Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 32 of 32
Found at i:15226109 original size:71 final size:71
Alignment explanation
Indices: 15225976--15226202 Score: 249
Period size: 71 Copynumber: 3.2 Consensus size: 71
15225966 ATTTGTGAAG
* * * * *
15225976 AAAGTATTGATACTTATAAGGAAGGTATTGATACTTGTTGTCCAGAATGTCTTGGGAAGCATTCT
1 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGCCATGGGAAGCATTCT
15226041 GTTTGA
66 GTTTGA
* * * * * *
15226047 AAAGTATCAATACCTATGAGGAAAGTATTCATTCTTGTTGTCCAAAATGCCATGTGG-TGCATTC
1 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGCCATG-GGAAGCATTC
15226111 TGTTTGA
65 TGTTTGA
* * * ** * * *
15226118 AAAGTATCGATACCTACAAAGAAGGTATTGATACTTGTTATCCAAAATGCTTTTAGAAAGTATTC
1 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGC-CATGGGAAGCATTC
*
15226183 TGTTTAA
65 TGTTTGA
15226190 AAAGTATCGATAC
1 AAAGTATCGATAC
15226203 TCATTTCTTA
Statistics
Matches: 127, Mismatches: 26, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
71 100 0.79
72 27 0.21
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (71 bp):
AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGCCATGGGAAGCATTCT
GTTTGA
Found at i:15228073 original size:22 final size:21
Alignment explanation
Indices: 15228046--15228094 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
15228036 CAAAGATTAA
*
15228046 TTTTTAGATTTTTTTCTTATAT
1 TTTTTAGATTCTTTTCTTAT-T
15228068 TTTTTAGATTCTTTTCTTATT
1 TTTTTAGATTCTTTTCTTATT
15228089 TTTTTA
1 TTTTTA
15228095 AAGAGATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTTAGATTCTTTTCTTATT
Found at i:15237078 original size:119 final size:121
Alignment explanation
Indices: 15236862--15237091 Score: 308
Period size: 119 Copynumber: 1.9 Consensus size: 121
15236852 AATTTTTTTC
* *
15236862 AAAATAATAGTTATTTTACTCTTTTTTAAATTTATCCATTTTCTTTTTCTTTGCTTTAATATTTA
1 AAAATAATAGTTATTTCACTCTTTTTTAAATTTATCCATTTTCTATTTCTTT-CTTTAATATTTA
* *
15236927 TAATCTTTTATTTGATTAACAAAAGAGAATTTTAAACA-TTTATAAATTTTGATCTTG
65 CAATCTCTTATTTGATTAACAAAAGAGAATTTTAAACACTTT-TAAATTTTGATCTTG
* * *
15236984 AAAATTATATTTATTTCACTTTTTTTTCAAATTTATCCATTTTC-ATTT-TTT-TTTAATATTTA
1 AAAATAATAGTTATTTCACTCTTTTTT-AAATTTATCCATTTTCTATTTCTTTCTTTAATATTTA
* *
15237046 CAATCTCTTATTTGATTAATAAAAGA-AGATTTTGAACACTTTTAAA
65 CAATCTCTTATTTGATTAACAAAAGAGA-ATTTTAAACACTTTTAAA
15237092 CGAAGAGAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
118 1 0.01
119 47 0.49
120 3 0.03
121 3 0.03
122 26 0.27
123 16 0.17
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (121 bp):
AAAATAATAGTTATTTCACTCTTTTTTAAATTTATCCATTTTCTATTTCTTTCTTTAATATTTAC
AATCTCTTATTTGATTAACAAAAGAGAATTTTAAACACTTTTAAATTTTGATCTTG
Found at i:15242332 original size:21 final size:21
Alignment explanation
Indices: 15242302--15242357 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
15242292 TTCCAAGAGT
15242302 TATCAAATTAGTTATTTT-GG
1 TATCAAATTAGTTATTTTAGG
* *
15242322 TACTTAAATTAGTTATTTTAGT
1 TA-TCAAATTAGTTATTTTAGG
15242344 TATCAAATTAGTTA
1 TATCAAATTAGTTA
15242358 ATGGTTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (21 bp):
TATCAAATTAGTTATTTTAGG
Found at i:15242369 original size:23 final size:21
Alignment explanation
Indices: 15242299--15242371 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
15242289 GCATTCCAAG
15242299 AGTTATCAAATTAGTTAT-TT
1 AGTTATCAAATTAGTTATGTT
* * * *
15242319 TGGTACTTAAATTAGTTATTTT
1 AGTTA-TCAAATTAGTTATGTT
15242341 AGTTATCAAATTAGTTAATGGTT
1 AGTTATCAAATTAGTT-AT-GTT
15242364 AGTTATCA
1 AGTTATCA
15242372 CATTTTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.07
21 22 0.52
22 7 0.17
23 10 0.24
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
AGTTATCAAATTAGTTATGTT
Found at i:15250355 original size:32 final size:32
Alignment explanation
Indices: 15250314--15250380 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
15250304 GACTAAGTCG
* * *
15250314 TCTGTCTCTGAAC-CTAGTTTCTAGTAGTAGGC
1 TCTGTCTCTGAACTC-AATTTCTAGCAGTAGCC
15250346 TCTGTCTCTGAACTCAATTTCTAGCAGTAGCC
1 TCTGTCTCTGAACTCAATTTCTAGCAGTAGCC
15250378 TCT
1 TCT
15250381 TAGTCGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.37
Consensus pattern (32 bp):
TCTGTCTCTGAACTCAATTTCTAGCAGTAGCC
Found at i:15297979 original size:31 final size:32
Alignment explanation
Indices: 15297941--15298021 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 32
15297931 CCATTTATTC
15297941 AAAACTAATCGAGTAAACACTTCCAAAAA-AA
1 AAAACTAATCGAGTAAACACTTCCAAAAAGAA
*
15297972 AAAACTAATCGAGTAAACATTTCCAAAAAGAA
1 AAAACTAATCGAGTAAACACTTCCAAAAAGAA
*
15298004 AAAACTAATTGAGTAAAC
1 AAAACTAATCGAGTAAAC
15298022 TCATATTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 28 0.60
32 19 0.40
ACGTcount: A:0.57, C:0.16, G:0.09, T:0.19
Consensus pattern (32 bp):
AAAACTAATCGAGTAAACACTTCCAAAAAGAA
Found at i:15300526 original size:78 final size:77
Alignment explanation
Indices: 15300388--15300552 Score: 197
Period size: 78 Copynumber: 2.1 Consensus size: 77
15300378 AATGCTATCT
* * * * *
15300388 ATTTTAATTTTAGTTGATTCATAAAAAAGTAGAAAATTTTTTCCAACTTTAAAAATATTCCTTAA
1 ATTTTAATTTTAGGTGATTCATAAAAAAGTAGAAAATTGTTTCCAACTTCAAAAAAATTCCTAAA
* *
15300453 ATTAAGGATGGAA
66 ATGAAGGATAG-A
* * * *
15300466 ATTTTAATTTTGGGTGATTCATAAAGAA-TAGGAAATTGTTTCCTACTTCAAAAGAAATTCCTAA
1 ATTTTAATTTTAGGTGATTCATAAAAAAGTAGAAAATTGTTTCCAACTTCAAAA-AAATTCCTAA
*
15300530 AATGAAGGATAGT
65 AATGAAGGATAGA
15300543 ATTTTAATTT
1 ATTTTAATTT
15300553 AAGAAATTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
77 31 0.42
78 43 0.58
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (77 bp):
ATTTTAATTTTAGGTGATTCATAAAAAAGTAGAAAATTGTTTCCAACTTCAAAAAAATTCCTAAA
ATGAAGGATAGA
Found at i:15311601 original size:68 final size:68
Alignment explanation
Indices: 15311529--15311743 Score: 279
Period size: 68 Copynumber: 3.2 Consensus size: 68
15311519 CATTCCAATT
* * **
15311529 GCATTCATCATGCATACTTAATTACCTTATATGGTATATGGAATTCGCATCATATACACAATATT
1 GCATTCATCATGCATACTTAATCATCTTATATGGTATATGGAATTTACATCATATACACAATATT
15311594 ATG
66 ATG
* * * * * *
15311597 GCATTGATCATACATACTTAATCATCTTATATGGTATATGAAATTTACATTATATACACATTTTT
1 GCATTCATCATGCATACTTAATCATCTTATATGGTATATGGAATTTACATCATATACACAATATT
15311662 ATG
66 ATG
* ** * *
15311665 GCATTCATCATGCATACTTAATCATCTCATATGGTGGATGGAATTTACATCATATACCCAATCTT
1 GCATTCATCATGCATACTTAATCATCTTATATGGTATATGGAATTTACATCATATACACAATATT
15311730 ATG
66 ATG
15311733 GCAATT-ATCAT
1 GC-ATTCATCAT
15311744 ACCAAACATG
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
68 123 0.98
69 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.38
Consensus pattern (68 bp):
GCATTCATCATGCATACTTAATCATCTTATATGGTATATGGAATTTACATCATATACACAATATT
ATG
Found at i:15311669 original size:136 final size:136
Alignment explanation
Indices: 15311471--15311745 Score: 345
Period size: 136 Copynumber: 2.0 Consensus size: 136
15311461 ACATCAATTG
* * *
15311471 TACATGCTTAATCATCTTATGTAGTATACGAAATCTACATCATACAAACATTCCAATTGCATTCA
1 TACATACTTAATCATCTTATATAGTATACGAAATCTACATCATACAAACATTCCAATGGCATTCA
* * * *
15311536 TCATGCATACTTAATTACCTTATATGGTATATGGAATTCGCATCATATACACAATATTATGGC-A
66 TCATGCATACTTAATCACCTCATATGGTAGATGGAATTCACATCATATACACAATATTATGGCAA
15311600 TTGATCA
131 TT-ATCA
* * * * * * ***
15311607 TACATACTTAATCATCTTATATGGTATATGAAATTTACATTATATACACATTTTTATGGCATTCA
1 TACATACTTAATCATCTTATATAGTATACGAAATCTACATCATACAAACATTCCAATGGCATTCA
* * * * *
15311672 TCATGCATACTTAATCATCTCATATGGTGGATGGAATTTACATCATATACCCAATCTTATGGCAA
66 TCATGCATACTTAATCACCTCATATGGTAGATGGAATTCACATCATATACACAATATTATGGCAA
15311737 TTATCA
131 TTATCA
15311743 TAC
1 TAC
15311746 CAAACATGCA
Statistics
Matches: 117, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
136 114 0.97
137 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (136 bp):
TACATACTTAATCATCTTATATAGTATACGAAATCTACATCATACAAACATTCCAATGGCATTCA
TCATGCATACTTAATCACCTCATATGGTAGATGGAATTCACATCATATACACAATATTATGGCAA
TTATCA
Found at i:15314914 original size:37 final size:34
Alignment explanation
Indices: 15314844--15315028 Score: 167
Period size: 36 Copynumber: 5.1 Consensus size: 34
15314834 AAGATTCTTT
*
15314844 CTTTTTAACGAGATCCAA-TGATAACCTTTACACTTG
1 CTTTTTAATG-GAT-CAAGTGATAACC-TTACACTTG
**
15314880 CTTTTTAATGAGATCAAAGCAATAACTCTTACACTTG
1 CTTTTTAATG-GATC-AAGTGATAAC-CTTACACTTG
*
15314917 CTTTTTAATGTGATCGAGTGATAACCCTTACACTTG
1 CTTTTTAATG-GATCAAGTGATAA-CCTTACACTTG
*
15314953 CTTTTTAACGGAATCAAGTGATAAACCTTACACTTG
1 CTTTTTAATGG-ATCAAGTGAT-AACCTTACACTTG
* * * *
15314989 CTTTTTTATAGGATCCAGTGGTATCCCTTACACTTG
1 CTTTTTAAT-GGATCAAGTGATA-ACCTTACACTTG
15315025 -TTTT
1 CTTTT
15315029 CTCACATGAC
Statistics
Matches: 127, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
35 7 0.06
36 86 0.68
37 33 0.26
38 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (34 bp):
CTTTTTAATGGATCAAGTGATAACCTTACACTTG
Found at i:15315024 original size:72 final size:73
Alignment explanation
Indices: 15314844--15315028 Score: 209
Period size: 73 Copynumber: 2.6 Consensus size: 73
15314834 AAGATTCTTT
* * * * *
15314844 CTTTTTAACGAGATCCAATGATAACCTTTACACTTGCTTTTTAATGAGATCAAAGCAATAACTCT
1 CTTTTTAATGTGATCCAGTGATAACCCTTACACTTGCTTTTTAAGGAGATCAAAGCAATAACTCT
15314909 TACACTTG
66 TACACTTG
* **
15314917 CTTTTTAATGTGATCGAGTGATAACCCTTACACTTGCTTTTTAACGGA-ATC-AAGTGATAAAC-
1 CTTTTTAATGTGATCCAGTGATAACCCTTACACTTGCTTTTTAA-GGAGATCAAAGCAAT-AACT
15314979 CTTACACTTG
64 CTTACACTTG
* * *
15314989 CTTTTTTATAG-GATCCAGTGGTATCCCTTACACTTG-TTTT
1 CTTTTTAAT-GTGATCCAGTGATAACCCTTACACTTGCTTTT
15315029 CTCACATGAC
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
71 4 0.04
72 45 0.46
73 46 0.47
74 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (73 bp):
CTTTTTAATGTGATCCAGTGATAACCCTTACACTTGCTTTTTAAGGAGATCAAAGCAATAACTCT
TACACTTG
Found at i:15316809 original size:37 final size:36
Alignment explanation
Indices: 15316718--15316809 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
15316708 CATTGCTTTT
**
15316718 TTAA-GATCAAGCACAACCTTTACAATGAAAATGCC
1 TTAAGGATCAAGCACAACCTTTACAACCAAAATGCC
* * *
15316753 TTAAGGTTCAAGCATAACCTTTAC-ACCCAAATGCC
1 TTAAGGATCAAGCACAACCTTTACAACCAAAATGCC
15316788 TTTCAAGGATCAAGCACAACCT
1 -TT-AAGGATCAAGCACAACCT
15316810 ATCATGACCC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 12 0.26
36 19 0.40
37 16 0.34
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (36 bp):
TTAAGGATCAAGCACAACCTTTACAACCAAAATGCC
Found at i:15324063 original size:35 final size:35
Alignment explanation
Indices: 15323988--15324243 Score: 347
Period size: 35 Copynumber: 7.3 Consensus size: 35
15323978 TCTCAAGCAC
15323988 TTGATTAAAATTGTTTAATTAAGTTA-T--GCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
15324021 TTCATTAAATTGTTTAATTAAGTCATTGAGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* **** *
15324056 TTTATTAAATTAAACAACTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
15324091 TTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* * *
15324127 TTAATTAAATTATTTAATTAAGTTATTAGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
*
15324162 TTGATTAAATTTTTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
15324198 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
15324233 TTGATTAAATT
1 TTGATTAAATT
15324244 AAATAATTAA
Statistics
Matches: 195, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
32 18 0.09
33 6 0.03
35 109 0.56
36 62 0.32
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:15324125 original size:71 final size:71
Alignment explanation
Indices: 15323995--15324243 Score: 353
Period size: 71 Copynumber: 3.6 Consensus size: 71
15323985 CACTTGATTA
* * * *
15323995 AAATTGTTTAATTAAGTTA-T--GCCTAATTCATTAAA-TTGTTTAATTAAGTCATTGAGCCTAA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAA
*
15324056 TTTATT
66 TTAATT
*** *
15324062 AAATTAAACAACTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAA
15324127 TTAATT
66 TTAATT
* *
15324133 AAATTATTTAATTAAGTTATTAGGCCTAATTGATTAAATTTTTTTAATTAAGTTATTGGGCCTAA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAA
*
15324198 TTGATT
66 TTAATT
*
15324204 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATT
15324244 AAATAATTAA
Statistics
Matches: 160, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
67 14 0.09
68 1 0.01
70 14 0.09
71 131 0.82
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (71 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAA
TTAATT
Found at i:15324160 original size:106 final size:106
Alignment explanation
Indices: 15323988--15324253 Score: 362
Period size: 106 Copynumber: 2.5 Consensus size: 106
15323978 TCTCAAGCAC
* *
15323988 TTGATTAAAATTGTTTAATTAAGTTA-T--GCCTAATTCATTAAATTGTTTAATTAAGTCATTGA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTATTTAATTAAGTCATTGA
*
15324050 GCCTAATTTATTAAA-TTAAACAACTAAGTTATTGGGCCTAA
65 GCCTAATTGATTAAATTTAAACAACTAAGTTATTGGGCCTAA
*
15324091 TTGATTAAATTTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTATTTAATTAAGTTATT-A
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTATTTAATTAAGTCATTGA
**** *
15324155 GGCCTAATTGATTAAATTTTTTTAATTAAGTTATTGGGCCTAA
65 -GCCTAATTGATTAAATTTAAACAACTAAGTTATTGGGCCTAA
* **
15324198 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAATAATTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTATTTAATTAA
15324254 ATTAATTGGG
Statistics
Matches: 145, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
102 3 0.02
103 22 0.15
104 1 0.01
105 1 0.01
106 88 0.61
107 30 0.21
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (106 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTATTTAATTAAGTCATTGAG
CCTAATTGATTAAATTTAAACAACTAAGTTATTGGGCCTAA
Found at i:15324198 original size:18 final size:18
Alignment explanation
Indices: 15324177--15324234 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
15324167 TAAATTTTTT
15324177 TAATTAAGTTATTGGGCC
1 TAATTAAGTTATTGGGCC
* **
15324195 TAATTGA-TTAAATT--GTT
1 TAATTAAGTT--ATTGGGCC
15324212 TAATTAAGTTATTGGGCC
1 TAATTAAGTTATTGGGCC
15324230 TAATT
1 TAATT
15324235 GATTAAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
16 3 0.10
17 9 0.31
18 14 0.48
19 3 0.10
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (18 bp):
TAATTAAGTTATTGGGCC
Found at i:15329923 original size:20 final size:20
Alignment explanation
Indices: 15329898--15329937 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
15329888 CAAAATTGAG
15329898 CCTTCACTTAGTTTCTCTTT
1 CCTTCACTTAGTTTCTCTTT
*
15329918 CCTTCACTTGGTTTCTCTTT
1 CCTTCACTTAGTTTCTCTTT
15329938 TTTTTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.55
Consensus pattern (20 bp):
CCTTCACTTAGTTTCTCTTT
Found at i:15332764 original size:84 final size:84
Alignment explanation
Indices: 15332666--15332835 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
15332656 GGACTCATAT
15332666 AACACCTTGCCCCTTGTGATGTTAATTAAATTAATTGCCAATAAAGATGAATTGTGGCTATTATT
1 AACACCTTGCCCCTTGTGATGTTAATTAAATTAATTGCCAATAAAGATGAATTGTGGCTATTATT
15332731 GATGAGAAAAGTTTTGTGA
66 GATGAGAAAAGTTTTGTGA
15332750 AACACCTTGCCCCTTGTGATGTTAATTAAATTAATTGCCAATAAAGATGAATTGTGGCTATTATT
1 AACACCTTGCCCCTTGTGATGTTAATTAAATTAATTGCCAATAAAGATGAATTGTGGCTATTATT
15332815 GATGAGAAAAGTTTTGTGA
66 GATGAGAAAAGTTTTGTGA
15332834 AA
1 AA
15332836 GTAGAGAACT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (84 bp):
AACACCTTGCCCCTTGTGATGTTAATTAAATTAATTGCCAATAAAGATGAATTGTGGCTATTATT
GATGAGAAAAGTTTTGTGA
Found at i:15351404 original size:16 final size:16
Alignment explanation
Indices: 15351385--15351415 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15351375 AGGAATGAGA
*
15351385 GAAGATGAGAAAGGAG
1 GAAGATGAAAAAGGAG
15351401 GAAGATGAAAAAGGA
1 GAAGATGAAAAAGGA
15351416 AAGGGAAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
GAAGATGAAAAAGGAG
Found at i:15365716 original size:15 final size:17
Alignment explanation
Indices: 15365687--15365721 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
15365677 TATATATATT
15365687 TTTTAACACTATAAATA
1 TTTTAACACTATAAATA
15365704 TTTT-ACACT-TAAATA
1 TTTTAACACTATAAATA
15365719 TTT
1 TTT
15365722 GAATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAACACTATAAATA
Found at i:15366130 original size:29 final size:29
Alignment explanation
Indices: 15366095--15366160 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
15366085 ATCAATGGAT
* *
15366095 TAAATTGCTTCAATTTCGAATACAAAGAC
1 TAAATTGATTCAATTTCGAATAAAAAGAC
*
15366124 TAAATTGATTCAATTTTGAATAAAAAGAC
1 TAAATTGATTCAATTTCGAATAAAAAGAC
15366153 TAAATTGA
1 TAAATTGA
15366161 ACCAAATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (29 bp):
TAAATTGATTCAATTTCGAATAAAAAGAC
Found at i:15372535 original size:49 final size:49
Alignment explanation
Indices: 15372482--15372622 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 49
15372472 CAAGTATCCT
* * ** * * *
15372482 TTGTGGAAAGGTTATCATTTCCCGTTAAGAAGAAAGAATCCTTTGTGGA
1 TTGTGTAAAAGTTATCGCTTCCCGTTAAAAAGCAAGAATCCTTTATGGA
** *
15372531 TTGTGTAAAAGTTATCGCTTCTTGTTAAAAAGCAATAATCTCTTTATGGA
1 TTGTGTAAAAGTTATCGCTTCCCGTTAAAAAGCAAGAATC-CTTTATGGA
*
15372581 TTGTGTAAAAGTTATCGCTT-CCATTAAAAAGCAAGAATCCTT
1 TTGTGTAAAAGTTATCGCTTCCCGTTAAAAAGCAAGAATCCTT
15372623 GATAGTGGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
48 3 0.04
49 46 0.60
50 28 0.36
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (49 bp):
TTGTGTAAAAGTTATCGCTTCCCGTTAAAAAGCAAGAATCCTTTATGGA
Found at i:15372587 original size:50 final size:48
Alignment explanation
Indices: 15372506--15372622 Score: 162
Period size: 50 Copynumber: 2.4 Consensus size: 48
15372496 TCATTTCCCG
* * * **
15372506 TTAAGAAGAAAGAATCCTTTGTGGATTGTGTAAAAGTTATCGCTTCTTG
1 TTAAAAAGCAAGAATCCTTTATGGATTGTGTAAAAGTTATCGCTTC-CA
*
15372555 TTAAAAAGCAATAATCTCTTTATGGATTGTGTAAAAGTTATCGCTTCCA
1 TTAAAAAGCAAGAATC-CTTTATGGATTGTGTAAAAGTTATCGCTTCCA
15372604 TTAAAAAGCAAGAATCCTT
1 TTAAAAAGCAAGAATCCTT
15372623 GATAGTGGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
48 3 0.05
49 28 0.47
50 29 0.48
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (48 bp):
TTAAAAAGCAAGAATCCTTTATGGATTGTGTAAAAGTTATCGCTTCCA
Found at i:15377937 original size:67 final size:67
Alignment explanation
Indices: 15377804--15377938 Score: 150
Period size: 67 Copynumber: 2.0 Consensus size: 67
15377794 TCTGTGATAT
* * *
15377804 TCTTACCCCAACACTGAGATTCATTAGAGGAAAAGATGGCATGTTCCCTAATCTTATCCTTATGG
1 TCTTACCCCAACACTGAGATTCATAAGAGGAAAAGATGGCACGTTCCCTAATCTTAACCTTATGG
15377869 TA
66 TA
* * * * *
15377871 TCTTACCCCAA-ACTGAGCTTTTATAAGGGGAACAGATGGCACGTTCTCC-AAT-TTCAACCTTG
1 TCTTACCCCAACACTGAG-ATTCATAAGAGGAAAAGATGGCACGTTC-CCTAATCTT-AACCTTA
15377933 TGGTA
63 TGGTA
15377938 T
1 T
15377939 TCTTGTCCAC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
66 8 0.14
67 47 0.82
68 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (67 bp):
TCTTACCCCAACACTGAGATTCATAAGAGGAAAAGATGGCACGTTCCCTAATCTTAACCTTATGG
TA
Found at i:15380024 original size:18 final size:18
Alignment explanation
Indices: 15379992--15380051 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
15379982 TAAATAAAGT
15379992 AAATGAAAAATTAAAATAAC
1 AAAT-AAAAA-TAAAATAAC
* *
15380012 AAATAAAAATAAACTAAT
1 AAATAAAAATAAAATAAC
*
15380030 AAAT-AAAACAAAATAAC
1 AAATAAAAATAAAATAAC
15380047 TAAAT
1 -AAAT
15380052 TCTAGCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.29
18 15 0.44
19 5 0.15
20 4 0.12
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAAAATAAAATAAC
Found at i:15380281 original size:20 final size:20
Alignment explanation
Indices: 15380240--15380291 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
15380230 CTCTGTTGCT
* *
15380240 ATCTATCGATAGATTTGGCC
1 ATCTATCGATAGATCTGACC
*
15380260 ATCTATGGATAGATCTGACC
1 ATCTATCGATAGATCTGACC
* *
15380280 ATTTATTGATAG
1 ATCTATCGATAG
15380292 CTGTTCTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
ATCTATCGATAGATCTGACC
Found at i:15382052 original size:12 final size:12
Alignment explanation
Indices: 15382043--15382080 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
15382033 GTCGCGGGGG
15382043 GCGGCGCGGGCC
1 GCGGCGCGGGCC
15382055 GCGGCGCGCGGCC
1 GCGGCGCG-GGCC
15382068 TGCGG-GCGGGCC
1 -GCGGCGCGGGCC
15382080 G
1 G
15382081 GCCTGCGCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.04
12 12 0.50
13 7 0.29
14 4 0.17
ACGTcount: A:0.00, C:0.39, G:0.58, T:0.03
Consensus pattern (12 bp):
GCGGCGCGGGCC
Found at i:15382097 original size:25 final size:26
Alignment explanation
Indices: 15382042--15382098 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
15382032 CGTCGCGGGG
* *
15382042 GGCGGCGCGGGCCGCGGCGCGCGGCC
1 GGCGGCGCGGGCCGCGCCGCGCGCCC
*
15382068 TGCGG-GCGGGCCG-GCCTGCGCGCCC
1 GGCGGCGCGGGCCGCGCC-GCGCGCCC
15382093 GGCGGC
1 GGCGGC
15382099 CACCGCCGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 2 0.08
25 19 0.76
26 4 0.16
ACGTcount: A:0.00, C:0.42, G:0.54, T:0.04
Consensus pattern (26 bp):
GGCGGCGCGGGCCGCGCCGCGCGCCC
Found at i:15384791 original size:20 final size:20
Alignment explanation
Indices: 15384758--15384809 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
15384748 TGATGAACAG
* * *
15384758 CTATCAATAAATGGTCAGAT
1 CTATCAATAGATGGCCACAT
*
15384778 CTATCCATAGATGGCCACAT
1 CTATCAATAGATGGCCACAT
*
15384798 CTATCGATAGAT
1 CTATCAATAGAT
15384810 AGCAACTAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (20 bp):
CTATCAATAGATGGCCACAT
Found at i:15387628 original size:69 final size:68
Alignment explanation
Indices: 15387527--15387709 Score: 151
Period size: 67 Copynumber: 2.7 Consensus size: 68
15387517 GTGAACATAT
* * *
15387527 CATCTATTCCCCGTATAAAAGCT-TGATATGGGGATAAGAATATCACAAGGTTGAA-ATT-GGAG
1 CATCTATTCCCCTTATAAAAGCTCAG-TATGGGG-TAAGAATATCACAAGGAT-AAGATTAGG-G
*
15387589 AACGTGC
62 AACATGC
* * * * *
15387596 CATCTCTTCCCCTTATAAAAGCTCAGTTTGGGGTAA-AATACCATAGGGATAAGATTAGGGAACA
1 CATCTATTCCCCTTATAAAAGCTCAGTATGGGGTAAGAATATCACAAGGATAAGATTAGGGAACA
15387660 TGC
66 TGC
* * * * * *
15387663 CATCTTTTCCTCTAAT-GAATCTCAGTGTGGGGGTAAGAATATCACAA
1 CATCTATTCCCCTTATAAAAGCTCAGTAT-GGGGTAAGAATATCACAA
15387710 AATTAAGTTG
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
66 11 0.12
67 40 0.44
68 12 0.13
69 27 0.30
70 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (68 bp):
CATCTATTCCCCTTATAAAAGCTCAGTATGGGGTAAGAATATCACAAGGATAAGATTAGGGAACA
TGC
Found at i:15391613 original size:44 final size:44
Alignment explanation
Indices: 15391549--15391651 Score: 127
Period size: 44 Copynumber: 2.4 Consensus size: 44
15391539 TGACAAAAGT
* * * **
15391549 GTGA-GAAAATAGTGATAATATTCTTTTATTGTGACAAATACAA
1 GTGACGAAATTAGTGACAATATTATCATATTGTGACAAATACAA
* **
15391592 GTGACGGAATTAGTGACAATATTATCATATTGTGACAAATATTA
1 GTGACGAAATTAGTGACAATATTATCATATTGTGACAAATACAA
15391636 GTGACGAAATTAGTGA
1 GTGACGAAATTAGTGA
15391652 TGAAATAGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (44 bp):
GTGACGAAATTAGTGACAATATTATCATATTGTGACAAATACAA
Found at i:15399361 original size:6 final size:6
Alignment explanation
Indices: 15399350--15399390 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
15399340 TATGTGTTTA
*
15399350 TATATG TATATG TATATG TATATGTG TATATA TATATG TAT
1 TATATG TATATG TATATG TATA--TG TATATG TATATG TAT
15399391 GATTTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 25 0.81
8 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:15399377 original size:14 final size:14
Alignment explanation
Indices: 15399350--15399388 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
15399340 TATGTGTTTA
15399350 TATATGTATA--TG
1 TATATGTATATGTG
15399362 TATATGTATATGTG
1 TATATGTATATGTG
*
15399376 TATATATATATGT
1 TATATGTATATGT
15399389 ATGATTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (14 bp):
TATATGTATATGTG
Found at i:15399377 original size:20 final size:20
Alignment explanation
Indices: 15399348--15399390 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
15399338 ATTATGTGTT
*
15399348 TATATATGTATATGTATATG
1 TATATATGTATATATATATG
*
15399368 TATATGTGTATATATATATG
1 TATATATGTATATATATATG
15399388 TAT
1 TAT
15399391 GATTTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (20 bp):
TATATATGTATATATATATG
Found at i:15400238 original size:27 final size:27
Alignment explanation
Indices: 15400161--15400238 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
15400151 TGCAAAAATT
* *
15400161 TTTTCTGCACGCCAAGTTCAAAAACAG
1 TTTTCTACATGCCAAGTTCAAAAACAG
* * ** * *
15400188 TTTGCTACATACCATTCTTGAAAAAGA-
1 TTTTCTACATGCCA-AGTTCAAAAACAG
15400215 TTTTCTACATGCCAAGTTCAAAAA
1 TTTTCTACATGCCAAGTTCAAAAA
15400239 TTTTGCTATA
Statistics
Matches: 37, Mismatches: 13, Indels: 3
0.70 0.25 0.06
Matches are distributed among these distances:
26 7 0.19
27 22 0.59
28 8 0.22
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (27 bp):
TTTTCTACATGCCAAGTTCAAAAACAG
Found at i:15407059 original size:42 final size:40
Alignment explanation
Indices: 15407011--15407093 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 40
15407001 TCGCCCCCCT
*
15407011 CCTCCACGAGTCCCGATTCCCCCGCCCCCCTCCCACGGGTCC
1 CCTCCACGAGTCCCGATT-CCCCGCCCCCCT-CCACGAGTCC
*
15407053 CCTCCACGAGTCCCGATTCCCCGGCCCCCTCCACGAGTCC
1 CCTCCACGAGTCCCGATTCCCCGCCCCCCTCCACGAGTCC
15407093 C
1 C
15407094 AATTCCGCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 10 0.26
41 11 0.28
42 18 0.46
ACGTcount: A:0.11, C:0.58, G:0.17, T:0.14
Consensus pattern (40 bp):
CCTCCACGAGTCCCGATTCCCCGCCCCCCTCCACGAGTCC
Found at i:15407107 original size:27 final size:27
Alignment explanation
Indices: 15407051--15407107 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
15407041 TCCCACGGGT
* *
15407051 CCCCTCCACGAGTCCCGATTCCCCGGC
1 CCCCTCCACGAGTCCCAATTCCCCGCC
*
15407078 CCCCTCCACGAGTCCCAATTCCGC-CC
1 CCCCTCCACGAGTCCCAATTCCCCGCC
15407104 CCCC
1 CCCC
15407108 ACTCAAGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.12, C:0.60, G:0.14, T:0.14
Consensus pattern (27 bp):
CCCCTCCACGAGTCCCAATTCCCCGCC
Found at i:15409597 original size:12 final size:13
Alignment explanation
Indices: 15409580--15409612 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15409570 TACATAGATA
15409580 AAGAAAATA-AGC
1 AAGAAAATAGAGC
*
15409592 AAGAAAAAAGAGC
1 AAGAAAATAGAGC
15409605 AAGAAAAT
1 AAGAAAAT
15409613 GAAAGAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.70, C:0.06, G:0.18, T:0.06
Consensus pattern (13 bp):
AAGAAAATAGAGC
Found at i:15410294 original size:16 final size:15
Alignment explanation
Indices: 15410263--15410314 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
15410253 AGGAGAAAAG
*
15410263 AAGAAAAAGATATAA
1 AAGAAAAAAATATAA
*
15410278 AAGGAAAAAAATTTAA
1 AA-GAAAAAAATATAA
*
15410294 AA-AAAAAAATGAAAA
1 AAGAAAAAAAT-ATAA
15410309 AAGAAA
1 AAGAAA
15410315 GAGAGGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 8 0.27
15 6 0.20
16 16 0.53
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAGAAAAAAATATAA
Found at i:15414121 original size:107 final size:109
Alignment explanation
Indices: 15413923--15414140 Score: 316
Period size: 107 Copynumber: 2.0 Consensus size: 109
15413913 CCCATCAAAT
* * *
15413923 ACAAGGACTAAAAATGCAGAAACCAAAGAAAACAGGAAACTGACTAGCTCAATAAATGAGGGAAA
1 ACAAGGACT-AAAATGCAGAAACCAAAGAAAACAGGAAAATGACTAGCTCAAGAAACGAGGGAAA
* *
15413988 CATCAAGAGCTTGAGTAAAATACCTAAATCATGGTGAACCACTTC
65 CATCAAGAGCTTGACTAAAATACCTAAAACATGGTGAACCACTTC
* *
15414033 ACAAGGACT-AAATGCAGAAGCCAAA-ATAAA-AGGAAAATGACTAGCTCAAGAAACGAGGGAAG
1 ACAAGGACTAAAATGCAGAAACCAAAGA-AAACAGGAAAATGACTAGCTCAAGAAACGAGGGAAA
* *
15414095 CATTAAGAGCTTGACTGAAATACCTAAAACATGGTGAACCACTTC
65 CATCAAGAGCTTGACTAAAATACCTAAAACATGGTGAACCACTTC
15414140 A
1 A
15414141 AAGAAAAGCC
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
107 71 0.72
108 18 0.18
110 9 0.09
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (109 bp):
ACAAGGACTAAAATGCAGAAACCAAAGAAAACAGGAAAATGACTAGCTCAAGAAACGAGGGAAAC
ATCAAGAGCTTGACTAAAATACCTAAAACATGGTGAACCACTTC
Found at i:15416019 original size:24 final size:23
Alignment explanation
Indices: 15415992--15416036 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
15415982 CAAATATTTA
15415992 TACATGTTAAGCATCCTATATTGG
1 TACATGTTAAGCATCCT-TATTGG
*
15416016 TACATGTTAAGTATCCTTATT
1 TACATGTTAAGCATCCTTATT
15416037 TGAGAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (23 bp):
TACATGTTAAGCATCCTTATTGG
Found at i:15418109 original size:21 final size:21
Alignment explanation
Indices: 15418085--15418154 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
15418075 TAGAAATTAT
15418085 AAAATCAATATTTTAAATTTA
1 AAAATCAATATTTTAAATTTA
**
15418106 AAAATCAA-ATTAAAAATTTATAA
1 AAAATCAATATTTTAAA-TT-T-A
* * *
15418129 AAAATTAATATTTTTAATCTA
1 AAAATCAATATTTTAAATTTA
15418150 AAAAT
1 AAAAT
15418155 TAAATTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.16
21 16 0.42
22 2 0.05
23 9 0.24
24 5 0.13
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATCAATATTTTAAATTTA
Found at i:15418115 original size:26 final size:26
Alignment explanation
Indices: 15418040--15418115 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
15418030 AAATAATTAT
* *
15418040 TATTTTAAATTTAAAAAATTAAATTAA
1 TATTTTAAATTT-AAAAATAAAATCAA
* ** *
15418067 AATTTT-AATAGAAATTATAAAATCAA
1 TATTTTAAATTTAAA-AATAAAATCAA
*
15418093 TATTTTAAATTTAAAAATCAAAT
1 TATTTTAAATTTAAAAATAAAAT
15418116 TAAAAATTTA
Statistics
Matches: 36, Mismatches: 11, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
25 3 0.08
26 22 0.61
27 11 0.31
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (26 bp):
TATTTTAAATTTAAAAATAAAATCAA
Found at i:15418122 original size:20 final size:22
Alignment explanation
Indices: 15418081--15418130 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
15418071 TTAATAGAAA
**
15418081 TTATAAAATCAATATTTTAAAT
1 TTATAAAATCAATATTAAAAAT
15418103 TTA-AAAATCAA-ATTAAAAAT
1 TTATAAAATCAATATTAAAAAT
15418123 TTATAAAA
1 TTATAAAA
15418131 AATTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 12 0.48
22 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TTATAAAATCAATATTAAAAAT
Found at i:15418125 original size:26 final size:26
Alignment explanation
Indices: 15418043--15418125 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
15418033 TAATTATTAT
*
15418043 TTTAAATTTAAAAAATTAAATT-AAAA
1 TTTAAATTT-AAAAATAAAATTAAAAA
* ** * * * *
15418069 TTTTAATAGAAATTATAAAATCAATAT
1 TTTAAATTTAAA-AATAAAATTAAAAA
*
15418096 TTTAAATTTAAAAATCAAATTAAAAA
1 TTTAAATTTAAAAATAAAATTAAAAA
15418122 TTTA
1 TTTA
15418126 TAAAAAATTA
Statistics
Matches: 39, Mismatches: 16, Indels: 4
0.66 0.27 0.07
Matches are distributed among these distances:
25 3 0.08
26 25 0.64
27 11 0.28
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (26 bp):
TTTAAATTTAAAAATAAAATTAAAAA
Found at i:15418133 original size:44 final size:44
Alignment explanation
Indices: 15418085--15418169 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
15418075 TAGAAATTAT
*
15418085 AAAATCAATATTTTAAATTTAAAAATCAAATTAAAAATTTATAA
1 AAAATCAATATTTTAAATCTAAAAATCAAATTAAAAATTTATAA
* * * *
15418129 AAAATTAATATTTTTAATCTAAAAATTAAATTAAAATTTTA
1 AAAATCAATATTTTAAATCTAAAAATCAAATTAAAAATTTA
15418170 AATAGTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (44 bp):
AAAATCAATATTTTAAATCTAAAAATCAAATTAAAAATTTATAA
Found at i:15418587 original size:40 final size:37
Alignment explanation
Indices: 15418533--15418614 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 37
15418523 CAAGAGGAGC
*
15418533 AAGCATAACCTCACAACA-TCAATGCCTTTTCAAGTTTA
1 AAGCATAACCTCACAA-AGTCAATGCCTTTTAAAG-TTA
**
15418571 AAGCATAACCTTTCACAAAGTCTTTGCCTTTTAAAGTTA
1 AAGCATAACC--TCACAAAGTCAATGCCTTTTAAAGTTA
15418610 AAGCA
1 AAGCA
15418615 CAACTTCTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 10 0.26
39 9 0.24
40 19 0.50
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (37 bp):
AAGCATAACCTCACAAAGTCAATGCCTTTTAAAGTTA
Found at i:15421282 original size:11 final size:11
Alignment explanation
Indices: 15421268--15421311 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 11
15421258 AAAAAGAATG
15421268 AAGAAAGGAGA
1 AAGAAAGGAGA
15421279 AAGAAAGAACGAAGA
1 AAGAAAG---G-AGA
15421294 AAGAAAGGAGA
1 AAGAAAGGAGA
15421305 AAGAAAG
1 AAGAAAG
15421312 AATGAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 17 0.59
12 1 0.03
14 1 0.03
15 10 0.34
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (11 bp):
AAGAAAGGAGA
Found at i:15421303 original size:26 final size:25
Alignment explanation
Indices: 15421268--15421321 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
15421258 AAAAAGAATG
15421268 AAGAAAGGAGAAAGAAAGAACGAAGA
1 AAGAAAGGAGAAAGAAAGAACGAA-A
*
15421294 AAGAAAGGAGAAAGAAAGAATGAAA
1 AAGAAAGGAGAAAGAAAGAACGAAA
15421319 AAG
1 AAG
15421322 GTGAGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (25 bp):
AAGAAAGGAGAAAGAAAGAACGAAA
Found at i:15421341 original size:21 final size:22
Alignment explanation
Indices: 15421260--15421341 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 22
15421250 TTGAAAGCAA
* *
15421260 AAAGAATGAAGAAAGGAGAAAG
1 AAAGAAAGAAAAAAGGAGAAAG
15421282 AAAGAACGAAGAAAGAAAGGAGAAAG
1 AAAG-A--AAGAAA-AAAGGAGAAAG
* * *
15421308 AAAGAATG-AAAAAGGTGAGAG
1 AAAGAAAGAAAAAAGGAGAAAG
15421329 AAA-AAAGAAAAAA
1 AAAGAAAGAAAAAA
15421342 TATAGGAGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.06
21 17 0.35
22 6 0.12
23 3 0.06
25 5 0.10
26 15 0.31
ACGTcount: A:0.67, C:0.01, G:0.28, T:0.04
Consensus pattern (22 bp):
AAAGAAAGAAAAAAGGAGAAAG
Found at i:15424723 original size:16 final size:16
Alignment explanation
Indices: 15424683--15424716 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15424673 AAACCAAAAA
15424683 TTAGATTTTGACTTTT
1 TTAGATTTTGACTTTT
15424699 TTAGATTTTGA-TTTT
1 TTAGATTTTGACTTTT
15424714 TTA
1 TTA
15424717 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.65
Consensus pattern (16 bp):
TTAGATTTTGACTTTT
Found at i:15425892 original size:68 final size:68
Alignment explanation
Indices: 15425812--15426027 Score: 207
Period size: 68 Copynumber: 3.2 Consensus size: 68
15425802 ATAAAATTTA
* * * * * ** *
15425812 GTATATAATGTAAATTTCATGTACCATATGAGATGATTAAGTATGCTTGATGTATACTATAAGAT
1 GTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTATGCATGATAAATACCATAAGAT
*
15425877 TGT
66 TAT
* * * * * *
15425880 GTATATGTTGTAAACTCCTTATACTATATGAGGTGATTAAGTATGCATGATAAATGCCATCAGAT
1 GTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTATGCATGATAAATACCATAAGAT
15425945 TAT
66 TAT
* * * * * * * * * *
15425948 GTATATGATGTATATTCCATATACTACATGAGATGATTGAGAAAGAATGATGAATGCCGTGAGAT
1 GTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTATGCATGATAAATACCATAAGAT
15426013 TAT
66 TAT
15426016 GTATATGATGTA
1 GTATATGATGTA
15426028 TTTCCCATAT
Statistics
Matches: 120, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 120 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (68 bp):
GTATATGATGTAAATTCCATATACTATATGAGATGATTAAGTATGCATGATAAATACCATAAGAT
TAT
Found at i:15430316 original size:21 final size:21
Alignment explanation
Indices: 15430283--15430324 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
15430273 AAAAAACACA
15430283 TAAAATGCTAAA-GTCTGAACC
1 TAAAATGCTAAAGGTCT-AACC
15430304 TAAAAT-CTCAAAGGTCTAACC
1 TAAAATGCT-AAAGGTCTAACC
15430325 CCTTAAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (21 bp):
TAAAATGCTAAAGGTCTAACC
Found at i:15434218 original size:23 final size:23
Alignment explanation
Indices: 15434189--15434237 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
15434179 AAATATATAC
15434189 TTATTAAATAATT-TATTAAAATA
1 TTATTAAATAATTGT-TTAAAATA
**
15434212 TTATTAAATTGTTGTTTAAAATA
1 TTATTAAATAATTGTTTAAAATA
15434235 TTA
1 TTA
15434238 ATATGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TTATTAAATAATTGTTTAAAATA
Found at i:15435448 original size:30 final size:30
Alignment explanation
Indices: 15435412--15435472 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
15435402 TAGTGTTGAA
**
15435412 GGTTATACCTCCTTGAAAAAGTAATATCTT
1 GGTTATACCTCCGAGAAAAAGTAATATCTT
* * *
15435442 GGTTATACTTTCGAGAAAAAGTAGTATCTT
1 GGTTATACCTCCGAGAAAAAGTAATATCTT
15435472 G
1 G
15435473 TGCTTCAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (30 bp):
GGTTATACCTCCGAGAAAAAGTAATATCTT
Found at i:15439570 original size:16 final size:17
Alignment explanation
Indices: 15439534--15439567 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
15439524 TTGTAGACAA
*
15439534 TTAATTAAAAA-TAAAC
1 TTAATCAAAAACTAAAC
15439550 TTAATCAAAAACTAAAC
1 TTAATCAAAAACTAAAC
15439567 T
1 T
15439568 AATTAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAATCAAAAACTAAAC
Found at i:15441568 original size:21 final size:22
Alignment explanation
Indices: 15441543--15441586 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
15441533 AAGTGATTAA
15441543 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
15441564 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
15441586 T
1 T
15441587 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:15443243 original size:22 final size:21
Alignment explanation
Indices: 15443218--15443258 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15443208 AAGGCCATTA
*
15443218 TGCCCAAAATGTATCGATACAT
1 TGCCC-AAATGTATCAATACAT
*
15443240 TGCCCTAATGTATCAATAC
1 TGCCCAAATGTATCAATAC
15443259 GTTCATTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (21 bp):
TGCCCAAATGTATCAATACAT
Found at i:15449174 original size:20 final size:20
Alignment explanation
Indices: 15449145--15449182 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15449135 TAAATAAGAG
*
15449145 CAAATATATCAATATATTGC
1 CAAATATATCAAAATATTGC
*
15449165 CAAATGTATCAAAATATT
1 CAAATATATCAAAATATT
15449183 TAAATGTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (20 bp):
CAAATATATCAAAATATTGC
Found at i:15452543 original size:19 final size:17
Alignment explanation
Indices: 15452514--15452559 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
15452504 AAATAAAATT
15452514 AAAATTAAAATAACTTAATA
1 AAAATT-AAATAA-TT-ATA
15452534 AAAATTAAATAATTATA
1 AAAATTAAATAATTATA
*
15452551 AAAAATAAA
1 AAAATTAAA
15452560 AATAACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 11 0.44
18 2 0.08
19 6 0.24
20 6 0.24
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATTAAATAATTATA
Found at i:15452562 original size:19 final size:19
Alignment explanation
Indices: 15452513--15452566 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
15452503 GAAATAAAAT
*
15452513 TAAAATTAAAATAACTTAA
1 TAAAAATAAAATAACTTAA
*
15452532 TAAAAATTAAATAA-TT-A
1 TAAAAATAAAATAACTTAA
15452549 TAAAAAATAAAAATAACT
1 T-AAAAAT-AAAATAACT
15452567 AAATTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.07
18 8 0.28
19 18 0.62
20 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAATAAAATAACTTAA
Found at i:15452562 original size:24 final size:24
Alignment explanation
Indices: 15452530--15452575 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
15452520 AAAATAACTT
15452530 AATAAAAATTAAAT-AATTATAAAA
1 AATAAAAA-TAAATAAATTATAAAA
*
15452554 AATAAAAATAACTAAATTATAA
1 AATAAAAATAAATAAATTATAA
15452576 TTAAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
AATAAAAATAAATAAATTATAAAA
Found at i:15469317 original size:14 final size:14
Alignment explanation
Indices: 15469294--15469332 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
15469284 CTACAACATG
*
15469294 AACATACATCAAGT
1 AACATTCATCAAGT
*
15469308 AACATTCATCAATT
1 AACATTCATCAAGT
15469322 AACATTCATCA
1 AACATTCATCA
15469333 TCAAACAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (14 bp):
AACATTCATCAAGT
Found at i:15469353 original size:14 final size:14
Alignment explanation
Indices: 15469307--15469355 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
15469297 ATACATCAAG
*
15469307 TAACATTCATCAAT
1 TAACATTCATCATT
*
15469321 TAACATTCATCATC
1 TAACATTCATCATT
* *
15469335 AAACAATCATCATT
1 TAACATTCATCATT
15469349 TAACATT
1 TAACATT
15469356 TATGATGGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
TAACATTCATCATT
Found at i:15472510 original size:21 final size:22
Alignment explanation
Indices: 15472484--15472537 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
15472474 ATTTTTTCTC
15472484 TTTTTCTCTTTTTATTAC-T-TT
1 TTTTTCTCTTTTTATT-CTTATT
15472505 TTTTTC-C-TTTTATTCTTATT
1 TTTTTCTCTTTTTATTCTTATT
*
15472525 TTTTTTTCTTTTT
1 TTTTTCTCTTTTT
15472538 CTTTAGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 8 0.29
20 8 0.29
21 7 0.25
22 4 0.14
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTCTTTTTATTCTTATT
Found at i:15472539 original size:19 final size:20
Alignment explanation
Indices: 15472484--15472540 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
15472474 ATTTTTTCTC
* *
15472484 TTTTTCTCTTTTTATTACTT
1 TTTTTTTCTTTTTCTTACTT
*
15472504 TTTTTTCCTTTTATTCTTA-TT
1 TTTTTTTC-TTT-TTCTTACTT
15472525 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTTCTT
15472541 TAGTAATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 12 0.39
22 5 0.16
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTCTTTTTCTTACTT
Found at i:15485524 original size:7 final size:7
Alignment explanation
Indices: 15485512--15485572 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
15485502 CTTTTAGCTA
15485512 TTCTTCT
1 TTCTTCT
15485519 TTCTTCT
1 TTCTTCT
*
15485526 TTCTGCT
1 TTCTTCT
*
15485533 TTCTGCT
1 TTCTTCT
15485540 TTC-TCTT
1 TTCTTC-T
*
15485547 TTCTTTT
1 TTCTTCT
*
15485554 TTCTCCT
1 TTCTTCT
*
15485561 TTCTTCC
1 TTCTTCT
15485568 TTCTT
1 TTCTT
15485573 TTTGTTGTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 1 0.02
7 43 0.96
8 1 0.02
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (7 bp):
TTCTTCT
Found at i:15485541 original size:21 final size:21
Alignment explanation
Indices: 15485499--15485571 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
15485489 AAGGCCAAAC
*
15485499 CTTCTTT-TAGCTATTCTTCTTT
1 CTTCTTTCT-GCT-TTCTCCTTT
*
15485521 CTTCTTTCTGCTTTCTGCTTT
1 CTTCTTTCTGCTTTCTCCTTT
**
15485542 C-TCTTTTCTTTTTTCTCCTTT
1 CTTC-TTTCTGCTTTCTCCTTT
*
15485563 CTTCCTTCT
1 CTTCTTTCT
15485572 TTTTGTTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.05
21 28 0.65
22 12 0.28
23 1 0.02
ACGTcount: A:0.03, C:0.29, G:0.04, T:0.64
Consensus pattern (21 bp):
CTTCTTTCTGCTTTCTCCTTT
Found at i:15489925 original size:73 final size:73
Alignment explanation
Indices: 15489774--15489927 Score: 184
Period size: 73 Copynumber: 2.1 Consensus size: 73
15489764 CCAAGAGATG
* * * *
15489774 TTGTTAGTTGACTAAGAGCTTATTATCAAAAACTAGGTTCAGAGATAGAAACAACTCAATCAACT
1 TTGTTAGTTGACTAAGAGCTCACTACCAAAAACTAGGATCAGAGATAGAAACAACTCAATCAACT
*
15489839 AAGAAGCA
66 AAAAAGCA
* * ** * * *
15489847 TTGTTAGTTGACTAAGAGCTCACTGCCAGAAGTTAGGATCAGAAGATAGAAACGACTTAATCGAC
1 TTGTTAGTTGACTAAGAGCTCACTACCAAAAACTAGGATCAG-AGATAGAAACAACTCAATCAAC
15489912 TAAAAAGCA
65 TAAAAAGCA
15489921 -TGTTAGT
1 TTGTTAGT
15489928 CAATTAAGAG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 41 0.60
74 27 0.40
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (73 bp):
TTGTTAGTTGACTAAGAGCTCACTACCAAAAACTAGGATCAGAGATAGAAACAACTCAATCAACT
AAAAAGCA
Found at i:15495534 original size:13 final size:13
Alignment explanation
Indices: 15495516--15495543 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15495506 GGCATGTTTA
15495516 TAGAGTAAATCTT
1 TAGAGTAAATCTT
15495529 TAGAGTAAATCTT
1 TAGAGTAAATCTT
15495542 TA
1 TA
15495544 TTTGTGGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
TAGAGTAAATCTT
Found at i:15503533 original size:36 final size:33
Alignment explanation
Indices: 15503486--15503598 Score: 138
Period size: 36 Copynumber: 3.3 Consensus size: 33
15503476 AATTGTTTAA
15503486 TTTAATCAATTAGGCTTGATAACTTAATTAAACAAT
1 TTTAATCAATTAGGC---ATAACTTAATTAAACAAT
*
15503522 TTTAATCAATTAGGCCCAATGACTTAATTAAACAA-
1 TTTAATCAATTAGG--C-ATAACTTAATTAAACAAT
* *
15503557 TTTAATTAATTAGGCATAAGTTAATTAAACAAT
1 TTTAATCAATTAGGCATAACTTAATTAAACAAT
15503590 TTTAATCAA
1 TTTAATCAA
15503599 GTGCTTTAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
32 15 0.22
33 9 0.13
35 13 0.19
36 30 0.44
38 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (33 bp):
TTTAATCAATTAGGCATAACTTAATTAAACAAT
Found at i:15508596 original size:59 final size:58
Alignment explanation
Indices: 15508496--15508624 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 58
15508486 CTTTAACATG
* * * * *
15508496 TTTGATCTTAATTTAGACAAGAAAATATGCTTGTCTTAATTTAAAACAA-AAAAAATATTT
1 TTTG-TCTTAATCTAGACAACAAAACATACTTGTCTCAATTT-AAACAAGAAAAAATA-TT
* * *
15508556 TTTGTCTTAATCTAGACAACAAAACATATTTGTCTCAATTTAGACAAGATAAAATATT
1 TTTGTCTTAATCTAGACAACAAAACATACTTGTCTCAATTTAAACAAGAAAAAATATT
*
15508614 TTTATCTTAAT
1 TTTGTCTTAAT
15508625 TAAAGAAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 17 0.29
59 38 0.64
60 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (58 bp):
TTTGTCTTAATCTAGACAACAAAACATACTTGTCTCAATTTAAACAAGAAAAAATATT
Found at i:15508612 original size:28 final size:27
Alignment explanation
Indices: 15508496--15508614 Score: 105
Period size: 28 Copynumber: 4.1 Consensus size: 27
15508486 CTTTAACATG
15508496 TTTGATCTTAATTTAGACAAG-AAAATA
1 TTTG-TCTTAATTTAGACAAGAAAAATA
* *
15508523 TGCTTGTCTTAATTTAAAACAAAAAAAATA
1 T--TTGTCTTAATTT-AGACAAGAAAAATA
* *
15508553 TTTTTTGTCTTAATCTAGACAACAAAACATA
1 ---TTTGTCTTAATTTAGACAAGAAAA-ATA
*
15508584 TTTGTCTCAATTTAGACAAGATAAAATA
1 TTTGTCTTAATTTAGACAAGA-AAAATA
15508612 TTT
1 TTT
15508615 TTATCTTAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.01
28 33 0.44
29 11 0.15
30 15 0.20
31 14 0.19
33 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTGTCTTAATTTAGACAAGAAAAATA
Found at i:15513807 original size:25 final size:25
Alignment explanation
Indices: 15513779--15513833 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
15513769 CCCAACCATG
* *
15513779 TATATCAACTCATGGCCTTACCACA
1 TATAACAACTCATGACCTTACCACA
* * *
15513804 TATAACAACTCGTGACCTTGCCATA
1 TATAACAACTCATGACCTTACCACA
15513829 TATAA
1 TATAA
15513834 TCACAAATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (25 bp):
TATAACAACTCATGACCTTACCACA
Found at i:15516071 original size:5 final size:5
Alignment explanation
Indices: 15516035--15516067 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
15516025 CTCCATCTAA
15516035 ATAAT ATAAT ATAAT ATAAT ATAAT ATAA- ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
15516068 AATATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:15521438 original size:10 final size:10
Alignment explanation
Indices: 15521419--15521451 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
15521409 TCACAACATA
15521419 ATAT-TTTAT
1 ATATATTTAT
15521428 ATATATTTAT
1 ATATATTTAT
*
15521438 ATATATATAT
1 ATATATTTAT
15521448 ATAT
1 ATAT
15521452 TATAACTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATATTTAT
Found at i:15524757 original size:37 final size:37
Alignment explanation
Indices: 15524701--15524913 Score: 209
Period size: 37 Copynumber: 5.9 Consensus size: 37
15524691 AGGAATCTTT
* * ** *
15524701 CTTTTTAATGTGATTAAGTGATAATTATTATAATCAG
1 CTTTTTCATGAGATTAAGTGATAACCATTACAATCAG
*
15524738 CTTTTTCATGAGATCAAGTGATAACCATTACAATCAG
1 CTTTTTCATGAGATTAAGTGATAACCATTACAATCAG
*
15524775 CTTTTTCATGAGATTAAGTGATAACCCTTACAAT-A-
1 CTTTTTCATGAGATTAAGTGATAACCATTACAATCAG
* * * ** * * *
15524810 ATTTTTAACGAGATTAAGCAATAACCCTTAC-ACCTG
1 CTTTTTCATGAGATTAAGTGATAACCATTACAATCAG
* * *
15524846 CTTTTTCATGGGATCAAGTGATAACCATTACAATGA-
1 CTTTTTCATGAGATTAAGTGATAACCATTACAATCAG
* * *
15524882 CTTTTTCACGAGATCAAGTGATAACCCTTACA
1 CTTTTTCATGAGATTAAGTGATAACCATTACA
15524914 CTGACTTTTT
Statistics
Matches: 144, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
34 1 0.01
35 26 0.18
36 53 0.37
37 64 0.44
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (37 bp):
CTTTTTCATGAGATTAAGTGATAACCATTACAATCAG
Found at i:15524923 original size:108 final size:108
Alignment explanation
Indices: 15524737--15524949 Score: 320
Period size: 108 Copynumber: 2.0 Consensus size: 108
15524727 ATTATAATCA
* *
15524737 GCTTTTTCATGAGATCAAGTGATAACCATTACAATCAGCTTTTTCATGAGATTAAGTGATAACCC
1 GCTTTTTCATGAGATCAAGTGATAACCATTACAATCAGCTTTTTCACGAGATCAAGTGATAACCC
* * * *
15524802 TTACAATAATTTTTAACGAGATTAAGCAATAACCCTTACACCT
66 TTACAATAATTTTTAACAAAATCAAGCAATAACCATTACACCT
* *
15524845 GCTTTTTCATGGGATCAAGTGATAACCATTACAATGA-CTTTTTCACGAGATCAAGTGATAACCC
1 GCTTTTTCATGAGATCAAGTGATAACCATTACAATCAGCTTTTTCACGAGATCAAGTGATAACCC
* *
15524909 TTACACTGACTTTTTAACAAAATCAAGCAATAACCATTACA
66 TTACAAT-AATTTTTAACAAAATCAAGCAATAACCATTACA
15524950 ATGCCTTTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 31 0.33
108 63 0.67
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (108 bp):
GCTTTTTCATGAGATCAAGTGATAACCATTACAATCAGCTTTTTCACGAGATCAAGTGATAACCC
TTACAATAATTTTTAACAAAATCAAGCAATAACCATTACACCT
Found at i:15524934 original size:36 final size:36
Alignment explanation
Indices: 15524738--15524958 Score: 194
Period size: 36 Copynumber: 6.1 Consensus size: 36
15524728 TTATAATCAG
* * * *
15524738 CTTTTTCATGAGATCAAGTGATAACCATTACAATCA
1 CTTTTTAACGAGATCAAGTGATAACCCTTACAATGA
* * *
15524774 GCTTTTTCATGAGATTAAGTGATAACCCTTACAAT-A
1 -CTTTTTAACGAGATCAAGTGATAACCCTTACAATGA
* * ** *
15524810 ATTTTTAACGAGATTAAGCAATAACCCTTACACCTG-
1 CTTTTTAACGAGATCAAGTGATAACCCTTACA-ATGA
* * * *
15524846 CTTTTTCATGGGATCAAGTGATAACCATTACAATGA
1 CTTTTTAACGAGATCAAGTGATAACCCTTACAATGA
* *
15524882 CTTTTTCACGAGATCAAGTGATAACCCTTACACTGA
1 CTTTTTAACGAGATCAAGTGATAACCCTTACAATGA
* * ** * *
15524918 CTTTTTAACAAAATCAAGCAATAACCATTACAATGC
1 CTTTTTAACGAGATCAAGTGATAACCCTTACAATGA
15524954 CTTTT
1 CTTTT
15524959 ATTGGGAGTA
Statistics
Matches: 152, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
35 29 0.19
36 91 0.60
37 32 0.21
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (36 bp):
CTTTTTAACGAGATCAAGTGATAACCCTTACAATGA
Found at i:15524934 original size:72 final size:72
Alignment explanation
Indices: 15524701--15524958 Score: 241
Period size: 72 Copynumber: 3.6 Consensus size: 72
15524691 AGGAATCTTT
* * * ** * * * *
15524701 CTTTTTAATGTGATTAAGTGATAATTATTATAATCAGCTTTTTCATGAGATCAAGTGATAACCAT
1 CTTTTTCATGAGATCAAGTGATAACCATTACAATGA-CTTTTTCACGAGATCAAGTGATAACCCT
* *
15524766 TACAATCA
65 TACACTGA
* * * * * **
15524774 GCTTTTTCATGAGATTAAGTGATAACCCTTACAAT-AATTTTTAACGAGATTAAGCAATAACCCT
1 -CTTTTTCATGAGATCAAGTGATAACCATTACAATGACTTTTTCACGAGATCAAGTGATAACCCT
15524838 TACACCTG-
65 TACA-CTGA
*
15524846 CTTTTTCATGGGATCAAGTGATAACCATTACAATGACTTTTTCACGAGATCAAGTGATAACCCTT
1 CTTTTTCATGAGATCAAGTGATAACCATTACAATGACTTTTTCACGAGATCAAGTGATAACCCTT
15524911 ACACTGA
66 ACACTGA
* ** * ** *
15524918 CTTTTTAACAAAATCAAGCAATAACCATTACAATGCCTTTT
1 CTTTTTCATGAGATCAAGTGATAACCATTACAATGACTTTT
15524959 ATTGGGAGTA
Statistics
Matches: 150, Mismatches: 31, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
71 34 0.23
72 86 0.57
73 2 0.01
74 28 0.19
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (72 bp):
CTTTTTCATGAGATCAAGTGATAACCATTACAATGACTTTTTCACGAGATCAAGTGATAACCCTT
ACACTGA
Found at i:15526158 original size:16 final size:16
Alignment explanation
Indices: 15526134--15526164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15526124 GAAGCAAGGT
15526134 TGAAATGCCAAAAAGA
1 TGAAATGCCAAAAAGA
*
15526150 TGAATTGCCAAAAAG
1 TGAAATGCCAAAAAG
15526165 TGTACAGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (16 bp):
TGAAATGCCAAAAAGA
Found at i:15528604 original size:21 final size:21
Alignment explanation
Indices: 15528578--15528617 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15528568 CTCATAGAGT
*
15528578 TTATCTACCGATAGATGTTCA
1 TTATCTACCGATAAATGTTCA
*
15528599 TTATCTATCGATAAATGTT
1 TTATCTACCGATAAATGTT
15528618 TTTTGTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (21 bp):
TTATCTACCGATAAATGTTCA
Found at i:15528722 original size:41 final size:41
Alignment explanation
Indices: 15528651--15528736 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
15528641 TTTTGACGAA
15528651 TATCTATCGATAGATATTCAACATCCATCGATAAACAAGCC
1 TATCTATCGATAGATATTCAACATCCATCGATAAACAAGCC
* * ** * *
15528692 TATCTATCGATAGATGTTCATCATTTATCGATAGACAAGCT
1 TATCTATCGATAGATATTCAACATCCATCGATAAACAAGCC
15528733 TATC
1 TATC
15528737 CATTAATAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (41 bp):
TATCTATCGATAGATATTCAACATCCATCGATAAACAAGCC
Found at i:15528746 original size:41 final size:41
Alignment explanation
Indices: 15528677--15528767 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
15528667 TTCAACATCC
* * * ** *
15528677 ATCGATAAACAAGCCTATCTATCGATAGATGTTCATCATTT
1 ATCGATAGACAAGCCTATCCATCAATAGATGCGCAACATTT
* *
15528718 ATCGATAGACAAGCTTATCCATTAATAGATGCGCAACATTT
1 ATCGATAGACAAGCCTATCCATCAATAGATGCGCAACATTT
*
15528759 ATGGATAGA
1 ATCGATAGA
15528768 TAGAAACCCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (41 bp):
ATCGATAGACAAGCCTATCCATCAATAGATGCGCAACATTT
Found at i:15530102 original size:32 final size:32
Alignment explanation
Indices: 15530066--15530138 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
15530056 CATCATAAAT
*
15530066 GCCCAAGGTGCAACGGAGATTGTGCATTGCCA
1 GCCCAAGGTGCAACGGAGATTGTACATTGCCA
* * **
15530098 GCCCAAGGTGCAATGGGGATTGTACATTGTTA
1 GCCCAAGGTGCAACGGAGATTGTACATTGCCA
15530130 GCCCAAGGT
1 GCCCAAGGT
15530139 TGATGGGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (32 bp):
GCCCAAGGTGCAACGGAGATTGTACATTGCCA
Found at i:15544965 original size:19 final size:19
Alignment explanation
Indices: 15544930--15544971 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
15544920 CCTTGAAGCT
15544930 AAGAAGAATTTGAAAGATTC
1 AAGAAGAATTTGAAAGA-TC
*
15544950 AAGAAG-ATTTGGAAGATC
1 AAGAAGAATTTGAAAGATC
15544968 AAGA
1 AAGA
15544972 TTACAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (19 bp):
AAGAAGAATTTGAAAGATC
Found at i:15551729 original size:376 final size:377
Alignment explanation
Indices: 15551032--15551767 Score: 1109
Period size: 376 Copynumber: 2.0 Consensus size: 377
15551022 ATAGGAGATT
* *
15551032 GTTAGGAATTTTAGGAATATGGTGCCCTAGAAAGCAAGTGTATTCTCATGCTTAATTTCATTAAA
1 GTTAGGAATTTTAAGAATATGGTGCCCTAGAAAGCAAGTATATTCTCATGCTTAATTTCATTAAA
* * *
15551097 TTTATTTGCAATGAAATTACATTTTGATAATAAGACGAAGAGTTTGTTTTAAGTAAGCATTCATT
66 TTTATTTGAAATAAAAGTACATTTTGATAATAAGACGAAGAGTTTGTTTTAAGTAAGCATTCATT
* * * * * *
15551162 ATGTAGGTTTTAAGGTACCATAATTCTATTTAGATATTAAAGTACTTTTGTATGAAGAGTCATGC
131 ATCTAGGTTTTAAGGTACCATAATTCTATTGAGATATTAAAATACATTTGTATAAAGAGTCATAC
* ** * *
15551227 ATAGGAAACATGTATTTTAATTGAATCTAAAAATTGTTTGTAGCCATATAATAAAGTTGGTCACT
196 ATAGGAAACATGTATTTTAATTAAATCTAAAAATTGTTCATAGCCATATAATAAAGCTCGTCACT
* * ** *
15551292 TTATTGTGTTAAGGCTATAGTGCCCATATTACTTCCAACGAAATGAATGTCATTCATTTCAAGGG
261 TTATTGTGTTAAGGCTATAGTACCCAGATTACTTCCAACGAAACCAATGTCATTCATTTCAAAGG
15551357 AATGATGAGTCTCAAATCATCAAAATGGTTGACTTCGTGTCATGGCACTATC
326 AATGATGAGTCTCAAATCATCAAAATGGTTGACTTCGTGTCATGGCACTATC
* * * *
15551409 GTTAGGAGTTTTAAGAATATGGTGCCGTAGAAAGCGAGTATATTCTCATGCTTAATTTCATTAAG
1 GTTAGGAATTTTAAGAATATGGTGCCCTAGAAAGCAAGTATATTCTCATGCTTAATTTCATTAAA
*
15551474 TTTATTTGAAATAAAAGTACATTTTGATAATAAGATGAAGAGTTTGTTTT-AGTAAGCATTCATT
66 TTTATTTGAAATAAAAGTACATTTTGATAATAAGACGAAGAGTTTGTTTTAAGTAAGCATTCATT
15551538 ATCTA-GTTATTAAGGTACCA-AGATTCTATTGAGATATTAAAATACATTTGTATAAAGAGTCAT
131 ATCTAGGTT-TTAAGGTACCATA-ATTCTATTGAGATATTAAAATACATTTGTATAAAGAGTCAT
* *
15551601 ACATAGGAGACATGTATTTTAATTAAATCTAATAATTGTTCATAGCCATATAATAAAGCTCGTCA
194 ACATAGGAAACATGTATTTTAATTAAATCTAAAAATTGTTCATAGCCATATAATAAAGCTCGTCA
* * * * * *
15551666 CTTTATTGTGTTAAGGCTGTAGTATCTAGATTACTTCCAACGATACCAATGTGATTTATTTCAAA
259 CTTTATTGTGTTAAGGCTATAGTACCCAGATTACTTCCAACGAAACCAATGTCATTCATTTCAAA
* *
15551731 GGAATGATGAGTCTTAAATCATCGAAATGGTTGACTT
324 GGAATGATGAGTCTCAAATCATCAAAATGGTTGACTT
15551768 TGAGTAATGA
Statistics
Matches: 321, Mismatches: 36, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
375 4 0.01
376 212 0.66
377 105 0.33
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (377 bp):
GTTAGGAATTTTAAGAATATGGTGCCCTAGAAAGCAAGTATATTCTCATGCTTAATTTCATTAAA
TTTATTTGAAATAAAAGTACATTTTGATAATAAGACGAAGAGTTTGTTTTAAGTAAGCATTCATT
ATCTAGGTTTTAAGGTACCATAATTCTATTGAGATATTAAAATACATTTGTATAAAGAGTCATAC
ATAGGAAACATGTATTTTAATTAAATCTAAAAATTGTTCATAGCCATATAATAAAGCTCGTCACT
TTATTGTGTTAAGGCTATAGTACCCAGATTACTTCCAACGAAACCAATGTCATTCATTTCAAAGG
AATGATGAGTCTCAAATCATCAAAATGGTTGACTTCGTGTCATGGCACTATC
Found at i:15552648 original size:30 final size:32
Alignment explanation
Indices: 15552600--15552661 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
15552590 GGTAAATATG
*
15552600 TTTATCTTAATTTAAGATAAGAAAA-ATATTT
1 TTTATCTTAATCTAAGATAAGAAAACATATTT
15552631 TTTATCTTAATCT-AGATAAGAAAACATATTT
1 TTTATCTTAATCTAAGATAAGAAAACATATTT
15552662 GTCTCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (32 bp):
TTTATCTTAATCTAAGATAAGAAAACATATTT
Found at i:15552671 original size:59 final size:59
Alignment explanation
Indices: 15552537--15552700 Score: 154
Period size: 59 Copynumber: 2.8 Consensus size: 59
15552527 TAGTAACTTT
* * * ** * *
15552537 AACATATTTGTCTTAATTT-AGACAAG-AAAACATGTTTGCTCTTAATATAGATAGGTA
1 AACATATTTGTCTTAATTTAAGAAAAGAAAAATATTTTTTATCTTAATATAGATAAGAA
* * * * *
15552594 AATATGTTTATCTTAATTTAAGATAAGAAAAATATTTTTTATCTTAATCTAGATAAGAA
1 AACATATTTGTCTTAATTTAAGAAAAGAAAAATATTTTTTATCTTAATATAGATAAGAA
* * * *
15552653 AACATATTTGTCTCAATTTAGACAAAATAAAAAT-TTTTTTGTCTTAAT
1 AACATATTTGTCTTAATTTA-AGAAAAGAAAAATATTTTTTATCTTAAT
15552701 TACAGACAAG
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
57 16 0.19
58 6 0.07
59 53 0.62
60 10 0.12
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (59 bp):
AACATATTTGTCTTAATTTAAGAAAAGAAAAATATTTTTTATCTTAATATAGATAAGAA
Found at i:15552888 original size:18 final size:17
Alignment explanation
Indices: 15552853--15552886 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
15552843 ATAATAATAA
15552853 AATAAGAGTTATTATTT
1 AATAAGAGTTATTATTT
15552870 AATAAGGAGTT-TTATTT
1 AATAA-GAGTTATTATTT
15552887 TATCAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (17 bp):
AATAAGAGTTATTATTT
Found at i:15554298 original size:28 final size:28
Alignment explanation
Indices: 15554241--15554383 Score: 142
Period size: 28 Copynumber: 4.9 Consensus size: 28
15554231 TGATAGTTTT
15554241 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
15554269 AACATGTTTGGTCTTAATTTAGACAAAAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
15554298 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * * **
15554328 AATATTTTTTTTTCTTAATCTAGATGAGAA
1 AACA--TGTTTGTCTTAATTTAGACAAGAA
* * *
15554358 AACATATTTATCTCAATTTAGACAAG
1 AACATGTTTGTCTTAATTTAGACAAG
15554384 GTAAAATATT
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
28 35 0.37
29 32 0.34
30 11 0.12
31 5 0.05
32 12 0.13
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:15554579 original size:17 final size:17
Alignment explanation
Indices: 15554557--15554589 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15554547 ATAATAATAA
15554557 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
15554574 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
15554590 TGATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:15555720 original size:17 final size:17
Alignment explanation
Indices: 15555698--15555732 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15555688 GGAATAATGA
15555698 TGAATTTATTGAATGCT
1 TGAATTTATTGAATGCT
* *
15555715 TGAATTTGTTGGATGCT
1 TGAATTTATTGAATGCT
15555732 T
1 T
15555733 CATCACATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.49
Consensus pattern (17 bp):
TGAATTTATTGAATGCT
Found at i:15558287 original size:23 final size:23
Alignment explanation
Indices: 15558236--15558281 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
15558226 CCCTAGCCCA
*
15558236 TGACCTAATCTC-CCCCCCCTCC
1 TGACCTAATTTCTCCCCCCCTCC
*
15558258 TGACCTAATTTCTCCCCCCTTCC
1 TGACCTAATTTCTCCCCCCCTCC
15558281 T
1 T
15558282 TTCCTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.13, C:0.52, G:0.04, T:0.30
Consensus pattern (23 bp):
TGACCTAATTTCTCCCCCCCTCC
Found at i:15558852 original size:14 final size:13
Alignment explanation
Indices: 15558827--15558859 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
15558817 ATTAAACATA
15558827 AGAATT-ATGTTT
1 AGAATTAATGTTT
15558839 GAGAATTAATGTTT
1 -AGAATTAATGTTT
15558853 AGAATTA
1 AGAATTA
15558860 TTGTGTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
AGAATTAATGTTT
Found at i:15558858 original size:84 final size:85
Alignment explanation
Indices: 15558679--15558990 Score: 350
Period size: 85 Copynumber: 3.7 Consensus size: 85
15558669 TTCAAAGACT
** * *
15558679 TTAATATTGAGAATTATTATTTGGATAATTAAATAAAATGATT--T-A-ATGCTAGAATTCAATA
1 TTAATATTGAGAATTATTATTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAATA
*
15558740 TGAAGATTTATGTTT-AGGAA
66 TGAAGAATTATGTTTGA-GAA
* * * *
15558760 TTAATATTTG-GAATTATTATTTGAATTTGTAATTAAAATGATTGGTAATATGTTAGAATTAAAC
1 TTAATA-TTGAGAATTATTATTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAAT
15558824 AT-AAGAATTATGTTTGAGAA
65 ATGAAGAATTATGTTTGAGAA
* * * * *
15558844 TTAATGTTTAGAATTATTGTGTGGATTTTTAATTAAAATGATTGGTAATATGTTAGAATTAAATA
1 TTAATATTGAGAATTATTATTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAATA
* * * *
15558909 TGAAAAATAATATTTGGGAA
66 TGAAGAATTATGTTTGAGAA
* * * * *
15558929 TTAATGTTGAGAATTATTTTTTTGATTTTTAATTAAAATGATTGGCAATATGCTATAATTAA
1 TTAATATTGAGAATTATTATTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAA
15558991 TCATTGGAAT
Statistics
Matches: 196, Mismatches: 27, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
81 34 0.17
82 3 0.02
83 3 0.02
84 72 0.37
85 84 0.43
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (85 bp):
TTAATATTGAGAATTATTATTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAATA
TGAAGAATTATGTTTGAGAA
Found at i:15563860 original size:66 final size:65
Alignment explanation
Indices: 15563777--15563975 Score: 299
Period size: 66 Copynumber: 3.0 Consensus size: 65
15563767 GAAATATTTT
* * *
15563777 AATATTATTTTAATAATAAGATATTATTTAATTCTAAATTTTTCCATTTGGCTTCTAGGGTTCCA
1 AATATTATTTTATTAATAAGATATTATTTAATTATAAAATTTTCCATTTGGCTTCT-GGGTTCCA
15563842 A
65 A
* * * *
15563843 AATATTATTTTATTAATAAGATATTATTCAATTGTAAAATTTTCTATTTGGCTTCTGGGTTTCTA
1 AATATTATTTTATTAATAAGATATTATTTAATTATAAAATTTTCCATTTGGCTTCTGGG-TTCCA
15563908 A
65 A
*
15563909 AATATTATTTTATTAATAAGATATTATTTAATTATAAAAGTTTCCATTTGGCTTCTGGGGTTCCA
1 AATATTATTTTATTAATAAGATATTATTTAATTATAAAATTTTCCATTTGGCTTCT-GGGTTCCA
15563974 A
65 A
15563975 A
1 A
15563976 GCATTTTAAT
Statistics
Matches: 120, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
65 3 0.03
66 114 0.95
67 3 0.03
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (65 bp):
AATATTATTTTATTAATAAGATATTATTTAATTATAAAATTTTCCATTTGGCTTCTGGGTTCCAA
Found at i:15570256 original size:69 final size:69
Alignment explanation
Indices: 15570145--15570285 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 69
15570135 ATTCATACAT
15570145 TGTGATGGTTTGACCCCCATCAACCTTTGGCCAGAAATGTATGAATTCCATTGCACCTTAGGTTG
1 TGTGATGGTTTGACCCCCATCAACCTTTGGCCAGAAATGTATGAATTCCATTGCACCTTAGGTTG
15570210 ACAA
66 ACAA
*
15570214 TGTGATGGTTTGACCCCCATCAACCTTTGGCCAGCAATGTATGAATTCCATTGCACCTTAGGTTG
1 TGTGATGGTTTGACCCCCATCAACCTTTGGCCAGAAATGTATGAATTCCATTGCACCTTAGGTTG
15570279 ACAA
66 ACAA
15570283 TGT
1 TGT
15570286 ACAATCCCCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (69 bp):
TGTGATGGTTTGACCCCCATCAACCTTTGGCCAGAAATGTATGAATTCCATTGCACCTTAGGTTG
ACAA
Found at i:15571785 original size:75 final size:74
Alignment explanation
Indices: 15571706--15571862 Score: 210
Period size: 75 Copynumber: 2.1 Consensus size: 74
15571696 CTTATTTATG
* *
15571706 TTAAATACCATTTAAGTAAATGTCCTTACTGTTACTTCTTT-CTTTGTTACTATT-CATTTACTT
1 TTAAATACCATTTAAGCAAATGTCCTCACTGTTACTTCTTTCCTTT-TTACT-TTACATTTACTT
*
15571769 AATATATTTACA
64 AAGATATTTA-A
* * *
15571781 TTAAATACCATTTAAGCAAATGTCCTCATTTTTACTTCTTTCCTTTTTACTTTATATTTACTTAA
1 TTAAATACCATTTAAGCAAATGTCCTCACTGTTACTTCTTTCCTTTTTACTTTACATTTACTTAA
15571846 GATATTTAA
66 GATATTTAA
15571855 TGTAAATA
1 T-TAAATA
15571863 AGCAAACAAC
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
74 4 0.05
75 65 0.89
76 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (74 bp):
TTAAATACCATTTAAGCAAATGTCCTCACTGTTACTTCTTTCCTTTTTACTTTACATTTACTTAA
GATATTTAA
Found at i:15576205 original size:171 final size:171
Alignment explanation
Indices: 15575975--15576600 Score: 750
Period size: 171 Copynumber: 3.7 Consensus size: 171
15575965 GTTTCCCATA
* *
15575975 AGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAAACATTCAATTTAAAATCAATT
1 AGGTAGACATTCAATTATAGTCTATTTTAGCCAAAAATGTAAAAACATTCAACTTAAAATCAATT
* * * *
15576040 ATGAGATTATAAAACAATTTAAAGTGAGTAGAAAGGCTTTTGCAGGAATGGGTGGCTATAAATGG
66 ATGAGATTATAAAACAATTTAAAGCGAGTAGAAAGGCTTTTGAAGGAATGGGAGACTATAAATGG
* *
15576105 ACTTTTCTTACCAATGAATGCTTGTTTCTTTATGTTTCTTG
131 ACTTTTCTTACCAATGAATGCTTGTTTCTTTACGTTTCTAG
* * *
15576146 AGGTAGACATTCAATTATAGTATGTTTTAGCAAAAAATGT-AAAACAATTCAACTTAAAATCAAT
1 AGGTAGACATTCAATTATAGTCTATTTTAGCCAAAAATGTAAAAAC-ATTCAACTTAAAATCAAT
* * * * * **
15576210 TATGAGATTATAAAACATTTTAAAGCAAGTA-ATAAAGCTTTTAAAGAAATAAGAGACTATAAAT
65 TATGAGATTATAAAACAATTTAAAGCGAGTAGA-AAGGCTTTTGAAGGAATGGGAGACTATAAAT
* *
15576274 AGACTTTTCTTACCAATGAATGCTTGTTTCTTTACATTTCTCA-
129 GGACTTTTCTTACCAATGAATGCTTGTTTCTTTACGTTTCT-AG
* * *
15576317 AGGTACAAATTCAATTATAGTCTATTTTAGCCAAAAATATAAAAACATTCAACTTAAAATCAATT
1 AGGTAGACATTCAATTATAGTCTATTTTAGCCAAAAATGTAAAAACATTCAACTTAAAATCAATT
* * * *
15576382 ATGAGATTATAAAATC-ATTTAAAGCGAGTGGTAAGGCTTTCGAAGGAA-CGGACGACTATAAAT
66 ATGAGATTATAAAA-CAATTTAAAGCGAGTAGAAAGGCTTTTGAAGGAATGGGA-GACTATAAAT
* *
15576445 GGACTTTT-TGTGCCAGTGAATGCCTT-TTT-TTTCACGTTTCTAG
129 GGACTTTTCT-TACCAATGAATG-CTTGTTTCTTT-ACGTTTCTAG
* * ** * *
15576488 AGGTAAACCTTCAATTATAGTCTATTTTAATCAAAAATGTGAAAAA-ATTCAACTTCAAGTCAAT
1 AGGTAGACATTCAATTATAGTCTATTTTAGCCAAAAATGT-AAAAACATTCAACTTAAAATCAAT
* * *
15576552 TATGAGATTATAAAACTATTTAAAGCAACTA-ATAAGGCTTTTGAAGGAA
65 TATGAGATTATAAAACAATTTAAAGCGAGTAGA-AAGGCTTTTGAAGGAA
15576601 NNNNNNNNNN
Statistics
Matches: 388, Mismatches: 53, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
170 14 0.04
171 360 0.93
172 14 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (171 bp):
AGGTAGACATTCAATTATAGTCTATTTTAGCCAAAAATGTAAAAACATTCAACTTAAAATCAATT
ATGAGATTATAAAACAATTTAAAGCGAGTAGAAAGGCTTTTGAAGGAATGGGAGACTATAAATGG
ACTTTTCTTACCAATGAATGCTTGTTTCTTTACGTTTCTAG
Done.