGCAGAATCAGGAC
1 GGGATATAATCCCATGCAGAATCAGGAC
3297370 GAGACTAAGC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
28 2 0.03
29 68 0.96
30 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (29 bp):
GGGATATAATCCCATGCAGAATCAGGACA
Found at i:3299038 original size:54 final size:54
Alignment explanation
Indices: 3298878--3299522 Score: 932
Period size: 54 Copynumber: 11.9 Consensus size: 54
3298868 TGAATATTAC
* * * * *
3298878 AACTCATTATAAATTCCATGGTTTTGCACACATAGCGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGG-GTTGCACACATAGTGTCGATACGGTAATTCACA
*
3298933 AACTCATTATGAATTACGTGGTTTTGCACACATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGG-GTTGCACACATAGTGTCGATACGGTAATTCACA
* *
3298988 AACTCATTATGAATTACGTGGGTTGCAAATATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
3299042 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * *
3299096 AACTCATTATGAATTATGTGGGTTGTACACATAATGTCGATACGATAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * *
3299150 AACTCATTATGAATTACGTGGGTTGAATACATAGT-ACTAATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTC-GATACGGTAATTCACA
*
3299204 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
**
3299258 AACTCATTATGAATTACGTGGGTTGCACACATAGTACCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* ** *
3299312 AACTCATTATGAATTACGTGGGTTGCACACATATTCCCGATACGATAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * **
3299366 AACTCATTATGAATTACGTAGGTTGCACACATAGTGCCGATACGATAATTTGCA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * * *
3299420 AACTCAATATGAATTATGTGGGTTGCACACATAGTGACAATACAGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * *
3299474 AACTCATTATGAATTACATGGGTTGCATACATAGTATCGATACGGTAAT
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAAT
3299523 GCAACATATG
Statistics
Matches: 538, Mismatches: 50, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 464 0.86
55 73 0.14
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
Found at i:3303555 original size:15 final size:15
Alignment explanation
Indices: 3303535--3303573 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3303525 TTAACTCAGT
3303535 TGGAGCCATTTGATA
1 TGGAGCCATTTGATA
3303550 TGGAGCCATTTGATA
1 TGGAGCCATTTGATA
3303565 TGGAGCCAT
1 TGGAGCCAT
3303574 AGAAACAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (15 bp):
TGGAGCCATTTGATA
Found at i:3306201 original size:54 final size:54
Alignment explanation
Indices: 3306064--3306627 Score: 803
Period size: 54 Copynumber: 10.5 Consensus size: 54
3306054 TTCCATGGTT
** * * *
3306064 TTGCACACATAGTGCATAAACGGTAATTCACAAACTCGTTATAAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
3306118 TTTGCACACATAGTGTCGATACGGTAATTCACAAACTTATTATGAATTACGTGGG
1 -TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
*
3306173 TTGCACACATAGTGCCGATACTGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
3306227 TTGTACAC--AGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
3306279 TT-CACACATAGTGCCGATATGGTAATTCAAAAACTTATTATGAATTACGTGGA
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
3306332 TTGCACAAATAGTGTCGATACGATAATTGACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
** * *
3306386 TTGCACACATAGTATCGATACGGTAATTCACAAACTTATTATGAATTACATGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
*
3306440 TT-CACACATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
3306493 TTACACACATAGTGCCGATACAGTAATTCACAAACTCGTTATAAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * *
3306547 TTGCACACAAAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGAG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
3306601 TTGCACAGATAGTGCAGATACGGTAAT
1 TTGCACACATAGTGCCGATACGGTAAT
3306628 GCAACATATG
Statistics
Matches: 452, Mismatches: 53, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
51 4 0.01
52 44 0.10
53 89 0.20
54 268 0.59
55 47 0.10
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (54 bp):
TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
Found at i:3306411 original size:161 final size:161
Alignment explanation
Indices: 3306083--3306627 Score: 821
Period size: 161 Copynumber: 3.4 Consensus size: 161
3306073 TAGTGCATAA
* * *
3306083 ACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTTGCACACATAGTGTCGATACGGTAATTC
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGG-TTGCACACATAGTGCCGATACGGTAATTC
3306148 ACAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATACTG-TAATTCACAAACTCAT
65 ACAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATAC-GATAATTCACAAACTCAT
*
3306212 TATGAATTACGTGGGTTGTACAC-AGTGTCGAT
129 TATGAATTACGTGGGTTGCACACAAGTGTCGAT
*
3306244 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTT-CACACATAGTGCCGATATGGTAATTCA
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCA
* * * * *
3306308 AAAACTTATTATGAATTACGTGGATTGCACAAATAGTGTCGATACGATAATTGACAAACTCATTA
66 CAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGATAATTCACAAACTCATTA
*
3306373 TGAATTACGTGGGTTGCACACATAGTATCGAT
131 TGAATTACGTGGGTTGCACACA-AGTGTCGAT
* * *
3306405 ACGGTAATTCACAAACTTATTATGAATTACATGGGTT-CACACATAGTGCTGATACGGTAATTCA
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCA
* * *
3306469 CAAACTCATTATGAATTACGTGGGTTACACACATAGTGCCGATAC-AGTAATTCACAAACTCGTT
66 CAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGA-TAATTCACAAACTCATT
*
3306533 ATAAATTACGTGGGTTGCACACAAAGTGTCGAT
130 ATGAATTACGTGGGTTGCACAC-AAGTGTCGAT
* * *
3306566 ACGGTAATTCACAAACTCATTATGAATTACGTGAGTTGCACAGATAGTGCAGATACGGTAAT
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAAT
3306628 GCAACATATG
Statistics
Matches: 348, Mismatches: 30, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
158 1 0.00
159 103 0.30
160 3 0.01
161 218 0.63
162 23 0.07
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (161 bp):
ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCA
CAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGATAATTCACAAACTCATTA
TGAATTACGTGGGTTGCACACAAGTGTCGAT
Found at i:3306451 original size:107 final size:108
Alignment explanation
Indices: 3306064--3306627 Score: 832
Period size: 107 Copynumber: 5.2 Consensus size: 108
3306054 TTCCATGGTT
** * * *
3306064 TTGCACACATAGTGCATAAACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTTGCACACAT
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG-TTGCACACAT
*
3306129 AGTGTCGATACGGTAATTCACAAACTTATTATGAATTACGTGGG
65 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
3306173 TTGCACACATAGTGCCGATACTGTAATTCACAAACTCATTATGAATTACGTGGGTTGTACAC--A
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATA
3306236 GTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
66 GTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * * *
3306279 TT-CACACATAGTGCCGATATGGTAATTCAAAAACTTATTATGAATTACGTGGATTGCACAAATA
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATA
* *
3306343 GTGTCGATACGATAATTGACAAACTCATTATGAATTACGTGGG
66 GTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
** * *
3306386 TTGCACACATAGTATCGATACGGTAATTCACAAACTTATTATGAATTACATGGGTT-CACACATA
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATA
3306450 GTG-CTGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
66 GTGTC-GATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * * *
3306493 TTACACACATAGTGCCGATACAGTAATTCACAAACTCGTTATAAATTACGTGGGTTGCACACAAA
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATA
*
3306558 GTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGAG
66 GTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
3306601 TTGCACAGATAGTGCAGATACGGTAAT
1 TTGCACACATAGTGCCGATACGGTAAT
3306628 GCAACATATG
Statistics
Matches: 409, Mismatches: 40, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
105 52 0.13
106 46 0.11
107 138 0.34
108 124 0.30
109 49 0.12
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (108 bp):
TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATA
GTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
Found at i:3307067 original size:20 final size:21
Alignment explanation
Indices: 3307044--3307093 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3307034 CTTCCTCTTG
*
3307044 GTATCGATAC-CCCCACATCA
1 GTATCGATACTACCCACATCA
**
3307064 GTATCGATACTACTTACATCA
1 GTATCGATACTACCCACATCA
3307085 GTATCGATA
1 GTATCGATA
3307094 TTGTTCCTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
GTATCGATACTACCCACATCA
Found at i:3312828 original size:2 final size:2
Alignment explanation
Indices: 3312823--3312853 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3312813 AAAAATCAAT
3312823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3312854 TATTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3314255 original size:23 final size:23
Alignment explanation
Indices: 3314203--3314263 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
3314193 TTGAAACTTT
* **
3314203 ATAAATAATAATATTTTTTTACA
1 ATAAATAATAATAATTTAATACA
3314226 ATAAATAATAATAATTTAATATCA
1 ATAAATAATAATAATTTAATA-CA
3314250 AT-AATAAT-ATAATT
1 ATAAATAATAATAATT
3314264 CTGTAGACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.18
23 24 0.71
24 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAATAATAATAATTTAATACA
Found at i:3314815 original size:48 final size:48
Alignment explanation
Indices: 3314760--3314863 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
3314750 TTGTAACAAA
3314760 AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
1 AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
*
3314808 AAGTAAATATAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
1 AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
3314856 AAGTAAAT
1 AAGTAAAT
3314864 GCAAACAGTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (48 bp):
AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
Found at i:3317955 original size:20 final size:20
Alignment explanation
Indices: 3317928--3317984 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3317918 ATGGATATTT
3317928 AATC-TTCGGTATGGAGACC
1 AATCTTTCGGTATGGAGACC
3317947 AATCTTTCGGTATGGAGACC
1 AATCTTTCGGTATGGAGACC
*
3317967 AATCTTTCGGTATAGAGA
1 AATCTTTCGGTATGGAGA
3317985 TCAACTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
AATCTTTCGGTATGGAGACC
Found at i:3323376 original size:14 final size:15
Alignment explanation
Indices: 3323357--3323390 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3323347 GTAAAAAAAA
*
3323357 ATAAACAGACGAA-T
1 ATAAACAAACGAATT
3323371 ATAAACAAACGAATT
1 ATAAACAAACGAATT
3323386 ATAAA
1 ATAAA
3323391 ACGTTCACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (15 bp):
ATAAACAAACGAATT
Found at i:3331084 original size:12 final size:12
Alignment explanation
Indices: 3331069--3331113 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
3331059 CGGTTTTTTT
*
3331069 ACCGGATAAAAA
1 ACCGGTTAAAAA
3331081 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
3331096 ACCGGTTAAAAA
1 ACCGGTTAAAAA
3331108 ACCGGT
1 ACCGGT
3331114 CTGGGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 16 0.55
13 1 0.03
14 2 0.07
15 10 0.34
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:3333415 original size:21 final size:21
Alignment explanation
Indices: 3333391--3333430 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3333381 TTTATTTTAT
3333391 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
3333412 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
3333431 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:3333478 original size:33 final size:33
Alignment explanation
Indices: 3333425--3333523 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3333415 TTTGTTTCAA
3333425 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3333457 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
3333490 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3333523 T
1 T
3333524 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3333552 original size:13 final size:13
Alignment explanation
Indices: 3333509--3333563 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3333499 TTGGAAGTAT
3333509 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
3333522 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
3333536 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
3333549 TTAAGTATTTAAA
1 TTAAGTATTTCAA
3333562 TT
1 TT
3333564 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:3333996 original size:17 final size:18
Alignment explanation
Indices: 3333976--3334009 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3333966 GTTTTTTTAT
3333976 AACCG-GTTTTTTAAAAA
1 AACCGAGTTTTTTAAAAA
*
3333993 AACCGATTTTTTTAAAA
1 AACCGAGTTTTTTAAAA
3334010 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGAGTTTTTTAAAAA
Found at i:3334009 original size:15 final size:15
Alignment explanation
Indices: 3333957--3334013 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3333947 ATCTGGAATA
* *
3333957 TTAAAATCGGTTTTT
1 TTAAAACCGATTTTT
* *
3333972 TTATAACCGGTTTTT
1 TTAAAACCGATTTTT
*
3333987 TAAAAAAACCGATTTTT
1 T--TAAAACCGATTTTT
3334004 TTAAAACCGA
1 TTAAAACCGA
3334014 AACCGGTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 22 0.65
17 12 0.35
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:3334129 original size:15 final size:17
Alignment explanation
Indices: 3334103--3334134 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3334093 TTCTATGAGA
3334103 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
3334119 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
3334135 CGGTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:3341664 original size:17 final size:17
Alignment explanation
Indices: 3341637--3341675 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3341627 AATTTACAAT
3341637 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
3341653 TAATTATAAATAATATC
1 TAATTATAAATAATATC
3341670 TAATTA
1 TAATTA
3341676 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:3343309 original size:17 final size:17
Alignment explanation
Indices: 3343282--3343320 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3343272 AATTTACAAT
3343282 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
3343298 TAATTATAAATAATATC
1 TAATTATAAATAATATC
3343315 TAATTA
1 TAATTA
3343321 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:3347391 original size:15 final size:15
Alignment explanation
Indices: 3347371--3347412 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3347361 TTACCGTCAC
3347371 CCAAAATCCCTAAAT
1 CCAAAATCCCTAAAT
* *
3347386 CCAAAACCCCAAAAT
1 CCAAAATCCCTAAAT
3347401 CC-AAATCCCTAA
1 CCAAAATCCCTAA
3347413 TTCTCAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (15 bp):
CCAAAATCCCTAAAT
Found at i:3356894 original size:31 final size:31
Alignment explanation
Indices: 3356858--3356939 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
3356848 ATGAAAAATA
3356858 AGTTGGCCACCTACCAAAGATTTTTCCAATG
1 AGTTGGCCACCTACCAAAGATTTTTCCAATG
3356889 AGTTGGCCACCTACCAAAGATTTTTCCAATG
1 AGTTGGCCACCTACCAAAGATTTTTCCAATG
*
3356920 AGTTGGCCACC-AACAAAGAT
1 AGTTGGCCACCTACCAAAGAT
3356940 GAAATTTCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 8 0.16
31 42 0.84
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (31 bp):
AGTTGGCCACCTACCAAAGATTTTTCCAATG
Found at i:3363460 original size:22 final size:22
Alignment explanation
Indices: 3363435--3363485 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3363425 TTTTTCTTGT
3363435 CTGCCTCTATGAAGCCTTCTAG
1 CTGCCTCTATGAAGCCTTCTAG
3363457 CTGCCTCTATGAAGCCTTCTAG
1 CTGCCTCTATGAAGCCTTCTAG
*
3363479 CCGCCTC
1 CTGCCTC
3363486 ATATAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.37, G:0.18, T:0.29
Consensus pattern (22 bp):
CTGCCTCTATGAAGCCTTCTAG
Found at i:3365501 original size:15 final size:15
Alignment explanation
Indices: 3365481--3365513 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3365471 AAAATCTTTC
*
3365481 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
3365496 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
3365511 TTT
1 TTT
3365514 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.15, T:0.55
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:3366269 original size:18 final size:18
Alignment explanation
Indices: 3366246--3366286 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3366236 CTCCGTCGAC
* *
3366246 AAATTTGTATTGTTGACA
1 AAATTTGTATTATTCACA
*
3366264 AAATTTTTATTATTCACA
1 AAATTTGTATTATTCACA
3366282 AAATT
1 AAATT
3366287 CACTATTCGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (18 bp):
AAATTTGTATTATTCACA
Found at i:3366345 original size:13 final size:13
Alignment explanation
Indices: 3366329--3366353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3366319 CTCGCAGAAA
3366329 AACCACCAAAATT
1 AACCACCAAAATT
3366342 AACCACCAAAAT
1 AACCACCAAAAT
3366354 CTCTTATACC
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:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (13 bp):
AACCACCAAAATT
Found at i:3372106 original size:64 final size:63
Alignment explanation
Indices: 3372021--3372181 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
3372011 TTGTTTAAGG
* * * *
3372021 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
3372085 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATTGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
3372149 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
3372182 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:3377030 original size:59 final size:60
Alignment explanation
Indices: 3376967--3377080 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
3376957 TTTCTATACC
* * *
3376967 TGTATTCAATCATTCACTC-CCTCATTATCTTGAAATATA-AAAAAAAACAAATCAATCCA
1 TGTATTCAATCAATCACTCATC-CAGTATCTTGAAATATATAAAAAAAACAAATCAATCCA
* * *
3377026 TGTATTTAATCAATCACTCATCCAGTATCTTTAAATATATATAAAAAACAAATCA
1 TGTATTCAATCAATCACTCATCCAGTATCTTGAAATATATAAAAAAAACAAATCA
3377081 TAACTTTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 32 0.68
60 15 0.32
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (60 bp):
TGTATTCAATCAATCACTCATCCAGTATCTTGAAATATATAAAAAAAACAAATCAATCCA
Found at i:3386486 original size:22 final size:21
Alignment explanation
Indices: 3386453--3386497 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3386443 ACTGATTACA
3386453 AACTAACTAACTACAAGCTGAT
1 AACTAACTAACTACAAGCT-AT
*
3386475 AACTAA-TCAACTATAAGCTAT
1 AACTAACT-AACTACAAGCTAT
3386496 AA
1 AA
3386498 AGATTACAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (21 bp):
AACTAACTAACTACAAGCTAT
Found at i:3393950 original size:19 final size:19
Alignment explanation
Indices: 3393899--3393950 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3393889 AACACCCAAA
3393899 TTTG-AATATAATCCATTTT
1 TTTGAAATATAAT-CATTTT
* *
3393918 TTCTTAAA-ACAATCATTTT
1 TT-TGAAATATAATCATTTT
3393937 TTTGAAATATAATC
1 TTTGAAATATAATC
3393951 CATCACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 5 0.19
21 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTGAAATATAATCATTTT
Found at i:3421919 original size:16 final size:16
Alignment explanation
Indices: 3421884--3421922 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3421874 TTTTGTTTTG
*
3421884 TTTTTTTATTTTTATT
1 TTTTTTTATTTTTATC
3421900 TTTTTTTATTTTT-TCC
1 TTTTTTTATTTTTAT-C
3421916 TTTTTTT
1 TTTTTTT
3421923 GAACTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTATTTTTATC
Found at i:3421919 original size:24 final size:24
Alignment explanation
Indices: 3421869--3421920 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3421859 AATCAAACTG
* * *
3421869 TTTTGTTTTGTTTTGTTTTTTTAT
1 TTTTATTTTGTTTTATTTTTTCAT
* *
3421893 TTTTATTTTTTTTTATTTTTTCCT
1 TTTTATTTTGTTTTATTTTTTCAT
3421917 TTTT
1 TTTT
3421921 TTGAACTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.04, G:0.06, T:0.85
Consensus pattern (24 bp):
TTTTATTTTGTTTTATTTTTTCAT
Found at i:3421922 original size:21 final size:21
Alignment explanation
Indices: 3421898--3421962 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
3421888 TTTATTTTTA
3421898 TTTTT-TTTTATTTTTTCCTT
1 TTTTTGTTTTATTTTTTCCTT
***
3421918 TTTTTGAACTATTTTTTCCTT
1 TTTTTGTTTTATTTTTTCCTT
3421939 TTCTGTTGTTTT-TTTTTT-CTT
1 TT-T-TTGTTTTATTTTTTCCTT
3421960 TTT
1 TTT
3421963 GTTGAACTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.17
21 19 0.53
22 7 0.19
23 4 0.11
ACGTcount: A:0.06, C:0.11, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTGTTTTATTTTTTCCTT
Found at i:3424950 original size:21 final size:21
Alignment explanation
Indices: 3424925--3425000 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 21
3424915 AGTATGTACA
3424925 GGGGGAACAGATTCCCCCTGG
1 GGGGGAACAGATTCCCCCTGG
* **
3424946 GGGGGTATTGATT-CCCC---
1 GGGGGAACAGATTCCCCCTGG
3424963 --GGGAACAGATTCCCCCTGG
1 GGGGGAACAGATTCCCCCTGG
*
3424982 GGGGGTATC-GATTCCCCCT
1 GGGGG-AACAGATTCCCCCT
3425001 AAATGAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
15 8 0.20
16 4 0.10
20 4 0.10
21 23 0.56
22 2 0.05
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAACAGATTCCCCCTGG
Found at i:3424974 original size:36 final size:36
Alignment explanation
Indices: 3424927--3424998 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
3424917 TATGTACAGG
*
3424927 GGGAACAGATTCCCCCTGGGGGGGTATTGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
3424963 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
3424999 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:3425425 original size:22 final size:20
Alignment explanation
Indices: 3425400--3425441 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3425390 CCAACGTGAA
3425400 ATGAAATAAGCTATATGAATAT
1 ATGAAATAA-C-ATATGAATAT
*
3425422 ATGAAATGACATATGAATAT
1 ATGAAATAACATATGAATAT
3425442 GCAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGAAATAACATATGAATAT
Found at i:3425623 original size:15 final size:15
Alignment explanation
Indices: 3425605--3425639 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3425595 CAAGGGTATT
3425605 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3425620 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
3425635 ATAGT
1 GTAGT
3425640 GGTCCTATGG
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:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:3431137 original size:35 final size:35
Alignment explanation
Indices: 3431091--3431160 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3431081 TATGTGCAGG
* *
3431091 GGGAACAGATTCCCCCTTGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGCATCGATTCCCC
3431126 GGGAACAGATTCCCCCTGGGGGGCATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGCATCGATTCCCC
3431161 CTAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGCATCGATTCCCC
Found at i:3431782 original size:15 final size:15
Alignment explanation
Indices: 3431764--3431822 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
3431754 GAGGGTATTA
*
3431764 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
3431779 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
3431794 TAGTCCTTCGGAACG
1 TAGTCCTTCGGGACG
*
3431809 TAGTCATTCGGGAC
1 TAGTCCTTCGGGAC
3431823 ATATATAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.17, C:0.24, G:0.31, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:3447883 original size:16 final size:15
Alignment explanation
Indices: 3447864--3447932 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
3447854 TTTCCTTTAA
3447864 TATTTTTTTTATTATT
1 TATTTTTTTTATT-TT
* *
3447880 TATTTCTTTTAAAATTT
1 TATTT-TTTT-TATTTT
* **
3447897 TCTTCATTTTA-TTT
1 TATTTTTTTTATTTT
3447911 TATTTTATTTTATTTT
1 TATTTT-TTTTATTTT
3447927 TATTTT
1 TATTTT
3447933 ACTTTTCTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 17 0.43
17 9 0.22
18 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTTTTTATTTT
Found at i:3447885 original size:28 final size:28
Alignment explanation
Indices: 3447839--3447897 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3447829 TTTATATTTC
*
3447839 TTTTTTAACTTATTTTTTCCTTTAATAT
1 TTTTTTAACTTATTTTTTCCTTTAAAAT
* *
3447867 TTTTTTTA-TTATTTATTTCTTTTAAAAT
1 TTTTTTAACTTATTT-TTTCCTTTAAAAT
3447895 TTT
1 TTT
3447898 CTTCATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTTTAACTTATTTTTTCCTTTAAAAT
Found at i:3447917 original size:10 final size:11
Alignment explanation
Indices: 3447903--3447938 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3447893 ATTTTCTTCA
3447903 TTTTATTTTA-
1 TTTTATTTTAC
*
3447913 TTTTATTTTAT
1 TTTTATTTTAC
3447924 TTTTATTTTAC
1 TTTTATTTTAC
3447935 TTTT
1 TTTT
3447939 CTCTTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTATTTTAC
Found at i:3447929 original size:6 final size:5
Alignment explanation
Indices: 3447902--3447938 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
3447892 AATTTTCTTC
3447902 ATTTT ATTTT ATTTT ATTTT ATTTTT ATTTT ACTTTT
1 ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT A-TTTT
3447939 CTCTTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:3453149 original size:38 final size:38
Alignment explanation
Indices: 3453098--3453173 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3453088 TATATTCTGA
3453098 ATTGAACGTTAACATGTTGACTATGATATGATAAAATT
1 ATTGAACGTTAACATGTTGACTATGATATGATAAAATT
3453136 ATTGAACGTTAACATGTTGACTATGATATGATAAAATT
1 ATTGAACGTTAACATGTTGACTATGATATGATAAAATT
3453174 TACTCTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (38 bp):
ATTGAACGTTAACATGTTGACTATGATATGATAAAATT
Found at i:3457408 original size:43 final size:43
Alignment explanation
Indices: 3457347--3457430 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
3457337 TGGATCATAC
* *
3457347 ATCGTAGTAGAGATAGTAGTAGGTATATACTTGCATATGCTTG
1 ATCGTAGTAGAGATAGTAGTACGTATATACTTACATATGCTTG
* * *
3457390 ATCGTAGTAGTGATAGTAGTTCGTATGTACTTACATATGCT
1 ATCGTAGTAGAGATAGTAGTACGTATATACTTACATATGCT
3457431 CAATCGAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (43 bp):
ATCGTAGTAGAGATAGTAGTACGTATATACTTACATATGCTTG
Found at i:3460183 original size:20 final size:21
Alignment explanation
Indices: 3460158--3460209 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3460148 TTTTCCTAAT
*
3460158 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3460178 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3460199 TCGCAATGCGA
1 TCGCAATGCGA
3460210 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3460223 original size:20 final size:20
Alignment explanation
Indices: 3460198--3460332 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
3460188 AATTGGGAAA
3460198 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
3460218 ATCGCAATGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
3460238 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3460259 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
3460279 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
3460299 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
3460319 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
3460333 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3460242 original size:61 final size:61
Alignment explanation
Indices: 3460195--3460326 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
3460185 GCGAATTGGG
* * * * *
3460195 AAAATCGCAATGCGATACTGACTATCGCAATGAGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * * *
3460256 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
3460317 ATAATCGCAA
1 AAAATCGCAA
3460327 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:3460528 original size:22 final size:22
Alignment explanation
Indices: 3460500--3460543 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3460490 CACTCTCTCA
3460500 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3460522 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3460544 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3461035 original size:25 final size:24
Alignment explanation
Indices: 3460981--3461035 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3460971 TGCTTATTAT
* *
3460981 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3461005 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3461031 TGTTT
1 TGTTT
3461036 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3462691 original size:20 final size:20
Alignment explanation
Indices: 3462666--3462711 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3462656 TAGTTTACTT
*
3462666 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
3462686 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3462706 TCGCAA
1 TCGCAA
3462712 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3462720 original size:19 final size:20
Alignment explanation
Indices: 3462677--3462732 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3462667 CGCAACATGA
3462677 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
3462697 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
3462716 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
3462733 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:3462740 original size:14 final size:14
Alignment explanation
Indices: 3462721--3462777 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3462711 ATGCGAAATG
3462721 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3462735 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3462754 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3462768 AAAATCGCAA
1 AAAATCGCAA
3462778 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3462747 original size:33 final size:33
Alignment explanation
Indices: 3462705--3462796 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
3462695 GGAAATGGCT
3462705 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3462738 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3462771 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3462797 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3462759 original size:19 final size:19
Alignment explanation
Indices: 3462705--3462801 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
3462695 GGAAATGGCT
3462705 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3462724 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3462738 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3462757 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3462771 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3462790 GTCGCAATGCGA
1 ATCGCAATGCGA
3462802 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3462835 original size:14 final size:14
Alignment explanation
Indices: 3462813--3462870 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
3462803 TTGTGTTTCG
3462813 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
3462827 CGTTACGATTTCATTT
1 CGTTGCGATTT--TGT
3462843 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3462859 CGTTGCGATTTT
1 CGTTGCGATTTT
3462871 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3462877 original size:33 final size:33
Alignment explanation
Indices: 3462808--3462919 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
3462798 GCGATTTGTG
* *
3462808 TTTCGCGTTGCGATTTTGTCGTTACGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3462840 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* * *
3462873 TTTCGCATTGCGATTTTTTCATTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3462906 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3462920 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 25 0.34
33 49 0.66
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3462885 original size:19 final size:19
Alignment explanation
Indices: 3462835--3462919 Score: 82
Period size: 19 Copynumber: 5.0 Consensus size: 19
3462825 GTCGTTACGA
3462835 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCATTGCGAT
*
3462853 TTT--TGTCG--TTGCGAT
1 TTTCATTTCGCATTGCGAT
3462868 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCATTGCGAT
3462886 TTT--TTT--CATTGCGAT
1 TTTCATTTCGCATTGCGAT
*
3462901 TTGCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
3462920 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
14 14 0.26
15 5 0.09
16 7 0.13
17 7 0.13
18 6 0.11
19 15 0.28
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (19 bp):
TTTCATTTCGCATTGCGAT
Found at i:3462897 original size:14 final size:14
Alignment explanation
Indices: 3462845--3462902 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
3462835 TTTCATTTCG
*
3462845 CATTGCGATTTTGT
1 CATTGCGATTTTTT
*
3462859 CGTTGCGATTTTCATTT
1 CATTGCGA-TTT--TTT
3462876 CGCATTGCGATTTTTT
1 --CATTGCGATTTTTT
3462892 CATTGCGATTT
1 CATTGCGATTT
3462903 GCATTTCGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 3 0.08
17 2 0.06
18 3 0.08
19 7 0.19
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (14 bp):
CATTGCGATTTTTT
Found at i:3462904 original size:21 final size:20
Alignment explanation
Indices: 3462867--3462908 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3462857 GTCGTTGCGA
*
3462867 TTTTCATTTCGCATTGCGATT
1 TTTTCATTGCGCATTGC-ATT
3462888 TTTTCATTGCG-ATTTGCATT
1 TTTTCATTGCGCA-TTGCATT
3462908 T
1 T
3462909 CGCATTGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTTCATTGCGCATTGCATT
Found at i:3462946 original size:20 final size:19
Alignment explanation
Indices: 3462904--3462959 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
3462894 TTGCGATTTG
*
3462904 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
* *
3462923 CATTTCCGCGTTGTGATAGT
1 CATTT-CGCGTTGCGATAGC
3462943 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3462960 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3464978 original size:20 final size:20
Alignment explanation
Indices: 3464962--3465008 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3464952 GATTTTCTCA
3464962 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
3464982 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
3465002 TTGCGAT
1 TTGCGAT
3465009 TTCCCCGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Done.