Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 98 of 210
Found at i:28690353 original size:2 final size:2
Alignment explanation
Indices: 28690346--28690386 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28690336 ATTGGAATTT
28690346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28690387 CTATCATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28694735 original size:23 final size:22
Alignment explanation
Indices: 28694679--28694735 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
28694669 ATCATGTGCA
*
28694679 TTTGAAATTACTATTGGTAATG
1 TTTGAAATTGCTATTGGTAATG
* *
28694701 TTTG-ATTATGCTATTGGTATATT
1 TTTGAAAT-TGCTATTGGTA-ATG
28694724 TTTGAAATTGCT
1 TTTGAAATTGCT
28694736 TGTATGAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 2 0.07
22 14 0.50
23 10 0.36
24 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (22 bp):
TTTGAAATTGCTATTGGTAATG
Found at i:28702340 original size:87 final size:87
Alignment explanation
Indices: 28702164--28702324 Score: 259
Period size: 87 Copynumber: 1.9 Consensus size: 87
28702154 TTGTTGAGTG
* * * *
28702164 AAAATTGAACTCCTAAAATTAAACAACTTCACATTGAATAAGGTTGTCTACTTTAGGATTTTCCA
1 AAAATTGAACACCTAAAATTAAACAACTTCACACTAAATAAGGTTATCTACTTTAGGATTTTCCA
* *
28702229 TTTGCAAAAACTTGATGTGCAA
66 TGTACAAAAACTTGATGTGCAA
*
28702251 AAAATTGAACACCTAAAATTAAACAACTTCACACTAAATAAGGTTATCTAGTTTAGGATTTTCCA
1 AAAATTGAACACCTAAAATTAAACAACTTCACACTAAATAAGGTTATCTACTTTAGGATTTTCCA
28702316 TGTACAAAA
66 TGTACAAAA
28702325 TTTAGGTAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (87 bp):
AAAATTGAACACCTAAAATTAAACAACTTCACACTAAATAAGGTTATCTACTTTAGGATTTTCCA
TGTACAAAAACTTGATGTGCAA
Found at i:28704446 original size:24 final size:24
Alignment explanation
Indices: 28704395--28704446 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28704385 ATAAAAGCAT
* *
28704395 TCCTTTTTAAATTTTTTGTTGGTT
1 TCCTTTTTAAATTTTTTGTTAGTG
*
28704419 TCCTTTTTAATTTTTTTGTTAGTG
1 TCCTTTTTAAATTTTTTGTTAGTG
28704443 TCCT
1 TCCT
28704447 CCATTGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (24 bp):
TCCTTTTTAAATTTTTTGTTAGTG
Found at i:28709499 original size:330 final size:330
Alignment explanation
Indices: 28708891--28709535 Score: 1128
Period size: 330 Copynumber: 2.0 Consensus size: 330
28708881 TTGGTCATGT
* *
28708891 GACCCATGTCAGAGAGTTACACAGGCATGGACACGGGCTGGGACACAGTCATGTGTCCCTACTTT
1 GACCCAAGTCAGAGAGTTACACAGGCATGGACACGGGCTGGGACACAGTCATATGTCCCTACTTT
* * *
28708956 GAATGTCCACACGGCCTAAGACACAGGCGTGTGTCTCAGCCGTGTGAGTCACACGACTGGGTGAC
66 GAATGTCAACACGGCCTAAGACACAGGCGTGTGTCTCAGCCGTGTGAGTCACACGACCGAGTGAC
* *
28709021 CCCTGCAGTGTAAAAAAATCCATCTTTTTCCATAAAATTTTAAATGTCTCCGATTTAGTCCCGAA
131 CCATGCAGTGTAAAAAAATCCATCTTTTTCCATAAAATTTAAAATGTCTCCGATTTAGTCCCGAA
28709086 TCGATTCTAAAGTGTTTCTAAGGCCTCAAAGGCTCGAATAAGGGACGATGTGTATATACTTGAAT
196 TCGATTCTAAAGTGTTTCTAAGGCCTCAAAGGCTCGAATAAGGGACGATGTGTATATACTTGAAT
28709151 GGATTTTTCTATGATTATGAAATGTTTAAAAATGATTGATTTTAAGTTACATTTTGTGACCCAAG
261 GGATTTTTCTATGATTATGAAATGTTTAAAAATGATTGATTTTAAGTTACATTTTGTGACCCAAG
28709216 TCAAA
326 TCAAA
* *
28709221 GACCCAAGTCAGAGAGTTACACAGGCATGGACACGGGTTGGGACACAGTCATATGTCGCTACTTT
1 GACCCAAGTCAGAGAGTTACACAGGCATGGACACGGGCTGGGACACAGTCATATGTCCCTACTTT
* * * *
28709286 GAATGTCAACATGGCCTAAGACACGGGTGTGTGTCTCAGCCGTGTGAGTCACACGGCCGAGTGAC
66 GAATGTCAACACGGCCTAAGACACAGGCGTGTGTCTCAGCCGTGTGAGTCACACGACCGAGTGAC
** * *
28709351 CCATGCAGTGTAAAAATGTCCATCTTTTTCCATAAAATTTAAAATTTCTCTGATTTAGTCCCGAA
131 CCATGCAGTGTAAAAAAATCCATCTTTTTCCATAAAATTTAAAATGTCTCCGATTTAGTCCCGAA
*
28709416 TCGGTTCTAAAGTGTTTCTAAGGCCTCAAAGGCTCGAATAAGGGACGATGTGTATATACTTGAAT
196 TCGATTCTAAAGTGTTTCTAAGGCCTCAAAGGCTCGAATAAGGGACGATGTGTATATACTTGAAT
28709481 GGATTTTTCTATGATTATGAAATGTTTAAAAATGATTGATTTTAAGTTACATTTT
261 GGATTTTTCTATGATTATGAAATGTTTAAAAATGATTGATTTTAAGTTACATTTT
28709536 TACAGTAATA
Statistics
Matches: 297, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
330 297 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (330 bp):
GACCCAAGTCAGAGAGTTACACAGGCATGGACACGGGCTGGGACACAGTCATATGTCCCTACTTT
GAATGTCAACACGGCCTAAGACACAGGCGTGTGTCTCAGCCGTGTGAGTCACACGACCGAGTGAC
CCATGCAGTGTAAAAAAATCCATCTTTTTCCATAAAATTTAAAATGTCTCCGATTTAGTCCCGAA
TCGATTCTAAAGTGTTTCTAAGGCCTCAAAGGCTCGAATAAGGGACGATGTGTATATACTTGAAT
GGATTTTTCTATGATTATGAAATGTTTAAAAATGATTGATTTTAAGTTACATTTTGTGACCCAAG
TCAAA
Found at i:28720009 original size:12 final size:12
Alignment explanation
Indices: 28719992--28720016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28719982 TAAATTGATA
28719992 TAAAAAATATAT
1 TAAAAAATATAT
28720004 TAAAAAATATAT
1 TAAAAAATATAT
28720016 T
1 T
28720017 CGTCAATCTG
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAATATAT
Found at i:28731552 original size:29 final size:29
Alignment explanation
Indices: 28731489--28731647 Score: 151
Period size: 29 Copynumber: 5.4 Consensus size: 29
28731479 TCATCGACAA
* * *
28731489 ATGAAAAGGGATAGTTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGACT
* * *
28731518 ACGAAAAGAGATAGCTTCGACTATCGACT
1 ATGAAAAGGGATAGCTTCGGCTATCGACT
* * * * *
28731547 ATGAAAAGGGAT-GGTGAT-GACCATCAACA
1 ATGAAAAGGGATAGCT--TCGGCTATCGACT
*
28731576 ATGAAAAGGGATGGCTTCGGCTATCGATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGA-CT
*
28731606 ATGAAAAGGGATAGCTTTGGCTATCGATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGA-CT
28731636 ATGAAAAGGGAT
1 ATGAAAAGGGAT
28731648 GGTGACGACC
Statistics
Matches: 106, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.03
29 59 0.56
30 44 0.42
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGACT
Found at i:28731612 original size:30 final size:30
Alignment explanation
Indices: 28731489--28731767 Score: 176
Period size: 30 Copynumber: 9.4 Consensus size: 30
28731479 TCATCGACAA
* *
28731489 ATGAAAAGGGATAGTTTCGGCTATC-AAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACT
* * *
28731518 ACGAAAAGAGATAGCTTCGACTATCG-ACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACT
* * * *
28731547 ATGAAAAGGGAT-GGTGAT-GACCATC-AACA
1 ATGAAAAGGGATAGCT--TCGGCTATCGAACT
* *
28731576 ATGAAAAGGGATGGCTTCGGCTATCGATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACT
* *
28731606 ATGAAAAGGGATAGCTTTGGCTATCGATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACT
* * * * * *
28731636 ATGAAAAGGGAT-GGTGACGACCATTGAACA
1 ATGAAAAGGGATAGCT-TCGGCTATCGAACT
* * * * *
28731666 ATGAAAAGGGATTG-TGACGACTATCAAATT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAACT
* **
28731696 ATGAAAATGGATAGCTTCAACTATCGAACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACT
** * * *
28731726 ATGAAAAGGGATAAATTCTGTTATCGAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACT
*
28731756 ACGAAAAGGGAT
1 ATGAAAAGGGAT
28731768 TGTCAACCAT
Statistics
Matches: 196, Mismatches: 44, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
28 3 0.02
29 60 0.31
30 131 0.67
31 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAACT
Found at i:28731699 original size:90 final size:87
Alignment explanation
Indices: 28731488--28731737 Score: 306
Period size: 90 Copynumber: 2.8 Consensus size: 87
28731478 ATCATCGACA
* *
28731488 AATGAAAAGGGATAGTTTCGGCTATCAAA-TACGAAAAGAGATAGCTTCGACTATCGACTATGAA
1 AATGAAAAGGGATAG-TTCGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCGACTATGAA
*
28731552 AAGGGATGGTGATGACCATCAAC
65 AAGGGATGGTGACGACCATCAAC
* * * *
28731575 AATGAAAAGGGATGGCTTCGGCTATC-GATCTATGAAAAGGGATAGCTTTGGCTATCGATCTATG
1 AATGAAAAGGGATAG-TTCGGCTATCAAAT-TATGAAAAGGGATAGCTTCGACTATCGA-CTATG
*
28731639 AAAAGGGATGGTGACGACCATTGAAC
63 AAAAGGGATGGTGACGACCA-TCAAC
* * * * *
28731665 AATGAAAAGGGATTGTGACGACTATCAAATTATGAAAATGGATAGCTTCAACTATCGAACTATGA
1 AATGAAAAGGGATAGT-TCGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCG-ACTATGA
28731730 AAAGGGAT
64 AAAGGGAT
28731738 AAATTCTGTT
Statistics
Matches: 139, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
86 1 0.01
87 24 0.17
88 24 0.17
89 25 0.18
90 62 0.45
91 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.24
Consensus pattern (87 bp):
AATGAAAAGGGATAGTTCGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCGACTATGAAA
AGGGATGGTGACGACCATCAAC
Found at i:28731730 original size:60 final size:59
Alignment explanation
Indices: 28731489--28731738 Score: 211
Period size: 60 Copynumber: 4.2 Consensus size: 59
28731479 TCATCGACAA
** * * *
28731489 ATGAAAAGGGATAGTTTCGGCTATCAAATACGAAAAGAGATAGCTTCGACTATCG-ACT
1 ATGAAAAGGGATAGTGACGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAACT
* * * * * *
28731547 ATGAAAAGGGATGGTGATGACCATCAACA-ATGAAAAGGGATGGCTTCGGCTATCGATCT
1 ATGAAAAGGGATAGTGACGACTATCAA-ATATGAAAAGGGATAGCTTCGACTATCGAACT
** * ** * * * * *
28731606 ATGAAAAGGGATAGCT-TTGGCTATCGATCTATGAAAAGGGAT-GGTGACGACCATTGAACA
1 ATGAAAAGGGATAG-TGACGACTATC-AAATATGAAAAGGGATAGCT-TCGACTATCGAACT
* * *
28731666 ATGAAAAGGGATTGTGACGACTATCAAATTATGAAAATGGATAGCTTCAACTATCGAACT
1 ATGAAAAGGGATAGTGACGACTATCAAA-TATGAAAAGGGATAGCTTCGACTATCGAACT
28731726 ATGAAAAGGGATA
1 ATGAAAAGGGATA
28731739 AATTCTGTTA
Statistics
Matches: 145, Mismatches: 38, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
58 43 0.30
59 26 0.18
60 74 0.51
61 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.24
Consensus pattern (59 bp):
ATGAAAAGGGATAGTGACGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAACT
Found at i:28732376 original size:2 final size:2
Alignment explanation
Indices: 28732369--28732409 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28732359 ATAAGAAAGG
28732369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28732410 GTCTATTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28734348 original size:25 final size:23
Alignment explanation
Indices: 28734305--28734355 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
28734295 TAACATCATT
*
28734305 AATATCTAATTTTTGAAATGTTAAA
1 AATATCTAATTATTGAAA--TTAAA
28734330 AATATCTAAATTATT-AAATTAAA
1 AATATCT-AATTATTGAAATTAAA
28734353 AAT
1 AAT
28734356 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (23 bp):
AATATCTAATTATTGAAATTAAA
Found at i:28735339 original size:18 final size:19
Alignment explanation
Indices: 28735318--28735367 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
28735308 TTTTAAATTT
28735318 TAAAAATTTAAAAACTT-A
1 TAAAAATTTAAAAACTTCA
*
28735336 TAAAAATTT-ATAACTTCA
1 TAAAAATTTAAAAACTTCA
28735354 -AAAAACTTTAAAAA
1 TAAAAA-TTTAAAAA
28735368 TTAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.41
18 13 0.48
19 3 0.11
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATTTAAAAACTTCA
Found at i:28738539 original size:26 final size:27
Alignment explanation
Indices: 28738503--28738567 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
28738493 TTAGCATTGT
*
28738503 TTTTAAAAAGT-ATTGTGAAAAAGTGC
1 TTTTAAGAAGTGATTGTGAAAAAGTGC
* * *
28738529 TTTTAAGAAGTGTTTGTGAAAAATTGT
1 TTTTAAGAAGTGATTGTGAAAAAGTGC
*
28738556 TTTTGAGAAGTG
1 TTTTAAGAAGTG
28738568 CTTTTGAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (27 bp):
TTTTAAGAAGTGATTGTGAAAAAGTGC
Found at i:28738545 original size:27 final size:27
Alignment explanation
Indices: 28738515--28738592 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
28738505 TTAAAAAGTA
28738515 TTGTGAAAAAGTGCTTTTAAGAAGTG-T
1 TTGTGAAAAA-TGCTTTTAAGAAGTGCT
* *
28738542 TTGTGAAAAATTGTTTTTGAGAAGTGCT
1 TTGTGAAAAA-TGCTTTTAAGAAGTGCT
* * *
28738570 TT-TGAGAAATACTTTTAAAAAGT
1 TTGTGAAAAATGCTTTTAAGAAGT
28738593 TTGGTTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 10 0.24
27 29 0.69
28 3 0.07
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (27 bp):
TTGTGAAAAATGCTTTTAAGAAGTGCT
Found at i:28738823 original size:24 final size:23
Alignment explanation
Indices: 28738795--28738846 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
28738785 TGAAATATAA
*
28738795 ATTAAATATTTTTAAATAATTA-AT
1 ATTAAATATTTAT-AA-AATTAGAT
*
28738819 ATTAATTATTTATAAAATTAGAT
1 ATTAAATATTTATAAAATTAGAT
28738842 ATTAA
1 ATTAA
28738847 CACATTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 9 0.36
24 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTAAATATTTATAAAATTAGAT
Found at i:28740894 original size:22 final size:22
Alignment explanation
Indices: 28740859--28740901 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28740849 GTCTTTCCCT
*
28740859 ATTATTATTATTTTAATTTTTC
1 ATTATTATTATTTTAAATTTTC
* *
28740881 ATTATTTTTCTTTTAAATTTT
1 ATTATTATTATTTTAAATTTT
28740902 AAATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTATTATTATTTTAAATTTTC
Found at i:28741204 original size:24 final size:24
Alignment explanation
Indices: 28741170--28741221 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28741160 TTTCCAGAAG
* **
28741170 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
28741194 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
28741218 ATTT
1 ATTT
28741222 GACTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:28749677 original size:18 final size:18
Alignment explanation
Indices: 28749641--28749677 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28749631 TGAATTTTCG
*
28749641 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
*
28749659 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCAAAT
28749677 A
1 A
28749678 TAAACTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:28749801 original size:7 final size:7
Alignment explanation
Indices: 28749789--28749813 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28749779 AAGATTTATT
28749789 TTCCCAA
1 TTCCCAA
28749796 TTCCCAA
1 TTCCCAA
28749803 TTCCCAA
1 TTCCCAA
28749810 TTCC
1 TTCC
28749814 TCCCCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (7 bp):
TTCCCAA
Found at i:28750163 original size:19 final size:19
Alignment explanation
Indices: 28750105--28750166 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
28750095 ATATTTGAAT
*
28750105 TATTGAATGATTTTAGCTC
1 TATTGAATGATTTTCGCTC
* *
28750124 TATTTGTAT-CTGTTTCGCTC
1 TA-TTGAATGAT-TTTCGCTC
*
28750144 TATTGAATGATTTTCTCTC
1 TATTGAATGATTTTCGCTC
28750163 TATT
1 TATT
28750167 TTCCTTCTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (19 bp):
TATTGAATGATTTTCGCTC
Found at i:28750578 original size:17 final size:17
Alignment explanation
Indices: 28750556--28750588 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28750546 AATTTCTCAA
*
28750556 AGTAATAATGTAATATT
1 AGTAATAATATAATATT
28750573 AGTAATAATATAATAT
1 AGTAATAATATAATAT
28750589 AAAATGTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
AGTAATAATATAATATT
Found at i:28750995 original size:91 final size:90
Alignment explanation
Indices: 28750876--28751274 Score: 575
Period size: 90 Copynumber: 4.4 Consensus size: 90
28750866 CTTCAATTAA
*
28750876 TTAATTTATGCTGTTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
1 TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
*
28750941 TATGGTTTAACAGACTTTTTTTTTGT
66 TATAGTTTAACAGAC-TTTTTTTTGT
*
28750967 TTAATTTATGCTATTGTACTATTATATTAATTTAGGTTTCAATTAACTAACTTTAAAGTTTAAAC
1 TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
* *
28751032 TATAGTTTAATATACTTTTTTTTGT
66 TATAGTTTAACAGACTTTTTTTTGT
*
28751057 TTAATTTACACTGTTGTACTTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGT
1 TTAATTT--A-TG--CTA-TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGT
**
28751122 TTAAA-TGATAACTTAACAGACTTTTTTTTGT
60 TTAAACT-ATAGTTTAACAGACTTTTTTTTGT
* * *
28751153 TTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACTTTAAAGTTTAAAA
1 TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
* *
28751218 TGTAGTTTAACAAACTTTTTTTTGT
66 TATAGTTTAACAGACTTTTTTTTGT
***
28751243 TTAATTTATGCTGCCGTACTATTATATTAATT
1 TTAATTTATGCTATTGTACTATTATATTAATT
28751275 AATTTTTAAT
Statistics
Matches: 278, Mismatches: 22, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
90 115 0.41
91 77 0.28
92 1 0.00
93 4 0.01
94 1 0.00
95 3 0.01
96 77 0.28
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (90 bp):
TTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
TATAGTTTAACAGACTTTTTTTTGT
Found at i:28751213 original size:186 final size:187
Alignment explanation
Indices: 28750889--28751250 Score: 611
Period size: 186 Copynumber: 1.9 Consensus size: 187
28750879 ATTTATGCTG
***
28750889 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTATGGTTTAACAG
1 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTATAACTTAACAG
* * *
28750954 ACTTTTTTTTTGTTTAATTTATGCTATTGTACTATTATATTAATTTAGGTTTCAATTAACTAACT
66 ACTTTTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACT
* * *
28751019 TTAAAGTTTAAACTATAGTTTAATATACTTTTTTTTGTTTAATTTACACTGTTGTAC
131 TTAAAGTTTAAAATATAGTTTAACAAACTTTTTTTTGTTTAATTTACACTGTTGTAC
28751076 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAA-TGATAACTTAACA
1 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACT-ATAACTTAACA
28751140 GAC-TTTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAAC
65 GACTTTTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAAC
*
28751204 TTTAAAGTTTAAAATGTAGTTTAACAAACTTTTTTTTGTTTAATTTA
130 TTTAAAGTTTAAAATATAGTTTAACAAACTTTTTTTTGTTTAATTTA
28751251 TGCTGCCGTA
Statistics
Matches: 164, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
186 102 0.62
187 62 0.38
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (187 bp):
TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTATAACTTAACAG
ACTTTTTTTTTGTTTAATTTATGCAATTGTACTATTATATTAATTTAGGCTTCAATTAAATAACT
TTAAAGTTTAAAATATAGTTTAACAAACTTTTTTTTGTTTAATTTACACTGTTGTAC
Found at i:28755013 original size:27 final size:26
Alignment explanation
Indices: 28754978--28755070 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 26
28754968 TCTCGCTAGA
*
28754978 CCTATTGGCGTATACTAGCTCGCCAAG
1 CCTACTGGCG-ATACTAGCTCGCCAAG
* *
28755005 CCTTCTGGCGA-ACTCTAACTCGCCAAG
1 CCTACTGGCGATA--CTAGCTCGCCAAG
28755032 CCTACTGGCGA-ACTCCAGCTCGCCAAG
1 CCTACTGGCGATACT--AGCTCGCCAAG
28755059 CCTACTGGCGAT
1 CCTACTGGCGAT
28755071 CACAGTTCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 52 0.93
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.22
Consensus pattern (26 bp):
CCTACTGGCGATACTAGCTCGCCAAG
Found at i:28755090 original size:26 final size:27
Alignment explanation
Indices: 28755033--28755111 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 27
28755023 CTCGCCAAGC
* * * * **
28755033 CTACTGGCGAACTCCAGCTCGCCAAGC
1 CTACTGGCGAACACTAGTTCACCAAAT
*
28755060 CTACTGGCGATCAC-AGTTCACCAAAT
1 CTACTGGCGAACACTAGTTCACCAAAT
* *
28755086 CTACTTGCGAACCCTAGTTCACCAAA
1 CTACTGGCGAACACTAGTTCACCAAA
28755112 GAAGTTGGCG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 19 0.45
27 23 0.55
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.20
Consensus pattern (27 bp):
CTACTGGCGAACACTAGTTCACCAAAT
Found at i:28757102 original size:2 final size:2
Alignment explanation
Indices: 28757095--28757129 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28757085 GTCTTTGTTA
28757095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28757130 AACCAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28757642 original size:18 final size:18
Alignment explanation
Indices: 28757597--28757642 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
28757587 AATTTTAAAA
28757597 AAAT-AAAT-TAAAAATT
1 AAATAAAATATAAAAATT
*
28757613 AGAAGAAAAATATAAAAATT
1 A-AA-TAAAATATAAAAATT
28757633 AAATAAAATA
1 AAATAAAATA
28757643 AATTTATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 1 0.04
17 2 0.08
18 6 0.25
19 6 0.25
20 9 0.38
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (18 bp):
AAATAAAATATAAAAATT
Found at i:28757810 original size:15 final size:17
Alignment explanation
Indices: 28757784--28757828 Score: 67
Period size: 15 Copynumber: 2.8 Consensus size: 17
28757774 CCCTTTTTTT
*
28757784 TCTTTCTTTCTTTCCC-
1 TCTTTCTCTCTTTCCCG
28757800 TC-TTCTCTCTTTCCCG
1 TCTTTCTCTCTTTCCCG
28757816 TCTTTCTCTCTTT
1 TCTTTCTCTCTTT
28757829 TTCTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 10 0.38
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (17 bp):
TCTTTCTCTCTTTCCCG
Found at i:28758807 original size:30 final size:30
Alignment explanation
Indices: 28758771--28758833 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
28758761 ACTTATTTTA
*
28758771 TTGTTAATTTTGTTACTATTTTAAAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
* *
28758801 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
28758831 TTG
1 TTG
28758834 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGACAT
Found at i:28761668 original size:30 final size:30
Alignment explanation
Indices: 28761634--28761691 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
28761624 ATTTTATTAT
*
28761634 TAATTTTGTTATTATTTTAAAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
*
28761664 TAATTTTGTTATTATTTTAGAGACATTT
1 TAATTTTGTTATTATTTTAAAGACATTT
28761692 ACTTGTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:28761831 original size:11 final size:11
Alignment explanation
Indices: 28761817--28761847 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28761807 TATATATGTT
28761817 TAAAAATTATA
1 TAAAAATTATA
*
28761828 TAAAAATAATA
1 TAAAAATTATA
28761839 TAAAAATTA
1 TAAAAATTA
28761848 ATACGAGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:28763129 original size:43 final size:43
Alignment explanation
Indices: 28763081--28763167 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
28763071 CTAAACTGTA
28763081 AAGTTTTCAAAATATCTCATATGGGTGTCGCGACTTTAAAGGC
1 AAGTTTTCAAAATATCTCATATGGGTGTCGCGACTTTAAAGGC
28763124 AAGTTTTCAAAATATCTCATATGGGTGTCGCGACTTTAAAGGC
1 AAGTTTTCAAAATATCTCATATGGGTGTCGCGACTTTAAAGGC
28763167 A
1 A
28763168 GTAGCCAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (43 bp):
AAGTTTTCAAAATATCTCATATGGGTGTCGCGACTTTAAAGGC
Found at i:28764354 original size:19 final size:19
Alignment explanation
Indices: 28764303--28764356 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
28764293 ACATATAGCA
* * *
28764303 CATATTGGCACATAAAGTG
1 CATACTGGCACACAAAGCG
* * *
28764322 CATCCTGACGCACAAAGCG
1 CATACTGGCACACAAAGCG
28764341 CATACTGGCACACAAA
1 CATACTGGCACACAAA
28764357 ATGCAATCTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (19 bp):
CATACTGGCACACAAAGCG
Found at i:28764629 original size:21 final size:23
Alignment explanation
Indices: 28764603--28764644 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28764593 TTTATTAGTT
28764603 TAATC-TTAATTAA-TTAAACAC
1 TAATCTTTAATTAACTTAAACAC
28764624 TAATCTTTAATTAACTTAAAC
1 TAATCTTTAATTAACTTAAAC
28764645 TAATGGCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (23 bp):
TAATCTTTAATTAACTTAAACAC
Found at i:28767572 original size:27 final size:27
Alignment explanation
Indices: 28767513--28767598 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 27
28767503 TATAAACTCT
28767513 ATTTTGCAACCAATATATT-TACGAACTCT-
1 ATTTTGCAACCAATATATTGT-CG---TCTA
28767542 ATTTTGCAACCAATATATTGTCGTCTA
1 ATTTTGCAACCAATATATTGTCGTCTA
* **
28767569 ATTTTTGTAACTGA-ATATTGTCGT-TA
1 A-TTTTGCAACCAATATATTGTCGTCTA
28767595 ATTT
1 ATTT
28767599 ATAAATTTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
25 3 0.06
26 6 0.12
27 11 0.22
28 9 0.18
29 21 0.41
30 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.44
Consensus pattern (27 bp):
ATTTTGCAACCAATATATTGTCGTCTA
Found at i:28777309 original size:24 final size:24
Alignment explanation
Indices: 28777280--28777328 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28777270 CGTTCTAGTC
28777280 CTTAACCTTCATCAATGAAACAGT
1 CTTAACCTTCATCAATGAAACAGT
*
28777304 CTTAACCTTCATCAATGAAATAGT
1 CTTAACCTTCATCAATGAAACAGT
28777328 C
1 C
28777329 AACCTATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (24 bp):
CTTAACCTTCATCAATGAAACAGT
Found at i:28782033 original size:2 final size:2
Alignment explanation
Indices: 28782026--28782076 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
28782016 TAAGGGAAGA
28782026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28782068 AT AT AT AT A
1 AT AT AT AT A
28782077 AATGAAATGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28795086 original size:22 final size:23
Alignment explanation
Indices: 28795056--28795099 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28795046 AATTTTATAT
28795056 TTTATTTTATATATAAATATTTA
1 TTTATTTTATATATAAATATTTA
* *
28795079 TTTA-TTTATATTTATATATTT
1 TTTATTTTATATATAAATATTT
28795100 GTTCGCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTTATATATAAATATTTA
Found at i:28795098 original size:14 final size:14
Alignment explanation
Indices: 28795049--28795099 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
28795039 ATTATTCAAT
28795049 TTTATAT-TTTAT-
1 TTTATATATTTATA
**
28795061 TTTATATATAAATA
1 TTTATATATTTATA
*
28795075 TTTATTTATTTATA
1 TTTATATATTTATA
28795089 TTTATATATTT
1 TTTATATATTT
28795100 GTTCGCTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATATATTTATA
Found at i:28795481 original size:41 final size:41
Alignment explanation
Indices: 28795404--28795720 Score: 469
Period size: 41 Copynumber: 7.7 Consensus size: 41
28795394 CCATTCAGGG
*
28795404 CTTTAGCGGCGTTTTTTTAGAAAAAGCGCCGCTAATGCT-TAGGGT
1 CTTTAGCGGCG--TTTTT-GGAAAAGCGCCGCTAATGCTCT--GGT
* *
28795449 -TTTAGCGGCGTTTTTAGAAAAGTGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
** *
28795489 CTTTAGCGGCGTTTTTGGGGAAGCGCCGATAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
28795530 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
28795571 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTTTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
28795612 CTTTAGCGGCGTTTTTGGAGAAGCGTCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
28795653 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
28795694 CTTTAGCGGCGTTTTT-GAGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGA-AAAGCGCC
28795721 ACAAAAACAT
Statistics
Matches: 250, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
40 5 0.02
41 229 0.92
42 6 0.02
44 10 0.04
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:28796116 original size:22 final size:24
Alignment explanation
Indices: 28796066--28796126 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
28796056 ATATGATTTA
28796066 GAGTTTAAGGTTTA-GGAGTTACT
1 GAGTTTAAGGTTTATGGAGTTACT
*
28796089 -ATTTTAAGGTTTATGGA-TTA-T
1 GAGTTTAAGGTTTATGGAGTTACT
* *
28796110 GAGTTTAGGGGTTATGG
1 GAGTTTAAGGTTTATGG
28796127 TTTACAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 28 0.88
23 3 0.09
ACGTcount: A:0.25, C:0.02, G:0.31, T:0.43
Consensus pattern (24 bp):
GAGTTTAAGGTTTATGGAGTTACT
Found at i:28796170 original size:21 final size:21
Alignment explanation
Indices: 28796145--28796198 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
28796135 TTATGCTTTA
28796145 AGATTTAGGGTTTAAGGGT-T
1 AGATTTAGGGTTTAAGGGTAT
*
28796165 ACGATTTATGGTTTAAGGGTAT
1 A-GATTTAGGGTTTAAGGGTAT
*
28796187 AGATTAAGGGTT
1 AGATTTAGGGTT
28796199 GGGGTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.31, T:0.39
Consensus pattern (21 bp):
AGATTTAGGGTTTAAGGGTAT
Found at i:28796238 original size:14 final size:14
Alignment explanation
Indices: 28796190--28796241 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
28796180 AGGGTATAGA
28796190 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
* *
28796203 TTTAAAGTTTAGGGG
1 -TTAAGGGTTAGGGG
28796218 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
28796232 TTGAGGGTTA
1 TTAAGGGTTA
28796242 AGAGTTAGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 28 0.88
15 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:28796239 original size:21 final size:21
Alignment explanation
Indices: 28796215--28796254 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28796205 TAAAGTTTAG
* *
28796215 GGGTTAAGGGTTAGGGGTTGA
1 GGGTTAAGAGTTAGAGGTTGA
28796236 GGGTTAAGAGTTAGAGGTT
1 GGGTTAAGAGTTAGAGGTT
28796255 TAAGATTTAA
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:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (21 bp):
GGGTTAAGAGTTAGAGGTTGA
Found at i:28796271 original size:22 final size:20
Alignment explanation
Indices: 28796239--28796281 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
28796229 GGGTTGAGGG
28796239 TTAAGAGTTAGAGGTTTAAGAT
1 TTAAGAGTTAG-GGTTT-AGAT
*
28796261 TTAAGATTTAGGGTTTAGAT
1 TTAAGAGTTAGGGTTTAGAT
28796281 T
1 T
28796282 AATTAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (20 bp):
TTAAGAGTTAGGGTTTAGAT
Found at i:28796397 original size:16 final size:17
Alignment explanation
Indices: 28796378--28796419 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
28796368 AAATTATTTA
28796378 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
28796394 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
28796411 TAAAATAAT
1 T-AAATAAT
28796420 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:28796636 original size:21 final size:22
Alignment explanation
Indices: 28796612--28796652 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28796602 ATGGTTTATT
28796612 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
* *
28796633 GTTTAGGGGTTAGGGGTTTA
1 GTTTAAGGGTTAGGGATTTA
28796653 GGATTTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:28803206 original size:86 final size:85
Alignment explanation
Indices: 28803107--28803378 Score: 282
Period size: 86 Copynumber: 3.2 Consensus size: 85
28803097 AAAGGTTTGT
* *
28803107 TCTATAGCGGCGTTTGTGGTAAAAGCGCTGCTAAAGGTCTTTAG-CTATAGCGGCGTTTGTGGGA
1 TCTATAGCGGCGTTTCTGGTAAAAGCGCTGCTAAAGGTC--TAGCCTTTAGCGGCGTTTGTGGGA
* ** *
28803171 AAAGTGCCGCTAAAGATCCTGC
64 AAAGCGCCGCTAAAGATCAGGA
* * * * *
28803193 TCTATAGCGGCGTTTCTCGTAAAAGCG-TCACTAAAGGTCAAGGTCTTTAGCGGCGTTTGTTGGA
1 TCTATAGCGGCGTTTCTGGTAAAAGCGCT-GCTAAAGGTCTA-GCCTTTAGCGGCGTTTGTGGGA
* *
28803257 GAAGCGCCGCTAAAGATTAGGA
64 AAAGCGCCGCTAAAGATCAGGA
* * * *
28803279 TCTTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAAAGGTCATAGCCTTTAGCGGCGTTTTTGGGAA
1 TCTATAGCGGCGTTTCTGGTAAAAGCGCTGCTAAAGGTC-TAGCCTTTAGCGGCGTTTGTGGGAA
*
28803343 AAGCGCCGCTAAAGGTCATGG-
65 AAGCGCCGCTAAAGATCA-GGA
* *
28803364 TCTTTAGCGGTGTTT
1 TCTATAGCGGCGTTT
28803379 ATTTCTAAAA
Statistics
Matches: 155, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
84 1 0.01
85 67 0.43
86 87 0.56
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (85 bp):
TCTATAGCGGCGTTTCTGGTAAAAGCGCTGCTAAAGGTCTAGCCTTTAGCGGCGTTTGTGGGAAA
AGCGCCGCTAAAGATCAGGA
Found at i:28803360 original size:43 final size:43
Alignment explanation
Indices: 28803111--28803378 Score: 253
Period size: 43 Copynumber: 6.3 Consensus size: 43
28803101 GTTTGTTCTA
* * * * *
28803111 TAGCGGCGTTTGTGGTAAAAGCGCTGCTAAAGGTCTTTAG-CTA
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTC-ATAGTCTT
* * * * *
28803154 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGATCCT-GCTCTA
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATAG-TCTT
* * * * *
28803197 TAGCGGCGTTTCTCGTAAAAGCGTCACTAAAGGTCA-AGGTCTT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATA-GTCTT
* *
28803240 TAGCGGCGTTTGTT-GGAGAAGCGCCGCTAAAGAT--TAGGATCTT
1 TAGCGGCGTTT-TTGGGAAAAGCGCCGCTAAAGGTCATA-G-TCTT
*
28803283 TAGCGGCGTTTTT-GGAAAAGCGCCGCTAAAGGTCATAGCCTT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATAGTCTT
*
28803325 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATAGTCTT
*
28803368 TAGCGGTGTTT
1 TAGCGGCGTTT
28803379 ATTTCTAAAA
Statistics
Matches: 189, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 40 0.21
43 144 0.76
44 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATAGTCTT
Found at i:28805800 original size:14 final size:15
Alignment explanation
Indices: 28805781--28805809 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28805771 ATTGATATAT
28805781 AAAAAAT-ATTTTTA
1 AAAAAATAATTTTTA
28805795 AAAAAATAATTTTTA
1 AAAAAATAATTTTTA
28805810 TAAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAATAATTTTTA
Found at i:28812278 original size:7 final size:7
Alignment explanation
Indices: 28812266--28812298 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28812256 CACGAAGTTG
28812266 ATGTGGA
1 ATGTGGA
28812273 ATGTGGA
1 ATGTGGA
28812280 ATGTGGA
1 ATGTGGA
28812287 ATGTGGA
1 ATGTGGA
28812294 ATGTG
1 ATGTG
28812299 TTATGTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.42, T:0.30
Consensus pattern (7 bp):
ATGTGGA
Found at i:28814747 original size:26 final size:27
Alignment explanation
Indices: 28814686--28814748 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
28814676 CTCTTTTGAG
28814686 TCAATAAA-TTCTCTTTGAGTTTTCTTT
1 TCAA-AAATTTCTCTTTGAGTTTTCTTT
*
28814713 TCAAGAATTTCTCTTT-AG-TTTCTTT
1 TCAAAAATTTCTCTTTGAGTTTTCTTT
*
28814738 TAGAAAAATTT
1 T-CAAAAATTT
28814749 TAACAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.26
26 11 0.35
27 12 0.39
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (27 bp):
TCAAAAATTTCTCTTTGAGTTTTCTTT
Found at i:28816095 original size:42 final size:42
Alignment explanation
Indices: 28816041--28816212 Score: 161
Period size: 42 Copynumber: 4.1 Consensus size: 42
28816031 CACTAAAGTA
* *
28816041 CATAAGTGCTAAACGGAAACCCGTAAAGGTTAAA-TGAAAGCT
1 CATAAGAGCTAAACGGAAACCCATAAAGGTTAAACTG-AAGCT
* * * * *
28816083 CATAGGAGCTAAACGAAAACCTATAAGGGTTAATCTGAAGCT
1 CATAAGAGCTAAACGGAAACCCATAAAGGTTAAACTGAAGCT
* * * *
28816125 CAGAAGAGCTAAACTGAAACCCATTAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACCCATAAAGGTTAAACTGAAGCT
* * * *
28816167 CAAAAGAGCTGAACTGAAA-CC-TAGAAGAGTTAAACTGAAACT
1 CATAAGAGCTAAACGGAAACCCATA-AAG-GTTAAACTGAAGCT
28816209 CATA
1 CATA
28816213 TGAGTTAACT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.01
41 4 0.04
42 100 0.93
43 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (42 bp):
CATAAGAGCTAAACGGAAACCCATAAAGGTTAAACTGAAGCT
Found at i:28816189 original size:84 final size:84
Alignment explanation
Indices: 28816048--28816210 Score: 195
Period size: 84 Copynumber: 1.9 Consensus size: 84
28816038 GTACATAAGT
* * * * *
28816048 GCTAAACGGAAACCCGTAAAGGTTAAATGAAAGCTCATAGGAGCTAAACGAAAACCTATAAGGGT
1 GCTAAACGGAAACCCATAAAGGTTAAATGAAAGCTCAAAAGAGCTAAACGAAAACCTAGAAGAGT
* *
28816113 TAATCTGAAGCTCAGAAGA
66 TAAACTGAAACTCAGAAGA
* * * *
28816132 GCTAAACTGAAACCCATTAGGGTTAAACTG-AAGCTCAAAAGAGCTGAACTG-AAACCTAGAAGA
1 GCTAAACGGAAACCCATAAAGGTTAAA-TGAAAGCTCAAAAGAGCTAAAC-GAAAACCTAGAAGA
28816195 GTTAAACTGAAACTCA
64 GTTAAACTGAAACTCA
28816211 TATGAGTTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 63 0.95
85 3 0.05
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (84 bp):
GCTAAACGGAAACCCATAAAGGTTAAATGAAAGCTCAAAAGAGCTAAACGAAAACCTAGAAGAGT
TAAACTGAAACTCAGAAGA
Found at i:28816217 original size:21 final size:21
Alignment explanation
Indices: 28816069--28816247 Score: 107
Period size: 21 Copynumber: 8.6 Consensus size: 21
28816059 ACCCGTAAAG
*
28816069 GTTAAA-TGAAAGCTCATAGGA
1 GTTAAACTGAAA-CTCATAAGA
* *
28816090 GCTAAAC-GAAAAC-CTATAAGG
1 GTTAAACTG-AAACTC-ATAAGA
* * *
28816111 GTTAATCTGAAGCTCAGAAGA
1 GTTAAACTGAAACTCATAAGA
* * * *
28816132 GCTAAACTGAAACCCATTAGG
1 GTTAAACTGAAACTCATAAGA
* *
28816153 GTTAAACTGAAGCTCAAAAGA
1 GTTAAACTGAAACTCATAAGA
* * *
28816174 GCTGAACTGAAAC-CTAGAAGA
1 GTTAAACTGAAACTC-ATAAGA
*
28816195 GTTAAACTGAAACTCATATGA
1 GTTAAACTGAAACTCATAAGA
* *
28816216 GTT-AACTGAAGCTCATGAGA
1 GTTAAACTGAAACTCATAAGA
* *
28816236 GCTAAACGGAAA
1 GTTAAACTGAAA
28816248 GAAAAAATGG
Statistics
Matches: 115, Mismatches: 35, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
20 18 0.16
21 91 0.79
22 6 0.05
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GTTAAACTGAAACTCATAAGA
Found at i:28817774 original size:13 final size:13
Alignment explanation
Indices: 28817756--28817780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28817746 ATTTATTGTT
28817756 CTATTTATTTATC
1 CTATTTATTTATC
28817769 CTATTTATTTAT
1 CTATTTATTTAT
28817781 TTATTTAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
CTATTTATTTATC
Found at i:28825239 original size:25 final size:25
Alignment explanation
Indices: 28825211--28825264 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
28825201 TGTAGTGGTA
*
28825211 AGGTGGCGGCACAGGTGTGGCAAAG
1 AGGTGGAGGCACAGGTGTGGCAAAG
* * *
28825236 AGGTGGAGTCACAGGTGTGGTAAGG
1 AGGTGGAGGCACAGGTGTGGCAAAG
28825261 AGGT
1 AGGT
28825265 CAGAGGTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.48, T:0.17
Consensus pattern (25 bp):
AGGTGGAGGCACAGGTGTGGCAAAG
Found at i:28826651 original size:27 final size:27
Alignment explanation
Indices: 28826621--28826711 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
28826611 TAAATGACTG
* **
28826621 AAATATCCTCAATGAATAAAATTTTCA
1 AAATACCCTCAATGAATAAAATTACCA
* *
28826648 AAATACCCTCGAT-AAGTAAAATTACCG
1 AAATACCCTCAATGAA-TAAAATTACCA
* * **
28826675 AAATATCGTCAATGGGTAAAATTACCA
1 AAATACCCTCAATGAATAAAATTACCA
28826702 AAATACCCTC
1 AAATACCCTC
28826712 TGTCGAAATC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (27 bp):
AAATACCCTCAATGAATAAAATTACCA
Found at i:28830292 original size:44 final size:44
Alignment explanation
Indices: 28830097--28830301 Score: 134
Period size: 44 Copynumber: 4.7 Consensus size: 44
28830087 TTTAATTCGA
****
28830097 TCCACTGCAAAC-TCAGGGAGATAAGATCCGCCATCTTCAATCTGC
1 TCCACTGC-AACTTCAGGGAGATAAGATCTATTAT-TTCAATCTGC
* * * * *
28830142 TCCACTGCAACTTCAGGGGGATAAGACCTGCTTA-CTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATCT-ATTATTTCAATCTGC
* * * * * * * *
28830186 TTCGCTGCAACCTCAGGGAGATAAGA-C-CTGA-TGCGATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATCTATTATTTCAATCTGC
* * * * *
28830227 TCTACTGCAATTTTAGAGAGATAAGATCTATTATTTGAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATCTATTATTTCAATCTGC
*
28830271 TCCACTGCAACTTCAGGGAGATAGGAT-TATT
1 TCCACTGCAACTTCAGGGAGATAAGATCTATT
28830302 GGCTTCGATC
Statistics
Matches: 119, Mismatches: 36, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
41 27 0.23
42 1 0.01
43 7 0.06
44 61 0.51
45 22 0.18
46 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATCTATTATTTCAATCTGC
Found at i:28830577 original size:88 final size:88
Alignment explanation
Indices: 28830384--28830757 Score: 237
Period size: 88 Copynumber: 4.2 Consensus size: 88
28830374 CGGAGGCAAT
* * * * * * * * *
28830384 GCTAGTGTTTTCAATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
1 GCTAGTGGTTTCAATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATCTTCAACCTACT
* * *
28830449 CCGCTGCTACTCGGGGAGATAAG
66 CCACTGCTGCTCAGGGAGATAAG
* * * * *
28830472 GCTGGTGCTTCCGATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATCTTCGACCTACT
1 GCTAGTGGTTTCAATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATCTTCAACCTACT
* *
28830537 CCACTGTTGCTTAGGGAGATAAG
66 CCACTGCTGCTCAGGGAGATAAG
* * * * * * *
28830560 GCTAGTGGTTTAAATCTGCTTC-C--CTACTACATTGGAAAGATAAGATTCGT-C-GTCTTCGAT
1 GCTAGTGGTTTCAATCTGCTTCACTGCCAGTACA---GAAAGACAAGA-TC-TACAATCTTCAAC
* *
28830620 CTACTCCACTACTGCTTAGGGAGATAAG
61 CTACTCCACTGCTGCTCAGGGAGATAAG
* ** * * * * *
28830648 ATCT-GTAATTTTCAACCTAC-TCTACTGCTGC-TTAC-G-AAGATAAGGTCTACAATCTTCAAC
1 -GCTAGT-GGTTTCAATCTGCTTC-ACTGC--CAGTACAGAAAGACAAGATCTACAATCTTCAAC
*
28830708 ATACTCCACTGCTGCTCAGGGAGATAAG
61 CTACTCCACTGCTGCTCAGGGAGATAAG
* *
28830736 GCTAGTGGCTTAAATCTGCTTC
1 GCTAGTGGTTTCAATCTGCTTC
28830758 CCTACTGCAT
Statistics
Matches: 217, Mismatches: 52, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
85 6 0.03
86 1 0.00
87 13 0.06
88 177 0.82
89 14 0.06
90 2 0.01
92 1 0.00
93 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (88 bp):
GCTAGTGGTTTCAATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTACAATCTTCAACCTACT
CCACTGCTGCTCAGGGAGATAAG
Found at i:28830644 original size:176 final size:176
Alignment explanation
Indices: 28830508--28831135 Score: 879
Period size: 176 Copynumber: 3.6 Consensus size: 176
28830498 CCAGTACAGA
* * * * * *
28830508 AAGACAAGATCTACAATCTTCGACCTACTCCACTGTTGCTTAGGGAGATAAGGCTAGTGGTTTAA
1 AAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAA
*
28830573 ATCTGCTTCCCTACTACATTGGAAAGATAAGATTCGTCGTCTTCGATCTACTCCACTACTGCTTA
66 ATCTGCTTCCCTACTACATTGGAAAGATAAGATTCG-CGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
28830638 GGGAGATAAGATCTGTAATTTTCAACCTACTCTACTG-CTGCTTACG
130 GGGAGATAAGATCTGTAATTTCCAACCTACTCCACTGCCTGCTCAGG
*
28830684 AAGATAAGGTCTACAATCTTCAACATACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAA
1 AAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAA
* * * *
28830749 ATCTGCTTCCCTACTGCATTGGGAAGATAAGATTTGCATTCTTCGATCTGCTCCACTACTGCTTA
66 ATCTGCTTCCCTACTACATTGGAAAGATAAGATTCGC-GTCTTCGATCTGCTCCACTACTGCTTA
*
28830814 GGGAGATAAGATCTGTAATTTCCAACCTACTCCACT-ACTGCTCAGG
130 GGGAGATAAGATCTGTAATTTCCAACCTACTCCACTGCCTGCTCAGG
* *
28830860 GAGATAAGGTCTACAATCTTCAACCTAC-CCTACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTA
1 AAGATAAGGTCTACAATCTTCAACCTACTCC-ACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTA
* * * * ** *
28830924 AATCTACTTCTCTACTACATTGGGAAGATAAGATTCGCCGTTTTTTATCTGTTCCACTACTGCTT
65 AATCTGCTTCCCTACTACATTGGAAAGATAAGATTCG-CGTCTTCGATCTGCTCCACTACTGCTT
*
28830989 AGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTG-CTGCTCAGG
129 AGGGAGATAAGATCTGTAATTTCCAACCTACTCCACTGCCTGCTCAGG
* * * * *
28831036 GAGATAAGGTCTACAATCTTTAAGCTACTCCACTACTGCTCAAGGAGATAAGGCTAGTGGCTTAA
1 AAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAA
*
28831101 ATCTGCTTCCCTACTACCTTGGGAAA-ATAAGATTC
66 ATCTGCTTCCCTACTACATT-GGAAAGATAAGATTC
28831136 ACCGTGGGAT
Statistics
Matches: 407, Mismatches: 38, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
175 3 0.01
176 397 0.98
177 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (176 bp):
AAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAA
ATCTGCTTCCCTACTACATTGGAAAGATAAGATTCGCGTCTTCGATCTGCTCCACTACTGCTTAG
GGAGATAAGATCTGTAATTTCCAACCTACTCCACTGCCTGCTCAGG
Found at i:28830777 original size:132 final size:131
Alignment explanation
Indices: 28830628--28830868 Score: 299
Period size: 132 Copynumber: 1.8 Consensus size: 131
28830618 ATCTACTCCA
* *
28830628 CTACTGCTTAGGGAGATAAGATCTGTAATT-TTCAACCTACTCTACTGCTGCTTACGAAGATAAG
1 CTACTGCTTAGGGAGATAAGATCTG-AATTCTTCAACCTACTCCACTACTGCTTACGAAGATAAG
* *
28830692 GTCTACAATCTT-CAACATACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCT
65 ATCTACAAT-TTCCAACATACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCT
28830756 TCC
129 TCC
* * * * * * *
28830759 CTACTGCATT-GGGAAGATAAGATTTGCATTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
1 CTACTGC-TTAGGG-AGATAAGATCTGAATTCTTCAACCTACTCCACTACTGCTTACGAAGATAA
** *
28830823 GATCTGTAATTTCCAACCTACTCCACTACTGCTCAGGGAGATAAGG
64 GATCTACAATTTCCAACATACTCCACTACTGCTCAGGGAGATAAGG
28830869 TCTACAATCT
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
131 15 0.16
132 77 0.84
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (131 bp):
CTACTGCTTAGGGAGATAAGATCTGAATTCTTCAACCTACTCCACTACTGCTTACGAAGATAAGA
TCTACAATTTCCAACATACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTC
C
Found at i:28831088 original size:44 final size:44
Alignment explanation
Indices: 28830620--28831088 Score: 236
Period size: 44 Copynumber: 10.7 Consensus size: 44
28830610 CGTCTTCGAT
* * **
28830620 CTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
* * * * * *
28830664 CTACTCTACTGCTGCTTACGAAGATAAGGTCTACAATCTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
* * ***** * *
28830708 ATACTCCACTGCTGCTCAGGGAGATAAGG-CTAGTGGCTTAAAT
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
* * * * * * *
28830751 CTGCTTCC-CTACTGCAT-TGGGAAGATAAGATTTGC-ATTCTTCGAT
1 CTAC-TCCACTACTGC-TCAGGG-AGATAAGGTCTACAATT-TTCAAC
* * * ** *
28830796 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
*
28830840 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATCTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
** ***** * *
28830884 CTAC-CCTACTGTTGCTCAGGGAGATAAGG-CTAGTGGCTTAAAT
1 CTACTCC-ACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
* * * * * * ** ** *
28830927 CTACTTCTCTACTACAT-TGGGAAGATAAGAT-TCGCCGTTTTTTAT
1 CTACTCCACTACTGC-TCAGGG-AGATAAGGTCT-ACAATTTTCAAC
** * * **
28830972 CTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAAC
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
* *
28831016 CTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTT-AAG
1 CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAAT-TTTCAAC
*
28831060 CTACTCCACTACTGCTCAAGGAGATAAGG
1 CTACTCCACTACTGCTCAGGGAGATAAGG
28831089 CTAGTGGCTT
Statistics
Matches: 319, Mismatches: 89, Indels: 34
0.72 0.20 0.08
Matches are distributed among these distances:
43 40 0.13
44 235 0.74
45 44 0.14
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATTTTCAAC
Found at i:28831227 original size:44 final size:43
Alignment explanation
Indices: 28831159--28831897 Score: 904
Period size: 44 Copynumber: 16.9 Consensus size: 43
28831149 ATCTGTAATA
* * *
28831159 TTCAACCTATTTCACTGATATCCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT-ACAATC
* * * *
28831203 TTCAACATATACCACTGCTGTCCAGGGAGATAGGACTTACCATG
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* **
28831247 TTCAACCTATTCCACTACTGTCCAATGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* * *
28831291 TTCAACCTATTCCACTACTATCTAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT-ACAATC
* * * *
28831335 TTTAACCTATTTCACTACTGTCTAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* * * *
28831379 TTCAACATATTCCAATGTTGTCCAAGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* * *
28831423 TTCAACCTATTTCACTGCTGTCCAGGGAGATAGGATTTATAACC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* * *
28831467 TTCAACCTATTCCCCTGCTGTCCAGGGAGATAAGATT-TAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTACAATC
* * *
28831509 TTCAACCTATTTCACTACTGTCTAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT-ACAATC
* * *
28831553 TTCAACCTATTCCACTGCTATCTAGGAAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT-ACAATC
* *
28831597 TTCAACCTATTCCACTGCTATCCAGGGAGATAGGACTTACAATA
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
*
28831641 TTCAGCCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT-ACAATC
**
28831685 TTCAACCTATTCCACTATTGTCCAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* * *
28831729 CTCAACCTATTCCACTGCTGTCTAGGGAGATAGGATTTACAATA
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* *
28831773 TTCAACCTATTCCACTACTTTCCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT-ACAATC
* * *
28831817 TTCAACTTATTCCACTGTTGTCTAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA-TTACAATC
* *
28831861 CTCAACATATTCCACTGCTGTCCAGGGAGATAGGATT
1 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATT
28831898 TATAACTTCA
Statistics
Matches: 605, Mismatches: 80, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
42 36 0.06
43 10 0.02
44 549 0.91
45 10 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTACAATC
Found at i:28832685 original size:9 final size:9
Alignment explanation
Indices: 28832666--28832699 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
28832656 GACAGAAATC
28832666 AAGAGAAAAA
1 AAGA-AAAAA
28832676 AAGAAAAAA
1 AAGAAAAAA
28832685 AAGAAAAAA
1 AAGAAAAAA
28832694 ATAGAA
1 A-AGAA
28832700 TAGAGCAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:28838113 original size:6 final size:6
Alignment explanation
Indices: 28838102--28838171 Score: 140
Period size: 6 Copynumber: 11.7 Consensus size: 6
28838092 AAGAGAGAAA
28838102 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
28838150 AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAA
28838172 AGAAAAGAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:28840640 original size:44 final size:44
Alignment explanation
Indices: 28840572--28841204 Score: 222
Period size: 44 Copynumber: 13.6 Consensus size: 44
28840562 TGAAGCCGAT
* * *
28840572 AATCCTATCTCCCTAAAGTTACAGTGGAGCGAATTAAAACAAAG
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGAATTAAGACAAAG
* * * *
28840616 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC-ACATTCGGTGAAGCCAGA-
1 AATCTTATCTCCCTGAAGTTACAGT-G-G-AG--CGA-A-T---T-AAGACAAAG
* * * ** *
28840669 AATCTTATCTCCCTGAAGTTACAGTCGAGC-AGATTGAGGCCGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAGACAAAG
* * * *
28840713 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGAATTAAGACAAAG
* * * * *
28840757 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGA-
1 AATCTTATCTCCCTGAAGTTACAGT-G-G-AG--CG-AAT---T-AAGACAAAG
* * * * ** *
28840810 AATCTTATGTCCCTGAATTTACAGTGGAGC-AGATTGAGGCCGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAGACAAAG
* * *
28840854 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAG
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGAATTAAGACAAAG
* * * * *
28840898 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGA-
1 AATCTTATCTCCCTGAAGTTACAGT-G-G-AG--CG-AAT---T-AAGACAAAG
* * * * ** *
28840951 AACCTTATCTCCCTAAAGTTACAGTGGAGC-AGATTGAGGCCGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAGACAAAG
* * * *
28840995 AATCCTATCTCCTTGAAGTTACAGCGGAGCGAATTAAAACAAAG
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGAATTAAGACAAAG
* * * *
28841039 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAAA-
1 AATCTTATCTCCCTGAAGTTACAGT-G-G-AG--CG-AAT---T-AAGACAAAG
* * * * ** *
28841092 AAACTTATCTCCCTGAAGTTATAGTGGAGC-AGATTGAGGCCGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAGACAAAG
* * *
28841136 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAG
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCGAATTAAGACAAAG
* *
28841180 TATCTTATCTCTCTGAAGTTACAGT
1 AATCTTATCTCCCTGAAGTTACAGT
28841205 AGAGTAGATC
Statistics
Matches: 429, Mismatches: 108, Indels: 104
0.67 0.17 0.16
Matches are distributed among these distances:
43 19 0.04
44 241 0.56
45 5 0.01
46 7 0.02
47 12 0.03
48 7 0.02
49 8 0.02
50 13 0.03
51 4 0.01
52 3 0.01
53 90 0.21
54 20 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCGAATTAAGACAAAG
Found at i:28840809 original size:141 final size:141
Alignment explanation
Indices: 28840555--28841458 Score: 1306
Period size: 141 Copynumber: 6.5 Consensus size: 141
28840545 AGTGTAAGGA
* * *
28840555 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTACAGTGGAGCGAATTAAAACAAAGGATC
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
*
28840620 TTATCTCTCTGAAGTTACAGTAGAGTAGATCACATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
*
28840685 AGTTACAGTCG
131 AGTTACAGTGG
*
28840696 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATC
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
*
28840761 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATGTCCCTGA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
*
28840826 ATTTACAGTGG
131 AGTTACAGTGG
28840837 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
* *
28840902 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAACCTTATCTCCCTAA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
28840967 AGTTACAGTGG
131 AGTTACAGTGG
* * *
28840978 AGCAGATTGAGGCCGATAATCCTATCTCCTTGAAGTTACAGCGGAGCGAATTAAAACAAAGGATC
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
* *
28841043 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAAAAAACTTATCTCCCTGA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
*
28841108 AGTTATAGTGG
131 AGTTACAGTGG
*
28841119 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGTATC
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
*
28841184 TTATCTCTCTGAAGTTACAGTAGAGTAGATCACATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
*
28841249 AGTTACAGTAG
131 AGTTACAGTGG
* * ** * *
28841260 AGCAGATTGAAGTCGATAATCCTATCTCCCT-AAGGTTGTAGTAGAGAGGATTAAAACAATA-GA
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAA-GTTACAGTGGAGCGGATTAAAACAA-AGGA
* * * *
28841323 TCTTATCTCCCT-AAG-TAGTAGTGGAGCAGATCGCA-TC------G---G---TCTTATCTCCC
64 TCTTATCTCTCTGAAGTTA-CAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCC
* *
28841373 TGAAGCTACAATGG
128 TGAAGTTACAGTGG
** ** *
28841387 AGCAGATTGAAACCGATAATCCTATCTCCCT-AAGGTTGTAGTGGAGAGGATTAAAACAATA-GA
1 AGCAGATTGAGGCCGATAATCCTATCTCCCTGAA-GTTACAGTGGAGCGGATTAAAACAA-AGGA
28841450 TCTTATCTC
64 TCTTATCTC
28841459 CCTAAGCAGT
Statistics
Matches: 713, Mismatches: 47, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
127 91 0.13
130 1 0.00
133 1 0.00
139 4 0.01
140 18 0.03
141 597 0.84
142 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (141 bp):
AGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGGATC
TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGGTGAAGCCAGAAATCTTATCTCCCTGA
AGTTACAGTGG
Found at i:28841286 original size:44 final size:44
Alignment explanation
Indices: 28841233--28841558 Score: 123
Period size: 44 Copynumber: 7.6 Consensus size: 44
28841223 TGAAGCCAGA
* **
28841233 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACCGAT
* ** * * *
28841277 AATCCTATCTCCCT-AAGGTTGTAGTAGAG-AGGATT-AAAACAAT
1 AATCTTATCTCCCTGAA-GTTACAGTGGAGCA-GATTGAAACCGAT
* * * *
28841320 AGATCTTATCTCCCT-AAG-TAGTAGTGGAGCAGATCG-CATCG--
1 A-ATCTTATCTCCCTGAAGTTA-CAGTGGAGCAGATTGAAACCGAT
* * *
28841361 -GTCTTATCTCCCTGAAGCTACAATGGAGCAGATTGAAACCGAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACCGAT
* ** * *
28841404 AATCCTATCTCCCT-AAGGTTGTAGTGGAG-AGGATT-AAAACAAT
1 AATCTTATCTCCCTGAA-GTTACAGTGGAGCA-GATTGAAACCGAT
* * * * *
28841447 AGATCTTATCTCCCT-AAG-CAGTAGTGGAGCAGATCG-CATCG--
1 A-ATCTTATCTCCCTGAAGTTA-CAGTGGAGCAGATTGAAACCGAT
** * * *
28841488 GGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAGAAAAC-A-
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT--GAAACCGAT
* * *
28841532 AGTCTTATCCCCCTGAAGTCACAGTGG
1 AATCTTATCTCCCTGAAGTTACAGTGG
28841559 GGTAGACTGA
Statistics
Matches: 210, Mismatches: 48, Indels: 48
0.69 0.16 0.16
Matches are distributed among these distances:
39 12 0.06
40 27 0.13
41 19 0.09
42 1 0.00
43 47 0.22
44 104 0.50
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACCGAT
Found at i:28841461 original size:127 final size:128
Alignment explanation
Indices: 28841235--28841524 Score: 492
Period size: 127 Copynumber: 2.3 Consensus size: 128
28841225 AAGCCAGAAA
* **
28841235 TCTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAGTCGATAATCCTATCTCCCTAAGGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACCGATAATCCTATCTCCCTAAGGTTGTA
*
28841300 GTAGAGAGGATTAAAACAATAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGCATC-GG
66 GTAGAGAGGATTAAAACAATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCGGG
* *
28841362 TCTTATCTCCCTGAAGCTACAATGGAGCAGATTGAAACCGATAATCCTATCTCCCTAAGGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACCGATAATCCTATCTCCCTAAGGTTGTA
*
28841427 GTGGAGAGGATTAAAACAATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCGGG
66 GTAGAGAGGATTAAAACAATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCGGG
* *
28841490 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
28841525 GAAAACAAGT
Statistics
Matches: 151, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
127 118 0.78
128 33 0.22
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACCGATAATCCTATCTCCCTAAGGTTGTA
GTAGAGAGGATTAAAACAATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCGGG
Found at i:28841659 original size:23 final size:23
Alignment explanation
Indices: 28841625--28841668 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28841615 AATCAATCCT
28841625 ATCAATCCTATCTCCCTGAAGAA
1 ATCAATCCTATCTCCCTGAAGAA
* *
28841648 ATCAATCTTATCTCTCTGAAG
1 ATCAATCCTATCTCCCTGAAG
28841669 TTGCAGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (23 bp):
ATCAATCCTATCTCCCTGAAGAA
Found at i:28841763 original size:45 final size:44
Alignment explanation
Indices: 28841691--28841818 Score: 145
Period size: 45 Copynumber: 2.9 Consensus size: 44
28841681 GGATCAGATT
*
28841691 AGGTCTTATCTCCCTGAAGTTATAGTGGAGCAGACT-AAGTAAGC
1 AGGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAG-AAGC
28841735 AGGTCTTATC-CCGACTGAAGTTACAGTGGAGCAGACTGAAGAAGC
1 AGGTCTTATCTCC--CTGAAGTTACAGTGGAGCAGACTGAAGAAGC
** * * *
28841780 AAATCTTATCTCCCT-AAGGTTGCAGTGGAGTAGATTGAA
1 AGGTCTTATCTCCCTGAA-GTTACAGTGGAGCAGACTGAA
28841819 TTCGATAATC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
43 4 0.05
44 30 0.41
45 34 0.47
46 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (44 bp):
AGGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAAGC
Found at i:28845901 original size:49 final size:50
Alignment explanation
Indices: 28845843--28845941 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
28845833 TTTGGTTTAT
* * *
28845843 TTTTTATTTTTT-GGACTCAAACAACCCTTTGCTGGTTTTCACCTTGGTC
1 TTTTTATTTTTTAGGAATCAAACAACCCTTTACGGGTTTTCACCTTGGTC
***
28845892 TTTTTATTTTTTAGGAATCAAAGTGCCCTTTACGGGTTTTCACCTTGGTC
1 TTTTTATTTTTTAGGAATCAAACAACCCTTTACGGGTTTTCACCTTGGTC
28845942 CCTTCTCCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 12 0.28
50 31 0.72
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (50 bp):
TTTTTATTTTTTAGGAATCAAACAACCCTTTACGGGTTTTCACCTTGGTC
Found at i:28846826 original size:14 final size:14
Alignment explanation
Indices: 28846809--28846865 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 14
28846799 TATCACTTTC
28846809 ATTTTTTTATTTTG
1 ATTTTTTTATTTTG
28846823 A-TTTTTTATTTTTG
1 ATTTTTTTA-TTTTG
*
28846837 ATTTTGATTTTTTTGATG
1 ATTTT--TTTATTT--TG
28846855 ATTTTTTTATT
1 ATTTTTTTATT
28846866 GAATCTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
13 7 0.20
14 7 0.20
15 3 0.09
16 8 0.23
17 3 0.09
18 7 0.20
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (14 bp):
ATTTTTTTATTTTG
Found at i:28846829 original size:13 final size:14
Alignment explanation
Indices: 28846811--28846841 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28846801 TCACTTTCAT
28846811 TTTTTTA-TTTTGA
1 TTTTTTATTTTTGA
28846824 TTTTTTATTTTTGA
1 TTTTTTATTTTTGA
28846838 TTTT
1 TTTT
28846842 GATTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTTATTTTTGA
Found at i:28846834 original size:20 final size:20
Alignment explanation
Indices: 28846811--28846849 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28846801 TCACTTTCAT
*
28846811 TTTTTTATTTTGATTTTTTA
1 TTTTTGATTTTGATTTTTTA
28846831 TTTTTGATTTTGATTTTTT
1 TTTTTGATTTTGATTTTTT
28846850 TGATGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTGATTTTGATTTTTTA
Found at i:28847938 original size:25 final size:25
Alignment explanation
Indices: 28847888--28847947 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
28847878 AAGAAAATCC
*
28847888 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
*
28847913 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
28847938 AAAATGAATG
1 AAAA-GAATG
28847948 CAAAAATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 3 0.10
25 23 0.74
26 5 0.16
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.22
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:28852805 original size:27 final size:27
Alignment explanation
Indices: 28852767--28853059 Score: 189
Period size: 27 Copynumber: 10.9 Consensus size: 27
28852757 TAGGTATTAC
* *
28852767 ACCCTCGATGGGTAAAATTACTGAAAT
1 ACCCCCGAAGGGTAAAATTACTGAAAT
*** * **
28852794 ACCATTGATGGGTAAAATTACCAAAAT
1 ACCCCCGAAGGGTAAAATTACTGAAAT
** * *
28852821 ACCCCTAAAAGATAAAATTACTGAAAT
1 ACCCCCGAAGGGTAAAATTACTGAAAT
* *
28852848 ACCCCCGAAGGGTCAAATTACTAAAAT
1 ACCCCCGAAGGGTAAAATTACTGAAAT
* * *
28852875 ACTCTCGAAGGGTAAAATTACCGAAAT
1 ACCCCCGAAGGGTAAAATTACTGAAAT
* * *
28852902 ACCCTCGAAAGGTAAAACTA-TCGAAAT
1 ACCCCCGAAGGGTAAAATTACT-GAAAT
* **
28852929 ACCCCCAAAGGGTAAAATTACCAAAAT
1 ACCCCCGAAGGGTAAAATTACTGAAAT
** * *
28852956 ACCCTGGATGGGTAAAACTA-TCGAAAT
1 ACCCCCGAAGGGTAAAATTACT-GAAAT
* *
28852983 ACTCCCGAAGGGTAAAATTA-TCAAAAT
1 ACCCCCGAAGGGTAAAATTACT-GAAAT
* * * **
28853010 TCCCTC-AATGTGTAAAATTACCAAAAT
1 ACCCCCGAA-GGGTAAAATTACTGAAAT
* * *
28853037 ACCCACGCAGGGTAAAATAACTG
1 ACCCCCGAAGGGTAAAATTACTG
28853060 TTGTACCCCT
Statistics
Matches: 202, Mismatches: 58, Indels: 12
0.74 0.21 0.04
Matches are distributed among these distances:
26 2 0.01
27 199 0.99
28 1 0.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.22
Consensus pattern (27 bp):
ACCCCCGAAGGGTAAAATTACTGAAAT
Found at i:28852842 original size:54 final size:54
Alignment explanation
Indices: 28852776--28853040 Score: 230
Period size: 54 Copynumber: 4.9 Consensus size: 54
28852766 CACCCTCGAT
* * * *
28852776 GGGTAAAATTACTGAAATACCATTGATGGGTAAAATTACCAAAATACCCCTAAA
1 GGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAAA
* * * * * * * *
28852830 AGATAAAATTACTGAAATACCCCCGAAGGGTCAAATTACTAAAATA-CTCTCGAA
1 GGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCCT-AAA
* * * * *
28852884 GGGTAAAATTACCGAAATACCCTCGAAAGGTAAAACTATCGAAATACCCCCAAA
1 GGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAAA
* * * * * * *
28852938 GGGTAAAATTACCAAAATACCCTGGATGGGTAAAACTATCGAAATACTCCC-GAA
1 GGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCAAAATAC-CCCTAAA
* * * *
28852992 GGGTAAAATTATCAAAATTCCCTC-AATGTGTAAAATTACCAAAATACCC
1 GGGTAAAATTACCGAAATACCCTCGAA-GGGTAAAATTACCAAAATACCC
28853041 ACGCAGGGTA
Statistics
Matches: 171, Mismatches: 36, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
53 6 0.04
54 160 0.94
55 5 0.03
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.22
Consensus pattern (54 bp):
GGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAAA
Found at i:28852918 original size:81 final size:79
Alignment explanation
Indices: 28852767--28853039 Score: 271
Period size: 81 Copynumber: 3.4 Consensus size: 79
28852757 TAGGTATTAC
* * * * * *
28852767 ACCCTCGATGGGTAAAATTACTGAAATACCATTGATGGGTAAAATTACCAAAATACCCCTAAAAG
1 ACCCCCGAAGGGTAAAATTACTAAAATACC-TCGATGGGTAAAATTACCGAAATACCCC-GAAAG
*
28852832 ATAAAATTA-CTGAAAT
64 GTAAAATTATC-GAAAT
* *
28852848 ACCCCCGAAGGGTCAAATTACTAAAATACTCTCGAAGGGTAAAATTACCGAAATACCCTCGAAAG
1 ACCCCCGAAGGGTAAAATTACTAAAATAC-CTCGATGGGTAAAATTACCGAAATACCC-CGAAAG
*
28852913 GTAAAACTATCGAAAT
64 GTAAAATTATCGAAAT
* * * * * *
28852929 ACCCCCAAAGGGTAAAATTACCAAAATACCCTGGATGGGTAAAACTATCGAAATACTCCCGAAGG
1 ACCCCCGAAGGGTAAAATTACTAAAATA-CCTCGATGGGTAAAATTACCGAAATAC-CCCGAAAG
*
28852994 GTAAAATTATCAAAAT
64 GTAAAATTATCGAAAT
* * * *
28853010 TCCCTC-AATGTGTAAAATTACCAAAATACC
1 ACCCCCGAA-GGGTAAAATTACTAAAATACC
28853040 CACGCAGGGT
Statistics
Matches: 163, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
80 4 0.02
81 153 0.94
82 6 0.04
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (79 bp):
ACCCCCGAAGGGTAAAATTACTAAAATACCTCGATGGGTAAAATTACCGAAATACCCCGAAAGGT
AAAATTATCGAAAT
Found at i:28853662 original size:26 final size:27
Alignment explanation
Indices: 28853626--28853685 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
28853616 CCTACAGTAG
28853626 TTTCAGAATATCATAACATATATCA-A
1 TTTCAGAATATCATAACATATATCAGA
* *
28853652 TTTCAGAATATCATAGCATGTATCAGA
1 TTTCAGAATATCATAACATATATCAGA
28853679 TTT-AGAA
1 TTTCAGAA
28853686 CGCTTACAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (27 bp):
TTTCAGAATATCATAACATATATCAGA
Found at i:28856046 original size:24 final size:24
Alignment explanation
Indices: 28856017--28856063 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
28856007 TTTTGGGTAA
28856017 TTGGAGAGAAAACCAAAACTCTAT
1 TTGGAGAGAAAACCAAAACTCTAT
28856041 TTGGAGAGAAAACCAAAACTCTA
1 TTGGAGAGAAAACCAAAACTCTA
28856064 CTTTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
TTGGAGAGAAAACCAAAACTCTAT
Found at i:28861618 original size:27 final size:30
Alignment explanation
Indices: 28861550--28861612 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
28861540 CATTGTTGCA
*
28861550 ATTGTATGCCACGAAGGCGTTCCTTTCATC
1 ATTGTGTGCCACGAAGGCGTTCCTTTCATC
28861580 ATTGTGTGCCACGAAGGCGTTCCTTTCATC
1 ATTGTGTGCCACGAAGGCGTTCCTTTCATC
28861610 ATT
1 ATT
28861613 TTCCACATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (30 bp):
ATTGTGTGCCACGAAGGCGTTCCTTTCATC
Found at i:28861656 original size:27 final size:27
Alignment explanation
Indices: 28861636--28861687 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28861626 TTCCTTTCCT
28861636 TAGATCGCCACAAAGGCTTCCATTTCA
1 TAGATCGCCACAAAGGCTTCCATTTCA
** *
28861663 TAGATTTCCACAAAGGCATCCATTT
1 TAGATCGCCACAAAGGCTTCCATTT
28861688 TCTGGTGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
TAGATCGCCACAAAGGCTTCCATTTCA
Found at i:28865106 original size:6 final size:6
Alignment explanation
Indices: 28865095--28865124 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28865085 TCGTTTATAT
28865095 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
28865125 ACATTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:28865722 original size:13 final size:14
Alignment explanation
Indices: 28865689--28865725 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
28865679 AAAAAGGCAA
28865689 TTAATAAATAAAAT
1 TTAATAAATAAAAT
28865703 TCT-ATAAA-AAAAT
1 T-TAATAAATAAAAT
28865716 TTAATAAATA
1 TTAATAAATA
28865726 GATAGGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.05
13 11 0.55
14 7 0.35
15 1 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAATAAATAAAAT
Found at i:28871352 original size:2 final size:2
Alignment explanation
Indices: 28871345--28871388 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28871335 TCCTGCAAGG
28871345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28871387 AT
1 AT
28871389 TAGTTCAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28874525 original size:37 final size:37
Alignment explanation
Indices: 28874483--28874556 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
28874473 ATTATTTGAG
28874483 AAAGGATTTAAGGGATAATTAAGCCTTAATTTAAGTA
1 AAAGGATTTAAGGGATAATTAAGCCTTAATTTAAGTA
28874520 AAAGGATTTAAGGGATAATTAAGCCTTAATTTAAGTA
1 AAAGGATTTAAGGGATAATTAAGCCTTAATTTAAGTA
28874557 GTGGGACGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (37 bp):
AAAGGATTTAAGGGATAATTAAGCCTTAATTTAAGTA
Found at i:28875598 original size:21 final size:21
Alignment explanation
Indices: 28875572--28875628 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
28875562 TGGGTGGATT
* *
28875572 AGCTCTCACGAGCTTCTATTC
1 AGCTCTTATGAGCTTCTATTC
*
28875593 AGCTCTTATGAGATTCTATTC
1 AGCTCTTATGAGCTTCTATTC
28875614 AGCTCTTATGAGCTT
1 AGCTCTTATGAGCTT
28875629 TTGTTGGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTATTC
Found at i:28876622 original size:17 final size:17
Alignment explanation
Indices: 28876600--28876642 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
28876590 CATGTAGCCA
28876600 GGCCGTGTGTGTCACAT
1 GGCCGTGTGTGTCACAT
*
28876617 GGCCGTGTATGTCACAT
1 GGCCGTGTGTGTCACAT
28876634 GGCCGTGTG
1 GGCCGTGTG
28876643 ATAGCCTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.23, G:0.37, T:0.28
Consensus pattern (17 bp):
GGCCGTGTGTGTCACAT
Found at i:28877410 original size:20 final size:20
Alignment explanation
Indices: 28877387--28877489 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
28877377 GAAGTACAAA
28877387 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
* * * *
28877407 CAGGGGTAC-TGAAGTACAAT
1 CAGGGGCACGT-ATGTGCATT
*
28877427 CAGGGACACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
* * * * *
28877447 CAGAGGTACCG-AAGTACAAAT
1 CAGGGGCA-CGTATGTGC-ATT
28877468 -AGGGGCACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
28877487 CAG
1 CAG
28877490 AGGTGCTGAA
Statistics
Matches: 57, Mismatches: 20, Indels: 12
0.64 0.22 0.13
Matches are distributed among these distances:
19 5 0.09
20 47 0.82
21 5 0.09
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.21
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCATT
Found at i:28877421 original size:40 final size:40
Alignment explanation
Indices: 28877377--28877528 Score: 234
Period size: 40 Copynumber: 3.8 Consensus size: 40
28877367 TACGGGCACC
*
28877377 GAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACT
1 GAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACT
* * *
28877417 GAAGTACAATCAGGGACACGTATGTGCATTCAGAGGTACC
1 GAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACT
* *
28877457 GAAGTACAAATAGGGGCACGTATGTGCATTCAGAGGTGCT
1 GAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACT
28877497 GAAGTACAAACAGGGGCA-GCTATGTGCATTCA
1 GAAGTACAAACAGGGGCACG-TATGTGCATTCA
28877529 CACAATAATT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 100 0.99
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (40 bp):
GAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACT
Found at i:28889426 original size:22 final size:23
Alignment explanation
Indices: 28889398--28889442 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
28889388 TTCACGCTGA
*
28889398 TTCTTCTTTTCTCT-TTTCTTTT
1 TTCTTCTTCTCTCTCTTTCTTTT
28889420 TTCTTCTTCTCTCTCTTTCTTTT
1 TTCTTCTTCTCTCTCTTTCTTTT
28889443 ATTGGGTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (23 bp):
TTCTTCTTCTCTCTCTTTCTTTT
Found at i:28894638 original size:22 final size:22
Alignment explanation
Indices: 28894596--28894638 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28894586 CAACCCAATT
* *
28894596 TTTATTATTATTTTTTCTTTAC
1 TTTATTATTATTTATTATTTAC
28894618 TTTATT-TTATTTTATTATTTA
1 TTTATTATTA-TTTATTATTTA
28894639 TTACTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTATTATTTATTATTTAC
Found at i:28905500 original size:5 final size:5
Alignment explanation
Indices: 28905490--28905529 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
28905480 GAGGTGTTCA
* *
28905490 TGAGT TGAGT TGAGT TGAGT TGAGT TAAGT TGAGT CGAGT
1 TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT
28905530 CAGGTTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (5 bp):
TGAGT
Found at i:28908753 original size:27 final size:27
Alignment explanation
Indices: 28908723--28908779 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
28908713 TAAATGCTAT
*
28908723 AAATATTATTAAATT-TAATAAAAAT-TA
1 AAATATTA-AAAATTATAA-AAAAATATA
28908750 AAATATTAAAAATTATAAAAAAATATA
1 AAATATTAAAAATTATAAAAAAATATA
28908777 AAA
1 AAA
28908780 ATTGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATATTAAAAATTATAAAAAAATATA
Found at i:28908795 original size:21 final size:21
Alignment explanation
Indices: 28908743--28908801 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
28908733 AAATTTAATA
28908743 AAAATTAAAATATTAAAAATTAT
1 AAAA-TAAAATA-TAAAAATTAT
*
28908766 -AAA-AAAATATAAAAATTGT
1 AAAATAAAATATAAAAATTAT
28908785 AAAATAAAATATAAAAA
1 AAAATAAAATATAAAAA
28908802 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.27
20 9 0.27
21 12 0.36
22 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATAAAATATAAAAATTAT
Found at i:28908810 original size:20 final size:19
Alignment explanation
Indices: 28908748--28908810 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
28908738 TAATAAAAAT
*
28908748 TAAAATATTAAAAATTATAA
1 TAAAATA-TAAAAATTTTAA
* *
28908768 AAAAATATAAAAATTGTAAAA
1 TAAAATATAAAAATT-T-TAA
28908789 TAAAATATAAAAAATTTTAA
1 TAAAATAT-AAAAATTTTAA
28908809 TA
1 TA
28908811 TTTTATCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 8 0.23
20 10 0.29
21 10 0.29
22 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAATATAAAAATTTTAA
Found at i:28908893 original size:29 final size:28
Alignment explanation
Indices: 28908748--28908894 Score: 95
Period size: 29 Copynumber: 5.1 Consensus size: 28
28908738 TAATAAAAAT
* * *
28908748 TAAAATATTA-AAAATTATAAAAAAATA
1 TAAAATTTTATAAAATCATAAAAAATTA
* *
28908775 TAAAAATTGTAAAATAAAAT-ATAAAAAATTT
1 T-AAAATT-T--TATAAAATCATAAAAAATTA
* * *
28908806 TAATATTTTATCAAAATCTTAAAAAACTA
1 TAAAATTTTAT-AAAATCATAAAAAATTA
*
28908835 TAAAA-TCTATAGAAAT-ATAAAAAAAGTTA
1 TAAAATTTTATA-AAATCAT-AAAAAA-TTA
*
28908864 TAAAATTTTATAAAGTCATAAGAAAATTA
1 TAAAATTTTATAAAATCATAA-AAAATTA
28908893 TA
1 TA
28908895 CAAAATGTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
27 5 0.05
28 24 0.26
29 31 0.34
30 16 0.17
31 11 0.12
32 5 0.05
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (28 bp):
TAAAATTTTATAAAATCATAAAAAATTA
Found at i:28909363 original size:94 final size:94
Alignment explanation
Indices: 28909231--28909409 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 94
28909221 ATAAGAGTAG
* * * * *
28909231 GGGCTTAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATACATTTTGAAAGTTTAAGTACC
1 GGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAATTCAAGTACC
*
28909296 CAATTGAGT-TAAAAAAAAAGAAAAGAAA
66 CAATTGAGTGCAAAAAAAAAGAAAAGAAA
* * *
28909324 GGGCTTAATTGCTTTTTTCGAATAAGTTTGAGGGCCTTTTTGATGCATTTTAAAAATTCAAGTGC
1 GGGCTTAATTGCTTTTTT-GAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAATTCAAGTAC
*
28909389 TCAATTGAGTGCAAAAAAAAA
65 CCAATTGAGTGCAAAAAAAAA
28909410 AAGAGTTTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 18 0.24
94 47 0.64
95 9 0.12
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (94 bp):
GGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAATTCAAGTACC
CAATTGAGTGCAAAAAAAAAGAAAAGAAA
Found at i:28917602 original size:17 final size:16
Alignment explanation
Indices: 28917573--28917620 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
28917563 TAGGTTAGGT
*
28917573 TTTCTTTCTCTTTTCC
1 TTTCTTTCCCTTTTCC
*
28917589 TTTCTTTTCCCTTTCCC
1 TTTC-TTTCCCTTTTCC
28917606 TTTCCTTT-CCTTTTC
1 TTT-CTTTCCCTTTTC
28917621 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.37
17 16 0.59
18 1 0.04
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCTTTCCCTTTTCC
Found at i:28917680 original size:25 final size:26
Alignment explanation
Indices: 28917626--28917680 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
28917616 TTTTCTTTTT
* * *
28917626 TTTTTTCTTTTCATTTTTAGTTTAGG
1 TTTTCTCTTTTCATTTTTAGGTTAGA
*
28917652 TTTTCTCTTTTC-TTTTTAGGTTATA
1 TTTTCTCTTTTCATTTTTAGGTTAGA
28917677 TTTT
1 TTTT
28917681 AATTTTGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (26 bp):
TTTTCTCTTTTCATTTTTAGGTTAGA
Found at i:28918932 original size:33 final size:32
Alignment explanation
Indices: 28918854--28918944 Score: 112
Period size: 34 Copynumber: 2.8 Consensus size: 32
28918844 TATGGGTTTT
* * *
28918854 GGTGTTATATATATAATATATATTTAAGTGTATG
1 GGTGTTATATGTAT-ATATATATTT-GGTGCATG
*
28918888 GATGTTATATGTATGATATATATTTGGTGCATG
1 GGTGTTATATGTAT-ATATATATTTGGTGCATG
28918921 GGTGTTATATGTATA-ATATATTTG
1 GGTGTTATATGTATATATATATTTG
28918945 CGTGGGTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 9 0.18
32 1 0.02
33 19 0.37
34 22 0.43
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (32 bp):
GGTGTTATATGTATATATATATTTGGTGCATG
Found at i:28924435 original size:27 final size:27
Alignment explanation
Indices: 28924376--28924437 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28924366 TGAAAATTTA
*
28924376 TTATAAATTAATTAAAATTAAATATGT
1 TTATAATTTAATTAAAATTAAATATGT
* * *
28924403 TAATAATTTAAGTTAAATTTAATTAT-T
1 TTATAATTTAA-TTAAAATTAAATATGT
28924430 TTATAATT
1 TTATAATT
28924438 ATATTATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (27 bp):
TTATAATTTAATTAAAATTAAATATGT
Found at i:28927995 original size:10 final size:11
Alignment explanation
Indices: 28927980--28928030 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 11
28927970 TTTATTAAGA
28927980 TAAATTTT-AT
1 TAAATTTTGAT
28927990 TAAATTTTGAT
1 TAAATTTTGAT
28928001 AATAAATTTT-AT
1 --TAAATTTTGAT
28928013 TAAATTTTGAT
1 TAAATTTTGAT
*
28928024 AAAATTT
1 TAAATTT
28928031 AAACTAATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 16 0.44
11 10 0.28
12 2 0.06
13 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (11 bp):
TAAATTTTGAT
Found at i:28928006 original size:23 final size:23
Alignment explanation
Indices: 28927979--28928025 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28927969 ATTTATTAAG
28927979 ATAAATTTTATTAAATTTTGATA
1 ATAAATTTTATTAAATTTTGATA
28928002 ATAAATTTTATTAAATTTTGATA
1 ATAAATTTTATTAAATTTTGATA
28928025 A
1 A
28928026 AATTTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATAAATTTTATTAAATTTTGATA
Found at i:28934683 original size:50 final size:50
Alignment explanation
Indices: 28934565--28934699 Score: 144
Period size: 50 Copynumber: 2.7 Consensus size: 50
28934555 AAAGTGATGG
* * * *
28934565 TCACGTGTGTAGTACTATGTGTAGGCTATTACGTGTACCAGAATGAAAGG
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGAAAGAAAGA
* * * * ***
28934615 TCGCATGTGGAGTTCTATGTGTAGGCTACTACGTGAACCAGAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGAAAGAAAGA
* * *
28934665 TCACGTCTGTAGTACTATGTGAAGGCTACTGCGTG
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTG
28934700 TATTGAATGA
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCAGAAAGAAAGA
Found at i:28935623 original size:20 final size:20
Alignment explanation
Indices: 28935608--28935677 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
28935598 TGGTATGGAG
* * *
28935608 TGGACTGGAATGGTATGGGA
1 TGGAATGGAATGGAATGGTA
*
28935628 TGGAATGAAATGGAATGGTA
1 TGGAATGGAATGGAATGGTA
*
28935648 TGGAATGGATTGGAATGGTA
1 TGGAATGGAATGGAATGGTA
28935668 TGGAATGGAA
1 TGGAATGGAA
28935678 AGAAATAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.01, G:0.40, T:0.26
Consensus pattern (20 bp):
TGGAATGGAATGGAATGGTA
Found at i:28935625 original size:5 final size:5
Alignment explanation
Indices: 28935602--28935677 Score: 80
Period size: 5 Copynumber: 15.2 Consensus size: 5
28935592 TATAATTGGT
* * * * * *
28935602 ATGGA GTGGA CTGGA ATGGT ATGGG ATGGA ATGAA ATGGA ATGGT ATGGA
1 ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA ATGGA
* *
28935652 ATGGA TTGGA ATGGT ATGGA ATGGA A
1 ATGGA ATGGA ATGGA ATGGA ATGGA A
28935678 AGAAATAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.33, C:0.01, G:0.41, T:0.25
Consensus pattern (5 bp):
ATGGA
Found at i:28938057 original size:25 final size:25
Alignment explanation
Indices: 28938029--28938079 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28938019 ACTTTCAGCC
28938029 AGTTGTGCATGTACCAGGAAAACCA
1 AGTTGTGCATGTACCAGGAAAACCA
28938054 AGTTGTGCATGTACCAGGAAAACCA
1 AGTTGTGCATGTACCAGGAAAACCA
28938079 A
1 A
28938080 CCTGAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
AGTTGTGCATGTACCAGGAAAACCA
Found at i:28943061 original size:20 final size:20
Alignment explanation
Indices: 28943006--28943062 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
28942996 TATATAAATA
*
28943006 TACCCCTGATCGCACTTACG
1 TACCCCTGATCGTACTTACG
* *
28943026 TGCCCCT-ATTGTACTT-CGG
1 TACCCCTGATCGTACTTAC-G
28943045 TACCCCTGATCGTACTTA
1 TACCCCTGATCGTACTTA
28943063 TATGCCCTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.18, C:0.35, G:0.16, T:0.32
Consensus pattern (20 bp):
TACCCCTGATCGTACTTACG
Found at i:28943062 original size:39 final size:39
Alignment explanation
Indices: 28943006--28943086 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
28942996 TATATAAATA
* *
28943006 TACCCCTGATCGCACTTACGTGCCCCTATTGTACTTCGG
1 TACCCCTGATCGCACTTACATGCCCCTATTGTACATCGG
* * * *
28943045 TACCCCTGATCGTACTTATATGCCCTTGTTGTACATCGG
1 TACCCCTGATCGCACTTACATGCCCCTATTGTACATCGG
28943084 TAC
1 TAC
28943087 TCTTGATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.33
Consensus pattern (39 bp):
TACCCCTGATCGCACTTACATGCCCCTATTGTACATCGG
Found at i:28948632 original size:50 final size:50
Alignment explanation
Indices: 28948521--28948767 Score: 230
Period size: 50 Copynumber: 4.8 Consensus size: 50
28948511 ATTTGGGTAA
*
28948521 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* * * *
28948577 AGAGGTCCCATGTAAGATCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * * *
28948627 AGAGGTCCCCCGTAAGGCCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
28948677 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
28948726 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28948768 TGTTATTATC
Statistics
Matches: 160, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
49 39 0.24
50 79 0.49
53 3 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28954637 original size:50 final size:50
Alignment explanation
Indices: 28954561--28954737 Score: 205
Period size: 50 Copynumber: 3.5 Consensus size: 50
28954551 TTTTGGAAAA
28954561 TAAGATTCGCCATTGTGGCTTTAATCTTTTTGACTGCAATGTCGGGGAAG
1 TAAGATTCGCCATTGTGGCTTTAATCTTTTTGACTGCAATGTCGGGGAAG
* * * * ** * * * *
28954611 CAAGATTCACCAATGTGGCTTTAATCTGTTCCATTGC-ATCGCCTGGGAGG
1 TAAGATTCGCCATTGTGGCTTTAATCTTTTTGACTGCAAT-GTCGGGGAAG
** *
28954661 TAAGATTCGCTGTTGTAGCTTTAATC-TTTTGAACTGCAATGTCGGGGAAG
1 TAAGATTCGCCATTGTGGCTTTAATCTTTTTG-ACTGCAATGTCGGGGAAG
28954711 TAAGATTCGCCATTGTGGCTTTAATCT
1 TAAGATTCGCCATTGTGGCTTTAATCT
28954738 GTTCCACTAC
Statistics
Matches: 97, Mismatches: 26, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
49 4 0.04
50 91 0.94
51 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (50 bp):
TAAGATTCGCCATTGTGGCTTTAATCTTTTTGACTGCAATGTCGGGGAAG
Found at i:28954734 original size:100 final size:100
Alignment explanation
Indices: 28954561--28954743 Score: 296
Period size: 100 Copynumber: 1.8 Consensus size: 100
28954551 TTTTGGAAAA
*
28954561 TAAGATTCGCCATTGTGGCTTTAATCTTTTTGACTGCAATGTCGGGGAAGCAAGATTCACCAATG
1 TAAGATTCGCCATTGTAGCTTTAATCTTTTTGACTGCAATGTCGGGGAAGCAAGATTCACCAATG
28954626 TGGCTTTAATCTGTTCCATTGCATCGCCTGGGAGG
66 TGGCTTTAATCTGTTCCATTGCATCGCCTGGGAGG
** * * *
28954661 TAAGATTCGCTGTTGTAGCTTTAATC-TTTTGAACTGCAATGTCGGGGAAGTAAGATTCGCCATT
1 TAAGATTCGCCATTGTAGCTTTAATCTTTTTG-ACTGCAATGTCGGGGAAGCAAGATTCACCAAT
28954725 GTGGCTTTAATCTGTTCCA
65 GTGGCTTTAATCTGTTCCA
28954744 CTACACCGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
99 5 0.07
100 71 0.93
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (100 bp):
TAAGATTCGCCATTGTAGCTTTAATCTTTTTGACTGCAATGTCGGGGAAGCAAGATTCACCAATG
TGGCTTTAATCTGTTCCATTGCATCGCCTGGGAGG
Found at i:28954892 original size:44 final size:44
Alignment explanation
Indices: 28954839--28955084 Score: 124
Period size: 44 Copynumber: 5.4 Consensus size: 44
28954829 TATTGTAACT
*
28954839 TCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATC
1 TCAGGGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATC
* * * * * * *
28954883 TCAGGGAGATAGGATTAC-TAGCTTCAATCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGA-TCCTTTGTTTTAATCCGCTCCACTGTAATC
* * *
28954927 TCAGGGAGATGAGAT--TTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAA-C
1 TCAGGGAGATAAGATCCTT-T-G-TT---T-TAATCCG--CT-C-C-ACTGTAATC
* * *
28954980 TTCAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAATC
1 -TCAGGGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATC
* * * * * * **
28955025 TCAAGGAGATAGGATTAC-TAGCTTTAATCTGCTCCGTTGTAATC
1 TCAGGGAGATAAGA-TCCTTTGTTTTAATCCGCTCCACTGTAATC
28955069 TCAGGGAGATAAGATC
1 TCAGGGAGATAAGATC
28955085 TGCAATTTCC
Statistics
Matches: 146, Mismatches: 37, Indels: 39
0.66 0.17 0.18
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 95 0.65
45 7 0.05
46 1 0.01
47 2 0.01
48 1 0.01
49 8 0.05
50 1 0.01
51 2 0.01
52 1 0.01
53 4 0.03
54 18 0.12
55 1 0.01
56 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (44 bp):
TCAGGGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATC
Found at i:28955069 original size:142 final size:142
Alignment explanation
Indices: 28954813--28955083 Score: 470
Period size: 142 Copynumber: 1.9 Consensus size: 142
28954803 GAGATAAGAC
* * *
28954813 CTGATGTGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
28954878 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATGAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
28954943 TCTGGCTTCAAT
131 TCTGGCTTCAAT
*
28954955 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
28955020 TAATCTCAAGGAGATAGGATTACTAGCTTTAATCTGCTCCGTTGTAATCTCAGGGAGATAAGAT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
28955084 CTGCAATTTC
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 121 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:28955265 original size:131 final size:130
Alignment explanation
Indices: 28955073--28955394 Score: 482
Period size: 131 Copynumber: 2.5 Consensus size: 130
28955063 GTAATCTCAG
* * * * **
28955073 GGAGATAAGATCTGCAATTTCCAACCTATTCCTCTGCTGGTCAGGGACATAGGACTTGTGGCTTA
1 GGAGACAAGATCTGCAATTTCCAACCTACTCCACTACTGACCAGGGACATAGGACTTGTGGCTTA
* *
28955138 AATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTA
66 AATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT-
28955203 A
130 A
* * *
28955204 GGAGACAAGATTTGCAATTTCCAACCTACTCCACTACTGACCAGGGACAAAGGACGTGTGGCTTA
1 GGAGACAAGATCTGCAATTTCCAACCTACTCCACTACTGACCAGGGACATAGGACTTGTGGCTTA
* * *
28955269 AATCTGTTTCCCTACTTCTAGGGAAGGTAAGATTCGCCGTCTTCGATCTGCTCCACTACTGGTTA
66 AATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTA
* *
28955334 GAGAAACAAGATCTGTAATTTCCAACCTACTCCACTACTGACCAGGGACATAGGACTTGTG
1 G-GAGACAAGATCTGCAATTTCCAACCTACTCCACTACTGACCAGGGACATAGGACTTGTG
28955395 ATTTCACCAT
Statistics
Matches: 171, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
130 2 0.01
131 169 0.99
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (130 bp):
GGAGACAAGATCTGCAATTTCCAACCTACTCCACTACTGACCAGGGACATAGGACTTGTGGCTTA
AATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTA
Found at i:28956630 original size:14 final size:14
Alignment explanation
Indices: 28956602--28956645 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28956592 CCTTAGCCTC
* *
28956602 TCCATTTTTACTTT
1 TCCATTTTCATTTT
28956616 TCCATTTTCATTTT
1 TCCATTTTCATTTT
* *
28956630 TTCATTCTCATTTT
1 TCCATTTTCATTTT
28956644 TC
1 TC
28956646 ATCATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.64
Consensus pattern (14 bp):
TCCATTTTCATTTT
Done.