Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 86 of 345
Found at i:28417262 original size:43 final size:42
Alignment explanation
Indices: 28417131--28417275 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 42
28417121 TTTTTCTTAT
* * * *
28417131 TAAAAGTCATGTTCTTT-AGCGTTGTTTGTGGGAAAAGCGTCGT
1 TAAAGGTCATGTTCTTTAAG-G-CGTTTGTGGGAAAAGCGCCGC
* * ** **
28417174 TAAAGGTTATGCTCTTT-AGCGCGTTT-TTTGAAAAGCGCTAC
1 TAAAGGTCATGTTCTTTAAG-GCGTTTGTGGGAAAAGCGCCGC
*
28417215 TAAAGGTCATGTTCTTTAATGGCGTTTGTGGGAAAATCGCCGC
1 TAAAGGTCATGTTCTTTAA-GGCGTTTGTGGGAAAAGCGCCGC
28417258 TAAAGGTCATGTTCTTTA
1 TAAAGGTCATGTTCTTTA
28417276 GCCCAAGATG
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
41 24 0.29
42 11 0.13
43 47 0.57
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (42 bp):
TAAAGGTCATGTTCTTTAAGGCGTTTGTGGGAAAAGCGCCGC
Found at i:28421200 original size:107 final size:107
Alignment explanation
Indices: 28421014--28421225 Score: 390
Period size: 107 Copynumber: 2.0 Consensus size: 107
28421004 GACATCCAAG
* *
28421014 GGGAGTGTTATGAATATCTTATTAAGTGGATGTCCATCATAGTCAAGATAAAGTTTTAATGTACT
1 GGGAGTATTATGAATATCTTATTAAGTGGATGTCCATCATAGTCAAGATAAAGTTTTAATATACT
28421079 TTAAATTCTAATAGTTATTAGAATAGATCTCTACTTCTATGA
66 TTAAATTCTAATAGTTATTAGAATAGATCTCTACTTCTATGA
28421121 GGGAGTATTATGAATATCTTATTAAGTGGATGTCCATCAT-GATCAAGATAAAGTTTTAATATAC
1 GGGAGTATTATGAATATCTTATTAAGTGGATGTCCATCATAG-TCAAGATAAAGTTTTAATATAC
28421185 TTTAAATTCTAATAGTTATTAGAATAGATCTCTACTTCTAT
65 TTTAAATTCTAATAGTTATTAGAATAGATCTCTACTTCTAT
28421226 TATACTTCTT
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
106 1 0.01
107 101 0.99
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (107 bp):
GGGAGTATTATGAATATCTTATTAAGTGGATGTCCATCATAGTCAAGATAAAGTTTTAATATACT
TTAAATTCTAATAGTTATTAGAATAGATCTCTACTTCTATGA
Found at i:28421713 original size:21 final size:21
Alignment explanation
Indices: 28421689--28421732 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28421679 AAAATTATAC
*
28421689 TTTTTATACTTGTTTAAATAA
1 TTTTAATACTTGTTTAAATAA
** *
28421710 TTTTAATTTTTTTTTAAATAA
1 TTTTAATACTTGTTTAAATAA
28421731 TT
1 TT
28421733 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAATACTTGTTTAAATAA
Found at i:28421740 original size:21 final size:21
Alignment explanation
Indices: 28421701--28421741 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28421691 TTTATACTTG
*
28421701 TTTAAATAATTTTAATTTTTT
1 TTTAAATAATTATAATTTTTT
28421722 TTTAAATAATTAT-ATTTTTT
1 TTTAAATAATTATAATTTTTT
28421742 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTAAATAATTATAATTTTTT
Found at i:28422269 original size:18 final size:20
Alignment explanation
Indices: 28422233--28422272 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
28422223 ATATAATTTT
*
28422233 AAAATATATATAAACCATCA
1 AAAATATATATAAAACATCA
28422253 AAAATAT-TA-AAAACATCA
1 AAAATATATATAAAACATCA
28422271 AA
1 AA
28422273 TAGATATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:28422389 original size:30 final size:28
Alignment explanation
Indices: 28422353--28422412 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
28422343 CAACTTAACA
28422353 AACAAATGT-TTCTAAAATAATAACAAAATT
1 AACAAATGTCTT-TAAAATAA-AA-AAAATT
28422383 AACAAATGTCTTTAAAATAAAAAAAATT
1 AACAAATGTCTTTAAAATAAAAAAAATT
28422411 AA
1 AA
28422413 TAATAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 8 0.28
29 2 0.07
30 17 0.59
31 2 0.07
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (28 bp):
AACAAATGTCTTTAAAATAAAAAAAATT
Found at i:28422470 original size:22 final size:22
Alignment explanation
Indices: 28422444--28422492 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28422434 ATATTCAAAT
28422444 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * *
28422466 TATAATAATAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
28422488 AATAA
1 AATAA
28422493 GGAGAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:28422500 original size:22 final size:22
Alignment explanation
Indices: 28422444--28422500 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
28422434 ATATTCAAAT
* *
28422444 AATAACAACAAAATAGTAGCAA
1 AATAAGAAGAAAATAGTAGCAA
* * *
28422466 TATAATAATAAAATAGTAGCAA
1 AATAAGAAGAAAATAGTAGCAA
*
28422488 AATAAGGAGAAAA
1 AATAAGAAGAAAA
28422501 CAATAAGAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.18
Consensus pattern (22 bp):
AATAAGAAGAAAATAGTAGCAA
Found at i:28428304 original size:22 final size:22
Alignment explanation
Indices: 28428278--28428333 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
28428268 CGGATTTTAA
* *
28428278 TACTGTTGTTTTTCCATTGTTT
1 TACTGTTATTTTTCCACTGTTT
*
28428300 TACTGTTATTTTTTCACTGTTT
1 TACTGTTATTTTTCCACTGTTT
*
28428322 TGCTGTTATTTT
1 TACTGTTATTTT
28428334 ACTATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.11, C:0.12, G:0.12, T:0.64
Consensus pattern (22 bp):
TACTGTTATTTTTCCACTGTTT
Found at i:28429627 original size:20 final size:20
Alignment explanation
Indices: 28429604--28429651 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
28429594 ATTATCTAGT
28429604 TTTTGCTCATTTTTAGCTCA
1 TTTTGCTCATTTTTAGCTCA
28429624 TTTTGCTCATTTTTAGCTCA
1 TTTTGCTCATTTTTAGCTCA
28429644 TTTTGCTC
1 TTTTGCTC
28429652 CCAAATGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.21, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTTGCTCATTTTTAGCTCA
Found at i:28429631 original size:9 final size:10
Alignment explanation
Indices: 28429603--28429651 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
28429593 AATTATCTAG
28429603 TTTTTGCTCA
1 TTTTTGCTCA
28429613 TTTTTAGCTCA
1 TTTTT-GCTCA
28429624 -TTTTGCTCA
1 TTTTTGCTCA
28429633 TTTTTAGCTCA
1 TTTTT-GCTCA
28429644 -TTTTGCTC
1 TTTTTGCTC
28429652 CCAAATGCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.25
10 17 0.47
11 10 0.28
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.57
Consensus pattern (10 bp):
TTTTTGCTCA
Found at i:28434512 original size:25 final size:25
Alignment explanation
Indices: 28434492--28434581 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
28434482 TTGATATTTG
28434492 GCTCGAAAGAGCTTCCCGATATACA
1 GCTCGAAAGAGCTTCCCGATATACA
* *
28434517 GCTCGTATGAGCTTCCCG-T-TACTTA
1 GCTCGAAAGAGCTTCCCGATATAC--A
* * *
28434542 GCTC-ACATGAGCTTCCCGTTATACG
1 GCTCGA-AAGAGCTTCCCGATATACA
*
28434567 GCTCGGAAGAGCTTC
1 GCTCGAAAGAGCTTC
28434582 TAATTTACGT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
23 3 0.06
24 1 0.02
25 45 0.85
26 1 0.02
27 3 0.06
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (25 bp):
GCTCGAAAGAGCTTCCCGATATACA
Found at i:28438275 original size:26 final size:26
Alignment explanation
Indices: 28438246--28438327 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
28438236 TGGTACAAAT
*
28438246 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
28438272 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
28438298 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
28438324 TGAT
1 TGAT
28438328 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:28444582 original size:21 final size:20
Alignment explanation
Indices: 28444558--28444603 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
28444548 AAAAATAATC
28444558 ATAAA-CTATTTTTTGAAAATT
1 ATAAAGCTA-TTTTT-AAAATT
28444579 ATAAAAGCTATTTTTAAAATT
1 AT-AAAGCTATTTTTAAAATT
28444600 ATAA
1 ATAA
28444604 GCATGCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.09
21 10 0.43
22 8 0.35
23 3 0.13
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
ATAAAGCTATTTTTAAAATT
Found at i:28446147 original size:16 final size:16
Alignment explanation
Indices: 28446110--28446149 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
28446100 TAATATTTAG
28446110 ATATT-TTGATTATTA
1 ATATTCTTGATTATTA
28446125 A-ATTCTTG-TTATTAA
1 ATATTCTTGATTATT-A
28446140 ATATTCTTGA
1 ATATTCTTGA
28446150 AATTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 7 0.33
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (16 bp):
ATATTCTTGATTATTA
Found at i:28450036 original size:22 final size:22
Alignment explanation
Indices: 28449994--28450043 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
28449984 AATGTCTCTG
*
28449994 TTATTTCTTTTCTTTGTTTCTTT
1 TTATTTCTATTCTTTGTTTC-TT
28450017 TTATTTC-ATTCTTT-TATTCTT
1 TTATTTCTATTCTTTGT-TTCTT
28450038 TTATTT
1 TTATTT
28450044 ACCTAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 9 0.36
22 9 0.36
23 7 0.28
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATTTCTATTCTTTGTTTCTT
Found at i:28450379 original size:3 final size:3
Alignment explanation
Indices: 28450371--28450431 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
28450361 ATCTTTAACT
** *
28450371 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA -AA CCA TAC TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
28450418 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
28450432 TCTTAGATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
4 3 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28461337 original size:12 final size:12
Alignment explanation
Indices: 28461320--28461345 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28461310 GTGCCACTGA
28461320 AAACAAATAAAT
1 AAACAAATAAAT
28461332 AAACAAATAAAT
1 AAACAAATAAAT
28461344 AA
1 AA
28461346 GATCATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACAAATAAAT
Found at i:28474224 original size:39 final size:39
Alignment explanation
Indices: 28474169--28474254 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
28474159 GAAATGTGTA
28474169 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * * * *
28474208 TGGAAATGTATTCGGGCTAAAGTCCTGCAGGCTTTGTGT
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
28474247 TGGTAATA
1 TGGAAATA
28474255 AAATTTCGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (39 bp):
TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:28476658 original size:27 final size:27
Alignment explanation
Indices: 28476628--28476805 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
28476618 ATATTGAGTC
* * *
28476628 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
28476655 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
28476682 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
28476710 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
28476737 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
28476764 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
28476791 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28476806 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:28476721 original size:55 final size:55
Alignment explanation
Indices: 28476628--28476805 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
28476618 ATATTGAGTC
* * *
28476628 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
28476682 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
28476737 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
28476791 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28476806 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:28476767 original size:82 final size:81
Alignment explanation
Indices: 28476649--28476804 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
28476639 TGCTATACAA
* * *
28476649 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
28476714 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
28476731 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
28476795 CACTTAGTGC
65 CACTTAGTGC
28476805 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28492703 original size:43 final size:43
Alignment explanation
Indices: 28492637--28492806 Score: 152
Period size: 43 Copynumber: 4.0 Consensus size: 43
28492627 AGCTCATGCA
*
28492637 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAAATATCG
*
28492680 ATGCC-ACTGTCCCAGACAG-GGTCTTACA-CAAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAAA-CAAATATCG
* * * * * * * * *
28492722 ATGTCGATGTCCTAGACATGGTCTTACACGTTAATCATAA-GTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATG-AAAACA-AATATCG
*
28492766 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACATAT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAAATAT
28492807 TGAATCCTAT
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
42 29 0.30
43 37 0.38
44 31 0.32
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAAATATCG
Found at i:28498947 original size:44 final size:43
Alignment explanation
Indices: 28498791--28498952 Score: 102
Period size: 43 Copynumber: 3.8 Consensus size: 43
28498781 AGCTCGTACA
* * * * *
28498791 ATGCCAAGATCTCAAACG-TGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCCAGACGTTGGTCTTACACGAAATCAAATA-CG
*** *
28498834 ATGCCATTGTCCCAAACAG--GGTCTTACACGAAATCAAATACG
1 ATGCCAACATCCCAGAC-GTTGGTCTTACACGAAATCAAATACG
* * *
28498876 ATTCCAACATCCCAGACGTT-GTTTTACACATAAATCATAAGT-CG
1 ATGCCAACATCCCAGACGTTGGTCTTACAC-GAAATCA-AA-TACG
* * *
28498920 ATGCCAGCATCTCAGAC-TTGGTCTTACATGAAA
1 ATGCCAACATCCCAGACGTTGGTCTTACACGAAA
28498953 ACACATATTG
Statistics
Matches: 93, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
41 1 0.01
42 22 0.24
43 43 0.46
44 26 0.28
45 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTTGGTCTTACACGAAATCAAATACG
Found at i:28500676 original size:25 final size:25
Alignment explanation
Indices: 28500648--28500717 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
28500638 TTCTTTTAAT
*
28500648 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTCAG-TA
*
28500673 AACTAGGGCAAAGCCCTTTTCAGTA
1 AACTGGGGCAAAGCCCTTTTCAGTA
*
28500698 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28500718 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 35 0.88
26 5 0.12
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCAGTA
Found at i:28501676 original size:27 final size:25
Alignment explanation
Indices: 28501646--28501753 Score: 83
Period size: 27 Copynumber: 4.0 Consensus size: 25
28501636 GTAAATCTAC
28501646 AAACCAATGGTATTTTAGTAATTTTGT
1 AAACCAATGGTATTTTA-TAATTTT-T
28501673 AAACCAATGGTATTTCTATAATTTTT
1 AAACCAATGGTATTT-TATAATTTTT
* *
28501699 AGAAAGTCAAAGGTATTTTTATAATTTTTT
1 --AAA-CCAATGGTA-TTTTATAA-TTTTT
* *
28501729 AAATCAGA-GGTATTTTGGTAATTTT
1 AAACCA-ATGGTATTTT-ATAATTTT
28501754 ACAAATTGAG
Statistics
Matches: 70, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
26 9 0.13
27 32 0.46
28 9 0.13
29 12 0.17
30 8 0.11
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.45
Consensus pattern (25 bp):
AAACCAATGGTATTTTATAATTTTT
Found at i:28501716 original size:29 final size:27
Alignment explanation
Indices: 28501654--28501743 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
28501644 ACAAACCAAT
* *
28501654 GGTATTT-TAGTAA-TTTTGTAAACCAAT
1 GGTATTTCTA-TAATTTTTG-AAATCAAA
28501681 GGTATTTCTATAATTTTTAGAAAGTCAAA
1 GGTATTTCTATAATTTTT-GAAA-TCAAA
* * *
28501710 GGTATTTTTATAATTTTTTAAATCAGA
1 GGTATTTCTATAATTTTTGAAATCAAA
28501737 GGTATTT
1 GGTATTT
28501744 TGGTAATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 21 0.39
28 12 0.22
29 21 0.39
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (27 bp):
GGTATTTCTATAATTTTTGAAATCAAA
Found at i:28501759 original size:27 final size:27
Alignment explanation
Indices: 28501720--28501913 Score: 171
Period size: 27 Copynumber: 7.2 Consensus size: 27
28501710 GGTATTTTTA
** *
28501720 TAATTTTTTAAATCAGAGGTATTTTGG
1 TAATTTTACAAATCAGAGGTATTTCGG
*
28501747 TAATTTTACAAAT-TGAGGGTATTTCGG
1 TAATTTTACAAATCAGA-GGTATTTCGG
* * *
28501774 TAATTTCACAAACCAGTGGTATTTCGG
1 TAATTTTACAAATCAGAGGTATTTCGG
* *
28501801 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTACAAATC-AGAGGTATTTCGG
* *
28501828 TAATTTTACAAAT-TGAGGGTATTTCAG
1 TAATTTTACAAATCAGA-GGTATTTCGG
* * * *
28501855 TAATTTCACAAACCAGTGGTATTTCGA
1 TAATTTTACAAATCAGAGGTATTTCGG
* *
28501882 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTACAAATC-AGAGGTATTTCGG
28501909 TAATT
1 TAATT
28501914 CTATCCTACA
Statistics
Matches: 135, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.04
27 128 0.95
28 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
TAATTTTACAAATCAGAGGTATTTCGG
Found at i:28501827 original size:81 final size:81
Alignment explanation
Indices: 28501737--28501913 Score: 336
Period size: 81 Copynumber: 2.2 Consensus size: 81
28501727 TTAAATCAGA
* *
28501737 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTCGGT
1 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTCGAT
28501802 AATTTTACAAACTAGG
66 AATTTTACAAACTAGG
28501818 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTCGAT
1 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTCGAT
28501883 AATTTTACAAACTAGG
66 AATTTTACAAACTAGG
28501899 GGTATTTTGGTAATT
1 GGTATTTTGGTAATT
28501914 CTATCCTACA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 94 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTCGAT
AATTTTACAAACTAGG
Found at i:28501963 original size:26 final size:27
Alignment explanation
Indices: 28501934--28501995 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28501924 AGGGGTATTT
*
28501934 TAGTAATTTCACAATC-GAGGGTAAAA
1 TAGTAATTTCACAAACTGAGGGTAAAA
***
28501960 TAGTAATTTTGTAAACTGAGGGTAAAA
1 TAGTAATTTCACAAACTGAGGGTAAAA
*
28501987 TGGTAATTT
1 TAGTAATTT
28501996 TGTAAATCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (27 bp):
TAGTAATTTCACAAACTGAGGGTAAAA
Found at i:28501976 original size:81 final size:79
Alignment explanation
Indices: 28501737--28501969 Score: 265
Period size: 81 Copynumber: 2.9 Consensus size: 79
28501727 TTAAATCAGA
* ** *
28501737 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTCGGT
1 GGTATTTTGGTAATTTTACAAA-TGAGGGTATTTCAGTAATTTCACAAACCAGTGGTAAAT-AGT
28501802 AATTTTACAAACTAGG
64 AATTTTACAAACTAGG
** *
28501818 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTCGAT
1 GGTATTTTGGTAATTTTACAAA-TGAGGGTATTTCAGTAATTTCACAAACCAGTGGTAAATAG-T
28501883 AATTTTACAAACTAGG
64 AATTTTACAAACTAGG
* * * *
28501899 GGTATTTTGGTAATTCTATCCTACAA-G-GGGTATTTTAGTAATTTCACAATCGAG-GGTAAAAT
1 GGTATTTTGGTAATT-T-TAC-A-AATGAGGGTATTTCAGTAATTTCACAAACCAGTGGT-AAAT
28501961 AGTAATTTT
61 AGTAATTTT
28501970 GTAAACTGAG
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
80 1 0.01
81 102 0.74
82 28 0.20
83 3 0.02
84 1 0.01
85 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (79 bp):
GGTATTTTGGTAATTTTACAAATGAGGGTATTTCAGTAATTTCACAAACCAGTGGTAAATAGTAA
TTTTACAAACTAGG
Found at i:28501980 original size:27 final size:27
Alignment explanation
Indices: 28501946--28502143 Score: 245
Period size: 27 Copynumber: 7.3 Consensus size: 27
28501936 GTAATTTCAC
*
28501946 AATCGAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
28501973 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
* *
28502000 AATCTAGGGTAAAATGATAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * *
28502027 AATCGAAGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
28502054 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * * * *
28502081 AATTGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* **
28502108 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTGTA
28502135 AATCGAGGG
1 AATCGAGGG
28502144 CATTTCAGTA
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 147 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:28502155 original size:81 final size:81
Alignment explanation
Indices: 28501989--28502163 Score: 217
Period size: 81 Copynumber: 2.2 Consensus size: 81
28501979 GGGTAAAATG
* * * *
28501989 GTAATTTTGTAAATCTAGGGTAAAATGATAATTTTGTAAATCGAAGGTAAAATGGTAATTCTATA
1 GTAATTTTGTAAATCTAGGGTAAAACGATAATTCTATAAATCGAAGGTAAAATGGTAATTCTACA
* *
28502054 AATCGAGGGTAAAACG
66 AATCGAGGGCAAAACA
* * *
28502070 GTAATTTTGTAAAT-TGAGGGTGAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTAC
1 GTAATTTTGTAAATCT-AGGGTAAAACGATAATTCTATAAATCGAAGGTAAAATGGTAATTCTAC
***
28502134 AAATCGAGGGCATTTCA
65 AAATCGAGGGCAAAACA
*
28502151 GTAATTTGGTAAA
1 GTAATTTTGTAAA
28502164 CTAAAGTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 1 0.01
81 79 0.99
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.32
Consensus pattern (81 bp):
GTAATTTTGTAAATCTAGGGTAAAACGATAATTCTATAAATCGAAGGTAAAATGGTAATTCTACA
AATCGAGGGCAAAACA
Found at i:28503676 original size:62 final size:62
Alignment explanation
Indices: 28503579--28503708 Score: 251
Period size: 62 Copynumber: 2.1 Consensus size: 62
28503569 ATGTGTTCAT
*
28503579 CTTCATCAAGCCTTGGCCGAACCTTACCTCTCTCCATAGCTAGGGTATCTTCAACTTCCAAG
1 CTTCATCAAGCCCTGGCCGAACCTTACCTCTCTCCATAGCTAGGGTATCTTCAACTTCCAAG
28503641 CTTCATCAAGCCCTGGCCGAACCTTACCTCTCTCCATAGCTAGGGTATCTTCAACTTCCAAG
1 CTTCATCAAGCCCTGGCCGAACCTTACCTCTCTCCATAGCTAGGGTATCTTCAACTTCCAAG
28503703 CTTCAT
1 CTTCAT
28503709 AGTAAGTGAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (62 bp):
CTTCATCAAGCCCTGGCCGAACCTTACCTCTCTCCATAGCTAGGGTATCTTCAACTTCCAAG
Found at i:28506326 original size:25 final size:26
Alignment explanation
Indices: 28506297--28506349 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
28506287 CTGTCATAAC
**
28506297 TTACC-ATAAGGGTATCTTAGTCATT
1 TTACCTATAAGGGTATAATAGTCATT
*
28506322 TTACCTTATAGGGGTATAATAGTCATT
1 TTACC-TATAAGGGTATAATAGTCATT
28506349 T
1 T
28506350 CATCAGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
27 18 0.78
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (26 bp):
TTACCTATAAGGGTATAATAGTCATT
Found at i:28524756 original size:16 final size:15
Alignment explanation
Indices: 28524729--28524762 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
28524719 ATCATTAATA
*
28524729 TATAATTATATCCAT
1 TATAATTATATCAAT
28524744 TATAATATATATCAAT
1 TATAAT-TATATCAAT
28524760 TAT
1 TAT
28524763 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATTATATCAAT
Found at i:28527476 original size:22 final size:22
Alignment explanation
Indices: 28527451--28527509 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
28527441 TCAACTCGGA
*
28527451 AGAGCTTACTGTTCAGCTTAAT
1 AGAGCTTACTGTTCAGCTCAAT
*
28527473 AGAGCTTACCATTTTCAGCTCAAT
1 AGAGCTTA-C-TGTTCAGCTCAAT
*
28527497 AGAGCTTATTGTT
1 AGAGCTTACTGTT
28527510 ATCATCTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 11 0.35
23 1 0.03
24 19 0.61
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:28537651 original size:22 final size:23
Alignment explanation
Indices: 28537611--28537700 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 23
28537601 TAGCTCGTAT
*
28537611 GAGCTTACTGTATCAGCTCAGA-A
1 GAGCTTATTGTATCAGCTCA-ATA
28537634 GAGCTTATTGT-TCAGCTCAATA
1 GAGCTTATTGTATCAGCTCAATA
*
28537656 AAGCTTACCATT-T-TCAGCTCAATA
1 GAGCTT---ATTGTATCAGCTCAATA
*
28537680 GAACTTATTGTTATCAGCTCA
1 GAGCTTATTG-TATCAGCTCA
28537701 TGAAGAGCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
21 4 0.07
22 14 0.25
23 11 0.20
24 24 0.43
25 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (23 bp):
GAGCTTATTGTATCAGCTCAATA
Found at i:28544490 original size:40 final size:40
Alignment explanation
Indices: 28544446--28544630 Score: 271
Period size: 40 Copynumber: 4.6 Consensus size: 40
28544436 AACCCAATTA
* * ** *
28544446 CCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* *
28544486 CCTTCGGGACTTAACCCGGAAATAGCAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
28544526 CCTTCGGGACTTAACCCAGAAATAACAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
28544566 CCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* *
28544606 CCTTCGGGACTTAACCTGGATATAA
1 CCTTCGGGACTTAACCCGGAAATAA
28544631 TCCTCAATTG
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 131 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.19
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
Found at i:28550061 original size:42 final size:42
Alignment explanation
Indices: 28550014--28550111 Score: 196
Period size: 42 Copynumber: 2.3 Consensus size: 42
28550004 TGTTGATTTC
28550014 GGCACTAAGTGTGCGGGTATAAACATTTACGATAATGAGATT
1 GGCACTAAGTGTGCGGGTATAAACATTTACGATAATGAGATT
28550056 GGCACTAAGTGTGCGGGTATAAACATTTACGATAATGAGATT
1 GGCACTAAGTGTGCGGGTATAAACATTTACGATAATGAGATT
28550098 GGCACTAAGTGTGC
1 GGCACTAAGTGTGC
28550112 AGACTTACTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.28
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAACATTTACGATAATGAGATT
Found at i:28552389 original size:153 final size:153
Alignment explanation
Indices: 28552111--28552413 Score: 606
Period size: 153 Copynumber: 2.0 Consensus size: 153
28552101 TTGATGTTCC
28552111 GTAATACACGCTCGTGTGCTAGGCCGTGTGATGAATTAAATTCTCACAAAAATGCTACAGACTCG
1 GTAATACACGCTCGTGTGCTAGGCCGTGTGATGAATTAAATTCTCACAAAAATGCTACAGACTCG
28552176 ACACGCCCTGGGTACATGACCACGTCCCCAGGCCGTGTCCCCCACACGGCCATGTCTTAACTCGT
66 ACACGCCCTGGGTACATGACCACGTCCCCAGGCCGTGTCCCCCACACGGCCATGTCTTAACTCGT
28552241 GTGGCCATTACTCAGGCTATATG
131 GTGGCCATTACTCAGGCTATATG
28552264 GTAATACACGCTCGTGTGCTAGGCCGTGTGATGAATTAAATTCTCACAAAAATGCTACAGACTCG
1 GTAATACACGCTCGTGTGCTAGGCCGTGTGATGAATTAAATTCTCACAAAAATGCTACAGACTCG
28552329 ACACGCCCTGGGTACATGACCACGTCCCCAGGCCGTGTCCCCCACACGGCCATGTCTTAACTCGT
66 ACACGCCCTGGGTACATGACCACGTCCCCAGGCCGTGTCCCCCACACGGCCATGTCTTAACTCGT
28552394 GTGGCCATTACTCAGGCTAT
131 GTGGCCATTACTCAGGCTAT
28552414 TTCCAAGCCT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 150 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.23
Consensus pattern (153 bp):
GTAATACACGCTCGTGTGCTAGGCCGTGTGATGAATTAAATTCTCACAAAAATGCTACAGACTCG
ACACGCCCTGGGTACATGACCACGTCCCCAGGCCGTGTCCCCCACACGGCCATGTCTTAACTCGT
GTGGCCATTACTCAGGCTATATG
Found at i:28554737 original size:28 final size:28
Alignment explanation
Indices: 28554705--28554761 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28554695 TCTCCTAGGC
28554705 TCGTAAAATAATTTTTATTCAATTTCCT
1 TCGTAAAATAATTTTTATTCAATTTCCT
*
28554733 TCGTAAAGTAATTTTTATTCAATTTCCT
1 TCGTAAAATAATTTTTATTCAATTTCCT
28554761 T
1 T
28554762 ACATTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (28 bp):
TCGTAAAATAATTTTTATTCAATTTCCT
Found at i:28560642 original size:44 final size:44
Alignment explanation
Indices: 28560575--28560662 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
28560565 GTGTTGGAGG
* *
28560575 TCTTGTGTTCGATTCTTTGCATTGGTAAGGGATAGTATTTTTTT
1 TCTTGTGTTCGATTCTCTACATTGGTAAGGGATAGTATTTTTTT
*
28560619 TCTTGTTTTCGATTCTCTACATTGGTAAGGGATAGTATTTTTTT
1 TCTTGTGTTCGATTCTCTACATTGGTAAGGGATAGTATTTTTTT
28560663 GTTTAGTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.52
Consensus pattern (44 bp):
TCTTGTGTTCGATTCTCTACATTGGTAAGGGATAGTATTTTTTT
Found at i:28562936 original size:5 final size:5
Alignment explanation
Indices: 28562926--28562973 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
28562916 AAAGAATTTA
* *
28562926 TTATT TTATT TTATT TTATT TTATT ATT-TA TTATT TTTTT ATTATT TT
1 TTATT TTATT TTATT TTATT TTATT -TTATT TTATT TTATT -TTATT TT
28562974 TTTAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:28562946 original size:15 final size:16
Alignment explanation
Indices: 28562923--28562982 Score: 65
Period size: 15 Copynumber: 4.0 Consensus size: 16
28562913 AAAAAAGAAT
28562923 TTATTATTTTATTTTA
1 TTATTATTTTATTTTA
*
28562939 TT-TTATTTTATTAT-
1 TTATTATTTTATTTTA
28562953 TTATTA-TTT-TTTTA
1 TTATTATTTTATTTTA
* *
28562967 TTATTTTTTTAATTTA
1 TTATTATTTTATTTTA
28562983 ACTTTAGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 3 0.08
14 10 0.28
15 17 0.47
16 6 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTATTTTATTTTA
Found at i:28562950 original size:23 final size:22
Alignment explanation
Indices: 28562922--28562981 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 22
28562912 AAAAAAAGAA
28562922 TTTATTATTTTATTTTATTTTAT
1 TTTATTATTTTATTTTATTTT-T
28562945 TTTATTA-TTTA--TTA-TTTT
1 TTTATTATTTTATTTTATTTTT
*
28562963 TTTATTATTTT-TTTAATTT
1 TTTATTATTTTATTTTATTT
28562982 AACTTTAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
18 8 0.25
19 6 0.19
20 5 0.16
21 2 0.06
22 4 0.12
23 7 0.22
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTATTATTTTATTTTATTTTT
Found at i:28562974 original size:10 final size:10
Alignment explanation
Indices: 28562922--28562975 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
28562912 AAAAAAAGAA
28562922 TTTATTATTT
1 TTTATTATTT
28562932 TATT-TTATTT
1 T-TTATTATTT
*
28562942 TATT-TTATTA
1 T-TTATTATTT
28562952 TTTATTATTTT
1 TTTATTA-TTT
28562963 TTTATTATTT
1 TTTATTATTT
28562973 TTT
1 TTT
28562976 TAATTTAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 2 0.05
10 26 0.67
11 11 0.28
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTATTT
Found at i:28572687 original size:27 final size:27
Alignment explanation
Indices: 28572660--28572877 Score: 285
Period size: 27 Copynumber: 8.1 Consensus size: 27
28572650 ACCAAAGTAC
* *
28572660 CCCT-GATTTATAGAATTACTGTTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
28572686 CCCTCGATTTACAAAATTACTGTTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
* *
28572713 CCCTTGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
* * * *
28572740 CCCTCGATTGATAGAATTACTATTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
28572767 CCCTCGATTTACAAAATTACTGTTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
* *
28572794 CCCTCGATTTATAAAATTACTATTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
* * *
28572821 CCCTCGATCTACAGAATTACCGTTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
* **
28572848 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACTGTTTTA
28572875 CCC
1 CCC
28572878 CTAGGATGTT
Statistics
Matches: 168, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
26 4 0.02
27 164 0.98
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACTGTTTTA
Found at i:28572715 original size:54 final size:55
Alignment explanation
Indices: 28572657--28572879 Score: 328
Period size: 54 Copynumber: 4.1 Consensus size: 55
28572647 ATTACCAAAG
* * *
28572657 TACCCCT-GATTTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGTTT
1 TACCCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTATAAAATTACTATTT
* * *
28572711 TA-CCCTTGATTTACAGAATTACTGTTTTACCCTCGATTGATAGAATTACTATTT
1 TACCCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTATAAAATTACTATTT
*
28572765 TA-CCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAAAATTACTATTT
1 TACCCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTATAAAATTACTATTT
* * *
28572819 TA-CCCTCGATCTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTT
1 TACCCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTATAAAATTACTATTT
28572873 TACCCCT
1 TACCCCT
28572880 AGGATGTTAA
Statistics
Matches: 154, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
53 4 0.03
54 146 0.95
55 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (55 bp):
TACCCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTATAAAATTACTATTT
Found at i:28572757 original size:81 final size:80
Alignment explanation
Indices: 28572667--28572877 Score: 314
Period size: 81 Copynumber: 2.6 Consensus size: 80
28572657 TACCCCTGAT
* *
28572667 TTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGTTTTACCCTTGATTTACAGAATTA
1 TTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTA
*
28572732 CTGTTTTACCCTCGA
66 CTATTTTACCCTCGA
* *
28572747 TTGATAGAATTACTATTTTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAAAATT
1 TT-ATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATT
28572812 ACTATTTTACCCTCGA
65 ACTATTTTACCCTCGA
* * * **
28572828 TCTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCC
1 T-TATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGTTTTACCC
28572878 CTAGGATGTT
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
80 2 0.02
81 115 0.97
82 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (80 bp):
TTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTA
CTATTTTACCCTCGA
Found at i:28573413 original size:6 final size:6
Alignment explanation
Indices: 28573382--28573475 Score: 68
Period size: 6 Copynumber: 15.3 Consensus size: 6
28573372 TTGCATTCAT
* *
28573382 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
28573431 -TCACCTG ATTCTG ATTCTA ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
28573476 AAGGTTTCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 56 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28573417 original size:31 final size:31
Alignment explanation
Indices: 28573382--28573454 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
28573372 TTGCATTCAT
* *
28573382 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
*
28573413 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
*
28573444 ATTCTAATTCT
1 ATTCTGATTCT
28573455 CATTTTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:28574500 original size:30 final size:30
Alignment explanation
Indices: 28574464--28574521 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
28574454 AAGTTCTAGT
28574464 TGAAGTGTGATAGTGATAGTAGGATCAGAG
1 TGAAGTGTGATAGTGATAGTAGGATCAGAG
28574494 TGAAGTGTGATAGTGATAGTAGGATCAG
1 TGAAGTGTGATAGTGATAGTAGGATCAG
28574522 TGTGCGCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (30 bp):
TGAAGTGTGATAGTGATAGTAGGATCAGAG
Found at i:28575551 original size:27 final size:27
Alignment explanation
Indices: 28575524--28575741 Score: 271
Period size: 27 Copynumber: 8.1 Consensus size: 27
28575514 ACCAAAGTAC
*
28575524 CCCT-GATTTACAAAATTATTATTTTA
1 CCCTCGATTTACAAAATTACTATTTTA
*
28575550 CCATCGATTTACAAAATTACTATTTTA
1 CCCTCGATTTACAAAATTACTATTTTA
* * *
28575577 CCCTTGATTTACAGAATTA-TCGTTTTA
1 CCCTCGATTTACAAAATTACT-ATTTTA
* * * *
28575604 CCC-CTGATTTATAGAATTATTGTTTTA
1 CCCTC-GATTTACAAAATTACTATTTTA
28575631 CCCTCGATTTACAAAATTACTATTTTA
1 CCCTCGATTTACAAAATTACTATTTTA
*
28575658 CCCTCGATTTACAGAATTACTATTTTA
1 CCCTCGATTTACAAAATTACTATTTTA
* *
28575685 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACTATTTTA
* *
28575712 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACTATTTTA
28575739 CCC
1 CCC
28575742 CTAGGGTGTT
Statistics
Matches: 171, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
26 4 0.02
27 165 0.96
28 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACTATTTTA
Found at i:28575622 original size:81 final size:81
Alignment explanation
Indices: 28575521--28575741 Score: 320
Period size: 81 Copynumber: 2.7 Consensus size: 81
28575511 ATTACCAAAG
* * *
28575521 TACCCCTGATTTACAAAATTATTATTTTACCATCGATTTACAAAATTACTATTTTACCCTTGATT
1 TACCCCTGATTTACAGAATTATTATTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
*
28575586 TACAGAATTA-TCGTTT
66 TACAGAATTACT-ATTT
* *
28575602 TACCCCTGATTTATAGAATTATTGTTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
1 TACCCCTGATTTACAGAATTATTATTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
28575667 TACAGAATTACTATTT
66 TACAGAATTACTATTT
** * *
28575683 TA-CCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAAAATTACCATTTTACCC
1 TACCCCT-GATTTACAGAATTATTATTTTACCCTCGATTTACAAAATTACTATTTTACCC
28575742 CTAGGGTGTT
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
80 4 0.03
81 121 0.96
82 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (81 bp):
TACCCCTGATTTACAGAATTATTATTTTACCCTCGATTTACAAAATTACTATTTTACCCTCGATT
TACAGAATTACTATTT
Found at i:28576022 original size:27 final size:26
Alignment explanation
Indices: 28575978--28576029 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28575968 CTCGCTGCAA
*
28575978 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28576005 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28576030 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28579602 original size:25 final size:25
Alignment explanation
Indices: 28579556--28579604 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28579546 CTGTTTTTGA
*
28579556 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATCCTGAAACTACTATAGG
*
28579581 TAGTATATGCT-AAGACTACTATAG
1 TAGTATATCCTGAA-ACTACTATAG
28579605 ATAGATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATCCTGAAACTACTATAGG
Found at i:28579841 original size:14 final size:15
Alignment explanation
Indices: 28579822--28579857 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
28579812 TACTCGAAGT
28579822 CGTGGTACAAGAGG-
1 CGTGGTACAAGAGGC
28579836 CGTGGTACAAGAGGC
1 CGTGGTACAAGAGGC
28579851 CGTGGTA
1 CGTGGTA
28579858 GAGGCCGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.25, C:0.17, G:0.42, T:0.17
Consensus pattern (15 bp):
CGTGGTACAAGAGGC
Found at i:28587968 original size:43 final size:43
Alignment explanation
Indices: 28587821--28587968 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
28587811 TGTGTTTTCC
* * * * * *
28587821 TGTAAGACCACGCCTGAGACATTGGCATCGACT-TATGATTTATG
1 TGTAAGACCACGTCTGGGATAGTGGCATCGA-TATTTGA-TTACG
* * *
28587865 TGTAAGACCACATCTGGGAT-GTTGGCATCG-TACTTGATTTCG
1 TGTAAGACCACGTCTGGGATAG-TGGCATCGATATTTGATTACG
*** * *
28587907 TGTAAGACGGTGTTTGGGATAGTGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGATAGTGGCATCGATATTTGATTACG
28587950 TGTAAGACCACGTCTGGGA
1 TGTAAGACCACGTCTGGGA
28587969 CATTAGCATT
Statistics
Matches: 79, Mismatches: 21, Indels: 9
0.72 0.19 0.08
Matches are distributed among these distances:
42 27 0.34
43 28 0.35
44 24 0.30
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGATAGTGGCATCGATATTTGATTACG
Found at i:28589731 original size:20 final size:20
Alignment explanation
Indices: 28589693--28589731 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28589683 ATAATTAAGA
* *
28589693 ACAAGTCAAATATTTATAAT
1 ACAAGTCAAATAATAATAAT
*
28589713 ACAATTCAAATAATAATAA
1 ACAAGTCAAATAATAATAA
28589732 CAAGATCCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (20 bp):
ACAAGTCAAATAATAATAAT
Found at i:28593243 original size:27 final size:26
Alignment explanation
Indices: 28593195--28593254 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28593185 GCGAGACTGC
*
28593195 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
28593222 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
28593248 CAGATAT
1 CAGATAT
28593255 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28593267 original size:33 final size:32
Alignment explanation
Indices: 28593216--28593279 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
28593206 ACGAAGTCAC
* *
28593216 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
28593248 CAGATATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCGAAGCCACCAGA
28593280 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:28593818 original size:10 final size:10
Alignment explanation
Indices: 28593803--28593833 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
28593793 ACACACCTAG
28593803 TTGATGACGA
1 TTGATGACGA
28593813 TTGATGACGA
1 TTGATGACGA
28593823 TTGATGACGA
1 TTGATGACGA
28593833 T
1 T
28593834 ATCTCCCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (10 bp):
TTGATGACGA
Found at i:28600083 original size:46 final size:47
Alignment explanation
Indices: 28599937--28600201 Score: 213
Period size: 47 Copynumber: 5.6 Consensus size: 47
28599927 CTGGTGGCTT
* * *
28599937 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTTTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT-AGAGCC
* ** * * *
28599983 AGTGTAAGACCATGTCTGAGACATGACATCAACATTGAGACG-AGAGCC
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCGAGATGTAGAGCC
* *
28600031 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
* ** * * *
28600077 AGTGTAAGACATGTATGGGGTATGTATCGG-CTACGAGATG-ATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGCC
* * * *
28600123 AGTTTAAGACCATGTCTGGGACATGGCATC-GACTTGAGATAT-GAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGCC
28600170 AGTGTAAGACTATGTCTGGGACATGGCATCGG
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGG
28600202 TACCTTACCC
Statistics
Matches: 175, Mismatches: 31, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
45 3 0.02
46 69 0.39
47 75 0.43
48 27 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
Found at i:28602471 original size:31 final size:31
Alignment explanation
Indices: 28602433--28602495 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
28602423 GTGAGAATGA
*
28602433 TGTTTGAGAATTATTTGTGAAATATTTTGAT
1 TGTTTGAGAATTATTTGTGAAATATTTCGAT
* *
28602464 TGTTTGAGCATTATTTGTGAAATGTTTCGAT
1 TGTTTGAGAATTATTTGTGAAATATTTCGAT
28602495 T
1 T
28602496 TGTCTGGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.21, T:0.51
Consensus pattern (31 bp):
TGTTTGAGAATTATTTGTGAAATATTTCGAT
Found at i:28611229 original size:42 final size:43
Alignment explanation
Indices: 28611110--28611271 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 43
28611100 CGATATGTGT
**
28611110 TTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGA
1 TTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTACTGA
* *
28611153 TTTACTTGTAGGACCACGTCTGGGACGTTGGCATCGTAC-ACT-A
1 TTT-CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTACTGA
*
28611196 TTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATTTGA
1 TTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACTA-CTGA
* * *
28611239 TTACATGTAAGACCACGTCTAGGACGTTGGCAT
1 TTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
28611272 TGTACGAGCT
Statistics
Matches: 100, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
41 3 0.03
42 28 0.28
43 35 0.35
44 32 0.32
45 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (43 bp):
TTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTACTGA
Found at i:28611270 original size:43 final size:43
Alignment explanation
Indices: 28611115--28611271 Score: 162
Period size: 42 Copynumber: 3.7 Consensus size: 43
28611105 TGTGTTTTCG
* *
28611115 TGTAAGACCACGTCTGGGACGTTGGCATCGACT-TGTGATTTACT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TATCTGA-TTACA
* * * *
28611159 TGTAGGACCACGTCTGGGACGTTGGCATCG-TACACT-ATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATA-TCTGATTACA
*
28611201 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATCTGATTACA
*
28611244 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
28611272 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 31 0.33
43 31 0.33
44 31 0.33
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATCTGATTACA
Found at i:28616098 original size:27 final size:25
Alignment explanation
Indices: 28616040--28616098 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
28616030 TCAAACTCTT
*
28616040 TTAAAAGAAAACTAAAGAAAAATTC
1 TTAAAAGAAAACTAAAGAAAAATTA
* *
28616065 TTGAAAAGAAAAAGTCAAAGAAAATTTA
1 TT-AAAAG-AAAACT-AAAGAAAAATTA
28616093 TTAAAA
1 TTAAAA
28616099 TGAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.07
26 5 0.18
27 9 0.32
28 12 0.43
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.22
Consensus pattern (25 bp):
TTAAAAGAAAACTAAAGAAAAATTA
Found at i:28618559 original size:27 final size:26
Alignment explanation
Indices: 28618511--28618570 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28618501 GCGAAGTTGG
*
28618511 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
28618538 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
28618564 CAGATAT
1 CAGATAT
28618571 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28619339 original size:27 final size:27
Alignment explanation
Indices: 28619309--28619507 Score: 245
Period size: 27 Copynumber: 7.4 Consensus size: 27
28619299 GGGCAAATTG
* * *
28619309 GTAATTTTACCCCACAAGGGTATCTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
28619336 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
28619363 GTATTTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
28619390 GTAATTCTATCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
28619417 GTAATTCTACCCTGCAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* * *
28619444 ATAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* * **
28619471 GTAATTCTACCTTACAGGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
28619498 GTAATTCTAC
1 GTAATTCTAC
28619508 AACTTATCCA
Statistics
Matches: 151, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:28626940 original size:27 final size:27
Alignment explanation
Indices: 28626910--28627055 Score: 175
Period size: 27 Copynumber: 5.4 Consensus size: 27
28626900 GGGGCAAAAT
* * *
28626910 GGTAATTTTACCCCACAAAGGTATCTC
1 GGTAATTCTACCCTACAAAGGTATTTC
** *
28626937 GGTAATTCTACCCTACAGGGGTATTTG
1 GGTAATTCTACCCTACAAAGGTATTTC
*
28626964 GGTATTTCTACCCTACAAAGGTATTTC
1 GGTAATTCTACCCTACAAAGGTATTTC
* **
28626991 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAAGGTATTTC
* **
28627018 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAAGGTATTTC
28627045 GGTAATTCTAC
1 GGTAATTCTAC
28627056 AACTTATCCA
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAAGGTATTTC
Found at i:28627012 original size:54 final size:54
Alignment explanation
Indices: 28626914--28627055 Score: 205
Period size: 54 Copynumber: 2.6 Consensus size: 54
28626904 CAAAATGGTA
* * *
28626914 ATTT-TACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTGGGT
1 ATTTCTACCCTACAAAGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
*
28626967 ATTTCTACCCTACAAAGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAAGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
* * **
28627021 AATTCTACCTTACAGGGGTATTTCGGTAATTCTAC
1 ATTTCTACCCTACAAAGGTATTTCGGTAATTCTAC
28627056 AACTTATCCA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
53 4 0.05
54 75 0.95
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (54 bp):
ATTTCTACCCTACAAAGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
Found at i:28628754 original size:55 final size:55
Alignment explanation
Indices: 28628648--28628755 Score: 128
Period size: 55 Copynumber: 2.0 Consensus size: 55
28628638 GACAGTTTTG
* * * * *
28628648 ACCACGGGTGGTGAGCACGAGAGTGTTACATGCCTGTGTTAATTGGACAGGATCA
1 ACCACAGGTGGTGAGCACGAGAGTGTCACACGCCCGTATTAATTGGACAGGATCA
* * *
28628703 ACCACAGGTGGTGGGCACGAGCGTGTCACACGCCCGTATTGATTTGG-CAGGAT
1 ACCACAGGTGGTGAGCACGAGAGTGTCACACGCCCGTATT-AATTGGACAGGAT
28628756 TGCCCACGGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
55 39 0.89
56 5 0.11
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (55 bp):
ACCACAGGTGGTGAGCACGAGAGTGTCACACGCCCGTATTAATTGGACAGGATCA
Found at i:28631509 original size:37 final size:37
Alignment explanation
Indices: 28631433--28631513 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
28631423 TTGCAGCAAT
****
28631433 AGTAGG-TCTAACTATACTCAATTCAGCTCCTGTTCA
1 AGTAGGTTCTAACTATACTCAATTCAGCTCCTACAAA
*
28631469 AGTAGGTTCTAACTATACTCAATTCATCTCCTACAAA
1 AGTAGGTTCTAACTATACTCAATTCAGCTCCTACAAA
28631506 AGTAGGTT
1 AGTAGGTT
28631514 TAGCATAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 6 0.15
37 33 0.85
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (37 bp):
AGTAGGTTCTAACTATACTCAATTCAGCTCCTACAAA
Found at i:28639656 original size:16 final size:16
Alignment explanation
Indices: 28639632--28639731 Score: 137
Period size: 16 Copynumber: 6.2 Consensus size: 16
28639622 TGGTTCACTA
*
28639632 TAATGGAATAGGGTTG
1 TAATGGAATAGAGTTG
* *
28639648 TAATTGAATAGAGGTG
1 TAATGGAATAGAGTTG
*
28639664 TAAAGGAATAGAGTTG
1 TAATGGAATAGAGTTG
* *
28639680 TAATTGAATAGAGGTG
1 TAATGGAATAGAGTTG
*
28639696 TAATGTAATAGAGTTG
1 TAATGGAATAGAGTTG
28639712 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
28639728 TAAT
1 TAAT
28639732 CAGTAATTCT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 71 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:28639731 original size:32 final size:32
Alignment explanation
Indices: 28639632--28639731 Score: 155
Period size: 32 Copynumber: 3.1 Consensus size: 32
28639622 TGGTTCACTA
*
28639632 TAATGGAATAGGGTTGTAATTGAATAGAGGTG
1 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
*
28639664 TAAAGGAATAGAGTTGTAATTGAATAGAGGTG
1 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
* * *
28639696 TAATGTAATAGAGTTGTAATGGAATAGAGTTG
1 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
28639728 TAAT
1 TAAT
28639732 CAGTAATTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (32 bp):
TAATGGAATAGAGTTGTAATTGAATAGAGGTG
Found at i:28639802 original size:44 final size:46
Alignment explanation
Indices: 28639713--28639805 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 46
28639703 ATAGAGTTGT
* * * *
28639713 AATGGAATAGAGTTGTAATCAGTAATTCTATTGTTTGGTTTAATGG
1 AATGGAATAAAGCTGTAATCAGTAATTCTATTGTTTCGTTGAATGG
28639759 AATGGAATAAAGCTGTAAT-AGT-ATTCT-TGTGTTTCGTTGAATGG
1 AATGGAATAAAGCTGTAATCAGTAATTCTAT-TGTTTCGTTGAATGG
28639803 AAT
1 AAT
28639806 AGATGTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.50
45 3 0.07
46 17 0.40
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (46 bp):
AATGGAATAAAGCTGTAATCAGTAATTCTATTGTTTCGTTGAATGG
Found at i:28642785 original size:42 final size:42
Alignment explanation
Indices: 28642680--28642837 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 42
28642670 ATATGTTTCT
* *
28642680 CGTGTAAGACCATGTCT-GGACTTTGGCATCG-ACTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTA-TT-TGA-TTA
*
28642723 CGTGCAAGACCACGTCTGGGACATTGGCATCGTATTTGCATT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTG-ATTA
* *
28642765 CGTGTAAGACC-CTGTTTGGGACAGTGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATTA
* *
28642808 CATGTAAGACCACATCTGGGACATTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
28642838 TGTACATGTT
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.31
43 49 0.50
44 17 0.17
45 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
Found at i:28642817 original size:85 final size:85
Alignment explanation
Indices: 28642679--28642837 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 85
28642669 GATATGTTTC
** * *
28642679 TCGTGTAAGACCATGTCTGGACTTTGGCATCGACTTATGATTTACGTGCAAGACCACGTCTGGGA
1 TCGTGTAAGACCATGTCTGGACAGTGGCATCGACTTATGATTTACATGCAAGACCACATCTGGGA
28642744 CATTGGCATCGTATTTGCAT
66 CATTGGCATCGTATTTGCAT
* * * *
28642764 TCGTGTAAGACCCTGTTTGGGACAGTGGCATCGA-TATTTGA-TTACATGTAAGACCACATCTGG
1 TCGTGTAAGACCATGTCT-GGACAGTGGCATCGACT-TATGATTTACATGCAAGACCACATCTGG
28642827 GACATTGGCAT
64 GACATTGGCAT
28642838 TGTACATGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 47 0.73
86 17 0.27
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (85 bp):
TCGTGTAAGACCATGTCTGGACAGTGGCATCGACTTATGATTTACATGCAAGACCACATCTGGGA
CATTGGCATCGTATTTGCAT
Found at i:28648073 original size:63 final size:63
Alignment explanation
Indices: 28647895--28648151 Score: 202
Period size: 68 Copynumber: 3.9 Consensus size: 63
28647885 ATATAGTTCG
* * * *
28647895 GCTCTCTTGTAC-ACATGGTGAACACTCAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTA
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATATATCTCGTA
* * *
28647958 GCTCTC-TGTCTACATGGTGTCCTTCACCT-GGAGCCACGCATGCGACCTAGCTACATATATC-C
1 GCTCTCTTGTCTACATGGTG---TACA-CTAGTA-CCACCCATGCGACCTAGCTACATATATCTC
28648020 GTA
61 GTA
* *
28648023 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTT
1 GCTCTCTTGTCTACATGGTGTACAC-TAGTACCACCCATGCGACCTAGCTACAT-AT-A--TCTC
28648088 GTA
61 GTA
* * * ** *
28648091 GCTCTCTTGTAC-ACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATACTATCT
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATA-TATCT
28648152 GTATTATCCA
Statistics
Matches: 157, Mismatches: 19, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
61 1 0.01
62 12 0.08
63 31 0.20
64 6 0.04
65 33 0.21
66 21 0.13
67 5 0.03
68 47 0.30
69 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (63 bp):
GCTCTCTTGTCTACATGGTGTACACTAGTACCACCCATGCGACCTAGCTACATATATCTCGTA
Found at i:28660644 original size:22 final size:22
Alignment explanation
Indices: 28660590--28660644 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
28660580 TATGGCCTTT
*
28660590 AGCCATTCTGTCTACAGCGTTG
1 AGCCATTCTGTCTACAGCATTG
* *
28660612 AGCCATCCTGTCTACGGCATTG
1 AGCCATTCTGTCTACAGCATTG
* *
28660634 AGTCGTTCTGT
1 AGCCATTCTGT
28660645 TGACTTAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (22 bp):
AGCCATTCTGTCTACAGCATTG
Found at i:28663198 original size:29 final size:29
Alignment explanation
Indices: 28663156--28663213 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28663146 TACTCTTATC
28663156 TCCATTGGATTTACCTTTAATTCCATCAT
1 TCCATTGGATTTACCTTTAATTCCATCAT
28663185 TCCATTGGATTTACCTTTAATTCCATCAT
1 TCCATTGGATTTACCTTTAATTCCATCAT
28663214 ACTTCTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (29 bp):
TCCATTGGATTTACCTTTAATTCCATCAT
Found at i:28667592 original size:16 final size:16
Alignment explanation
Indices: 28667566--28667616 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
28667556 GTAGATCGGC
* * *
28667566 AAATCCCGAAATGCCG
1 AAATGCCGAAAAGTCG
*
28667582 AAAAGCCGAAAAGTCG
1 AAATGCCGAAAAGTCG
*
28667598 AAATGCCAAAAAGTCG
1 AAATGCCGAAAAGTCG
28667614 AAA
1 AAA
28667617 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.10
Consensus pattern (16 bp):
AAATGCCGAAAAGTCG
Found at i:28667869 original size:29 final size:29
Alignment explanation
Indices: 28667827--28667979 Score: 227
Period size: 29 Copynumber: 5.3 Consensus size: 29
28667817 AAAGAATATT
* *
28667827 TATGAATGTGATTTGGGCCTAATGGGTCG
1 TATGAATGTGATTTGGGCCTAATGGGCCA
28667856 TATGAATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
28667885 TATGAATGTGATTTGGGCCTAGTGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
* *
28667914 TACGAATATGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
* *
28667943 TATGAATGAGA-TTGGGCCTAGTGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
28667971 TATGCATGT
1 TATGAATGT
28667980 ATGTAGACCT
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
28 23 0.21
29 89 0.79
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.31
Consensus pattern (29 bp):
TATGAATGTGATTTGGGCCTAATGGGCCA
Found at i:28672811 original size:45 final size:45
Alignment explanation
Indices: 28672762--28672862 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
28672752 TACGATGCTG
* * *
28672762 ATGTCCTAGACATAGTCTTGCACATAACCACATAGATCGATGCCA
1 ATGTCCCAGACATAGCCTTACACATAACCACATAGATCGATGCCA
** * *
28672807 ATGTCCCAGATGTGGCCTTACACGTAACCACATAGATCGATGCCA
1 ATGTCCCAGACATAGCCTTACACATAACCACATAGATCGATGCCA
*
28672852 ACGTCCCAGAC
1 ATGTCCCAGAC
28672863 GTGGTCTTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (45 bp):
ATGTCCCAGACATAGCCTTACACATAACCACATAGATCGATGCCA
Found at i:28672872 original size:45 final size:45
Alignment explanation
Indices: 28672776--28672917 Score: 171
Period size: 45 Copynumber: 3.2 Consensus size: 45
28672766 CCTAGACATA
* * * *
28672776 GTCTTGCACATAACCACATAGATCGATGCCAATGTCCCAGATGTG
1 GTCTTACACGTAACCACATAGATCGATGCCAACGTCCCAGACGTG
*
28672821 GCCTTACACGTAACCACATAGATCGATGCCAACGTCCCAGACGTG
1 GTCTTACACGTAACCACATAGATCGATGCCAACGTCCCAGACGTG
* * * *
28672866 GTCTTACATGAAAACA-ATTATG-TCGATGCCAACATCCCAGACGTG
1 GTCTTACACGTAACCACA-TA-GATCGATGCCAACGTCCCAGACGTG
28672911 GTCTTAC
1 GTCTTAC
28672918 TCGGAAACAC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
44 1 0.01
45 83 0.98
46 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
GTCTTACACGTAACCACATAGATCGATGCCAACGTCCCAGACGTG
Found at i:28675826 original size:42 final size:44
Alignment explanation
Indices: 28675745--28675882 Score: 147
Period size: 42 Copynumber: 3.2 Consensus size: 44
28675735 CCGGACGTGG
* * * * *
28675745 TCTTACATGTAATTCAG-TATCAATGCCTCTGTCCCAGACAGGG
1 TCTTACATGTAAATCAGATATCGATGCCTATGTCCCAGACACGA
* *
28675788 TCTTACATG-AAATCAGATAT-GATTCCTATGTCCCAGACATGA
1 TCTTACATGTAAATCAGATATCGATGCCTATGTCCCAGACACGA
* ** * *
28675830 TCTTACACGTAAATCTCAAATCGAGGCCTATGTCCCAGACACGA
1 TCTTACATGTAAATCAGATATCGATGCCTATGTCCCAGACACGA
28675874 TCTTACATG
1 TCTTACATG
28675883 ATATCTCAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
42 31 0.40
43 20 0.26
44 27 0.35
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
TCTTACATGTAAATCAGATATCGATGCCTATGTCCCAGACACGA
Found at i:28679891 original size:60 final size:59
Alignment explanation
Indices: 28679764--28679902 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
28679754 ATCAGATTTA
* * *
28679764 ACTGGGCCTTAGCCCTTATCAATAACAATCTGGGCCATAGCCCCTTACTGTATCAGAGTAT
1 ACTGGGCC-TAGCCCATATCAATAACAATATGGGCCATAGCCCCTTACAG-ATCAGAGTAT
* * *
28679825 ACTGGGCCTAGCCCATATCAGTATCAATATGGGCCGTAGCCCTCTTACA-AGTC-GAGATAT
1 ACTGGGCCTAGCCCATATCAATAACAATATGGGCCATAGCCC-CTTACAGA-TCAGAG-TAT
* *
28679885 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
28679903 TAACACAGTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 50 0.75
61 13 0.19
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATAACAATATGGGCCATAGCCCCTTACAGATCAGAGTAT
Found at i:28693203 original size:5 final size:5
Alignment explanation
Indices: 28693186--28693216 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
28693176 ATAGAGTGAC
28693186 TTCTT TT-TT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
28693217 TCTATCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTCTT
Found at i:28697547 original size:23 final size:24
Alignment explanation
Indices: 28697521--28697569 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
28697511 AATAGTGATC
* *
28697521 AAGAAATAAG-AGAAAATTGGGAA
1 AAGAAAGAAGAAGAAAATTGAGAA
*
28697544 AAGAAAGAAGAAGAAAGTTGAGAA
1 AAGAAAGAAGAAGAAAATTGAGAA
28697568 AA
1 AA
28697570 ATTTTACTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (24 bp):
AAGAAAGAAGAAGAAAATTGAGAA
Found at i:28697942 original size:17 final size:18
Alignment explanation
Indices: 28697909--28697943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28697899 ACATAGGGTC
28697909 ACACGCCCATGTGCCCTCG
1 ACACGCCCA-GTGCCCTCG
28697928 ACACGCCCA-TGCCCTC
1 ACACGCCCAGTGCCCTC
28697944 AATCCGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.17, C:0.51, G:0.17, T:0.14
Consensus pattern (18 bp):
ACACGCCCAGTGCCCTCG
Found at i:28704898 original size:15 final size:15
Alignment explanation
Indices: 28704869--28704908 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
28704859 AAAGATGACA
* *
28704869 AGAAAACCAAGATAG
1 AGAAATCCAAAATAG
*
28704884 AGGAATCCAAAATAG
1 AGAAATCCAAAATAG
28704899 AGAAATCCAA
1 AGAAATCCAA
28704909 GATACGATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.10
Consensus pattern (15 bp):
AGAAATCCAAAATAG
Found at i:28710591 original size:30 final size:31
Alignment explanation
Indices: 28710512--28710594 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
28710502 TCAGTCTCGA
*
28710512 CATAT-ACTGGGCCGAAGCCTTTTCATAATT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
28710542 CATATCATTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
28710573 CATATCACT-GGTCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
28710595 ACTGTAAGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.35
31 31 0.65
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:28710851 original size:25 final size:25
Alignment explanation
Indices: 28710814--28710908 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
28710804 CTCTTTTAAT
* * *
28710814 AACTAGGGTAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
28710839 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
28710864 AACTGGGGCAAAGACCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
28710889 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28710909 AGCACTTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:28711753 original size:27 final size:26
Alignment explanation
Indices: 28711718--28711795 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
28711708 GGGCATATTC
28711718 GTCATTTTACCATATAGGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
* *
28711745 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTA-CCTATAGGGG-TATTACG
*
28711772 GTCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTA-TAGGGGTATT
28711796 TTAGTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 5 0.12
27 34 0.81
28 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:28711866 original size:27 final size:28
Alignment explanation
Indices: 28711836--28711943 Score: 100
Period size: 27 Copynumber: 3.9 Consensus size: 28
28711826 GTAAATCTAC
28711836 AAACCAAGGGTATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
*
28711863 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTCTAGTAATTTTGT
* *
28711889 AGAAAGTCAATGGTATTTCT-GTAATTTTGT
1 --AAA-CCAAGGGTATTTCTAGTAATTTTGT
* * *
28711919 AAATCAGGGGTATTT-TGGTAATTTT
1 AAACCAAGGGTATTTCTAGTAATTTT
28711944 ACAAATTGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
26 2 0.03
27 39 0.56
28 8 0.11
29 20 0.29
30 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (28 bp):
AAACCAAGGGTATTTCTAGTAATTTTGT
Found at i:28711949 original size:27 final size:26
Alignment explanation
Indices: 28711900--28712041 Score: 133
Period size: 27 Copynumber: 5.3 Consensus size: 26
28711890 GAAAGTCAAT
**
28711900 GGTATTTCT-GTAATTTTGTAAATCAGG
1 GGTATTT-TGGTAATTTTACAAAT-AGG
*
28711927 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTGGTAATTTTACAAATAG-G
* * *
28711954 GGTATTTCGGTAATTTCACAAAGTAGT
1 GGTATTTTGGTAATTTTACAAA-TAGG
*
28711981 GGAATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAA-TAGG
* **
28712008 GGTATTTTGGTAATTCTACCCTATAGG
1 GGTATTTTGGTAATTTTA-CAAATAGG
28712035 GGTATTT
1 GGTATTT
28712042 CAATAATTTC
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.02
27 89 0.94
28 4 0.04
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTACAAATAGG
Found at i:28712084 original size:27 final size:27
Alignment explanation
Indices: 28712054--28712145 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
28712044 ATAATTTCAC
*
28712054 AATCGAGGGTAAAACACTAATTTTGTA
1 AATCGAGGGTAAAACAATAATTTTGTA
* *
28712081 AATCGAGGGTAAAAGAGTAATTTTGTA
1 AATCGAGGGTAAAACAATAATTTTGTA
* * *
28712108 AATCAAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACAATAATTTTGTA
28712135 AATCGAGGGTA
1 AATCGAGGGTA
28712146 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACAATAATTTTGTA
Found at i:28712276 original size:27 final size:27
Alignment explanation
Indices: 28712245--28712301 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
28712235 CCATTCTCGA
*
28712245 CCCAAATGGGCCCACACGCTCGTGTGG
1 CCCAAATAGGCCCACACGCTCGTGTGG
28712272 CCCAAATAGGCCCACACGCTCGTGTGG
1 CCCAAATAGGCCCACACGCTCGTGTGG
28712299 CCC
1 CCC
28712302 TTTTAGCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.40, G:0.26, T:0.14
Consensus pattern (27 bp):
CCCAAATAGGCCCACACGCTCGTGTGG
Found at i:28717969 original size:93 final size:93
Alignment explanation
Indices: 28717855--28718025 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
28717845 GCCCCTAAGT
* *
28717855 GAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28717919 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
*
28717948 GAACTCGGGCTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28718013 CGAGTTCGGATGC
66 CGAGTTCGGATGC
28718026 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28718022 original size:46 final size:46
Alignment explanation
Indices: 28717850--28718022 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 46
28717840 AACCCGCCCC
* *
28717850 TAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCA
*
28717896 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
28717944 TCA-CGAACTCGGGCTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28717989 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28718023 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 58 0.54
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:28718479 original size:30 final size:30
Alignment explanation
Indices: 28718445--28718504 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28718435 ATTTAATACG
28718445 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
28718475 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
28718505 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:28724365 original size:35 final size:34
Alignment explanation
Indices: 28724324--28724433 Score: 98
Period size: 37 Copynumber: 3.0 Consensus size: 34
28724314 AAGAGCCTCT
*
28724324 TGTGCGAGATACTAAATCCGGTTAGCCCGAAGGCA
1 TGTGCGAG-TACTAAATCCGGTTAGTCCGAAGGCA
28724359 TGTGCGAGT-CATGAAATCCGGGTTAAGTCCGAAGGCAA
1 TGTGCGAGTAC-T-AAATCC-GGTT-AGTCCGAAGGC-A
* *
28724397 TTGTGGGAGTTACTAAA-CCGGCTATGTCCGAAGGCA
1 -TGTGCGAG-TACTAAATCCGGTTA-GTCCGAAGGCA
28724433 T
1 T
28724434 TTGAATGGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
33 1 0.02
34 2 0.03
35 15 0.24
36 6 0.10
37 23 0.37
38 3 0.05
39 10 0.16
40 2 0.03
41 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (34 bp):
TGTGCGAGTACTAAATCCGGTTAGTCCGAAGGCA
Found at i:28730180 original size:40 final size:39
Alignment explanation
Indices: 28730136--28730238 Score: 136
Period size: 38 Copynumber: 2.6 Consensus size: 39
28730126 CATATCCAGA
*
28730136 CTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGG
1 CTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGG
* *
28730176 CTAAGCCCGAA-GCATTTGTGCGAGTTACTAAATCCGGG
1 CTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGG
* *
28730214 TTAAGTCCCGAAGGCAATTGTGCGA
1 CTAAGT-CCGAAGGCATTTGTGCGA
28730239 TTACTATAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 29 0.53
39 10 0.18
40 16 0.29
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (39 bp):
CTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGG
Found at i:28730193 original size:38 final size:40
Alignment explanation
Indices: 28730094--28730269 Score: 147
Period size: 40 Copynumber: 4.5 Consensus size: 40
28730084 AATGATGTCC
* * * *
28730094 GGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCA
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAATCCG
* *
28730134 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAATCCG
*
28730174 GGCTAAG-CCCGAA-GCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCG
* * *
28730212 GGTTAAGTCCCGAAGGCAATTGTGCGA-TTACTATAA--C-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AATCCG
*
28730249 -GCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
28730270 AACGAGTAGC
Statistics
Matches: 115, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
36 18 0.16
38 30 0.26
39 17 0.15
40 39 0.34
41 10 0.09
42 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCG
Found at i:28732451 original size:10 final size:12
Alignment explanation
Indices: 28732426--28732451 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28732416 TTTGAGAGTT
28732426 ACACGGCCTAAC
1 ACACGGCCTAAC
28732438 ACACGGCCTAAC
1 ACACGGCCTAAC
28732450 AC
1 AC
28732452 CCAAGTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.42, G:0.15, T:0.08
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:28735542 original size:43 final size:43
Alignment explanation
Indices: 28735494--28735664 Score: 152
Period size: 43 Copynumber: 4.0 Consensus size: 43
28735484 GTTACTGAAA
*
28735494 TGTGATTACATGTAAGACCATGTCTGAGACATTGGAATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATTGTAT
* * *
28735537 TGTGATTACGTGTAAGACCATGTAT-AGGATATTGGCATTGTTAT
1 TGTGATTACATGTAAGACCATGTCTGA-GACATTGGCATTG-TAT
* * * * * * *
28735581 T-TTATTTCGTGTAAGACCTTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATTGTAT
* * * *
28735622 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 -TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATTGTAT
28735665 GAGTTATATG
Statistics
Matches: 102, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 9 0.09
43 87 0.85
44 4 0.04
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATTGTAT
Found at i:28735653 original size:86 final size:85
Alignment explanation
Indices: 28735504--28735662 Score: 203
Period size: 86 Copynumber: 1.9 Consensus size: 85
28735494 TGTGATTACA
* * * * *
28735504 TGTAAGACCATGTCTGAGACATTGGAATTGTATTGTGATTACGTGTAAGACCATGTATAGGATAT
1 TGTAAGACCATGTCTGAGACAGTGGAATCGTATTGTGATAACATGTAAGACCATATATAGGATA-
28735569 TGGCATTGTTATTTTATTTCG
65 TGGCATTGTTATTTTATTTCG
* * * * *
28735590 TGTAAGACCTTGTCTGGGACAGTGGCATCG-ATATGTGATAACATGTAAGACCATATCTGGGATA
1 TGTAAGACCATGTCTGAGACAGTGGAATCGTAT-TGTGATAACATGTAAGACCATATATAGGATA
28735654 TGGCATTGT
65 TGGCATTGT
28735663 ATGAGTTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
85 11 0.18
86 51 0.82
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (85 bp):
TGTAAGACCATGTCTGAGACAGTGGAATCGTATTGTGATAACATGTAAGACCATATATAGGATAT
GGCATTGTTATTTTATTTCG
Found at i:28742143 original size:43 final size:43
Alignment explanation
Indices: 28742094--28742252 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
28742084 GGTTACTAAG
28742094 ATGTGATTACATGTAAGACCATGTCTGGGACATTGACA-CTG-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGACATC-GAT
* * * * *
28742136 ACTGTGATCACGTGTAAGACCATGTCTAGGATATTGACATCGTT
1 A-TGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGAT
* * * * * *
28742180 ATTTGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGAT
* * *
28742223 ATGTGATAACATGTAAAACCATATCTGGGA
1 ATGTGATTACATGTAAGACCATGTCTGGGA
28742253 TATGGCATTG
Statistics
Matches: 94, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
42 1 0.01
43 90 0.96
44 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGAT
Found at i:28743791 original size:12 final size:12
Alignment explanation
Indices: 28743774--28743798 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28743764 TTGTAAGGCC
28743774 TTGTAACCCTAT
1 TTGTAACCCTAT
28743786 TTGTAACCCTAT
1 TTGTAACCCTAT
28743798 T
1 T
28743799 CTGGCGACGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TTGTAACCCTAT
Found at i:28748975 original size:19 final size:19
Alignment explanation
Indices: 28748950--28749075 Score: 174
Period size: 19 Copynumber: 6.9 Consensus size: 19
28748940 ATAATCTTCA
28748950 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
* *
28748969 GTGATATGTAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28748988 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
28749005 ATGAT-TGCAATATTAGAT
1 ATGATATGCAATCTTAGAT
28749023 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
28749040 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
28749058 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
28749076 AGATATGATT
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
17 30 0.32
18 31 0.33
19 33 0.35
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:28748990 original size:14 final size:16
Alignment explanation
Indices: 28748959--28749063 Score: 93
Period size: 17 Copynumber: 6.0 Consensus size: 16
28748949 AATGATATGC
*
28748959 AATCTTAGATGTGATA
1 AATCTTAGATATGATA
28748975 TGTAATCTTAGATATGATA
1 ---AATCTTAGATATGATA
*
28748994 CAATCTTAGATATGATTGC
1 -AATCTTAGATATGA-T-A
*
28749013 AATATTAGATATGATA
1 AATCTTAGATATGATA
*
28749029 CAATCTTAGATATGATTGC
1 -AATCTTAGATATGA-T-A
28749048 AATCTTAGATATGATA
1 AATCTTAGATATGATA
28749064 TACAATCTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
17 29 0.40
18 29 0.40
19 15 0.21
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (16 bp):
AATCTTAGATATGATA
Found at i:28749020 original size:18 final size:18
Alignment explanation
Indices: 28748950--28749075 Score: 157
Period size: 18 Copynumber: 6.9 Consensus size: 18
28748940 ATAATCTTCA
28748950 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
* *
28748969 GTGATATGTAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
28748988 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
28749005 ATGATTGCAATATTAGAT
1 ATGATTGCAATCTTAGAT
*
28749023 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
28749040 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
28749058 ATGATATACAATCTTAGA
1 ATGAT-TGCAATCTTAGA
28749076 AGATATGATT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
17 30 0.32
18 32 0.34
19 31 0.33
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:28749027 original size:35 final size:35
Alignment explanation
Indices: 28748958--28749075 Score: 182
Period size: 35 Copynumber: 3.3 Consensus size: 35
28748948 CAATGATATG
* *
28748958 CAATCTTAGATGTGATATGTAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
*
28748994 CAATCTTAGATATGATTGCAATATTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
28749029 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
28749066 CAATCTTAGA
1 CAATCTTAGA
28749076 AGATATGATT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
35 48 0.63
36 15 0.20
37 13 0.17
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:28754864 original size:21 final size:21
Alignment explanation
Indices: 28754833--28754906 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 21
28754823 GACTTCTATT
28754833 TAAAA-AAAAAG-GCAAAAAAG
1 TAAAAGAAAAAGAG-AAAAAAG
*
28754853 TAAAAGAAAAAGAGAAAAAAA
1 TAAAAGAAAAAGAGAAAAAAG
28754874 TAAAATGAAAAAAGAGAAAAAAG
1 TAAAA-G-AAAAAGAGAAAAAAG
*
28754897 -AAAAAAAAAA
1 TAAAAGAAAAA
28754907 TGGAGAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 10 0.21
21 17 0.36
22 6 0.13
23 14 0.30
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (21 bp):
TAAAAGAAAAAGAGAAAAAAG
Found at i:28754873 original size:16 final size:16
Alignment explanation
Indices: 28754854--28754903 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
28754844 GCAAAAAAGT
28754854 AAAAGAAAAAGAGAAA
1 AAAAGAAAAAGAGAAA
* *
28754870 AAAATAAAATGA-AAA
1 AAAAGAAAAAGAGAAA
*
28754885 AAGAGAAAAA-AGAAA
1 AAAAGAAAAAGAGAAA
28754900 AAAA
1 AAAA
28754904 AAATGGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 1 0.04
15 16 0.59
16 10 0.37
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAA
Found at i:28754900 original size:22 final size:22
Alignment explanation
Indices: 28754837--28754906 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
28754827 TCTATTTAAA
*
28754837 AAAAAAG-GCAAAAAAGTAAAAG
1 AAAAAAGAGAAAAAAAG-AAAAG
*
28754859 -AAAAAGAGAAAAAAATAAAATG
1 AAAAAAGAGAAAAAAAGAAAA-G
28754881 AAAAAAGAG-AAAAAAGAAAA-
1 AAAAAAGAGAAAAAAAGAAAAG
28754901 AAAAAA
1 AAAAAA
28754907 TGGAGAGGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.14
21 10 0.24
22 18 0.43
23 8 0.19
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (22 bp):
AAAAAAGAGAAAAAAAGAAAAG
Found at i:28755892 original size:43 final size:41
Alignment explanation
Indices: 28755844--28755970 Score: 116
Period size: 43 Copynumber: 3.0 Consensus size: 41
28755834 TTGAAAATTA
28755844 CAAAATTCAGCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT
1 CAAAATT--GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT
* * * *
28755887 CAAAATTGCGGATCTT-ATCTCCCTAAACAGTAGTGG-AGCAGAT
1 CAAAATTGC-G-CCTTAATC-CCCTAAGCAGTAG-GGTAACAGGT
* *
28755930 CGAAGA-TGCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGT
1 C-AAAATTGCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT
28755971 TAAAGTATAG
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
40 2 0.03
41 22 0.33
42 7 0.10
43 31 0.46
44 5 0.07
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (41 bp):
CAAAATTGCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT
Found at i:28756458 original size:207 final size:207
Alignment explanation
Indices: 28756096--28757434 Score: 2309
Period size: 207 Copynumber: 6.5 Consensus size: 207
28756086 CGACGGAGAG
* * * *
28756096 CAAATCGAAGACATAACTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
* * * * *
28756161 GCATCTTTGTATTGTTAGAGAATAAATCGAAGTTTGGCGTCTCCATATTTGATGGAGGGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
* *
28756226 CATAGCAGATCTGGCCTTTAGATGTTTATACTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
28756291 GCTTACAAGGAA
196 GCTTACAAGGAA
* * * *
28756303 CAAACCAAAGACATAGCTGATTTGGCTTTCATGTGTTTATGTTGAAGCAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
* *
28756368 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAAACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
28756433 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
28756498 GCTTACAAGGAA
196 GCTTACAAGGAA
28756510 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
** *
28756575 GCATCTCTGTATTGTCAGAGAACAAATTAAAGTTTGGCGTCTCCATATTCGATGGAGGGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
28756640 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
28756705 GCTTACAAGGAA
196 GCTTACAAGGAA
* * * *
28756717 CAAATTGAAGACATAGCTGATTTGGCTTTCATGTGTTTACATTGAAACAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
*
28756782 GCATCTCTGTATTGTCAGAGAACAAATCGATGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
*
28756847 CATAGCAGATCTGGCCTTCAGATGTTTATATTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
28756912 GCTTACAAGGAA
196 GCTTACAAGGAA
28756924 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
* *
28756989 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTAGGCGTCTCCATATTCGACGGAGAGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
* * *
28757054 CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGCAAGATCTAAGATAGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
28757119 GCTTACAAGGAA
196 GCTTACAAGGAA
28757131 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
* * *
28757196 ACATCTCTATATTGTCCGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
* * *
28757261 CGTAGCAGATCTAGCCTTCAGATGTTTATACTGGAGCAAGATCCAAGATGGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
28757326 GCTTACAAGGAA
196 GCTTACAAGGAA
* *
28757338 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTATGTTGAAGTAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
* *
28757403 GCATCTCTGTATTGTCAAAGAACAAATTGAAG
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAG
28757435 AAGCAGATTT
Statistics
Matches: 1068, Mismatches: 64, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
207 1068 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (207 bp):
CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
GCTTACAAGGAA
Found at i:28757839 original size:17 final size:18
Alignment explanation
Indices: 28757826--28757948 Score: 87
Period size: 18 Copynumber: 6.8 Consensus size: 18
28757816 TAATCTTCAA
28757826 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
28757845 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
28757862 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
28757881 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
28757897 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
* *
28757916 TGAT-TGTAATCTTAGATA
1 TGATATGCAATCTTAGA-G
*
28757934 TGATATACAATCTTA
1 TGATATGCAATCTTA
28757949 AAAGATATGA
Statistics
Matches: 87, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.02
16 3 0.03
17 24 0.28
18 27 0.31
19 27 0.31
20 4 0.05
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Done.