Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, 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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:2856274 original size:16 final size:16
Alignment explanation
Indices: 2856253--2856293 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
2856243 NNNNNNNNNN
*
2856253 TTCTTTCTTTCTCCCT
1 TTCTTTCTTGCTCCCT
2856269 TTCTTTCTTGCTCCCT
1 TTCTTTCTTGCTCCCT
2856285 TTCTCTTCT
1 TTCT-TTCT
2856294 CACTTTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.61
Consensus pattern (16 bp):
TTCTTTCTTGCTCCCT
Found at i:2859059 original size:35 final size:35
Alignment explanation
Indices: 2858986--2859332 Score: 358
Period size: 35 Copynumber: 9.8 Consensus size: 35
2858976 NNNNNNNNNN
* *
2858986 GATTAAAATTGTTTAATTAAG---TTGTGCCTAATT
1 GATT-AAATTATTTAATTAAGTTATTGGGCCTAATT
* * * *
2859019 CATTAAATTATTTAATTATGTCATTGGACCTAATT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATT
* *** *
2859054 AATTAAATTAAACAATTAAGTTATTGGGCCTAACT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATT
* * * * *
2859089 AATTAAATTTGTTTAATCAATTTATTGGGCATAATT
1 GATTAAA-TTATTTAATTAAGTTATTGGGCCTAATT
* *
2859125 GATTAAATTGTTTAATTAAGTTATTGGGCTTAATT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATT
* * * *
2859160 GATTAATTTGTTTAATCAAGTTATTGGGTCTAATT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATT
* *
2859195 GATTAAAATTGTTTAATCAAGTTATTGGGCCTAATT
1 GATT-AAATTATTTAATTAAGTTATTGGGCCTAATT
* *
2859231 GATTAAATTTGCTTTAATCAAGTTATTGGGCCTAATT
1 GATTAAA-TT-ATTTAATTAAGTTATTGGGCCTAATT
*
2859268 GATTAAATTATTTAATTAAGTTATTAGGCCTAATT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATT
**
2859303 GATTAAATTAAATAATTAAGTTAATTGGGC
1 GATTAAATTATTTAATTAAGTT-ATTGGGC
2859333 TTCTTAAAGA
Statistics
Matches: 268, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
32 14 0.05
33 3 0.01
35 150 0.56
36 69 0.26
37 32 0.12
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (35 bp):
GATTAAATTATTTAATTAAGTTATTGGGCCTAATT
Found at i:2859130 original size:71 final size:70
Alignment explanation
Indices: 2858986--2859311 Score: 374
Period size: 71 Copynumber: 4.6 Consensus size: 70
2858976 NNNNNNNNNN
* * * * * * *
2858986 GATTAAAATTGTTTAATTAAG---TTGTGCCTAATTCATTAAA-TTATTTAATTATGTCATTGGA
1 GATT-AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGG-
*
2859047 CCTAATT
64 GCTAATT
* *** * * *
2859054 AATTAAATTAAACAATTAAGTTATTGGGCCTAACTAATTAAATTTGTTTAATCAATTTATTGGGC
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGC
2859119 ATAATT
66 -TAATT
* *
2859125 GATTAAATTGTTTAATTAAGTTATTGGGCTTAATTGATT-AATTTGTTTAATCAAGTTATTGGGT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG-
2859189 CTAATT
65 CTAATT
* *
2859195 GATTAAAATTGTTTAATCAAGTTATTGGGCCTAATTGATTAAATTTGCTTTAATCAAGTTATTGG
1 GATT-AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTG-TTTAATCAAGTTATTGG
2859260 GCCTAATT
64 G-CTAATT
*
2859268 GATTAAATTATTTAATTAAGTTATTAGGCCTAATTGATTAAATT
1 GATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATT
2859312 AAATAATTAA
Statistics
Matches: 220, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
67 12 0.05
68 3 0.01
70 49 0.22
71 85 0.39
72 43 0.20
73 28 0.13
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.44
Consensus pattern (70 bp):
GATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGC
TAATT
Found at i:2859151 original size:106 final size:106
Alignment explanation
Indices: 2859014--2859311 Score: 389
Period size: 106 Copynumber: 2.8 Consensus size: 106
2859004 AAGTTGTGCC
* * * * * * ***
2859014 TAATTCATTAAATTATTTAATTATGTCATTGGACCTAATTAATTAAATTAAACAATTAAGTTATT
1 TAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAGTTATT
* * *
2859079 GGGCCTAACTAATTAAATTTGTTTAATCAATTTATTGGGCA
66 GGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCA
* * * *
2859120 TAATTGATTAAATTGTTTAATTAAGTTATTGGGCTTAATTGATTAATTTGTTTAATCAAGTTATT
1 TAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAGTTATT
* * *
2859185 GGGTCTAATTGATTAAAATTGTTTAATCAAGTTATTGGGCC
66 GGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCA
*
2859226 TAATTGATTAAATTTGCTTTAATCAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAGTTA
1 TAATTGATTAAA-TTG-TTTAATTAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAGTTA
*
2859291 TTAGGCCTAATTGATTAAATT
64 TTGGGCCTAATTGATTAAATT
2859312 AAATAATTAA
Statistics
Matches: 163, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
106 99 0.61
107 3 0.02
108 61 0.37
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (106 bp):
TAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAGTTATT
GGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCA
Found at i:2859324 original size:143 final size:143
Alignment explanation
Indices: 2859071--2859331 Score: 398
Period size: 143 Copynumber: 1.8 Consensus size: 143
2859061 TTAAACAATT
* *
2859071 AAGTTATTGGGCCTAACTAATTAAATTTGTTTAATCAATTTATTGGGCATAATTGATTAAATTGT
1 AAGTTATTGGGCCTAACTAATTAAATTTGTTTAATCAAGTTATTGGGCATAATTGATTAAATTAT
* * * ***
2859136 TTAATTAAGTTATTGGGCTTAATTGATTAATTTGTTTAATCAAGTT-ATTGGGTCTAATTGATTA
66 TTAATTAAGTTATTAGGCCTAATTGATTAAATTAAATAATCAAGTTAATTGGGTCTAATTGATTA
2859200 AAATTGTTTAATC
131 AAATTGTTTAATC
* * *
2859213 AAGTTATTGGGCCTAATTGATTAAATTTGCTTTAATCAAGTTATTGGGCCTAATTGATTAAATTA
1 AAGTTATTGGGCCTAACTAATTAAATTTG-TTTAATCAAGTTATTGGGCATAATTGATTAAATTA
*
2859278 TTTAATTAAGTTATTAGGCCTAATTGATTAAATTAAATAATTAAGTTAATTGGG
65 TTTAATTAAGTTATTAGGCCTAATTGATTAAATTAAATAATCAAGTTAATTGGG
2859332 CTTCTTAAAG
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
142 27 0.26
143 72 0.69
144 6 0.06
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.44
Consensus pattern (143 bp):
AAGTTATTGGGCCTAACTAATTAAATTTGTTTAATCAAGTTATTGGGCATAATTGATTAAATTAT
TTAATTAAGTTATTAGGCCTAATTGATTAAATTAAATAATCAAGTTAATTGGGTCTAATTGATTA
AAATTGTTTAATC
Found at i:2861478 original size:26 final size:27
Alignment explanation
Indices: 2861449--2861501 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2861439 TCAACCCACA
2861449 TATA-CTC-TTGTCTATAAATAAGACAT
1 TATACCTCTTTGTCTA-AAATAAGACAT
*
2861475 TATACGCTCTTTGTCTAAATTAAGACA
1 TATAC-CTCTTTGTCTAAAATAAGACA
2861502 ACTCTTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (27 bp):
TATACCTCTTTGTCTAAAATAAGACAT
Found at i:2863242 original size:36 final size:35
Alignment explanation
Indices: 2863193--2863267 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
2863183 GGAATGTGCT
* *
2863193 TTTTAATGGGATCAAG-AATAAACCCTCACAAATGCC
1 TTTTAACGAGATCAAGCAAT-AACCCTCAC-AATGCC
*
2863229 TTTTAACGAGATCAAGCAATAACCCTCACAATGGC
1 TTTTAACGAGATCAAGCAATAACCCTCACAATGCC
2863264 TTTT
1 TTTT
2863268 CTCAAGCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 9 0.26
36 23 0.66
37 3 0.09
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (35 bp):
TTTTAACGAGATCAAGCAATAACCCTCACAATGCC
Found at i:2868614 original size:112 final size:112
Alignment explanation
Indices: 2868401--2868602 Score: 305
Period size: 112 Copynumber: 1.8 Consensus size: 112
2868391 AAAGATTGCT
* * * * * *
2868401 CAAGGTCGAGGCCATCACTATGAACTAACCGTGGGTTTATGCTATCAGTGGCAATTACACCACTT
1 CAAGGTCGAGGCAATCACTAGGAACTAACCGTGGGTTTACGCAATCAGTGGCAACTACAACACTT
2868466 AGGGTGACACCATCTTCTAAGAATGCTAGGGGTGATAAAGGCAAGGG
66 AGGGTGACACCATCTTCTAAGAATGCTAGGGGTGATAAAGGCAAGGG
* * * **
2868513 CAAGGTCTAGGCAATCATTAGGAACTAACTGTGGGTTTACGCAATCAGTGGCAACTACAATGCTT
1 CAAGGTCGAGGCAATCACTAGGAACTAACCGTGGGTTTACGCAATCAGTGGCAACTACAACACTT
2868578 AGGGTGACACCATCTTCTAAGAATG
66 AGGGTGACACCATCTTCTAAGAATG
2868603 TTTGTGGTGA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 79 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (112 bp):
CAAGGTCGAGGCAATCACTAGGAACTAACCGTGGGTTTACGCAATCAGTGGCAACTACAACACTT
AGGGTGACACCATCTTCTAAGAATGCTAGGGGTGATAAAGGCAAGGG
Found at i:2873384 original size:17 final size:16
Alignment explanation
Indices: 2873358--2873401 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2873348 TTACTTATTT
2873358 TTAG-TTATTTTTATAG
1 TTAGTTTATTTTTA-AG
2873374 TTAGTTTATTTTTAAG
1 TTAGTTTATTTTTAAG
*
2873390 TGAGTTTATTTT
1 TTAGTTTATTTT
2873402 AATTTTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.64
Consensus pattern (16 bp):
TTAGTTTATTTTTAAG
Found at i:2882316 original size:18 final size:18
Alignment explanation
Indices: 2882295--2882329 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2882285 TTAGCTGAGT
*
2882295 AATTTTAAGTTTAATTAG
1 AATTTAAAGTTTAATTAG
*
2882313 AATTTAAATTTTAATTA
1 AATTTAAAGTTTAATTA
2882330 TTTGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
AATTTAAAGTTTAATTAG
Found at i:2892548 original size:72 final size:72
Alignment explanation
Indices: 2892431--2892636 Score: 234
Period size: 72 Copynumber: 2.8 Consensus size: 72
2892421 CAATAAGGTG
* * * ***
2892431 AATGTGGATGGTAAAATACCTATAAACATAATTA-AGAAAGTGGATGAGTAAGTCTCCACTGTTT
1 AATGTGGATGGTAAAATGCCCATAAACAAAATTATA-AAAGTGGATGAGTAAGTCTCCACCACTT
2892495 AATTGTTA
65 AATTGTTA
* * * *
2892503 AATGTGGATGGTAAAATGCCCATAAACACAGTTATAATAGTGGATGAGTAAGTCTCCACCACTTG
1 AATGTGGATGGTAAAATGCCCATAAACAAAATTATAAAAGTGGATGAGTAAGTCTCCACCACTTA
2892568 ATTGTTA
66 ATTGTTA
** * * * * *
2892575 AACATGAATGGTAAAATGCCCACAAATATAAATTATGAGAGTGGATGAGTAAGTCTCCACCA
1 AATGTGGATGGTAAAATGCCCATAAACA-AAATTATAAAAGTGGATGAGTAAGTCTCCACCA
2892637 TTTACTAGTT
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
72 84 0.74
73 30 0.26
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (72 bp):
AATGTGGATGGTAAAATGCCCATAAACAAAATTATAAAAGTGGATGAGTAAGTCTCCACCACTTA
ATTGTTA
Found at i:2892837 original size:36 final size:36
Alignment explanation
Indices: 2892784--2892853 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
2892774 CATGAATGCA
* **
2892784 TAAAGGCCAGATGTGGGGTGTCATAACACACATGTT
1 TAAAGGCAAGATGTGGGGCATCATAACACACATGTT
* *
2892820 TAAAGGCAAGATTTGGGGCATCATACCACACATG
1 TAAAGGCAAGATGTGGGGCATCATAACACACATG
2892854 ACAAAGGCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (36 bp):
TAAAGGCAAGATGTGGGGCATCATAACACACATGTT
Found at i:2892872 original size:35 final size:36
Alignment explanation
Indices: 2892785--2892872 Score: 90
Period size: 36 Copynumber: 2.5 Consensus size: 36
2892775 ATGAATGCAT
* ** **
2892785 AAAGGCCAGATGTGGGGTGTCATAACACACATGTTT
1 AAAGGCCAAATGTGGGGCATCATAACACACATGTAC
* *
2892821 AAAGG-CAAGATTTGGGGCATCATACCACACATG-AC
1 AAAGGCCAA-ATGTGGGGCATCATAACACACATGTAC
2892856 AAAGGCCAAATGTGGGG
1 AAAGGCCAAATGTGGGG
2892873 TGTTATTCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
35 14 0.33
36 28 0.67
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (36 bp):
AAAGGCCAAATGTGGGGCATCATAACACACATGTAC
Found at i:2895824 original size:15 final size:15
Alignment explanation
Indices: 2895804--2895839 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2895794 AATGGCTTCT
2895804 CAAATGTTTTAAACC
1 CAAATGTTTTAAACC
2895819 CAAATGTTTTAAACC
1 CAAATGTTTTAAACC
2895834 CAAATG
1 CAAATG
2895840 ATTTCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (15 bp):
CAAATGTTTTAAACC
Found at i:2903225 original size:2 final size:2
Alignment explanation
Indices: 2903208--2903247 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2903198 TTGGGATTTG
2903208 AT AT AT A- AT -T AT -T AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2903246 AT
1 AT
2903248 CCATCCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.12
2 30 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2903226 original size:13 final size:15
Alignment explanation
Indices: 2903208--2903247 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2903198 TTGGGATTTG
*
2903208 ATATATA-AT-TATT
1 ATATATATATATATA
2903221 ATATATATATATATA
1 ATATATATATATATA
2903236 ATATATATATAT
1 ATATATATATAT
2903248 CCATCCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.29
14 2 0.08
15 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2903228 original size:15 final size:17
Alignment explanation
Indices: 2903208--2903247 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2903198 TTGGGATTTG
*
2903208 ATATATA-AT-TATTAT
1 ATATATATATATAATAT
2903223 ATATATATATATAATAT
1 ATATATATATATAATAT
2903240 ATATATAT
1 ATATATAT
2903248 CCATCCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 2 0.09
17 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:2906048 original size:2 final size:2
Alignment explanation
Indices: 2906041--2906070 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2906031 TACGTGATTG
*
2906041 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2906071 GTAAATGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2910503 original size:80 final size:80
Alignment explanation
Indices: 2910349--2910509 Score: 252
Period size: 80 Copynumber: 2.0 Consensus size: 80
2910339 ATGTGTGAAA
** *
2910349 GCATTATGAATGCTTATATGTATTTATTTATCCATGCTATTACATTTGATTTATTTACATCCTCT
1 GCATTATGAATGCTTATATGTATTTATTTATCCACACTATTACATTTGATTTATTTACATCCTCA
* *
2910414 CATTGAGTATTGGAT
66 CATTCAGTATTAGAT
*
2910429 GCATTATGAATGCTTATATGTATTTATTTATCTACACTATTACATTTGATTTATTTACATTCCT-
1 GCATTATGAATGCTTATATGTATTTATTTATCCACACTATTACATTTGATTTATTTACA-TCCTC
2910493 ACATTCAGTATTAGAT
65 ACATTCAGTATTAGAT
2910509 G
1 G
2910510 ATTCACCTCT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
80 70 0.95
81 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (80 bp):
GCATTATGAATGCTTATATGTATTTATTTATCCACACTATTACATTTGATTTATTTACATCCTCA
CATTCAGTATTAGAT
Found at i:2911676 original size:22 final size:22
Alignment explanation
Indices: 2911650--2911709 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
2911640 AATTACTATG
2911650 TGATTGATTTTTAGGCATTACA
1 TGATTGATTTTTAGGCATTACA
* * * ***
2911672 TGATTGGTTATGA-GCATTGTG
1 TGATTGATTTTTAGGCATTACA
2911693 TGATTGATTTTTAGGCA
1 TGATTGATTTTTAGGCA
2911710 ATACCTAAGT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.45
Consensus pattern (22 bp):
TGATTGATTTTTAGGCATTACA
Found at i:2911743 original size:23 final size:23
Alignment explanation
Indices: 2911716--2911777 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
2911706 GGCAATACCT
2911716 AAGTCACACAATGCCTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
* *
2911739 TAGTCACGCAATGCCTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
2911762 AAGTCACACAATGCCT
1 AAGTCACACAATGCCT
2911778 ACCAGTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGTCACACAATGCCTTACTAAC
Found at i:2911832 original size:21 final size:21
Alignment explanation
Indices: 2911787--2911866 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
2911777 TACCAGTTAA
* * *
2911787 TCACGCAATACCTAAAAATAAG
1 TCACGCAATGCC-CAAAGTAAG
* *
2911809 TCACGTAATGCCCAAAGTTAG
1 TCACGCAATGCCCAAAGTAAG
** *
2911830 TCACGCAATGTACAGAGTAAG
1 TCACGCAATGCCCAAAGTAAG
2911851 TCACGCAATGCCCAAA
1 TCACGCAATGCCCAAA
2911867 AACCACCAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 35 0.78
22 10 0.22
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (21 bp):
TCACGCAATGCCCAAAGTAAG
Found at i:2912080 original size:60 final size:60
Alignment explanation
Indices: 2911965--2912091 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
2911955 TGCCTACTTG
*** * * *
2911965 ATAAAGAATGCTCAAAATGTTCAAAAGTTTTTCTTCATATATCAAAATCATTCCAAAATGC
1 ATAAA-AATGCTCAAAACACTCAAAAGGTTTTCTTCATATATCAAAAACACTCCAAAATGC
*
2912026 ATAAAAATGCTCAAAACACTC-AAAGGTTTTCTTCGTATATCAAAAACTACTCCAAAATGC
1 ATAAAAATGCTCAAAACACTCAAAAGGTTTTCTTCATATATCAAAAAC-ACTCCAAAATGC
*
2912086 TTAAAA
1 ATAAAA
2912092 TACTTTAACG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 23 0.40
60 29 0.51
61 5 0.09
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (60 bp):
ATAAAAATGCTCAAAACACTCAAAAGGTTTTCTTCATATATCAAAAACACTCCAAAATGC
Found at i:2915699 original size:45 final size:46
Alignment explanation
Indices: 2915648--2915742 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 46
2915638 TATGAGAGCT
2915648 CAAAATTTA-ATTT-AAGTTGAACTTTTTTGAT-TTTATTCTTGAAAC
1 CAAAATTTAGATTTGAAGTTG-ACTTTTTTGATATTT-TTCTTGAAAC
* * * *
2915693 CAAAATTTAGATTTGAATTTGATTTTTTTGATATTTTTGTTGAATC
1 CAAAATTTAGATTTGAAGTTGACTTTTTTGATATTTTTCTTGAAAC
2915739 CAAA
1 CAAA
2915743 TTAGGGTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
45 9 0.21
46 26 0.60
47 8 0.19
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (46 bp):
CAAAATTTAGATTTGAAGTTGACTTTTTTGATATTTTTCTTGAAAC
Found at i:2932863 original size:22 final size:22
Alignment explanation
Indices: 2932822--2932864 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2932812 CACTTCATTC
***
2932822 TTTTTCTTTTTCTTTCTTTCAT
1 TTTTTCTTTTTCTCAATTTCAT
2932844 TTTTTCTTTTTCTCAATTTCA
1 TTTTTCTTTTTCTCAATTTCA
2932865 CACCTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTCTTTTTCTCAATTTCAT
Found at i:2940982 original size:31 final size:31
Alignment explanation
Indices: 2940944--2941002 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2940934 ATAATTGACC
* *
2940944 TTCTAATATTGAAGAATCGATTCTGAGTCAA
1 TTCTAATAGTGAAGAATCAATTCTGAGTCAA
2940975 TTCTAATAGTGAAGAATCAATTCTGAGT
1 TTCTAATAGTGAAGAATCAATTCTGAGT
2941003 GAAATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (31 bp):
TTCTAATAGTGAAGAATCAATTCTGAGTCAA
Found at i:2960297 original size:22 final size:24
Alignment explanation
Indices: 2960256--2960304 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2960246 TGGAGACCCA
*
2960256 AAAATTTGAAATTAAGCTAA-TTC
1 AAAAGTTGAAATTAAGCTAATTTC
*
2960279 AAAAGTTGAATTTAA-CTAATTTC
1 AAAAGTTGAAATTAAGCTAATTTC
2960302 AAA
1 AAA
2960305 TAAATCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (24 bp):
AAAAGTTGAAATTAAGCTAATTTC
Found at i:2999856 original size:18 final size:19
Alignment explanation
Indices: 2999835--2999881 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2999825 GTGACAGGTG
*
2999835 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
2999853 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
2999872 AAAATAATAT
1 AAAATAATAT
2999882 AAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:3000960 original size:4 final size:4
Alignment explanation
Indices: 3000940--3001019 Score: 85
Period size: 4 Copynumber: 20.8 Consensus size: 4
3000930 ACGAAGAAGA
* * * *
3000940 AAAG AAAG AGAG -GAG AAAG AAAG AAAG GAAG AAAG AAAG AAAG GAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
3000987 AAAG GAAG AAAG AAAG AAAG -GAG AAA- AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
3001020 AAGCTAAGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
3 8 0.13
4 55 0.87
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3001008 original size:16 final size:16
Alignment explanation
Indices: 3000935--3001006 Score: 101
Period size: 16 Copynumber: 4.5 Consensus size: 16
3000925 TAGAAACGAA
*
3000935 GAAGAAAAGAAAGAGAG
1 GAAG-AAAGAAAGAAAG
3000952 G-AGAAAGAAAGAAAG
1 GAAGAAAGAAAGAAAG
3000967 GAAGAAAGAAAGAAAG
1 GAAGAAAGAAAGAAAG
*
3000983 GAAGAAAGGAAGAAAG
1 GAAGAAAGAAAGAAAG
*
3000999 AAAGAAAG
1 GAAGAAAG
3001007 GAGAAAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.24
16 38 0.75
17 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAAGAAAG
Found at i:3002165 original size:35 final size:36
Alignment explanation
Indices: 3002114--3002201 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 36
3002104 AGGCAGATAG
*
3002114 GCGTGGCGAGGGCCACGGCCTGTG-ATATATATATAT
1 GCGTGGCTA-GGCCACGGCCTGTGAATATATATATAT
3002150 GCGTGGCTAGGCCACGGCCTGTGATATATATATATAT
1 GCGTGGCTAGGCCACGGCCTGTGA-ATATATATATAT
3002187 GCGTGGCTAGGCCAC
1 GCGTGGCTAGGCCAC
3002202 TAGTGATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
35 14 0.29
36 8 0.16
37 27 0.55
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.25
Consensus pattern (36 bp):
GCGTGGCTAGGCCACGGCCTGTGAATATATATATAT
Found at i:3004556 original size:6 final size:6
Alignment explanation
Indices: 3004547--3004603 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
3004537 TTTGCTTATC
* * *
3004547 TTCTTC TTCTTT CTCCTTT TT-TTCT TTTTTT TTCTTT TTCTTT TTCTTT
1 TTCTTT TTCTTT -TTCTTT TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT
3004596 TTCTTT TT
1 TTCTTT TT
3004604 TGCTGCCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 2 0.05
6 35 0.80
7 7 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:3011478 original size:477 final size:477
Alignment explanation
Indices: 3010584--3011540 Score: 1720
Period size: 477 Copynumber: 2.0 Consensus size: 477
3010574 AAATCAAGAT
*
3010584 TAATTTATGGTGGTGGCATCTGGTCACTTTTTCCCATAAAACATAAAGGCGTTTCTTTGGATATT
1 TAATTTATGGTGGTGGCATCTGGTCACTTTTCCCCATAAAACATAAAGGCGTTTCTTTGGATATT
3010649 TCATATAAAAAACCTCCTTAGCCAACTCGTCAACTACATCCACTCTATGGAAACTTTCTATAGAA
66 TCATATAAAAAACCTCCTTAGCCAACTCGTCAACTACATCCACTCTATGGAAACTTTCTATAGAA
*
3010714 GAAGGATAATTAGTTGTCTTTAATATATTAAACTCAACTATCTCTTCTTTAACTTTGAAAGTTAT
131 GAAGGATAATTAGTTGTCTTTAATATATTAAACTCAACTATCTCTTCTCTAACTTTGAAAGTTAT
* *
3010779 CTTGCCATTCTTCACATCTATGATTGCTCTAATTGTAGCTAAGACTAATTATCCGAAAATAAGAG
196 CTTGCCATTCTTCACATCTATGATTGCTCTAATTGTAGCCAAGACTAATTATCCAAAAATAAGAG
* *
3010844 GAATTTTATCATCCTCTTCCATCTAAAGCACAATAAAGTCCATCGAAATGCACAACTTCCTAACT
261 GAATTTAATCATCCTCTTCCATCTAAAGCACAATAAAGTCCATCAAAATGCACAACTTCCTAACT
*
3010909 TTAACTGAAACATCCTTTATAATCCTAGCAAGGTACCTAATTGTTTTGTTTGGTAACTACAAAGA
326 TTAACTGAAACATCCTTTATAATCCTAGCAAGGTACCTAATTGTTTTGCTTGGTAACTACAAAGA
3010974 AACCATAGGAGGTTGTACCTGTAACACCCCGTACACTCGTATAAGAGCCAATATGATCTCATCAA
391 AACCATAGGAGGTTGTACCTGTAACACCCCGTACACTCGTATAAGAGCCAATATGATCTCATCAA
3011039 CGAGACAGAGGGTTGATGGATG
456 CGAGACAGAGGGTTGATGGATG
* *
3011061 TAATTTATGGTGGTGGCATCTGGTCAGTTTTCCCCATAAAAACGTAAAAGG-GTTTCTTTGGATA
1 TAATTTATGGTGGTGGCATCTGGTCACTTTTCCCCAT-AAAACAT-AAAGGCGTTTCTTTGGATA
* * * *
3011125 TTTCATGTAAAAAACCTCCTTAGCCAACTCGTCAACTATATCCACTCTCTGGAAACTTTCTGTAG
64 TTTCATATAAAAAACCTCCTTAGCCAACTCGTCAACTACATCCACTCTATGGAAACTTTCTATAG
3011190 AAGAAGGATAATTAGTTGTCTTTAATATATTAAACTCAACTATCTCTTCTCTAACTTTGAAAGTT
129 AAGAAGGATAATTAGTTGTCTTTAATATATTAAACTCAACTATCTCTTCTCTAACTTTGAAAGTT
3011255 AT-TTGCCATTCTTCACATCTATGATTGCTCTAATTGTAGCCAAGACTAATTATCCAAAAATAAG
194 ATCTTGCCATTCTTCACATCTATGATTGCTCTAATTGTAGCCAAGACTAATTATCCAAAAATAAG
3011319 AGGAATTTAATCATCCTCTTCCATCTAAAGCACAATAAAGTCCATCAAAATGCACAACTTCCTAA
259 AGGAATTTAATCATCCTCTTCCATCTAAAGCACAATAAAGTCCATCAAAATGCACAACTTCCTAA
* *
3011384 CTTTAACTGAAACATCCTTTATAATTCTAGTAAGGTACCTAATTGTTTTGCTTGGTAACTACAAA
324 CTTTAACTGAAACATCCTTTATAATCCTAGCAAGGTACCTAATTGTTTTGCTTGGTAACTACAAA
* *
3011449 GAAACCATAGTAGGTTGTACCTGTAACACCCCGTATACTCGTATAAGAGCCAATATGATCTCATC
389 GAAACCATAGGAGGTTGTACCTGTAACACCCCGTACACTCGTATAAGAGCCAATATGATCTCATC
*
3011514 AATGAGACAGAGGGTTGATGGATG
454 AACGAGACAGAGGGTTGATGGATG
3011538 TAA
1 TAA
3011541 ATCTACGTGC
Statistics
Matches: 460, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
477 309 0.67
478 146 0.32
479 5 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (477 bp):
TAATTTATGGTGGTGGCATCTGGTCACTTTTCCCCATAAAACATAAAGGCGTTTCTTTGGATATT
TCATATAAAAAACCTCCTTAGCCAACTCGTCAACTACATCCACTCTATGGAAACTTTCTATAGAA
GAAGGATAATTAGTTGTCTTTAATATATTAAACTCAACTATCTCTTCTCTAACTTTGAAAGTTAT
CTTGCCATTCTTCACATCTATGATTGCTCTAATTGTAGCCAAGACTAATTATCCAAAAATAAGAG
GAATTTAATCATCCTCTTCCATCTAAAGCACAATAAAGTCCATCAAAATGCACAACTTCCTAACT
TTAACTGAAACATCCTTTATAATCCTAGCAAGGTACCTAATTGTTTTGCTTGGTAACTACAAAGA
AACCATAGGAGGTTGTACCTGTAACACCCCGTACACTCGTATAAGAGCCAATATGATCTCATCAA
CGAGACAGAGGGTTGATGGATG
Found at i:3037451 original size:68 final size:68
Alignment explanation
Indices: 3037265--3037441 Score: 230
Period size: 68 Copynumber: 2.6 Consensus size: 68
3037255 TATGCATGAA
** * **
3037265 AAATGCCATGAGATTATGTAAATGATGTATATTCAATATACTACAAAAGATGATTAACAAAGCAT
1 AAATGCCATGAGATTATGTGTATGATGTATATTCCATATACTACATGAGATGATTAACAAAGCAT
*
3037330 GAT
66 AAT
* * * *
3037333 GAATGTCATGAGAGTATGTGTATGATGTATATTCCATATACTACATGAGATGATT-GCAAAAGCA
1 AAATGCCATGAGATTATGTGTATGATGTATATTCCATATACTACATGAGATGATTAAC-AAAGCA
3037397 TAAT
65 TAAT
* *
3037401 AAATGCCATGAGATTATGTGTATGATGTGTTTTCCATATAC
1 AAATGCCATGAGATTATGTGTATGATGTATATTCCATATAC
3037442 CTTATGAGAT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
67 1 0.01
68 92 0.99
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (68 bp):
AAATGCCATGAGATTATGTGTATGATGTATATTCCATATACTACATGAGATGATTAACAAAGCAT
AAT
Found at i:3051471 original size:12 final size:12
Alignment explanation
Indices: 3051441--3051475 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
3051431 CAGAATAGTT
3051441 TCTTGCTGCCTC
1 TCTTGCTGCCTC
3051453 T-TTGCTGCCTC
1 TCTTGCTGCCTC
3051464 TCTTGCTGCCTC
1 TCTTGCTGCCTC
3051476 AAAAATCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.43
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:3057451 original size:2 final size:2
Alignment explanation
Indices: 3057416--3057442 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3057406 CCAGGTATGG
3057416 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3057443 CACATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3058186 original size:2 final size:2
Alignment explanation
Indices: 3058179--3058207 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3058169 TTTCCTACCC
3058179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3058208 CAATGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3067758 original size:27 final size:27
Alignment explanation
Indices: 3067720--3067774 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3067710 ATCAATTGGT
3067720 AAAGCACTAGTAAAGACTTCCCTTATC
1 AAAGCACTAGTAAAGACTTCCCTTATC
3067747 AAAGCACTAGTAAAGACTTCCCTTATC
1 AAAGCACTAGTAAAGACTTCCCTTATC
3067774 A
1 A
3067775 TTAAGCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (27 bp):
AAAGCACTAGTAAAGACTTCCCTTATC
Found at i:3067884 original size:19 final size:19
Alignment explanation
Indices: 3067857--3067898 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3067847 GAGAAAAGAC
3067857 AATTATAAAGCTTGATGCT
1 AATTATAAAGCTTGATGCT
* *
3067876 AATTTTAAAGCTTGATTCT
1 AATTATAAAGCTTGATGCT
3067895 AATT
1 AATT
3067899 GTGAAAACTT
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:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTATAAAGCTTGATGCT
Found at i:3070521 original size:15 final size:16
Alignment explanation
Indices: 3070501--3070543 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3070491 ACATAAAACT
*
3070501 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
3070516 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
3070533 AAAATAACTAA
1 AAAATAACTAA
3070544 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:3071941 original size:44 final size:43
Alignment explanation
Indices: 3071873--3071960 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
3071863 TGTGTGATAG
* * *
3071873 AAAACAGTGACAATATTCTCACATTGTGACAAATACTAGTGAC
1 AAAACAGTGACAACATTATCACATTGTGACAAACACTAGTGAC
*
3071916 AAAACTAGTGGCAACATTATCACATTGTGACAAACACTAGTGAC
1 AAAAC-AGTGACAACATTATCACATTGTGACAAACACTAGTGAC
3071960 A
1 A
3071961 GATTTAGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 5 0.12
44 35 0.88
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (43 bp):
AAAACAGTGACAACATTATCACATTGTGACAAACACTAGTGAC
Found at i:3072717 original size:13 final size:13
Alignment explanation
Indices: 3072699--3072723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3072689 AACGGCATTA
3072699 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
3072712 TTTTTTTTTTTT
1 TTTTTTTTTTTT
3072724 TTTAACTTGC
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:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:3074785 original size:14 final size:14
Alignment explanation
Indices: 3074766--3074792 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3074756 GAGAGAGATT
3074766 AAAAAAAGAAAAAC
1 AAAAAAAGAAAAAC
3074780 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
3074793 AACCTTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAC
Found at i:3077980 original size:6 final size:6
Alignment explanation
Indices: 3077971--3078042 Score: 96
Period size: 6 Copynumber: 12.5 Consensus size: 6
3077961 ACCAAATGCC
* *
3077971 AGGTGG AGGTGG AGGTGG AGGTGG A---GG AGGAGG AGGTGG AGGCGG
1 AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG
*
3078016 AGGTGG AGGTGG AGGCGG AGGTGG AGG
1 AGGTGG AGGTGG AGGTGG AGGTGG AGG
3078043 CATTGGAGGG
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 3 0.05
6 55 0.95
ACGTcount: A:0.19, C:0.03, G:0.67, T:0.11
Consensus pattern (6 bp):
AGGTGG
Found at i:3078010 original size:27 final size:27
Alignment explanation
Indices: 3077975--3078030 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3077965 AATGCCAGGT
*
3077975 GGAGGTGGAGGTGGAGGTGGAGGAGGA
1 GGAGGTGGAGGCGGAGGTGGAGGAGGA
*
3078002 GGAGGTGGAGGCGGAGGTGGAGGTGGA
1 GGAGGTGGAGGCGGAGGTGGAGGAGGA
3078029 GG
1 GG
3078031 CGGAGGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.02, G:0.68, T:0.11
Consensus pattern (27 bp):
GGAGGTGGAGGCGGAGGTGGAGGAGGA
Found at i:3078700 original size:41 final size:44
Alignment explanation
Indices: 3078643--3078728 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
3078633 AGGTAATATG
3078643 TCTTCTTTTGGTTGTTT-CT-TA-TGTTGTCTCTTTGGTACTTA
1 TCTTCTTTTGGTTGTTTCCTATATTGTTGTCTCTTTGGTACTTA
*
3078684 TCTTCTTTTGGTTGTTTCCTATATTTGTTGTCTCTTTGGTGCTTA
1 TCTTCTTTTGGTTGTTTCCTATA-TTGTTGTCTCTTTGGTACTTA
3078729 CTGCATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 17 0.43
42 2 0.05
43 2 0.05
45 19 0.47
ACGTcount: A:0.07, C:0.15, G:0.17, T:0.60
Consensus pattern (44 bp):
TCTTCTTTTGGTTGTTTCCTATATTGTTGTCTCTTTGGTACTTA
Found at i:3088322 original size:35 final size:35
Alignment explanation
Indices: 3088283--3088382 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
3088273 TTAATTGTTT
**
3088283 AATTTAATCAATTAAGCATAATAACTTGATTAAAC
1 AATTTAATCAATTAAGCCCAATAACTTGATTAAAC
* * *
3088318 AATTTAATTAATT-AGACCCAATAACTTAATTAAAT
1 AATTTAATCAATTAAG-CCCAATAACTTGATTAAAC
* *
3088353 AATTTGATCAATTAGGCCCAATAACTTGAT
1 AATTTAATCAATTAAGCCCAATAACTTGAT
3088383 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 2 0.04
35 51 0.94
36 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAAGCCCAATAACTTGATTAAAC
Found at i:3095762 original size:73 final size:73
Alignment explanation
Indices: 3095673--3095812 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
3095663 CAAGAGACAG
* * * *
3095673 TGTTAGTTGACTAAGAGATTACTGCTAGAAA-TCAGGTTCAGAGACAGAAATGACTTAATCGACT
1 TGTTAGTCGACTAAGAGACTACTGCCAGAAACT-AGGTTCAGAGACAGAAACGACTTAATCGACT
3095737 AAGAAATTT
65 AAGAAATTT
* * * *
3095746 TGTTAGTCGACTAAGAGGCTATTGCCAGAAACTAGGTTCAGAGACAGAGACGACTTACTCGACTA
1 TGTTAGTCGACTAAGAGACTACTGCCAGAAACTAGGTTCAGAGACAGAAACGACTTAATCGACTA
3095811 AG
66 AG
3095813 TGGTAATGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 57 0.98
74 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (73 bp):
TGTTAGTCGACTAAGAGACTACTGCCAGAAACTAGGTTCAGAGACAGAAACGACTTAATCGACTA
AGAAATTT
Found at i:3104617 original size:73 final size:73
Alignment explanation
Indices: 3104515--3104654 Score: 176
Period size: 73 Copynumber: 1.9 Consensus size: 73
3104505 CAAGAGACAG
* * * * *
3104515 TGTTAGTCAATTAAGAGATTACTGCCAGAAACT-GGATTCAGAGATAGAA-ATGACTTAATCGAC
1 TGTTAGTCAACTAAAAGACTACTGCCAGAAACTAGG-TTCAGAGACA-AAGACGACTTAATCGAC
3104578 TAAGAAGTTT
64 TAAGAAGTTT
* * *
3104588 TGTTAGTCGACTAAAAGACTACTGTCAGAAACTAGGTTCAGAGACAAAGACGACTTACTCGACTA
1 TGTTAGTCAACTAAAAGACTACTGCCAGAAACTAGGTTCAGAGACAAAGACGACTTAATCGACTA
3104653 AG
66 AG
3104655 TGGTAATGAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
72 2 0.04
73 53 0.93
74 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (73 bp):
TGTTAGTCAACTAAAAGACTACTGCCAGAAACTAGGTTCAGAGACAAAGACGACTTAATCGACTA
AGAAGTTT
Found at i:3106883 original size:52 final size:52
Alignment explanation
Indices: 3106747--3106906 Score: 175
Period size: 52 Copynumber: 3.1 Consensus size: 52
3106737 ATAATCAATT
* * * *
3106747 CATATCTTAACACATTTACTTATATGTATAAACATT-CATCTAGTCATATTCCATT
1 CATAGCTTAACACATATACTTATGTGTATAAACATTGCATCTAGTCATA----ATC
* *
3106802 CATAGCTT-A-ACTTATACTTATGTGCATAAACATTGCATCTAGTCATAATC
1 CATAGCTTAACACATATACTTATGTGTATAAACATTGCATCTAGTCATAATC
* *
3106852 CATAGCTTAACACATATACTTATGTGTATAAACA-TGTCATCTAATCATAACC
1 CATAGCTTAACACATATACTTATGTGTATAAACATTG-CATCTAGTCATAATC
3106904 CAT
1 CAT
3106907 TCAGGGCTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
50 10 0.11
51 3 0.03
52 37 0.41
53 21 0.23
54 13 0.14
55 7 0.08
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.37
Consensus pattern (52 bp):
CATAGCTTAACACATATACTTATGTGTATAAACATTGCATCTAGTCATAATC
Found at i:3107960 original size:31 final size:31
Alignment explanation
Indices: 3107883--3107993 Score: 132
Period size: 31 Copynumber: 3.5 Consensus size: 31
3107873 TACCATTGTT
3107883 TTTCTTTTCAATTTGGTCTTCCAACATTTTC
1 TTTCTTTTCAATTTGGTCTTCCAACATTTTC
* * *
3107914 TTTTTTTTTTTTCAATTTGGTTTTCCAAGATTTTC
1 ----TTTCTTTTCAATTTGGTCTTCCAACATTTTC
* * *
3107949 TTTCTTTTCAATTTAGTCCTCTAACATTTTC
1 TTTCTTTTCAATTTGGTCTTCCAACATTTTC
3107980 TTTCTTTTCAATTT
1 TTTCTTTTCAATTT
3107994 AGCCTTTTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 39 0.58
35 28 0.42
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.60
Consensus pattern (31 bp):
TTTCTTTTCAATTTGGTCTTCCAACATTTTC
Found at i:3107984 original size:35 final size:35
Alignment explanation
Indices: 3107883--3107986 Score: 117
Period size: 35 Copynumber: 3.1 Consensus size: 35
3107873 TACCATTGTT
*
3107883 TTTCTTTTCAATTTGGTCTTCCAACATTTTCTTTT
1 TTTCTTTTCAATTTGGTCTTCCAACATTTTCTTTC
* * *
3107918 TTTTTTTTCAATTTGGTTTTCCAAGA---T-TTTC
1 TTTCTTTTCAATTTGGTCTTCCAACATTTTCTTTC
* * *
3107949 TTTCTTTTCAATTTAGTCCTCTAACATTTTCTTTC
1 TTTCTTTTCAATTTGGTCTTCCAACATTTTCTTTC
3107984 TTT
1 TTT
3107987 TCAATTTAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
31 23 0.42
32 1 0.02
34 1 0.02
35 30 0.55
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (35 bp):
TTTCTTTTCAATTTGGTCTTCCAACATTTTCTTTC
Found at i:3108103 original size:44 final size:44
Alignment explanation
Indices: 3108050--3108147 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
3108040 GGATATAGAT
* ** *
3108050 TATTCTCCTTGGAAGGTTAGTATTACAGAA-TCAAGGATTTCAAC
1 TATTATCCTTGGAAACTTAGCATTACA-AACTCAAGGATTTCAAC
*
3108094 TATTATCCTTGGAAACTTAGCATTACAAACTCAAGGATTTCAAT
1 TATTATCCTTGGAAACTTAGCATTACAAACTCAAGGATTTCAAC
*
3108138 TGTTATCCTT
1 TATTATCCTT
3108148 AGAACTCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 2 0.04
44 45 0.96
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (44 bp):
TATTATCCTTGGAAACTTAGCATTACAAACTCAAGGATTTCAAC
Found at i:3112380 original size:81 final size:84
Alignment explanation
Indices: 3112168--3112396 Score: 347
Period size: 85 Copynumber: 2.8 Consensus size: 84
3112158 ACCATAGTTC
* *
3112168 AAATAATATAAATTAATTTTATATTTGTTAGTTTACAAGTTTAATTAATATAAAAATTTTATATA
1 AAATAATATAAATTAATTTTATATTTGTTAGTTTACAAATTTAACTAATATAAAAATTTTATATA
*
3112233 TTAAATTTTTATCATAATTT
66 TTAAATATTTATCATAA-TT
* *
3112253 AAGTAATATAAATTAATTTTATATTTGTTAGTTTATAAATTTAACTAATATAAAAATTTTATATA
1 AAATAATATAAATTAATTTTATATTTGTTAGTTTACAAATTTAACTAATATAAAAATTTTATATA
*
3112318 TTAAA-ATTTA-CATCA-T
66 TTAAATATTTATCATAATT
* * *
3112334 AAATAATATAAATTAATTTTATATTTATTAATTTACAAATTCAACTAATATAAAAATTTTATA
1 AAATAATATAAATTAATTTTATATTTGTTAGTTTACAAATTTAACTAATATAAAAATTTTATA
3112397 AATAATATTA
Statistics
Matches: 133, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
81 59 0.44
83 4 0.03
84 4 0.03
85 66 0.50
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (84 bp):
AAATAATATAAATTAATTTTATATTTGTTAGTTTACAAATTTAACTAATATAAAAATTTTATATA
TTAAATATTTATCATAATT
Found at i:3113374 original size:1 final size:1
Alignment explanation
Indices: 3113368--3113410 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
3113358 GGAGAGTTTC
3113368 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3113411 CATACTAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3117339 original size:26 final size:26
Alignment explanation
Indices: 3117283--3117332 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3117273 ATATATATAT
*
3117283 AAAGACAAAAACATCTCTAAAGAGCA
1 AAAGACAAAAACATCTCTAAAAAGCA
* *
3117309 AAAGATAAAAACATCTTTAAAAAG
1 AAAGACAAAAACATCTCTAAAAAG
3117333 AAGAAGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.60, C:0.14, G:0.10, T:0.16
Consensus pattern (26 bp):
AAAGACAAAAACATCTCTAAAAAGCA
Found at i:3131853 original size:68 final size:68
Alignment explanation
Indices: 3131658--3131924 Score: 232
Period size: 68 Copynumber: 3.9 Consensus size: 68
3131648 CATGTTTGGT
* * * *
3131658 ATGATGAATGTCATAAGATTATGTGTATGATGTAAATTCCATATACCATATGAGATGATAAAGTA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
3131723 TGC
66 TGC
* * * * * * *
3131726 ATGATATATACTATAAGATTGTGTATATGATGTAAAATT-CATAAACCATATAAGGTGATTAAGT
1 ATGATAAATGCCATAAGATTATGTATATGATGT-AAATTCCATATACCATATGAGATGATTAAGT
3131790 ATGC
65 ATGC
* * * * * * * * *
3131794 ATAATAAATGCCATGAGATTATGTATATGGTGTATATTCCATATACTACACGAGATGATTGAGAA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
*
3131859 AGC
66 TGC
* * * * * ** * *
3131862 ATGATGAATGCGATGAGATTATGTCTATAATGTATTTTCCATATA-CATTATGAAATGAATAAG
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCCATATACCA-TATGAGATGATTAAG
3131925 CTTATAAGTG
Statistics
Matches: 155, Mismatches: 41, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
67 5 0.03
68 145 0.94
69 5 0.03
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (68 bp):
ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
TGC
Found at i:3136421 original size:29 final size:28
Alignment explanation
Indices: 3136382--3136543 Score: 137
Period size: 28 Copynumber: 5.6 Consensus size: 28
3136372 ACAGCTTTAC
3136382 CATGTTTGTCTTAATTTAGACAAAAAAA
1 CATGTTTGTCTTAATTTAGACAAAAAAA
*
3136410 CATGTTTGGTCTTAATTTAGAC-AAAAAC
1 CATGTTT-GTCTTAATTTAGACAAAAAAA
*
3136438 CTATGTTTGTCTTAATTTAAGACAAGAGAAA
1 C-ATGTTTGTCTTAATTT-AGACAA-AAAAA
* * * * **
3136469 TATTTTTTATCTTAATCTAGACAAGTAAA
1 CA-TGTTTGTCTTAATTTAGACAAAAAAA
* * *
3136498 TATATTTGTCTCAATTTAGACAAGATAAAA
1 CATGTTTGTCTTAATTTAGACAA-A-AAAA
* *
3136528 TATTTTTGTCTTAATT
1 CATGTTTGTCTTAATT
3136544 AAAGATAAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
28 40 0.37
29 29 0.27
30 25 0.23
31 15 0.14
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (28 bp):
CATGTTTGTCTTAATTTAGACAAAAAAA
Found at i:3136493 original size:30 final size:30
Alignment explanation
Indices: 3136386--3136543 Score: 141
Period size: 29 Copynumber: 5.4 Consensus size: 30
3136376 CTTTACCATG
* * *
3136386 TTTGTCTTAATTTAGACAA-AAAAACATGT
1 TTTGTCTTAATTTAGACAAGATAAATATTT
* * *
3136415 TTGGTCTTAATTTAGACAA-A-AACCTA-TG
1 TTTGTCTTAATTTAGACAAGATAA-ATATTT
*
3136443 TTTGTCTTAATTTAAGACAAGAGAAATATTT
1 TTTGTCTTAATTT-AGACAAGATAAATATTT
* * *
3136474 TTTATCTTAATCTAGACAAG-TAAATA-TA
1 TTTGTCTTAATTTAGACAAGATAAATATTT
*
3136502 TTTGTCTCAATTTAGACAAGATAAA-ATATT
1 TTTGTCTTAATTTAGACAAGATAAATAT-TT
3136532 TTTGTCTTAATT
1 TTTGTCTTAATT
3136544 AAAGATAAGA
Statistics
Matches: 104, Mismatches: 17, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
28 33 0.32
29 35 0.34
30 22 0.21
31 14 0.13
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTGTCTTAATTTAGACAAGATAAATATTT
Found at i:3136506 original size:59 final size:56
Alignment explanation
Indices: 3136386--3136542 Score: 165
Period size: 59 Copynumber: 2.7 Consensus size: 56
3136376 CTTTACCATG
* * * *
3136386 TTTGTCTTAATTTAGACAA-AAAAACATGTTTGGTCTTAATTTAGACAAAAACCTATG
1 TTTGTCTTAATTTAGACAAGAAAAA-ATTTTTTGTCTTAATCTAGACAAAAA-CTATA
* *
3136443 TTTGTCTTAATTTAAGACAAGAGAAATATTTTTTATCTTAATCTAGACAAGTAAA-TATA
1 TTTGTCTTAATTT-AGACAAGA-AAAAATTTTTTGTCTTAATCTAGACAA--AAACTATA
* *
3136502 TTTGTCTCAATTTAGACAAGATAAAATATTTTTGTCTTAAT
1 TTTGTCTTAATTTAGACAAGAAAAAAT-TTTTTGTCTTAAT
3136543 TAAAGATAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
57 17 0.20
58 26 0.31
59 35 0.42
60 3 0.04
61 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (56 bp):
TTTGTCTTAATTTAGACAAGAAAAAATTTTTTGTCTTAATCTAGACAAAAACTATA
Found at i:3136717 original size:17 final size:17
Alignment explanation
Indices: 3136695--3136727 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3136685 ATAATAATAA
3136695 AATAAG-AGTTATTATTC
1 AATAAGAAGTT-TTATTC
3136712 AATAAGAAGTTTTATT
1 AATAAGAAGTTTTATT
3136728 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAAGAAGTTTTATTC
Found at i:3138873 original size:2 final size:2
Alignment explanation
Indices: 3138868--3138902 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3138858 TGAGCGTGTG
3138868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3138903 TGAATTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3140104 original size:2 final size:2
Alignment explanation
Indices: 3140097--3140124 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3140087 ATTAAATTAC
3140097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3140125 GATCATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3140714 original size:36 final size:34
Alignment explanation
Indices: 3140631--3140815 Score: 194
Period size: 35 Copynumber: 5.3 Consensus size: 34
3140621 TTAATTGTTT
*
3140631 AATTTAATCAATTAGGCCGAATAAGTTAATTAAAC
1 AATTTAATCAATTAGGCC-AATAACTTAATTAAAC
* *
3140666 AATTTAATCAATTAAGCTCAATAACTTGATTAAAC
1 AATTTAATCAATTAGGC-CAATAACTTAATTAAAC
* ****
3140701 ACATTTATTCAATTAGGCCCAATAACTTAATTTTTT
1 A-ATTTAATCAATTAGG-CCAATAACTTAATTAAAC
* *
3140737 AATTTAATTAATTAGGCCCACTAACTTAATTAAAC
1 AATTTAATCAATTAGG-CCAATAACTTAATTAAAC
* *
3140772 AATTTAATGAATTAGG-C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCAATAACTTAATTAAAC
3140804 AATTTTAATCAA
1 AA-TTTAATCAA
3140816 GTGCTTAAGA
Statistics
Matches: 125, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
32 15 0.12
33 9 0.07
35 73 0.58
36 27 0.22
37 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (34 bp):
AATTTAATCAATTAGGCCAATAACTTAATTAAAC
Found at i:3140716 original size:71 final size:69
Alignment explanation
Indices: 3140608--3140815 Score: 204
Period size: 71 Copynumber: 3.0 Consensus size: 69
3140598 AGTCCTTAAG
**** *
3140608 AAGCCCAATTAACTTAATTGTTTAATTTAATCAATTAGGCCGAATAAGTTAATTAAACAATTTAA
1 AAGCCCAA-TAACTTAATTAAACAATTTAATCAATTAGGCC-AATAACTTAATTAAACAATTTAA
3140673 TCAATT
64 TCAATT
* * * ****
3140679 AAGCTCAATAACTTGATTAAACACATTTATTCAATTAGGCCCAATAACTTAATTTTTTAATTTAA
1 AAGCCCAATAACTTAATTAAACA-ATTTAATCAATTAGG-CCAATAACTTAATTAAACAATTTAA
*
3140744 TTAATT
64 TCAATT
* * * *
3140750 AGGCCCACTAACTTAATTAAACAATTTAATGAATTAGG-C-ACAACTTAATTAAACAATTTTAAT
1 AAGCCCAATAACTTAATTAAACAATTTAATCAATTAGGCCAATAACTTAATTAAACAA-TTTAAT
3140813 CAA
65 CAA
3140816 GTGCTTAAGA
Statistics
Matches: 109, Mismatches: 25, Indels: 9
0.76 0.17 0.06
Matches are distributed among these distances:
67 12 0.11
68 9 0.08
70 23 0.21
71 63 0.58
72 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (69 bp):
AAGCCCAATAACTTAATTAAACAATTTAATCAATTAGGCCAATAACTTAATTAAACAATTTAATC
AATT
Found at i:3148903 original size:51 final size:51
Alignment explanation
Indices: 3148826--3148948 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
3148816 ACTTCGTGGA
* * *
3148826 AATTGAGGGCTTATGTGTAGAATGGTTAATTGGGTGG-AAATTTCCTTATGG
1 AATTGAGGGCTTATGTGTTGAATGGTTAATTGGG-GGTAAACTGCCTTATGG
*
3148877 AATTGAGGGCTTATGTGTTGATTGGTTAATTGGGGGTTCAAACTGCCTTATGG
1 AATTGAGGGCTTATGTGTTGAATGGTTAATTGGGGG-T-AAACTGCCTTATGG
* *
3148930 AATAGAGGGTTTATGTGTT
1 AATTGAGGGCTTATGTGTT
3148949 AAAAAGGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
50 2 0.03
51 32 0.51
53 29 0.46
ACGTcount: A:0.24, C:0.07, G:0.32, T:0.38
Consensus pattern (51 bp):
AATTGAGGGCTTATGTGTTGAATGGTTAATTGGGGGTAAACTGCCTTATGG
Found at i:3148945 original size:53 final size:51
Alignment explanation
Indices: 3148830--3148948 Score: 150
Period size: 53 Copynumber: 2.3 Consensus size: 51
3148820 CGTGGAAATT
* * * *
3148830 GAGGGCTTATGTGTAGAATGGTTAATTGGGTGGAAATTTCCTTATGGAATT
1 GAGGGCTTATGTGTTGAATGGTTAATTGGGTGGAAACTGCCTTATGGAATA
*
3148881 GAGGGCTTATGTGTTGATTGGTTAATTGGG-GGTTCAAACTGCCTTATGGAATA
1 GAGGGCTTATGTGTTGAATGGTTAATTGGGTGG---AAACTGCCTTATGGAATA
*
3148934 GAGGGTTTATGTGTT
1 GAGGGCTTATGTGTT
3148949 AAAAAGGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 28 0.47
53 29 0.49
ACGTcount: A:0.23, C:0.07, G:0.33, T:0.38
Consensus pattern (51 bp):
GAGGGCTTATGTGTTGAATGGTTAATTGGGTGGAAACTGCCTTATGGAATA
Found at i:3149772 original size:60 final size:61
Alignment explanation
Indices: 3149708--3149869 Score: 175
Period size: 61 Copynumber: 2.7 Consensus size: 61
3149698 ACCGTATTGG
* *
3149708 TGTTGATGAT-GTGGATAACCATGTGTGTAGAGAGGAAGGCACATGTTTGTAATGTCTTGA
1 TGTTGATGATCGTAGATAACCATGTGTGTAAAGAGGAAGGCACATGTTTGTAATGTCTTGA
* * * * * * * *
3149768 TGTTGATGATCATAGACAATCATGTGTCTACAGAGAAAGGCACATGTTTGTGATGTGTTGA
1 TGTTGATGATCGTAGATAACCATGTGTGTAAAGAGGAAGGCACATGTTTGTAATGTCTTGA
* * * **
3149829 TGGTG-TTATGGTAGATGGCCATGTGTGTAAAGAGGAAGGCA
1 TGTTGATGATCGTAGATAACCATGTGTGTAAAGAGGAAGGCA
3149870 TGTCTATGGT
Statistics
Matches: 81, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 36 0.44
61 45 0.56
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (61 bp):
TGTTGATGATCGTAGATAACCATGTGTGTAAAGAGGAAGGCACATGTTTGTAATGTCTTGA
Found at i:3152029 original size:14 final size:14
Alignment explanation
Indices: 3152007--3152038 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3151997 CCAAACATTC
*
3152007 AAAATTAATTAACT
1 AAAACTAATTAACT
3152021 AAAACTAATTAACT
1 AAAACTAATTAACT
3152035 AAAA
1 AAAA
3152039 TTTAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAACTAATTAACT
Found at i:3155563 original size:24 final size:24
Alignment explanation
Indices: 3155536--3155582 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3155526 AAAGATAAGT
3155536 AAATAAAAATAAATAAAGACACAC
1 AAATAAAAATAAATAAAGACACAC
* * *
3155560 AAATAAAAGTACATAAAGGCACA
1 AAATAAAAATAAATAAAGACACA
3155583 TAATAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.66, C:0.13, G:0.09, T:0.13
Consensus pattern (24 bp):
AAATAAAAATAAATAAAGACACAC
Found at i:3160127 original size:16 final size:17
Alignment explanation
Indices: 3160100--3160137 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3160090 GGATTCAATA
3160100 AAAATATCAAAAAAATC
1 AAAATATCAAAAAAATC
* *
3160117 CAAAT-TCAAAAGAATC
1 AAAATATCAAAAAAATC
3160133 AAAAT
1 AAAAT
3160138 CTAAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.13, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATATCAAAAAAATC
Found at i:3163920 original size:19 final size:18
Alignment explanation
Indices: 3163891--3163928 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3163881 TTGTTACTTA
*
3163891 TTTAGTTAATTAATTATT
1 TTTAGTTAATTAATCATT
3163909 TTTAGTTTAATTAATCATT
1 TTTAG-TTAATTAATCATT
3163928 T
1 T
3163929 GAAATTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTAGTTAATTAATCATT
Found at i:3169944 original size:12 final size:13
Alignment explanation
Indices: 3169925--3169961 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
3169915 CAGAATAGTT
3169925 TCTTGCTGCCTCA
1 TCTTGCTGCCTCA
3169938 T-TTGCTGCCTC-
1 TCTTGCTGCCTCA
3169949 TCTTGCTGCCTCA
1 TCTTGCTGCCTCA
3169962 AAAATCTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.05, C:0.38, G:0.16, T:0.41
Consensus pattern (13 bp):
TCTTGCTGCCTCA
Found at i:3176271 original size:77 final size:77
Alignment explanation
Indices: 3176143--3176307 Score: 260
Period size: 77 Copynumber: 2.1 Consensus size: 77
3176133 GAATGTCATC
* * *
3176143 TATTTTAATTTTGGGTGATTCATAAAGAATAGAAAATTATTTCCTACTTTAAAAGCAATTCCTAA
1 TATTTTAATTTTAGGTGATTCATAAAGAATAGAAAATTATTTCCCACTTTAAAAGAAATTCCTAA
3176208 AATTAAGGATA-
66 AATTAAGGATAG
* * *
3176219 TAATTTTAATTTTAGGTGATTCATAAAGAATAGGAAATTGTTTCCCACTTTAAAAGAAATTCTTA
1 T-ATTTTAATTTTAGGTGATTCATAAAGAATAGAAAATTATTTCCCACTTTAAAAGAAATTCCTA
3176284 AAATTAAGGATAG
65 AAATTAAGGATAG
3176297 TATTTTAATTT
1 TATTTTAATTT
3176308 AGGAAATTCA
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
76 1 0.01
77 79 0.98
78 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (77 bp):
TATTTTAATTTTAGGTGATTCATAAAGAATAGAAAATTATTTCCCACTTTAAAAGAAATTCCTAA
AATTAAGGATAG
Found at i:3182470 original size:77 final size:76
Alignment explanation
Indices: 3182384--3182531 Score: 201
Period size: 77 Copynumber: 1.9 Consensus size: 76
3182374 TAAAACACTG
* * * *
3182384 TCTTGAATTTTA-AGAATTTCTTTTAAAGTAGGAAACAATTTTCTATTTTTTATGAATCGCCCAA
1 TCTTGAATTTTAGA-AATTACTTTTAAAGCAGAAAACAA-TTTCT-TTTTTTATGAATCACCCAA
3182448 AATTAAAATTTTAT
63 AATTAAAATTTTAT
* *
3182462 TCTT-AATTTTAGAAATTACTTTTAAAGCAGAAAATAATTTCTTTTTTTATGAATCACTCAAAAT
1 TCTTGAATTTTAGAAATTACTTTTAAAGCAGAAAACAATTTCTTTTTTTATGAATCACCCAAAAT
3182526 TAAAAT
66 TAAAAT
3182532 AGATGGCATT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
75 26 0.41
76 5 0.08
77 27 0.43
78 5 0.08
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (76 bp):
TCTTGAATTTTAGAAATTACTTTTAAAGCAGAAAACAATTTCTTTTTTTATGAATCACCCAAAAT
TAAAATTTTAT
Found at i:3201289 original size:16 final size:17
Alignment explanation
Indices: 3201264--3201303 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3201254 TTTAAATTAT
*
3201264 TAATATTTTAATGATAA
1 TAATATTTAAATGATAA
*
3201281 TAATATTTAAATTATAA
1 TAATATTTAAATGATAA
3201298 -AATATT
1 TAATATT
3201304 AATATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATGATAA
Found at i:3201315 original size:16 final size:16
Alignment explanation
Indices: 3201296--3201329 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3201286 TTTAAATTAT
*
3201296 AAAATATTAATATTTA
1 AAAATACTAATATTTA
*
3201312 AAAATGCTAATATTTA
1 AAAATACTAATATTTA
3201328 AA
1 AA
3201330 TTATCACTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATACTAATATTTA
Found at i:3201580 original size:27 final size:26
Alignment explanation
Indices: 3201548--3201605 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
3201538 TATTAATATT
3201548 TAAATTATCAA-TGATTAATATTTTAAA
1 TAAATTAT-AACTGATTAATA-TTTAAA
*
3201575 TAAATTATAACTTATTAATATTTAAA
1 TAAATTATAACTGATTAATATTTAAA
*
3201601 AAAAT
1 TAAAT
3201606 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (26 bp):
TAAATTATAACTGATTAATATTTAAA
Found at i:3203437 original size:19 final size:21
Alignment explanation
Indices: 3203395--3203438 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3203385 AAACAATATG
* *
3203395 ATAATCATATAACTCATTTCA
1 ATAACCATATAACGCATTTCA
3203416 ATAACCATA-AACGCATTT-A
1 ATAACCATATAACGCATTTCA
3203435 ATAA
1 ATAA
3203439 ATCTAAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAACCATATAACGCATTTCA
Found at i:3203988 original size:69 final size:70
Alignment explanation
Indices: 3203891--3204027 Score: 161
Period size: 69 Copynumber: 2.0 Consensus size: 70
3203881 ACACTAGGAC
* ** *
3203891 TCATAAAAAGAAGAAAAGTGATATAATGCCCAACTTAACCCTGTGATATTCTTACCCCCACA-TC
1 TCATAAAAAGAAGAAAAGTGATACAATGCCCAACCAAACCCTGTGATATTCTTACCCCAACACTC
3203955 GGGTT
66 GGGTT
* * * * * *
3203960 TCATAAAAA-AAGAAAAGGTGGTGCAATGCCTAACCAAATCTTGTGGTATTCTTACCCCAACACT
1 TCATAAAAAGAAGAAAA-GTGATACAATGCCCAACCAAACCCTGTGATATTCTTACCCCAACACT
3204024 CGGG
65 CGGG
3204028 CAAAAACCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
68 7 0.12
69 44 0.79
70 5 0.09
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (70 bp):
TCATAAAAAGAAGAAAAGTGATACAATGCCCAACCAAACCCTGTGATATTCTTACCCCAACACTC
GGGTT
Found at i:3213406 original size:21 final size:21
Alignment explanation
Indices: 3213380--3213422 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3213370 CTCTTAAAGT
3213380 AATTTAAATAAAATAACCTAA
1 AATTTAAATAAAATAACCTAA
* *
3213401 AATTTAACTAAAATAACTTAA
1 AATTTAAATAAAATAACCTAA
3213422 A
1 A
3213423 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTTAAATAAAATAACCTAA
Found at i:3215545 original size:18 final size:17
Alignment explanation
Indices: 3215509--3215542 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3215499 GTTCTTGATA
3215509 AAATAAAATTCCTTATT
1 AAATAAAATTCCTTATT
3215526 AAATAATAATT-CTTATT
1 AAATAA-AATTCCTTATT
3215543 TAATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAAAATTCCTTATT
Found at i:3215794 original size:59 final size:60
Alignment explanation
Indices: 3215694--3215856 Score: 172
Period size: 64 Copynumber: 2.7 Consensus size: 60
3215684 TCTTGTTTGT
* *
3215694 AATTAAGACAAAAATA-TTTTATTTTGTCTAAATTGAGACAAATATTTT-TTCT-T-ATCCA
1 AATTAAGACAAAAA-AGGTTT-TTTTGTCTAAATTAAGACAAATATTTTCTTCTCTAATCCA
* * *
3215752 GATTAAGATAAAAAAGGTTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTCTCTAATCTA
1 AATTAAGACAAAAAAGGTTTTT-TTGTC-TAAATTAAGAC-AA-ATATTTTCTTCTCTAATCCA
* * *
3215816 AATTAAGACCAAACATGTTTTTTTGTCTAAATTAAGACAAA
1 AATTAAGACAAAAAAGGTTTTTTTGTCTAAATTAAGACAAA
3215857 CATGTTAAAG
Statistics
Matches: 87, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
57 3 0.03
58 20 0.23
59 10 0.11
60 3 0.03
61 9 0.10
62 15 0.17
63 6 0.07
64 21 0.24
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (60 bp):
AATTAAGACAAAAAAGGTTTTTTTGTCTAAATTAAGACAAATATTTTCTTCTCTAATCCA
Found at i:3215820 original size:33 final size:28
Alignment explanation
Indices: 3215694--3215862 Score: 106
Period size: 30 Copynumber: 5.6 Consensus size: 28
3215684 TCTTGTTTGT
* * *
3215694 AATTAAGACAAAAATATTTTATTTTGTCTA
1 AATTAAGACAAACAT-GTTT-TTTTATCTA
* * *
3215724 AATTGAGACAAATAT-TTTTTCTTATCCA
1 AATTAAGACAAACATGTTTTT-TTATCTA
* * * * *
3215752 GATTAAGATAAAAAAGGTTTTTCTTGTCTTA
1 AATTAAGA-CAAACATGTTTTT-TTATC-TA
*
3215783 AATTAAGACAAACATATTTTCTTCTCTAATCTA
1 AATTAAGACAAACAT-GTTT-TT-T-T-ATCTA
*
3215816 AATTAAGACCAAACATGTTTTTTTGTCTA
1 AATTAAGA-CAAACATGTTTTTTTATCTA
3215845 AATTAAGACAAACATGTT
1 AATTAAGACAAACATGTT
3215863 AAAGCTGTCA
Statistics
Matches: 111, Mismatches: 19, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.02
28 24 0.22
29 16 0.14
30 28 0.25
31 12 0.11
32 6 0.05
33 14 0.13
34 9 0.08
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTTTTATCTA
Found at i:3215845 original size:34 final size:33
Alignment explanation
Indices: 3215781--3215859 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
3215771 TTTCTTGTCT
3215781 TAAATTAAGACAAACATATTTTCTTCTCTAATC
1 TAAATTAAGACAAACATATTTTCTTCTCTAATC
* *
3215814 TAAATTAAGACCAAACAT-GTTT-TT-T-T-GTC
1 TAAATTAAGA-CAAACATATTTTCTTCTCTAATC
3215843 TAAATTAAGACAAACAT
1 TAAATTAAGACAAACAT
3215860 GTTAAAGCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 7 0.16
29 12 0.28
30 1 0.02
31 1 0.02
32 2 0.05
33 13 0.30
34 7 0.16
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (33 bp):
TAAATTAAGACAAACATATTTTCTTCTCTAATC
Found at i:3215855 original size:62 final size:59
Alignment explanation
Indices: 3215694--3215859 Score: 176
Period size: 62 Copynumber: 2.7 Consensus size: 59
3215684 TCTTGTTTGT
* *
3215694 AATTAAGACAAAAATA-TTTTATTTTGTCTAAATTGAGAC-AA-ATATTTTTTCTTATCCA
1 AATTAAGACAAAAA-AGGTTT-TTTTGTCTAAATTAAGACAAACATATTTTTTCTTATCCA
* * *
3215752 GATTAAGATAAAAAAGGTTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTCTCTAATCTA
1 AATTAAGACAAAAAAGGTTTTT-TTGTC-TAAATTAAGACAAACATATTTT-TTCT-T-ATCCA
* * *
3215816 AATTAAGACCAAACATGTTTTTTTGTCTAAATTAAGACAAACAT
1 AATTAAGACAAAAAAGGTTTTTTTGTCTAAATTAAGACAAACAT
3215860 GTTAAAGCTG
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
57 3 0.03
58 20 0.22
59 10 0.11
60 2 0.02
61 7 0.08
62 21 0.23
63 6 0.07
64 21 0.23
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (59 bp):
AATTAAGACAAAAAAGGTTTTTTTGTCTAAATTAAGACAAACATATTTTTTCTTATCCA
Found at i:3215871 original size:29 final size:29
Alignment explanation
Indices: 3215812--3215871 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3215802 TCTTCTCTAA
****
3215812 TCTAAATTAAGACCAAACATGTTTTTTTG
1 TCTAAATTAAGACCAAACATGTTAAGCTG
3215841 TCTAAATTAAGA-CAAACATGTTAAAGCTG
1 TCTAAATTAAGACCAAACATGTT-AAGCTG
3215870 TC
1 TC
3215872 ATTTTTATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (29 bp):
TCTAAATTAAGACCAAACATGTTAAGCTG
Found at i:3222428 original size:15 final size:15
Alignment explanation
Indices: 3222408--3222438 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3222398 TCCCCCTTTT
3222408 TTTTAATAAAAAATA
1 TTTTAATAAAAAATA
3222423 TTTTAATAAAAAATA
1 TTTTAATAAAAAATA
3222438 T
1 T
3222439 ATATTTTTAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTTAATAAAAAATA
Found at i:3223763 original size:28 final size:27
Alignment explanation
Indices: 3223716--3223873 Score: 156
Period size: 28 Copynumber: 5.4 Consensus size: 27
3223706 TCTAGTATGT
3223716 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGAC--AAATATTTT-TCTTGTCTA
*
3223746 AATTGAGACAAATATTTTTTCTTGTCTA
1 AATTAAGACAAATA-TTTTTCTTGTCTA
* *
3223774 GATTAAGATAAAAAATATTTTTCTTGTCTTA
1 AATTAAG---ACAAATATTTTTCTTGTC-TA
*
3223805 AATTAAGACAAATATATTTTCTTGTCCA
1 AATTAAGACAAATAT-TTTTCTTGTCTA
*
3223833 AATTAAGACTAAACATGTTTT-TTGGTCTA
1 AATTAAGAC-AAATAT-TTTTCTT-GTCTA
3223862 AATTAAGACAAA
1 AATTAAGACAAA
3223874 AATGTTAAAG
Statistics
Matches: 110, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
28 41 0.37
29 36 0.33
30 19 0.17
31 14 0.13
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (27 bp):
AATTAAGACAAATATTTTTCTTGTCTA
Found at i:3223814 original size:59 final size:57
Alignment explanation
Indices: 3223716--3223873 Score: 201
Period size: 59 Copynumber: 2.7 Consensus size: 57
3223706 TCTAGTATGT
* * * *
3223716 AATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATTTTTTCTTGTCTA
1 AATTAAGATAAAAATATTTT-TCTTGTCTAAATTAAGACAAATATATTTTCTTGTCCA
*
3223774 GATTAAGATAAAAAATATTTTTCTTGTCTTAAATTAAGACAAATATATTTTCTTGTCCA
1 AATTAAGAT-AAAAATATTTTTCTTGTC-TAAATTAAGACAAATATATTTTCTTGTCCA
* * *
3223833 AATTAAGACTAAACATGTTTTT-TGGTCTAAATTAAGACAAA
1 AATTAAGA-TAAAAATATTTTTCTTGTCTAAATTAAGACAAA
3223874 AATGTTAAAG
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
57 14 0.16
58 18 0.20
59 55 0.62
60 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (57 bp):
AATTAAGATAAAAATATTTTTCTTGTCTAAATTAAGACAAATATATTTTCTTGTCCA
Found at i:3223827 original size:29 final size:28
Alignment explanation
Indices: 3223716--3223876 Score: 171
Period size: 29 Copynumber: 5.5 Consensus size: 28
3223706 TCTAGTATGT
3223716 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATA-TTT-TCTTGTCTA
* * *
3223746 AATTGAGACAAATATTTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTCTTGTCTA
* *
3223774 GATTAAGATAAAAAATATTTTTCTTGTCTTA
1 AATTAAGA-CAAAAATA-TTTTCTTGTC-TA
* *
3223805 AATTAAGACAAATATATTTTCTTGTCCA
1 AATTAAGACAAAAATATTTTCTTGTCTA
* *
3223833 AATTAAGACTAAACATGTTTT-TTGGTCTA
1 AATTAAGAC-AAAAATATTTTCTT-GTCTA
3223862 AATTAAGACAAAAAT
1 AATTAAGACAAAAAT
3223877 GTTAAAGCTG
Statistics
Matches: 110, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
28 32 0.29
29 40 0.36
30 29 0.26
31 9 0.08
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAAAATATTTTCTTGTCTA
Found at i:3224501 original size:63 final size:63
Alignment explanation
Indices: 3224411--3224530 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
3224401 ATCTTTCTCT
* * *
3224411 CTCAACTCTCTGAACTATATCAACTCTGTTAACTCTCTATTAAGCACCATTGTCATCAGGTCG
1 CTCAACTCTCTAAACTATATCAACTCTGTCAACTCTCTATTAAGCACCATCGTCATCAGGTCG
* * * * *
3224474 CTCAACTCTCTAAACTGTATGAGCTCTGTCAACTCTCTGTTGAGCACCATCGTCATC
1 CTCAACTCTCTAAACTATATCAACTCTGTCAACTCTCTATTAAGCACCATCGTCATC
3224531 GTGTTGTGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (63 bp):
CTCAACTCTCTAAACTATATCAACTCTGTCAACTCTCTATTAAGCACCATCGTCATCAGGTCG
Found at i:3224794 original size:23 final size:23
Alignment explanation
Indices: 3224767--3224820 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3224757 AGCACAGGAC
*
3224767 GTGTAACACGTAATGAACATGGT
1 GTGTAACAAGTAATGAACATGGT
* ** *
3224790 GTGTAACAATTTTTGAGCATGGT
1 GTGTAACAAGTAATGAACATGGT
3224813 GTGTAACA
1 GTGTAACA
3224821 TAGTTGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (23 bp):
GTGTAACAAGTAATGAACATGGT
Found at i:3228572 original size:31 final size:31
Alignment explanation
Indices: 3228527--3228798 Score: 239
Period size: 31 Copynumber: 8.6 Consensus size: 31
3228517 AACATGGCAT
* *
3228527 AAATGTGGTTACACGCCATGCATAACAGGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
*
3228558 AAATGAGGTCACACGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
*
3228589 ACATGTGGTCACACGCCATGCATAAC--G--
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* * *
3228616 AAAGGTCGTCACACGCCACGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
*
3228647 AAATGTCATCACATGTCATCACATGCCATGCATAACAAGTA
1 AAATG---T----GGTCA-CAC--GCCATGCATAACAAGTA
* **
3228688 AAAGGTCATCACACGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
**
3228719 AAATGTGGTCACACGCCATGCATAATGAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* ** *
3228750 AAA-GCTCGTCACACATCATGCATAACAAGTC
1 AAATG-TGGTCACACGCCATGCATAACAAGTA
* *
3228781 AAATGTTGTAACACGCCA
1 AAATGTGGTCACACGCCA
3228799 ACCATGCCGT
Statistics
Matches: 195, Mismatches: 30, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
27 22 0.11
29 2 0.01
30 1 0.01
31 134 0.69
32 1 0.01
33 3 0.02
34 4 0.02
38 5 0.03
39 3 0.02
41 20 0.10
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (31 bp):
AAATGTGGTCACACGCCATGCATAACAAGTA
Found at i:3228740 original size:62 final size:62
Alignment explanation
Indices: 3228527--3228798 Score: 273
Period size: 62 Copynumber: 4.3 Consensus size: 62
3228517 AACATGGCAT
* * * **
3228527 AAATGTGGTTACACGCCATGCATAACAGGTAAAATGAGGTCACACGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTAAAAGGTCGTCACACGCCATGCATAACAAGTA
* *
3228589 ACATGTGGTCACACGCCATGCATAAC--G--AAAGGTCGTCACACGCCACGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTAAAAGGTCGTCACACGCCATGCATAACAAGTA
* *
3228647 AAATGTCATCACATGTCATCACATGCCATGCATAACAAGTAAAAGGTCATCACACGCCATGCATA
1 AAATG---T----GGTCA-CAC--GCCATGCATAACAAGTAAAAGGTCGTCACACGCCATGCATA
3228712 ACAAGTA
56 ACAAGTA
** * ** *
3228719 AAATGTGGTCACACGCCATGCATAATGAGTAAAAGCTCGTCACACATCATGCATAACAAGTC
1 AAATGTGGTCACACGCCATGCATAACAAGTAAAAGGTCGTCACACGCCATGCATAACAAGTA
* *
3228781 AAATGTTGTAACACGCCA
1 AAATGTGGTCACACGCCA
3228799 ACCATGCCGT
Statistics
Matches: 176, Mismatches: 20, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
58 31 0.18
60 1 0.01
61 1 0.01
62 81 0.46
64 3 0.02
65 8 0.05
66 3 0.02
68 12 0.07
69 1 0.01
70 1 0.01
72 34 0.19
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (62 bp):
AAATGTGGTCACACGCCATGCATAACAAGTAAAAGGTCGTCACACGCCATGCATAACAAGTA
Found at i:3229539 original size:24 final size:24
Alignment explanation
Indices: 3229485--3229565 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 24
3229475 ATTCTCTCAG
* *
3229485 TGGCATGTCAC-AACCCTGAATGC
1 TGGCGTGTCACAAACCCTGAATGT
3229508 T-GCTGTGTCACAAACCCTGAATGT
1 TGGC-GTGTCACAAACCCTGAATGT
* **
3229532 TGGCGTGT--CAAACTCTGAACCT
1 TGGCGTGTCACAAACCCTGAATGT
3229554 TGGCGTGTCACA
1 TGGCGTGTCACA
3229566 GATTCCCTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 21 0.44
23 7 0.15
24 18 0.38
25 2 0.04
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
TGGCGTGTCACAAACCCTGAATGT
Found at i:3229585 original size:23 final size:23
Alignment explanation
Indices: 3229554--3229631 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
3229544 CTCTGAACCT
3229554 TGGCGTGTCACAGATTCCCTCCA
1 TGGCGTGTCACAGATTCCCTCCA
* * *
3229577 TGGCATGTCACA-A-ACCCTAAACCT
1 TGGCGTGTCACAGATTCCCT---CCA
*
3229601 TGCCGTGTCACAGATTCCCTCCA
1 TGGCGTGTCACAGATTCCCTCCA
3229624 TGGCGTGT
1 TGGCGTGT
3229632 TGCAAACTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
21 4 0.10
22 1 0.02
23 20 0.48
24 12 0.29
25 1 0.02
26 4 0.10
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.26
Consensus pattern (23 bp):
TGGCGTGTCACAGATTCCCTCCA
Found at i:3230119 original size:47 final size:47
Alignment explanation
Indices: 3229540--3230123 Score: 471
Period size: 47 Copynumber: 12.6 Consensus size: 47
3229530 GTTGGCGTGT
** *
3229540 CAAACTCTGAAC-CTTGGCGTGTCACAGATTCCCTCCATGGCATGTCA
1 CAAACTCTGAACTC-TACCGTGTCACAGATTCCCTCCATGCCATGTCA
* * * * * **
3229587 CAAACCCTAAAC-CTTGCCGTGTCACAGATTCCCTCCATGGCGTGTTG
1 CAAACTCTGAACTC-TACCGTGTCACAGATTCCCTCCATGCCATGTCA
* * *
3229634 CAAACTCTGAA-TACTACCATGTCACAGATTCCCTCCATGTCGTGTCA
1 CAAACTCTGAACT-CTACCGTGTCACAGATTCCCTCCATGCCATGTCA
* *** *
3229681 CAAACTCTTAA-TACTGGTGTGTCACAGATTCCGTCCAT-CGCATGTCA
1 CAAACTCTGAACT-CTACCGTGTCACAGATTCCCTCCATGC-CATGTCA
* * * * *** *
3229728 CAAACCCTGAACCCTGCCGTGTCACAAATTCCCTCCATGGGGTCTCA
1 CAAACTCTGAACTCTACCGTGTCACAGATTCCCTCCATGCCATGTCA
* *
3229775 CAAACTCTGAA-TACTACCGTGTCACAGATTCCCTCGATGCCGTGT--
1 CAAACTCTGAACT-CTACCGTGTCACAGATTCCCTCCATGCCATGTCA
* * * * * *
3229820 CAAACTCTAAACTCTAGCATGTCACAGATTCCCTCCATGTCGTGTCG
1 CAAACTCTGAACTCTACCGTGTCACAGATTCCCTCCATGCCATGTCA
* * * * *
3229867 TAAACTCTAAACACTAGCATGTCACAGATTCCCTCCATGCCATGT--
1 CAAACTCTGAACTCTACCGTGTCACAGATTCCCTCCATGCCATGTCA
* * *
3229912 TAAACTCTGAACTCTGA-TGTGTCACAGATTCCCTTCATGCCATGTCA
1 CAAACTCTGAACTCT-ACCGTGTCACAGATTCCCTCCATGCCATGTCA
*** * * * *
3229959 CAAACTCTGAACTCTGGAGTGTTATAGCTTCCCT-CATGGCATGT--
1 CAAACTCTGAACTCTACCGTGTCACAGATTCCCTCCATGCCATGTCA
* *
3230003 CAAACTCTGAACTCTGA-CATGTCACAGATTCCTTCCATGCCATGTCA
1 CAAACTCTGAACTCT-ACCGTGTCACAGATTCCCTCCATGCCATGTCA
* **
3230050 CAAACTCTAAACTCTAGAGTGTCACAGATTCCCTCCATAG-CATGTCA
1 CAAACTCTGAACTCTACCGTGTCACAGATTCCCTCCAT-GCCATGTCA
* *
3230097 CAAACTCTAAACCCTACCGTGTCACAG
1 CAAACTCTGAACTCTACCGTGTCACAG
3230124 CCCTGTCACA
Statistics
Matches: 442, Mismatches: 76, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
44 26 0.06
45 85 0.19
46 12 0.03
47 317 0.72
48 2 0.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (47 bp):
CAAACTCTGAACTCTACCGTGTCACAGATTCCCTCCATGCCATGTCA
Found at i:3261699 original size:21 final size:23
Alignment explanation
Indices: 3261674--3261722 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3261664 GAACTACTTC
*
3261674 AATGTTAT-TATGAATAACT-AA
1 AATGTTATACATGAATAACTCAA
*
3261695 AATGTTATACATGAATATCTCAA
1 AATGTTATACATGAATAACTCAA
3261718 AATGT
1 AATGT
3261723 AATTCTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (23 bp):
AATGTTATACATGAATAACTCAA
Found at i:3272510 original size:17 final size:17
Alignment explanation
Indices: 3272480--3272512 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3272470 TTCTTGATAA
3272480 AATAAAACTCCTTGTTG
1 AATAAAACTCCTTGTTG
3272497 AATAATAACT-CTTGTT
1 AATAA-AACTCCTTGTT
3272513 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTGTTG
Found at i:3272815 original size:86 final size:87
Alignment explanation
Indices: 3272689--3272867 Score: 240
Period size: 86 Copynumber: 2.1 Consensus size: 87
3272679 NNNNNNNNNN
*
3272689 AACATATTTTTTTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAACACA-AAGCA-
1 AACATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAACACATAA-CAT
3272752 GGTTTCTTGCCTAAATTAAGACA
65 GGTTTCTTGCCTAAATTAAGACA
* * * *
3272775 AACATGTTTTTCTTGTC-TAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACATTACAT
1 AACATATTTTTCTTGTCTTAAATTAAGAC-AAACATATTTTCTTGTCTAAATTAACACATAACAT
* * *
3272839 GTTTTCTTGTCTAAATTAAGATA
65 GGTTTCTTGCCTAAATTAAGACA
3272862 AA-ATAT
1 AACATAT
3272868 GTTAAACTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
85 11 0.14
86 47 0.58
87 23 0.28
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (87 bp):
AACATATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAACACATAACATG
GTTTCTTGCCTAAATTAAGACA
Found at i:3272869 original size:29 final size:29
Alignment explanation
Indices: 3272696--3272870 Score: 221
Period size: 29 Copynumber: 6.1 Consensus size: 29
3272686 NNNAACATAT
* *
3272696 TTTTTTTGTCTTAAATTAAGAC-AAACATA
1 TTTTCTTGTC-TAAATTAAGACAAAACATG
* *
3272725 TTTTCTTGTCTAAATTAACACAAAGCA-G
1 TTTTCTTGTCTAAATTAAGACAAAACATG
* *
3272753 GTTTCTTGCCTAAATTAAGAC-AAACATG
1 TTTTCTTGTCTAAATTAAGACAAAACATG
3272781 TTTTTCTTGTCTAAATTAAGACAAAACATG
1 -TTTTCTTGTCTAAATTAAGACAAAACATG
**
3272811 TTTTCTTGTCTAAATTAAGACATTACATG
1 TTTTCTTGTCTAAATTAAGACAAAACATG
* *
3272840 TTTTCTTGTCTAAATTAAGATAAAATATG
1 TTTTCTTGTCTAAATTAAGACAAAACATG
3272869 TT
1 TT
3272871 AAACTTGCCA
Statistics
Matches: 126, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
27 4 0.03
28 29 0.23
29 86 0.68
30 7 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (29 bp):
TTTTCTTGTCTAAATTAAGACAAAACATG
Found at i:3283809 original size:21 final size:22
Alignment explanation
Indices: 3283780--3283823 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3283770 AAGTGATTAA
3283780 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
3283801 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
3283823 T
1 T
3283824 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:3303341 original size:51 final size:51
Alignment explanation
Indices: 3303262--3303404 Score: 137
Period size: 51 Copynumber: 2.8 Consensus size: 51
3303252 AGTTAATGTT
*
3303262 AGGGTTATCACTTCCTGTTAAAACGCAAGAATCTCTTTTGTAAATTGTGCA
1 AGGGTTATCACTTCCTGTTAAAAAGCAAGAATCTCTTTTGTAAATTGTGCA
** * * **
3303313 AGGGTTATTGCTTCCCT-TTAAAAAGCAAGAATTTCTTTTGTGAATTGTATA
1 AGGGTTATCACTT-CCTGTTAAAAAGCAAGAATCTCTTTTGTAAATTGTGCA
* * * *
3303364 AAGGTTGTCACTTAATTCTGTTAAAAGGCAAGAATC-CTTTT
1 AGGGTTATCAC-T--TCCTGTTAAAAAGCAAGAATCTCTTTT
3303405 AGTAGATAGG
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
51 47 0.64
52 4 0.05
53 7 0.10
54 15 0.21
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (51 bp):
AGGGTTATCACTTCCTGTTAAAAAGCAAGAATCTCTTTTGTAAATTGTGCA
Found at i:3309537 original size:16 final size:16
Alignment explanation
Indices: 3309516--3309556 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
3309506 GCAAGATTTC
3309516 TTCACTCTTCTCCCAA
1 TTCACTCTTCTCCCAA
3309532 TTCACTCTTCTCCCAA
1 TTCACTCTTCTCCCAA
*
3309548 ATCACTCTT
1 TTCACTCTT
3309557 ACTCTCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (16 bp):
TTCACTCTTCTCCCAA
Found at i:3313644 original size:91 final size:89
Alignment explanation
Indices: 3313541--3313726 Score: 291
Period size: 91 Copynumber: 2.1 Consensus size: 89
3313531 GCCCAACACT
3313541 TAATTAAACCTTTTTAATTAAATCATTGTAAATTAAAATTAAAATAAATTTACTTTTTATTTGTT
1 TAATTAAACCTTTTTAATTAAATCATTGTAAATTAAAATTAAAATAAATTTAC--TTTATTTGTT
* * *
3313606 TGCAATTAATGCTTTAATATTATAAC
64 TACAATTAAGGCTTTAATATTAGAAC
* * *
3313632 TAATTAAACCTTTTTAATTAAATCATTGTAAATTAAAATTTAATTTAATTTACTTTATTTGTTTA
1 TAATTAAACCTTTTTAATTAAATCATTGTAAATTAAAATTAAAATAAATTTACTTTATTTGTTTA
*
3313697 TAATTAAGGCTTTAATATTAGAAC
66 CAATTAAGGCTTTAATATTAGAAC
3313721 TAATTA
1 TAATTA
3313727 TAATGTTGGC
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 38 0.43
91 50 0.57
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (89 bp):
TAATTAAACCTTTTTAATTAAATCATTGTAAATTAAAATTAAAATAAATTTACTTTATTTGTTTA
CAATTAAGGCTTTAATATTAGAAC
Found at i:3319404 original size:35 final size:35
Alignment explanation
Indices: 3319356--3319632 Score: 245
Period size: 35 Copynumber: 7.9 Consensus size: 35
3319346 TCTTTAAGAA
***
3319356 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATCAATTAG
* * * * *
3319392 GCCTAATAACTTAATTAAACAATTTAATTAATCAA
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
3319427 GCCCAACAATTTAATTAAACAATGCTAATCAATTAG
1 GCCCAATAACTTAATTAAATAAT-TTAATCAATTAG
** *
3319463 GCCCAATGGCTTAATTAAACAAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAA-TAATTTAATCAATTAG
** *
3319499 GCCCAATAACTTAATTATTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * *
3319534 GCCTAATGACTTAATTAAATAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * * * *
3319569 GCCTAATGATTTAATTAAAAAATTTATTTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
*
3319604 G--C-ATAACTTAATTAAACAATTTTAATCAA
1 GCCCAATAACTTAATTAAATAA-TTTAATCAA
3319633 GTACTTGATT
Statistics
Matches: 198, Mismatches: 40, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
32 14 0.07
33 7 0.04
35 120 0.61
36 54 0.27
37 3 0.02
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATCAATTAG
Found at i:3319495 original size:107 final size:104
Alignment explanation
Indices: 3319377--3319625 Score: 295
Period size: 107 Copynumber: 2.4 Consensus size: 104
3319367 TTAATTGTTT
*
3319377 AATTTAATCAATTAGGCCTAATAACTTAATTAAACAATTTAATTAATCAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCC-AATAACTTAATTAAACAATTTAATTAATCAAGCCCAACAACTTAAT
*
3319442 TAAACAATGCTAATCAATTAGGCCCAATGGCTTAATTAAACA
65 TAAACAAT-CTAATCAATTAGGCCCAATGACTTAATTAAA-A
*** * * * **
3319484 AATTTAATCAATTAGGCCCAATAACTTAATTATTTAATTTAATTAATTAGGCCTAATGACTTAAT
1 AATTTAATCAATTAGG-CCAATAACTTAATTAAACAATTTAATTAATCAAGCCCAACAACTTAAT
* * * * *
3319549 TAAATAATTTAATTAATTAGGCCTAATGATTTAATTAAAA
65 TAAACAATCTAATCAATTAGGCCCAATGACTTAATTAAAA
* *
3319589 AATTTATTTAATTAGG-C-ATAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCAATAACTTAATTAAACAATTT
3319626 TAATCAAGTA
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
102 17 0.14
103 1 0.01
105 15 0.12
106 26 0.21
107 60 0.50
108 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (104 bp):
AATTTAATCAATTAGGCCAATAACTTAATTAAACAATTTAATTAATCAAGCCCAACAACTTAATT
AAACAATCTAATCAATTAGGCCCAATGACTTAATTAAAA
Found at i:3327603 original size:11 final size:11
Alignment explanation
Indices: 3327584--3327616 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3327574 ATTTCCTCTT
3327584 TTTTC-TTCTC
1 TTTTCTTTCTC
3327594 TTTTCTTTCTC
1 TTTTCTTTCTC
*
3327605 TTTTCTTCCTC
1 TTTTCTTTCTC
3327616 T
1 T
3327617 CGGGTGGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:3329460 original size:35 final size:35
Alignment explanation
Indices: 3329419--3329656 Score: 148
Period size: 35 Copynumber: 6.8 Consensus size: 35
3329409 AGTTCAATTA
** *
3329419 ACTTAATTGTTTAATTTAATCAATTAGGCCAAATT
1 ACTTAATTAATTAATTTAATCAATTAGGCCAAATG
* * *
3329454 ACTTAATTAAATAATTTAATTAATTAAGCACAACA--
1 ACTTAATTAATTAATTTAATCAATTAGGC-CAA-ATG
* **
3329489 ATTTAATTAAACAATTTTAATCAATTAGGTCC-AATG
1 ACTTAATTAATTAA-TTTAATCAATTAGG-CCAAATG
* * *
3329525 ACTTAATTAAATAAATTTAATCAATTAGGCCCAAGG
1 ACTTAATT-AATTAATTTAATCAATTAGGCCAAATG
** * * *
3329561 ACTTAATTGTTTAATTTAATTAATTAAGCCCAATG
1 ACTTAATTAATTAATTTAATCAATTAGGCCAAATG
* * *
3329596 ACTTAA--AA-CAATTTAATTAATTACG-CATAATG
1 ACTTAATTAATTAATTTAATCAATTAGGCCA-AATG
* ** * *
3329628 ATTTAATTAAAAAATTTATTTAATTAGGC
1 ACTTAATTAATTAATTTAATCAATTAGGC
3329657 ACAACTTAAT
Statistics
Matches: 162, Mismatches: 28, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
31 1 0.01
32 24 0.15
34 3 0.02
35 80 0.49
36 48 0.30
37 6 0.04
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (35 bp):
ACTTAATTAATTAATTTAATCAATTAGGCCAAATG
Found at i:3329515 original size:36 final size:35
Alignment explanation
Indices: 3329430--3329593 Score: 118
Period size: 36 Copynumber: 4.6 Consensus size: 35
3329420 CTTAATTGTT
*
3329430 TAATTTAATCAATT-AGGCCAA-ATTACTTAATTAAA
1 TAATTTAATCAATTAAGTCCAACA--ACTTAATTAAA
* *
3329465 TAATTTAATTAATTAAG-CACAACAATTTAATTAAA
1 TAATTTAATCAATTAAGTC-CAACAACTTAATTAAA
* * **
3329500 CAATTTTAATCAATTAGGTCCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAAGTCCAACAACTTAATTAAA
* * ** ***
3329536 TAAATTTAATCAATTAGGCCCAAGGACTTAATTGTT
1 T-AATTTAATCAATTAAGTCCAACAACTTAATTAAA
* *
3329572 TAATTTAATTAATTAAGCCCAA
1 TAATTTAATCAATTAAGTCCAA
3329594 TGACTTAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
35 45 0.42
36 58 0.54
37 4 0.04
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (35 bp):
TAATTTAATCAATTAAGTCCAACAACTTAATTAAA
Found at i:3329579 original size:71 final size:69
Alignment explanation
Indices: 3329418--3329601 Score: 206
Period size: 71 Copynumber: 2.6 Consensus size: 69
3329408 AAGTTCAATT
* *
3329418 AACTTAATTGTTTAATTTAATCAATTAGGCCAAATTACTTAATTAAATAATTTAATTAATTAAGC
1 AACTTAATTGTTTAATTTAATCAATTAGGCC-AATGACTTAATTAAATAATTTAATCAATTAAGC
3329483 ACAAC
65 ACAAC
* **** *
3329488 AATTTAATTAAACAATTTTAATCAATTAGGTCCAATGACTTAATTAAATAAATTTAATCAATTAG
1 AACTTAATTGTTTAA-TTTAATCAATTAGG-CCAATGACTTAATTAAAT-AATTTAATCAATTAA
* *
3329553 GCCCAAG
63 GCACAAC
* * *
3329560 GACTTAATTGTTTAATTTAATTAATTAAGCCCAATGACTTAA
1 AACTTAATTGTTTAATTTAATCAATT-AGGCCAATGACTTAA
3329602 AACAATTTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
70 10 0.11
71 51 0.55
72 31 0.34
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.38
Consensus pattern (69 bp):
AACTTAATTGTTTAATTTAATCAATTAGGCCAATGACTTAATTAAATAATTTAATCAATTAAGCA
CAAC
Found at i:3329628 original size:32 final size:32
Alignment explanation
Indices: 3329573--3329660 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
3329563 TTAATTGTTT
*
3329573 AATTTAATTAATTAAGCCCAATGACTTAAAAC
1 AATTTAATTAATTAAGCACAATGACTTAAAAC
* * * *
3329605 AATTTAATTAATTACGCATAATGATTTAATTAAAA
1 AATTTAATTAATTAAGCACAATGACTT-A--AAAC
* *
3329640 AATTTATTTAATTAGGCACAA
1 AATTTAATTAATTAAGCACAA
3329661 CTTAATTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
32 23 0.51
33 1 0.02
35 21 0.47
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (32 bp):
AATTTAATTAATTAAGCACAATGACTTAAAAC
Found at i:3329672 original size:67 final size:66
Alignment explanation
Indices: 3329431--3329676 Score: 170
Period size: 67 Copynumber: 3.5 Consensus size: 66
3329421 TTAATTGTTT
* * *
3329431 AATTTAATCAATTAGGCCAAATTACTTAATTAAATAATTTAATTAATTAAGCACAACAATTTAAT
1 AATTTAATTAATTAGGCC--A--ACTTAATTAAACAATTTAATTAATTAAGCACAACGATTTAAT
3329496 TAAACA
62 TAAA-A
* * * * * * * *
3329502 ATTTTAATCAATTAGGTCCAATGACTTAATTAAATAAATTTAATCAATTAGGCCCAAGGACTTAA
1 AATTTAATTAATTAGG-CC-A--ACTTAATTAAA-CAATTTAATTAATTAAGCACAACGATTTAA
****
3329567 TTGTTT
61 TTAAAA
* * * * * *
3329573 AATTTAATTAATTAAGCCCAA-TGACTTAAAACAATTTAATTAATTACGCATAATGATTTAATTA
1 AATTTAATTAATT-AGGCCAACTTAATT-AAACAATTTAATTAATTAAGCACAACGATTTAATTA
3329637 AAA
64 AAA
*
3329640 AATTTATTTAATTAGGCACAACTTAATTAAACAATTT
1 AATTTAATTAATTAGGC-CAACTTAATTAAACAATTT
3329677 TAATCAAGTG
Statistics
Matches: 136, Mismatches: 33, Indels: 16
0.74 0.18 0.09
Matches are distributed among these distances:
66 3 0.02
67 53 0.39
68 8 0.06
70 1 0.01
71 42 0.31
72 29 0.21
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (66 bp):
AATTTAATTAATTAGGCCAACTTAATTAAACAATTTAATTAATTAAGCACAACGATTTAATTAAA
A
Found at i:3348030 original size:17 final size:17
Alignment explanation
Indices: 3348010--3348042 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3348000 TTCTTCATAA
3348010 AATAA-AACTTCTTATTG
1 AATAATAAC-TCTTATTG
3348027 AATAATAACTCTTATT
1 AATAATAACTCTTATT
3348043 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:3348343 original size:29 final size:28
Alignment explanation
Indices: 3348280--3348353 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
3348270 TTTATTATTT
*
3348280 TAAATTAAGACAAACATATTTTTTTCTC
1 TAAATTAAGACAAACATATTTTCTTCTC
* * *
3348308 TAAATTAAGACAAATCTTGTTTTCTTGTC
1 TAAATTAAGACAAA-CATATTTTCTTCTC
*
3348337 TCAATTAAGACAAACAT
1 TAAATTAAGACAAACAT
3348354 GTTAAAGCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 16 0.41
29 23 0.59
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAATTAAGACAAACATATTTTCTTCTC
Found at i:3349502 original size:38 final size:38
Alignment explanation
Indices: 3349451--3349525 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
3349441 AATATACTTG
3349451 TTTTCTAGGGCATCATATTCTTTGAATTCCTAACATTT
1 TTTTCTAGGGCATCATATTCTTTGAATTCCTAACATTT
3349489 TTTTCTAGGGCATCATATTCTTTGAATTCCTAACATT
1 TTTTCTAGGGCATCATATTCTTTGAATTCCTAACATT
3349526 GAATATATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.47
Consensus pattern (38 bp):
TTTTCTAGGGCATCATATTCTTTGAATTCCTAACATTT
Found at i:3366998 original size:59 final size:59
Alignment explanation
Indices: 3366923--3367034 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 59
3366913 TATAAATTTG
** * *
3366923 TCTATTCCATAAAGTGAATGTGACATCATTTAATAATTATGGTCATGGTCATGAATCTA
1 TCTATTCCATAAAGTGAATACGACATCATTTAATAATTATGATCATGGACATGAATCTA
* *
3366982 TCTATTCCCTGAAGTGAATACGACATCATTTAATAATTATGATCATGGACATG
1 TCTATTCCATAAAGTGAATACGACATCATTTAATAATTATGATCATGGACATG
3367035 GAAGAGATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (59 bp):
TCTATTCCATAAAGTGAATACGACATCATTTAATAATTATGATCATGGACATGAATCTA
Found at i:3371300 original size:21 final size:21
Alignment explanation
Indices: 3371276--3371319 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3371266 GAATAAGATC
3371276 TTCTTACTCCCTCTAAATACT
1 TTCTTACTCCCTCTAAATACT
* *
3371297 TTCTTTCTCTCTCTAAATACT
1 TTCTTACTCCCTCTAAATACT
3371318 TT
1 TT
3371320 ATCTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (21 bp):
TTCTTACTCCCTCTAAATACT
Found at i:3372650 original size:21 final size:21
Alignment explanation
Indices: 3372608--3372650 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3372598 TGCGTCTCAG
* *
3372608 TTTATTGGGTTTTGCTTCTTA
1 TTTATTGGGTTATGCTTATTA
3372629 TTTATTGGGTTAATGC-TATTA
1 TTTATTGGGTT-ATGCTTATTA
3372650 T
1 T
3372651 CTTTAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.16, C:0.07, G:0.19, T:0.58
Consensus pattern (21 bp):
TTTATTGGGTTATGCTTATTA
Done.