Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 9 of 14
Found at i:2843161 original size:27 final size:27
Alignment explanation
Indices: 2843079--2843221 Score: 98
Period size: 27 Copynumber: 5.3 Consensus size: 27
2843069 ATATTACAGG
*
2843079 CTTTCCATTCTA-AATATGCCACAAAAG-
1 CTTTCCATT-TAGAATACGCCA-AAAAGA
* * *
2843106 CTTT-C-TTTAAAATACGCCACAAAGC
1 CTTTCCATTTAGAATACGCCAAAAAGA
*
2843131 CTTTCCATTTAGAATACACCATAAAAG-
1 CTTTCCATTTAGAATACGCCA-AAAAGA
* ** * *
2843158 CTTTCTATTCCGAATACACCACAAAGGA
1 CTTTCCATTTAGAATACGCCA-AAAAGA
* * *
2843186 TTTTCCATTCAGAATACGCCACAAAGA
1 CTTTCCATTTAGAATACGCCAAAAAGA
2843213 CTTTCCATT
1 CTTTCCATT
2843222 ACTGTTGTGT
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
24 6 0.06
25 14 0.15
26 2 0.02
27 50 0.54
28 21 0.23
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (27 bp):
CTTTCCATTTAGAATACGCCAAAAAGA
Found at i:2843200 original size:28 final size:27
Alignment explanation
Indices: 2843116--2843221 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
2843106 CTTTCTTTAA
* * *
2843116 AATACGCCACAAAGCCTTTCCATTTAG
1 AATACACCACAAAGACTTTCCATTCAG
* * *
2843143 AATACACCATAAA-AGCTTTCTATTCCG
1 AATACACCACAAAGA-CTTTCCATTCAG
*
2843170 AATACACCACAAAGGATTTTCCATTCAG
1 AATACACCACAAA-GACTTTCCATTCAG
*
2843198 AATACGCCACAAAGACTTTCCATT
1 AATACACCACAAAGACTTTCCATT
2843222 ACTGTTGTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
27 42 0.66
28 21 0.33
29 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.26
Consensus pattern (27 bp):
AATACACCACAAAGACTTTCCATTCAG
Found at i:2851722 original size:7 final size:7
Alignment explanation
Indices: 2851710--2851744 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2851700 AACTTGAACT
2851710 CTCGACC
1 CTCGACC
2851717 CTCGACC
1 CTCGACC
2851724 CTCGACC
1 CTCGACC
*
2851731 CTTGACC
1 CTCGACC
*
2851738 CTAGACC
1 CTCGACC
2851745 TTGAAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.17, C:0.51, G:0.14, T:0.17
Consensus pattern (7 bp):
CTCGACC
Found at i:2851759 original size:20 final size:21
Alignment explanation
Indices: 2851731--2851770 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2851721 ACCCTCGACC
2851731 CTTGACCCT-AGACCTTGAAA
1 CTTGACCCTCAGACCTTGAAA
*
2851751 CTTGGCCCTCAGACCTTGAA
1 CTTGACCCTCAGACCTTGAA
2851771 CCATGAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (21 bp):
CTTGACCCTCAGACCTTGAAA
Found at i:2851830 original size:49 final size:49
Alignment explanation
Indices: 2851762--2851862 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 49
2851752 TTGGCCCTCA
* *
2851762 GACCTTGAACCATGAACCTTAAACCCTAAAGC-TTAGGCCTTAAACCTTG
1 GACCCTGAACCATGAACCTTAAACCCTAAA-CTTTAGACCTTAAACCTTG
* * * * *
2851811 GACCCTGAACCTTGGACCTTAGACCTTAGACTTTAGACCTTAAACCTTG
1 GACCCTGAACCATGAACCTTAAACCCTAAACTTTAGACCTTAAACCTTG
2851860 GAC
1 GAC
2851863 ACTAGACCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (49 bp):
GACCCTGAACCATGAACCTTAAACCCTAAACTTTAGACCTTAAACCTTG
Found at i:2851836 original size:14 final size:14
Alignment explanation
Indices: 2851799--2851851 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2851789 AAAGCTTAGG
*
2851799 CCTTAAACCTTGGA
1 CCTTAGACCTTGGA
*
2851813 CCCT-GAACCTTGGA
1 CCTTAG-ACCTTGGA
*
2851827 CCTTAGACCTTAGA
1 CCTTAGACCTTGGA
*
2851841 CTTTAGACCTT
1 CCTTAGACCTT
2851852 AAACCTTGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 31 0.97
15 1 0.03
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (14 bp):
CCTTAGACCTTGGA
Found at i:2851852 original size:14 final size:14
Alignment explanation
Indices: 2851819--2851858 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2851809 TGGACCCTGA
*
2851819 ACCTTGGACCTTAG
1 ACCTTAGACCTTAG
*
2851833 ACCTTAGACTTTAG
1 ACCTTAGACCTTAG
*
2851847 ACCTTAAACCTT
1 ACCTTAGACCTT
2851859 GGACACTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (14 bp):
ACCTTAGACCTTAG
Found at i:2851868 original size:21 final size:21
Alignment explanation
Indices: 2851825--2851870 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2851815 CTGAACCTTG
* **
2851825 GACCTTAGACCTTAGACTTTA
1 GACCTTAAACCTTAGACACTA
*
2851846 GACCTTAAACCTTGGACACTA
1 GACCTTAAACCTTAGACACTA
2851867 GACC
1 GACC
2851871 ATGGGCTATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (21 bp):
GACCTTAAACCTTAGACACTA
Found at i:2857622 original size:14 final size:14
Alignment explanation
Indices: 2857593--2857638 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
2857583 AATTTACAAC
*
2857593 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
2857607 ATTTACAAATATAT
1 ATATACAAATAAAT
2857621 ATATACAAATACAAT
1 ATATACAAATA-AAT
2857636 ATA
1 ATA
2857639 ACAGTAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:2861493 original size:3 final size:3
Alignment explanation
Indices: 2861487--2861528 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2861477 ATGTGCATGT
2861487 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2861529 ATAATTGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2861734 original size:21 final size:22
Alignment explanation
Indices: 2861710--2861751 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2861700 CTTATTATAT
2861710 TAAA-TATATATGATT-AAATAC
1 TAAAGTAT-TATGATTCAAATAC
*
2861731 TAAAGTATTATTATTCAAATA
1 TAAAGTATTATGATTCAAATA
2861752 ATTACTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAAGTATTATGATTCAAATAC
Found at i:2881305 original size:35 final size:35
Alignment explanation
Indices: 2881264--2881414 Score: 178
Period size: 35 Copynumber: 4.3 Consensus size: 35
2881254 AATCCAACCA
* * **
2881264 AAACACACCAGATGCTCATAAGAGCCAATTCAACCG
1 AAACACACCA-ATGCTCATAAGAGCTAATCCCTCCG
* *
2881300 -AACACACCAATGCTCGTAAGAGCTAATCCCTTCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
2881334 AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
* * * ***
2881369 AAACACACTAGTGCTCATAAGAGCTAGTCAAACCG
1 AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
2881404 AAACACACCAA
1 AAACACACCAA
2881415 AATAAAGAGT
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
34 19 0.19
35 79 0.81
ACGTcount: A:0.40, C:0.31, G:0.13, T:0.16
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCCTCCG
Found at i:2890006 original size:81 final size:81
Alignment explanation
Indices: 2889891--2890121 Score: 317
Period size: 81 Copynumber: 2.9 Consensus size: 81
2889881 AAATATCCCG
*
2889891 GAGGGTAAAATGACCGAAATACCCTTAAAGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAAT
1 GAGGGTAAAATGACTGAAATACCC-TAAAGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAAT
2889956 GACT-GAAATACCCTCA
65 GACTAGAAATACCCTCA
* * **
2889972 GAGGATAAAATGACTGAAATACCTCTAAAGGGTAAAATGATCGAAATACCCCTGGAGGGTAAAAT
1 GAGGGTAAAATGACTGAAATACC-CTAAAGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAAT
2890037 GA-TAGAAATACCCTCA
65 GACTAGAAATACCCTCA
* * * *
2890053 GAGGGTAAAAT-AATCGAAATACCCCAAAGGGTAAAATGACTGAAATACCAC-AATAGGGTAAAA
1 GAGGGTAAAATGACT-GAAATACCCTAAAGGGTAAAATGACCGAAATACCCCTAA-AGGGTAAAA
2890116 TGACTA
64 TGACTA
2890122 TTATACCCCT
Statistics
Matches: 132, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
80 39 0.30
81 92 0.70
82 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (81 bp):
GAGGGTAAAATGACTGAAATACCCTAAAGGGTAAAATGACCGAAATACCCCTAAAGGGTAAAATG
ACTAGAAATACCCTCA
Found at i:2890120 original size:27 final size:26
Alignment explanation
Indices: 2889892--2890120 Score: 250
Period size: 27 Copynumber: 8.5 Consensus size: 26
2889882 AATATCCCGG
*
2889892 AGGGTAAAATGACCGAAATACCCTTAA
1 AGGGTAAAATGACTGAAATACCC-TAA
*
2889919 AGGGTAAAATGACCGAAATACCCCTAA
1 AGGGTAAAATGACTGAAATA-CCCTAA
*
2889946 AGGGTAAAATGACTGAAATACCCTCAG
1 AGGGTAAAATGACTGAAATACCCT-AA
*
2889973 AGGATAAAATGACTGAAATACCTCTAA
1 AGGGTAAAATGACTGAAATACC-CTAA
**
2890000 AGGGTAAAATGA-TCGAAATACCCCTGG
1 AGGGTAAAATGACT-GAAATA-CCCTAA
*
2890027 AGGGTAAAATGA-TAGAAATACCCTCAG
1 AGGGTAAAATGACT-GAAATACCCT-AA
* *
2890054 AGGGTAAAAT-AATCGAAATACCCCAA
1 AGGGTAAAATGACT-GAAATACCCTAA
2890080 AGGGTAAAATGACTGAAATACCAC-AA
1 AGGGTAAAATGACTGAAATACC-CTAA
2890106 TAGGGTAAAATGACT
1 -AGGGTAAAATGACT
2890121 ATTATACCCC
Statistics
Matches: 179, Mismatches: 13, Indels: 20
0.84 0.06 0.09
Matches are distributed among these distances:
26 31 0.17
27 141 0.79
28 7 0.04
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (26 bp):
AGGGTAAAATGACTGAAATACCCTAA
Found at i:2890507 original size:28 final size:28
Alignment explanation
Indices: 2890464--2890590 Score: 193
Period size: 28 Copynumber: 4.5 Consensus size: 28
2890454 CATTATTGCA
*
2890464 CCACACTGGTTACTGTATTGGGCTAAGGC
1 CCACACT-ATTACTGTATTGGGCTAAGGC
2890493 CCACACTATTACTGTATTGGGCTAAGGC
1 CCACACTATTACTGTATTGGGCTAAGGC
2890521 CCACACTATTACTGTATTGGGCTAAGGC
1 CCACACTATTACTGTATTGGGCTAAGGC
* * * *
2890549 CCACATTGTTACTGTTTTGGGCTAAGAC
1 CCACACTATTACTGTATTGGGCTAAGGC
2890577 CCACACTA-TACTGT
1 CCACACTATTACTGT
2890591 TACTGTATAG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 6 0.07
28 78 0.86
29 7 0.08
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (28 bp):
CCACACTATTACTGTATTGGGCTAAGGC
Found at i:2896858 original size:20 final size:21
Alignment explanation
Indices: 2896833--2896874 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2896823 CGAACCTTCT
*
2896833 CTTTTCGCTTC-TCTTCTCTA
1 CTTTTCGCTTCTTCTCCTCTA
*
2896853 CTTTTCTCTTCTTCTCCTCTA
1 CTTTTCGCTTCTTCTCCTCTA
2896874 C
1 C
2896875 ATTCCAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.05, C:0.38, G:0.02, T:0.55
Consensus pattern (21 bp):
CTTTTCGCTTCTTCTCCTCTA
Found at i:2897583 original size:27 final size:27
Alignment explanation
Indices: 2897553--2897702 Score: 210
Period size: 27 Copynumber: 5.6 Consensus size: 27
2897543 GAATCGTGGG
* * *
2897553 AAAATGACCAAAATACCCCCGGAGGGT
1 AAAATGACCGAAATACCCTCAGAGGGT
* *
2897580 AAAATGACCGAAATACCCTCAAAGGCT
1 AAAATGACCGAAATACCCTCAGAGGGT
* *
2897607 AAAATGACCGAAATAGCCTCGGAGGGT
1 AAAATGACCGAAATACCCTCAGAGGGT
* *
2897634 AAAATGACTGAAATACCCTTAGAGGGT
1 AAAATGACCGAAATACCCTCAGAGGGT
*
2897661 AAAATGACCGAAATACCTTCAGAGGGT
1 AAAATGACCGAAATACCCTCAGAGGGT
2897688 AAAATGACCGAAATA
1 AAAATGACCGAAATA
2897703 GCCCCAACCC
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 107 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCAGAGGGT
Found at i:2897779 original size:27 final size:26
Alignment explanation
Indices: 2897553--2897794 Score: 76
Period size: 27 Copynumber: 8.8 Consensus size: 26
2897543 GAATCGTGGG
* **
2897553 AAAATGACCAAAATACCCCCGGAGGGT
1 AAAATGACAAAAATACCCCTAGA-GGT
** *
2897580 AAAATGACCGAAATA-CCCTCAAAGGCT
1 AAAATGACAAAAATACCCCT-AGAGG-T
** * *
2897607 AAAATGACCGAAATA-GCCTCGGAGGGT
1 AAAATGACAAAAATACCCCT-AGA-GGT
** *
2897634 AAAATGACTGAAATACCCTTAGAGGGT
1 AAAATGACAAAAATACCCCTAGA-GGT
** *
2897661 AAAATGACCGAAATA-CCTTCAGAGGGT
1 AAAATGACAAAAATACCCCT-AGA-GGT
** * *
2897688 AAAATGACCGAAATAGCCCCAACCCAAATGGT
1 AAAATGACAAAAATA---CC--CCTAGA-GGT
* ** * *
2897720 AAAATAACTGAAATACCCCGAAAGGT
1 AAAATGACAAAAATACCCCTAGAGGT
2897746 AAAATGACAAAAATACCCCTAGAGTGT
1 AAAATGACAAAAATACCCCTAGAG-GT
* **
2897773 AAAATGACTATTATACCCCTAG
1 AAAATGACAAAAATACCCCTAG
2897795 GAGATGAAAT
Statistics
Matches: 176, Mismatches: 27, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
26 31 0.18
27 119 0.68
28 4 0.02
29 2 0.01
31 1 0.01
32 18 0.10
33 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (26 bp):
AAAATGACAAAAATACCCCTAGAGGT
Found at i:2897804 original size:27 final size:26
Alignment explanation
Indices: 2897758--2897811 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2897748 AATGACAAAA
*
2897758 ATACCCCTAGAGTGTAAAATGACTATT
1 ATACCCCTAGAGTG-AAAATAACTATT
2897785 ATACCCCTAGGAGATG-AAATAACTATT
1 ATACCCCTA-GAG-TGAAAATAACTATT
2897812 TTAGCCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 19 0.79
28 3 0.12
29 2 0.08
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (26 bp):
ATACCCCTAGAGTGAAAATAACTATT
Found at i:2898162 original size:28 final size:28
Alignment explanation
Indices: 2898122--2898205 Score: 141
Period size: 28 Copynumber: 3.0 Consensus size: 28
2898112 CACTATACTG
2898122 ATTACTGTATTGGGCTAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACACT
*
2898150 ATTACTGTATTGGGCTAAGGCCCACATT
1 ATTACTGTATTGGGCTAAGGCCCACACT
* *
2898178 GTTACTGTTTTGGGCTAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACACT
2898206 GTACTGTTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (28 bp):
ATTACTGTATTGGGCTAAGGCCCACACT
Found at i:2912390 original size:16 final size:17
Alignment explanation
Indices: 2912357--2912390 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2912347 CGCATTCAGT
*
2912357 ATACAAAAAATTCGAGG
1 ATACAAAAAATTCAAGG
2912374 ATACAAAAAA-TCAAGG
1 ATACAAAAAATTCAAGG
2912390 A
1 A
2912391 AAGAAAGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
ATACAAAAAATTCAAGG
Found at i:2918408 original size:13 final size:13
Alignment explanation
Indices: 2918392--2918422 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2918382 AAAAAAAATC
2918392 AAAATAAAAATAA
1 AAAATAAAAATAA
2918405 AAAATAAAAATAA
1 AAAATAAAAATAA
2918418 AAAAT
1 AAAAT
2918423 TAGAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:2918408 original size:19 final size:19
Alignment explanation
Indices: 2918384--2918420 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2918374 ATCCTTTCAA
*
2918384 AAAAAATCAAAATAAAAAT
1 AAAAAATAAAAATAAAAAT
2918403 AAAAAATAAAAATAAAAA
1 AAAAAATAAAAATAAAAA
2918421 ATTAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAAATAAAAAT
Found at i:2918422 original size:7 final size:6
Alignment explanation
Indices: 2918385--2918420 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2918375 TCCTTTCAAA
*
2918385 AAAAAT CAAAAT AAAAAT AAAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAA
2918421 ATTAGAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:2918460 original size:8 final size:7
Alignment explanation
Indices: 2918397--2918461 Score: 51
Period size: 7 Copynumber: 8.7 Consensus size: 7
2918387 AAATCAAAAT
*
2918397 AAAAATA
1 AAAAAGA
*
2918404 AAAAATA
1 AAAAAGA
2918411 AAAATA-A
1 AAAA-AGA
2918418 AAAATTAGA
1 AAAA--AGA
2918427 GAAAAAGA
1 -AAAAAGA
*
2918435 AAGAAGA
1 AAAAAGA
2918442 AAAGAAGA
1 AAA-AAGA
2918450 AAAAAGA
1 AAAAAGA
2918457 AAAAA
1 AAAAA
2918462 TCTAGATGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
7 33 0.65
8 13 0.25
9 1 0.02
10 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (7 bp):
AAAAAGA
Found at i:2919371 original size:7 final size:7
Alignment explanation
Indices: 2919354--2919403 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
2919344 AAAAATGTGC
2919354 GAAAAATT
1 GAAAAA-T
2919362 GAAAAAT
1 GAAAAAT
2919369 G-AAAAT
1 GAAAAAT
*
2919375 GGAAAAT
1 GAAAAAT
*
2919382 GAAAAAG
1 GAAAAAT
2919389 GAAAAA-
1 GAAAAAT
2919395 GTAAAAAT
1 G-AAAAAT
2919403 G
1 G
2919404 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 7 0.19
7 23 0.62
8 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (7 bp):
GAAAAAT
Found at i:2919382 original size:13 final size:13
Alignment explanation
Indices: 2919364--2919393 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2919354 GAAAAATTGA
*
2919364 AAAATGAAAATGG
1 AAAATGAAAAAGG
2919377 AAAATGAAAAAGG
1 AAAATGAAAAAGG
2919390 AAAA
1 AAAA
2919394 AGTAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (13 bp):
AAAATGAAAAAGG
Found at i:2920735 original size:43 final size:43
Alignment explanation
Indices: 2920655--2921037 Score: 158
Period size: 43 Copynumber: 8.9 Consensus size: 43
2920645 AAGATTACGG
* ** *
2920655 ATCTTATCTTCCCCAAGAGTAGGGAAGTAGATCTAAGCGGTGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCGGTGA
* **
2920698 ATCTTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACT-A
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG-CGGTGA
* * * * * * ****
2920741 GTCCTATC-TCCCTGGTCAGCAGT-GGG--ATAGGTTAAAGTTACGA
1 ATCTTATCTTCCC----CAGGAGTAGGGAAACAGATTTAAGCGGTGA
* * * **
2920784 ATCTTATCTTCCCCAGGAGTTGGGAAGA-AAATCTAAGCGGCAA
1 ATCTTATCTTCCCCAGGAGTAGGGAA-ACAGATTTAAGCGGTGA
* * **
2920827 ATTTTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACT-A
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG-CGGTGA
* * * * * * * ** *
2920870 GTCCTATC-T-CCCTGGTCAGTAGTGG-GATAGGTTGAAG-ATTACGG
1 ATCTTATCTTCCCCAGG--AGTAG-GGAAACAGATTTAAGCGGT--GA
* * *
2920914 ATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGTGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCGGTGA
* ** * * *
2920957 ATTTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGCGGCGG
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCGGTGA
* *
2921000 ATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGC
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGC
2921038 CACTAGTCCT
Statistics
Matches: 248, Mismatches: 69, Indels: 46
0.68 0.19 0.13
Matches are distributed among these distances:
40 6 0.02
41 10 0.04
42 6 0.02
43 183 0.74
44 27 0.11
45 5 0.02
46 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (43 bp):
ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCGGTGA
Found at i:2920879 original size:129 final size:130
Alignment explanation
Indices: 2920645--2920982 Score: 561
Period size: 129 Copynumber: 2.6 Consensus size: 130
2920635 CAGATCAATG
* * *
2920645 AAGATTACGGATCTTATCTTCCCCAAGAGTAGGGAAGTAGATCTAAGCGGTGAATCTTATCTTCC
1 AAGATTACGGATCTTATCTTCCCCAGGAGTAGGGAAGAAGATCTAAGCGGTGAATTTTATCTTCC
2920710 CCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTA
66 CCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTA
* * * **
2920775 AAG-TTACGAATCTTATCTTCCCCAGGAGTTGGGAAGAAAATCTAAGCGGCAAATTTTATCTTCC
1 AAGATTACGGATCTTATCTTCCCCAGGAGTAGGGAAGAAGATCTAAGCGGTGAATTTTATCTTCC
* *
2920839 CCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGGGATAGGTTG
66 CCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTA
* *
2920904 AAGATTACGGATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGTGAATTTTATCTTCC
1 AAGATTACGGATCTTATCTTCCCCAGGAGTAGGGAAGAAGATCTAAGCGGTGAATTTTATCTTCC
2920969 CCAGGAGTAGGGAA
66 CCAGGAGTAGGGAA
2920983 GTAGATCTAA
Statistics
Matches: 190, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 119 0.63
130 71 0.37
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (130 bp):
AAGATTACGGATCTTATCTTCCCCAGGAGTAGGGAAGAAGATCTAAGCGGTGAATTTTATCTTCC
CCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTA
Found at i:2920934 original size:87 final size:87
Alignment explanation
Indices: 2920830--2921112 Score: 299
Period size: 87 Copynumber: 3.3 Consensus size: 87
2920820 GCGGCAAATT
2920830 TTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGG
1 TTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGG
2920895 GATAGGTTGAAGATTACGGATC
66 GATAGGTTGAAGATTACGGATC
* * * * ** * ** *
2920917 TTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAG-CGGTGAATTTTATCTTCCCCAGG--AGTAG
1 TTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACT-AGTCCTATC-T-CCCTGGTCAGTAG
* * ***
2920979 -GGAAGTAGATCT-AAG-CGGCGGATC
63 TGGGA-TAGGT-TGAAGATTACGGATC
* ** *
2921003 TTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATAGCCCTGGTCAGCAGTGG
1 TTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGG
2921068 GATAGGTTGAAGATTACGGATC
66 GATAGGTTGAAGATTACGGATC
*
2921090 TTATCTTTCCCAGGAGTAGGGAA
1 TTATCTTCCCCAGGAGTAGGGAA
2921113 GCAGATCTAA
Statistics
Matches: 149, Mismatches: 36, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
84 5 0.03
85 1 0.01
86 56 0.38
87 80 0.54
88 2 0.01
89 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (87 bp):
TTATCTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGG
GATAGGTTGAAGATTACGGATC
Found at i:2920994 original size:173 final size:173
Alignment explanation
Indices: 2920782--2921167 Score: 628
Period size: 173 Copynumber: 2.2 Consensus size: 173
2920772 TTAAAGTTAC
* * * *
2920782 GAATCTTATCTTCCCCAGGAGTTGGGAAGAAAATCTAAGCGGCAAATTTTATCTTCCCCAGGAGT
1 GAATCTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGCGGCAAATCTTATCTTCCCCAGGAGT
** *
2920847 AGGGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGGGATAGGTTGAAGATTAC
66 AGGGAAACAAATTTAAGCCACTAGTCCTATAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTAC
2920912 GGATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGT
131 GGATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGT
* ** *
2920955 GAATTTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGCGGCGGATCTTATCTTCCCTAGGAGT
1 GAATCTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGCGGCAAATCTTATCTTCCCCAGGAGT
2921020 AGGGAAACAAATTTAAGCCACTAGTCCTATAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTAC
66 AGGGAAACAAATTTAAGCCACTAGTCCTATAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTAC
* *
2921085 GGATCTTATCTTTCCCAGGAGTAGGGAAGCAGATCTAAGCGGT
131 GGATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGT
* * *
2921128 GAATCTTATCTTCCCCAGGAGTAGGAAAATAGATTTAAGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGC
2921168 CACTAGTCCT
Statistics
Matches: 196, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
173 196 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (173 bp):
GAATCTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGCGGCAAATCTTATCTTCCCCAGGAGT
AGGGAAACAAATTTAAGCCACTAGTCCTATAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTAC
GGATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGT
Found at i:2921396 original size:303 final size:303
Alignment explanation
Indices: 2920655--2921426 Score: 684
Period size: 303 Copynumber: 2.6 Consensus size: 303
2920645 AAGATTACGG
* ** *** * * * *
2920655 ATCTTATCTTCCCCAAGAGTAGGGAAGTAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTAG
1 ATCTTATCTTCCCAAAGAGTAGGGAAACAGATCTAAGCCACGGATCCTATCTTCCCTAGGAGCAG
* * * ** * * * * ** **
2920720 GGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTAAAG-TTACGA
66 GGAAACAAATTGAAGCCACAAATCCTATAGCCCTAGTCAACAGTGGGACAGATCGAAGACGACGA
* * * * *
2920784 ATCTTATCTTCCCCAGGAGTTGGGAAGAAAATCTAAGCGGCAAATTTTATCTTCCCCAGGAGTAG
131 ATCTTATCTTTCCCAGGAGTAGGGAAGCAGATCTAAGCGGCAAATCTTATCTTCCCCAGGAGTAG
* * *
2920849 GGAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGTAGTGGGATAGGTTGAAGATTACGG
196 GAAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAG
* * * * *
2920914 ATCTTATCCTCCCCAGGAGTAGGGAAGCAGATCTAAGCGGTGA
261 ATCTTATCCTCCCAAGCAATAGGGAAGCAGATCGAAGCGGCGA
* * * ** ** * *
2920957 ATTTTATCTTCCCCAGGAGTAGGGAAGTAGATCTAAGCGGCGGATCTTATCTTCCCTAGGAGTAG
1 ATCTTATCTTCCCAAAGAGTAGGGAAACAGATCTAAGCCACGGATCCTATCTTCCCTAGGAGCAG
* * * * * * * * ** *
2921022 GGAAACAAATTTAAGCCACTAGTCCTATAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACGG
66 GGAAACAAATTGAAGCCACAAATCCTATAGCCCTAGTCAACAGTGGGACAGATCGAAGACGACGA
**
2921087 ATCTTATCTTTCCCAGGAGTAGGGAAGCAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTAG
131 ATCTTATCTTTCCCAGGAGTAGGGAAGCAGATCTAAGCGGCAAATCTTATCTTCCCCAGGAGTAG
* *
2921152 GAAAATAGATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAG
196 GAAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAG
*
2921217 AT-TTGT-CTCCCTAAGCAATAGTGG-AGCAGATCGAAGACGGCGA
261 ATCTTATCCTCCC-AAGCAATAG-GGAAGCAGATCGAAG-CGGCGA
* * *
2921260 ATCTTATCTTCCCAAAGAGTAGGGAAACAGATTTAAGCCAC-TATCCTATC-T-CCTTGGTCAGC
1 ATCTTATCTTCCCAAAGAGTAGGGAAACAGATCTAAGCCACGGATCCTATCTTCCCTAGG--AGC
* * ** ** * ** *
2921322 AGTGG-GATAGGTTGAAGATTACAAATCTTATCTCCCTAAG-CAATAGT-GGAGCAGATCGAAGA
64 AG-GGAAACAAATTGAAG-CCACAAATCCTATAGCCCT-AGTCAACAGTGGGA-CAGATCGAAGA
* * * *
2921384 CGGCGAATCTTATC-TTCCCAGGAGTAAGGAAACAGATTTAAGC
125 CGACGAATCTTATCTTTCCCAGGAGTAGGGAAGCAGATCTAAGC
2921427 CACTAGTCCT
Statistics
Matches: 396, Mismatches: 64, Indels: 20
0.82 0.13 0.04
Matches are distributed among these distances:
300 5 0.01
301 6 0.02
302 182 0.46
303 202 0.51
304 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (303 bp):
ATCTTATCTTCCCAAAGAGTAGGGAAACAGATCTAAGCCACGGATCCTATCTTCCCTAGGAGCAG
GGAAACAAATTGAAGCCACAAATCCTATAGCCCTAGTCAACAGTGGGACAGATCGAAGACGACGA
ATCTTATCTTTCCCAGGAGTAGGGAAGCAGATCTAAGCGGCAAATCTTATCTTCCCCAGGAGTAG
GAAAACAAATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAG
ATCTTATCCTCCCAAGCAATAGGGAAGCAGATCGAAGCGGCGA
Found at i:2921594 original size:131 final size:131
Alignment explanation
Indices: 2920985--2921876 Score: 1334
Period size: 130 Copynumber: 6.9 Consensus size: 131
2920975 GTAGGGAAGT
* * * *
2920985 AGATCTAAG-CGGCGGATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
** * * *
2921049 TAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACGGATCTTATCTTTCCC--AGGAGTAG-GG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATC--TCCCTAAGCAATAGTGG
2921111 AAGC
129 -AGC
* * * *
2921115 AGATCTAAG-CGGTGAATCTTATCTTCCCCAGGAGTAGGAAAATAGATTTAAGCCACTAGTCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
*
2921179 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGAT-TTGTCTCCCTAAGCAATAGTGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921243 C
131 C
* *
2921244 AGATCGAAGACGGCGAATCTTATCTTCCCAAAGAGTAGGGAAACAGATTTAAGCCACTA-TCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
* *
2921308 TCTCCTTGGTCAGCAGTGGGATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAATAGTGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921373 C
131 C
*
2921374 AGATCGAAGACGGCGAATCTTATCTT-CCCAGGAGTAAGGAAACAGATTTAAGCCACTAGTCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
* *
2921438 TCTCCCTGGTCAGCAGTGGGATAGGTTAAAGATTACAGATCTTATCTCCCTAAGCAACAGTGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921503 C
131 C
* * ** * *
2921504 AGATAGAAGGCGGAAAATCTTATTTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
* * *
2921569 TCTCCCTGGTCAGCAATGGGATAGGTTGAAGAATACAGATCTTATCTCCCTAAGCAATAATGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921634 C
131 C
* **
2921635 AGATCGAAGACGACGAATCTTATCTT-CCCAGGAGTAGGGAAATGGATTTAAGCCACTAGTCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
* *
2921699 TCTCCCTGGTCTGCAGTGGGATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAATAGTGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921764 C
131 C
* * * *
2921765 AGATCGAAGGCGGCGAATCTTATTTTCCCTAGGAGTAGGGAAACAGATTTAAGCGACTAGTCCTA
1 AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
*
2921830 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACGGATCTTATCT
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCT
2921877 TCCCCAGGAG
Statistics
Matches: 690, Mismatches: 64, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
127 4 0.01
129 93 0.13
130 398 0.58
131 195 0.28
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (131 bp):
AGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTAGTCCTA
TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
C
Found at i:2921899 original size:261 final size:260
Alignment explanation
Indices: 2920985--2921876 Score: 1355
Period size: 261 Copynumber: 3.4 Consensus size: 260
2920975 GTAGGGAAGT
* *
2920985 AGATCTAA-GCGGCGGATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
1 AGATCGAAGGCGGCGAATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
** * * *
2921049 TAGCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACGGATCTTATCTTTCCC--AGGAGTAGGGA
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATC--TCCCTAAGCAATAGGG-
* * *
2921112 AGCAGATCTAAG-CGGTGAATCTTATCTTCCCCAGGAGTAGGAAAATAGATTTAAGCCACTAGTC
128 AGCAGATCGAAGACGGCGAATCTTATCTT-CCCAGGAGTAGGGAAATAGATTTAAGCCACTAGTC
*
2921176 CTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGAT-TTGTCTCCCTAAGCAATAGTG
192 CTATCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTG
2921240 GAGC
257 GAGC
* * * *
2921244 AGATCGAAGACGGCGAATCTTATCTTCCCAAAGAGTAGGGAAACAGATTTAAGCCACTA-TCCTA
1 AGATCGAAGGCGGCGAATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
* *
2921308 TCTCCTTGGTCAGCAGTGGGATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAATAGTGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAG-GGAG
* *
2921373 CAGATCGAAGACGGCGAATCTTATCTTCCCAGGAGTAAGGAAACAGATTTAAGCCACTAGTCCTA
130 CAGATCGAAGACGGCGAATCTTATCTTCCCAGGAGTAGGGAAATAGATTTAAGCCACTAGTCCTA
* *
2921438 TCTCCCTGGTCAGCAGTGGGATAGGTTAAAGATTACAGATCTTATCTCCCTAAGCAACAGTGGAG
195 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921503 C
260 C
* ** * *
2921504 AGATAGAAGGCGGAAAATCTTATTTTCCCCAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
1 AGATCGAAGGCGGCGAATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
* * *
2921569 TCTCCCTGGTCAGCAATGGGATAGGTTGAAGAATACAGATCTTATCTCCCTAAGCAATAATGGAG
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAAT-AGGGAG
* *
2921634 CAGATCGAAGACGACGAATCTTATCTTCCCAGGAGTAGGGAAATGGATTTAAGCCACTAGTCCTA
130 CAGATCGAAGACGGCGAATCTTATCTTCCCAGGAGTAGGGAAATAGATTTAAGCCACTAGTCCTA
* *
2921699 TCTCCCTGGTCTGCAGTGGGATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAATAGTGGAG
195 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAG
2921764 C
260 C
* * *
2921765 AGATCGAAGGCGGCGAATCTTATTTTCCCTAGGAGTAGGGAAACAGATTTAAGCGACTAGTCCTA
1 AGATCGAAGGCGGCGAATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
*
2921830 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACGGATCTTATCT
66 TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCT
2921877 TCCCCAGGAG
Statistics
Matches: 574, Mismatches: 51, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
257 4 0.01
259 144 0.25
260 136 0.24
261 289 0.50
262 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (260 bp):
AGATCGAAGGCGGCGAATCTTATCTTCCCTAGGAGTAGGGAAACAAATTTAAGCCACTAGTCCTA
TCTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGGGAGC
AGATCGAAGACGGCGAATCTTATCTTCCCAGGAGTAGGGAAATAGATTTAAGCCACTAGTCCTAT
CTCCCTGGTCAGCAGTGGGATAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGC
Found at i:2923072 original size:19 final size:19
Alignment explanation
Indices: 2923048--2923103 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
2923038 GACCCGATCA
*
2923048 GGGAAGGATCTGCGTATCC
1 GGGAAGGATCTGCGCATCC
2923067 GGGAAGGATCTGCGCATCC
1 GGGAAGGATCTGCGCATCC
*
2923086 GGGAAGGATCCGCGCATC
1 GGGAAGGATCTGCGCATC
2923104 AAGGATCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.16
Consensus pattern (19 bp):
GGGAAGGATCTGCGCATCC
Found at i:2934183 original size:16 final size:16
Alignment explanation
Indices: 2934162--2934192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2934152 TCGTATTGAA
2934162 ATTGTAATTAATTAAC
1 ATTGTAATTAATTAAC
*
2934178 ATTGTATTTAATTAA
1 ATTGTAATTAATTAA
2934193 TGCATGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
ATTGTAATTAATTAAC
Found at i:2935999 original size:120 final size:120
Alignment explanation
Indices: 2935872--2936099 Score: 296
Period size: 120 Copynumber: 1.9 Consensus size: 120
2935862 TTATACTTCG
** ** * * * *
2935872 GTACCCCTAAATTGTACATATGTGACCC-TATTTGTACTTTAGTACCCTTAAATTGCACATACGT
1 GTACCCCTAAATTACACATACAT-ACCCTTATTTATACTTCAGTACCCCTAAATTACACATACGT
* * * * * *
2935936 GCCTCTTTTTGTACTTCTGTACCCCTGAATTGCACATATGTGCCTTTTTTATTTTT
65 GCCCCTGTTTGCACTTCGGTACCCCTAAATAGCACATATGTGCCTTTTTTATTTTT
* *
2935992 GTACCCCTAAATTACACATACATACCCTTATTTATACTTCGGTACCCCTGAATTACACATACGTG
1 GTACCCCTAAATTACACATACATACCCTTATTTATACTTCAGTACCCCTAAATTACACATACGTG
2936057 CCCCTGTTTGCACTTCGGTACCCCTAAATAGCACATATGTGCC
66 CCCCTGTTTGCACTTCGGTACCCCTAAATAGCACATATGTGCC
2936100 CTTGTTTACA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 4 0.04
120 87 0.96
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (120 bp):
GTACCCCTAAATTACACATACATACCCTTATTTATACTTCAGTACCCCTAAATTACACATACGTG
CCCCTGTTTGCACTTCGGTACCCCTAAATAGCACATATGTGCCTTTTTTATTTTT
Found at i:2936117 original size:41 final size:41
Alignment explanation
Indices: 2935835--2936117 Score: 243
Period size: 41 Copynumber: 7.0 Consensus size: 41
2935825 ATTAATTATA
* * *
2935835 CCCTAAATTGCACATCTGTACCCCTATTTATACTTCGGTAC
1 CCCTAAATTGCACATATGTGCCCTTATTTATACTTCGGTAC
* * **
2935876 CCCTAAATTGTACATATGTGACCC-TATTTGTACTTTAGTAC
1 CCCTAAATTGCACATATGTG-CCCTTATTTATACTTCGGTAC
* * * *
2935917 CCTTAAATTGCACATACGTGCCTCTT-TTTGTACTTCTGTAC
1 CCCTAAATTGCACATATGTGCC-CTTATTTATACTTCGGTAC
* * **
2935958 CCCTGAATTGCACATATGTG-CCTT-TTT-TATTTTTGTAC
1 CCCTAAATTGCACATATGTGCCCTTATTTATACTTCGGTAC
* ** *
2935996 CCCTAAATTACACATACATACCCTTATTTATACTTCGGTAC
1 CCCTAAATTGCACATATGTGCCCTTATTTATACTTCGGTAC
* * * * * **
2936037 CCCTGAATTACACATACGTGCCCCTGTTTGCACTTCGGTAC
1 CCCTAAATTGCACATATGTGCCCTTATTTATACTTCGGTAC
* * * *
2936078 CCCTAAATAGCACATATGTGCCCTTGTTTACACTCCGGTA
1 CCCTAAATTGCACATATGTGCCCTTATTTATACTTCGGTA
2936118 ATTTCAAATC
Statistics
Matches: 198, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
38 24 0.12
39 10 0.05
40 6 0.03
41 154 0.78
42 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (41 bp):
CCCTAAATTGCACATATGTGCCCTTATTTATACTTCGGTAC
Found at i:2943459 original size:41 final size:41
Alignment explanation
Indices: 2943406--2943842 Score: 466
Period size: 41 Copynumber: 10.7 Consensus size: 41
2943396 ATTAATTATA
* * *
2943406 CCCTAAATTGCACATACGTGCCCCTGTTTGTTCTTCGATAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * ** * ** *
2943447 CCTTTAATTGCACATGTGTACCTTTGTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
** * * *
2943488 CATTGAATTGCACATACGTGCCCTTTTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * * *
2943529 CCCTGAATTGCACATATGTGCCCCTATTTTTACTTCGATGC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * *
2943570 CCCTGAATTGCACATATGTGCTCCTATTTGTACTTCGAT-C
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
*
2943610 CCTTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * * *
2943651 CTCTGAATTCCACATACATACCCCTCTTTGTACTTCGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* * * *
2943692 CCCTAAATTACACATACGTGGCCCTGTTTGTACTTCGATA-
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* *
2943732 CCCTGAATTACACATACGTAG-CCCTGTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACGT-GCCCCTGTTTGTACTTCGGTAC
*
2943773 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
* ** *
2943814 CCCTAAATAACACATATGTGCCCCTGTTT
1 CCCTGAATTGCACATACGTGCCCCTGTTT
2943843 ACACTCCGGT
Statistics
Matches: 334, Mismatches: 58, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
40 71 0.21
41 263 0.79
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (41 bp):
CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
Found at i:2943552 original size:21 final size:21
Alignment explanation
Indices: 2943528--2943590 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
2943518 TACTTTGGTA
2943528 CCCCTGAATTGCACATATGTG
1 CCCCTGAATTGCACATATGTG
* **
2943549 CCCCT-ATTTTTAC-T-TCGATG
1 CCCCTGAATTGCACATAT-G-TG
2943569 CCCCTGAATTGCACATATGTG
1 CCCCTGAATTGCACATATGTG
2943590 C
1 C
2943591 TCCTATTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 12 0.39
21 13 0.42
22 2 0.06
23 1 0.03
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (21 bp):
CCCCTGAATTGCACATATGTG
Found at i:2943665 original size:122 final size:122
Alignment explanation
Indices: 2943406--2943842 Score: 529
Period size: 122 Copynumber: 3.6 Consensus size: 122
2943396 ATTAATTATA
* * * * * * * * *
2943406 CCCTAAATTGCACATACGTGCCCCTGTTTGTTCTTCGATACCCTTTAATTGCACATGTGTACCTT
1 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTAAATTACACATATGTGCC-C
* * * * *
2943471 TGTTTGTACTTTGGTACCATTGAATTGCACATACGTGCCCTTTTTTGTACTTTGGTAC
65 TGTTTGTACTTCGATACCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTAC
* * * * *
2943529 CCCTGAATTGCACATATGTGCCCCTATTTTTACTTCGATGCCCCTGAATTGCACATATGTGCTCC
1 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTAAATTACACATATGTGC-CC
* *
2943594 TATTTGTACTTCGAT-CCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
65 TGTTTGTACTTCGATACCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTAC
* * * * * * *
2943651 CTCTGAATTCCACATACATACCCCTCTTTGTACTTCGGTACCCCTAAATTACACATACGTGGCCC
1 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTAAATTACACATATGT-GCCC
*
2943716 TGTTTGTACTTCGATACCC-TGAATTACACATACGTAG-CCCTGTTTGTACTTTGGTAC
65 TGTTTGTACTTCGATACCCTTGAATTGCACATACGT-GCCCCTGTTTGTACTTTGGTAC
* *
2943773 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAATAACACATATGTGCCCC
1 CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTAAATTACACATATGTG-CCC
2943838 TGTTT
65 TGTTT
2943843 ACACTCCGGT
Statistics
Matches: 269, Mismatches: 40, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
121 1 0.00
122 197 0.73
123 70 0.26
124 1 0.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (122 bp):
CCCTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCCTAAATTACACATATGTGCCCT
GTTTGTACTTCGATACCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTAC
Found at i:2943683 original size:163 final size:162
Alignment explanation
Indices: 2943403--2943814 Score: 504
Period size: 163 Copynumber: 2.5 Consensus size: 162
2943393 ATAATTAATT
* * * ** *
2943403 ATACCCTAAATTGCACATACGTGCCCCTGTTTGTTCTTCGATACCCTTTAATTGCACATGTGTAC
1 ATACCCTGAATTGCACATACGTG-CCCTGTTTGTACTTCGATACCCTTGAATTGCACATACGTGC
** * * * * * * *
2943468 CTTTGTTTGTACTTTGGTACCATTGAATTGCACATACGTGCCCTTTTTTGTACTTTGGTACCCCT
65 CCCTGTTTGTACTTCGGTACCATTGAATTCCACATACATACCCCTCTTTGTACTTCGGTACCCCT
* * * *
2943533 GAATTGCACATATGTGCCCCTATTTTTACTTCG
130 AAATTACACATACGTGCCCCTATTTGTACTTCG
* * *
2943566 ATGCCCCTGAATTGCACATATGTGCTCCTATTTGTACTTCGAT-CCCTTGAATTGCACATACGTG
1 AT-ACCCTGAATTGCACATACGTGC-CCTGTTTGTACTTCGATACCCTTGAATTGCACATACGTG
2943630 CCCCTGTTTGTACTTCGGTACC-TCTGAATTCCACATACATACCCCTCTTTGTACTTCGGTACCC
64 CCCCTGTTTGTACTTCGGTACCAT-TGAATTCCACATACATACCCCTCTTTGTACTTCGGTACCC
* *
2943694 CTAAATTACACATACGTGGCCCTGTTTGTACTTCG
128 CTAAATTACACATACGTGCCCCTATTTGTACTTCG
* * * *
2943729 ATACCCTGAATTACACATACGTAGCCCTGTTTGTACTTTGGTACCCCTGAATTGCACATACGTGC
1 ATACCCTGAATTGCACATACGT-GCCCTGTTTGTACTTCGATACCCTTGAATTGCACATACGTGC
*
2943794 CCCTATTTGTACTTCGGTACC
65 CCCTGTTTGTACTTCGGTACC
2943815 CCTAAATAAC
Statistics
Matches: 212, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
162 32 0.15
163 147 0.69
164 33 0.16
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (162 bp):
ATACCCTGAATTGCACATACGTGCCCTGTTTGTACTTCGATACCCTTGAATTGCACATACGTGCC
CCTGTTTGTACTTCGGTACCATTGAATTCCACATACATACCCCTCTTTGTACTTCGGTACCCCTA
AATTACACATACGTGCCCCTATTTGTACTTCG
Found at i:2943818 original size:20 final size:20
Alignment explanation
Indices: 2943753--2943818 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
2943743 ACATACGTAG
* *
2943753 CCCTGTTTGTACTTTGGTAC
1 CCCTATTTGTACTTCGGTAC
* * * *
2943773 CCCTGAATTGCACATAC-GTGC
1 CCCT-ATTTGTAC-TTCGGTAC
2943794 CCCTATTTGTACTTCGGTAC
1 CCCTATTTGTACTTCGGTAC
2943814 CCCTA
1 CCCTA
2943819 AATAACACAT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 18 0.55
21 12 0.36
22 1 0.03
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.35
Consensus pattern (20 bp):
CCCTATTTGTACTTCGGTAC
Found at i:2959822 original size:18 final size:17
Alignment explanation
Indices: 2959795--2959830 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2959785 AAAATACAAT
*
2959795 TAAAAAACATTATTTAA
1 TAAAAAACATTAGTTAA
2959812 TAAACAAACATTAGTTAA
1 TAAA-AAACATTAGTTAA
2959830 T
1 T
2959831 CATGATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAAACATTAGTTAA
Found at i:2959982 original size:21 final size:21
Alignment explanation
Indices: 2959935--2959974 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2959925 ATCTTGAACA
*
2959935 AAGTGTTGATATCTTTATAAT
1 AAGTATTGATATCTTTATAAT
*
2959956 AAGTATTGATATTTTTATA
1 AAGTATTGATATCTTTATA
2959975 TATGGTATCG
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:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (21 bp):
AAGTATTGATATCTTTATAAT
Found at i:2971531 original size:30 final size:29
Alignment explanation
Indices: 2971496--2971553 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2971486 GAGTTTGTAA
2971496 ATAGTATT-TATTAATATTTATGAGTTGATT
1 ATAGTATTATATTAA-ATTT-TGAGTTGATT
*
2971526 ATAGTATTATATTAAATTTTGATTTGAT
1 ATAGTATTATATTAAATTTTGAGTTGAT
2971554 AATTTTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 12 0.46
31 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (29 bp):
ATAGTATTATATTAAATTTTGAGTTGATT
Found at i:2973140 original size:13 final size:13
Alignment explanation
Indices: 2973114--2973261 Score: 84
Period size: 13 Copynumber: 11.2 Consensus size: 13
2973104 AATGTAGAAA
* *
2973114 ATGAAATAGATAT
1 ATGAAATGGTTAT
*
2973127 AAGAAATGGTTAT
1 ATGAAATGGTTAT
* *
2973140 ACGAAAAGGTTAT
1 ATGAAATGGTTAT
*
2973153 ATGAAATGGTTAC
1 ATGAAATGGTTAT
2973166 ATGAAATGGTTAT
1 ATGAAATGGTTAT
* * *
2973179 ATGGAAATAGATAC
1 AT-GAAATGGTTAT
* * *
2973193 ATGGAATGATTTT
1 ATGAAATGGTTAT
*
2973206 ATG-AATCGATTAT
1 ATGAAAT-GGTTAT
* *
2973219 ATACAAATAGTTAT
1 AT-GAAATGGTTAT
* *
2973233 AT-AAACTGCTTTT
1 ATGAAA-TGGTTAT
*
2973246 ATGAAATGTTTAT
1 ATGAAATGGTTAT
2973259 ATG
1 ATG
2973262 GATATAGATA
Statistics
Matches: 102, Mismatches: 27, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
12 6 0.06
13 74 0.73
14 19 0.19
15 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:2973193 original size:27 final size:26
Alignment explanation
Indices: 2973142--2973210 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
2973132 ATGGTTATAC
* * *
2973142 GAAAAGGTTATATGAAATGGTTACAT
1 GAAATGGTTATATGAAATAGATACAT
2973168 GAAATGGTTATATGGAAATAGATACAT
1 GAAATGGTTATAT-GAAATAGATACAT
* * *
2973195 GGAATGATTTTATGAA
1 GAAATGGTTATATGAA
2973211 TCGATTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (26 bp):
GAAATGGTTATATGAAATAGATACAT
Found at i:2985405 original size:27 final size:27
Alignment explanation
Indices: 2985349--2985420 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
2985339 CAGAACGGAA
* *
2985349 AGCACCAAAATGCTAATCAAAACAACG
1 AGCACCAAAGTGCTAATTAAAACAACG
* *
2985376 AGCACCAAAGTGCTAATTAGAATAGA-G
1 AGCACCAAAGTGCTAATTAAAACA-ACG
*
2985403 AGCACCGAAGTGCTAATT
1 AGCACCAAAGTGCTAATT
2985421 TCCATTCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (27 bp):
AGCACCAAAGTGCTAATTAAAACAACG
Found at i:2986874 original size:115 final size:114
Alignment explanation
Indices: 2986468--2986915 Score: 580
Period size: 114 Copynumber: 3.9 Consensus size: 114
2986458 TTCCACCCAT
* * * * *
2986468 TCAGGGCTTTAACGGCGATTTTGTGGAAGCGCCGCAAA-AAACCGAAGCCCAACGATGCCGTTTG
1 TCAGGACTTTAGCGGCGTTTTTGTGGAAGCGCCGCAAAGAAACCGAAGCCCAACGATGCCATTTT
* * *
2986532 CTGAG-ATTCGGGGATTTAGTAGTGTTTTCGGTGAAGCACCGCTAATGC
66 CTGAGCATTCGGGGATTTAGTGGCGTTTTCGGTGAAGCGCCGCTAATGC
* * * *
2986580 TCAAGACTTTAGCGGCTTTTTTG-GGTAAGCGCCGCAAATAAACCGAAGCCCAACGACGCCATTT
1 TCAGGACTTTAGCGGCGTTTTTGTGG-AAGCGCCGCAAAGAAACCGAAGCCCAACGATGCCATTT
*
2986644 TCTGAGCATTCGGGGATTTAGTGGCGTTTTCGGTAAAGCGCCGCTAATGC
65 TCTGAGCATTCGGGGATTTAGTGGCGTTTTCGGTGAAGCGCCGCTAATGC
* * * * * *
2986694 TCTGGACTTTAGCGGCGTTTTTGAGTAAGCGCCGCAAAGAAACTGAAGCCCAACGATGTCGTTTT
1 TCAGGACTTTAGCGGCGTTTTTGTGGAAGCGCCGCAAAGAAACCGAAGCCCAACGATGCCATTTT
* *
2986759 CTGAGCATTCGGGGATTTAGTGGCGCTTTCGGTGGAAGCGCCGCTAATGA
66 CTGAGCATTCGGGGATTTAGTGGCGTTTTCGGT-GAAGCGCCGCTAATGC
* * * *
2986809 TCAGGGCTTTAGTGGCGTTTTTTGTGGAAGCGCCGCAAA-AAACCTAAGCCCAATGATGCCATTT
1 TCAGGACTTTAGCGGCG-TTTTTGTGGAAGCGCCGCAAAGAAACCGAAGCCCAACGATGCCATTT
** * *
2986873 TCTGAGCATTCGGGGATTTAGCAGCGTTTTTGATGAAGCGCCG
65 TCTGAGCATTCGGGGATTTAGTGGCGTTTTCGGTGAAGCGCCG
2986916 TAAAATAATT
Statistics
Matches: 291, Mismatches: 39, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
111 2 0.01
112 30 0.10
113 28 0.10
114 134 0.46
115 78 0.27
116 19 0.07
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (114 bp):
TCAGGACTTTAGCGGCGTTTTTGTGGAAGCGCCGCAAAGAAACCGAAGCCCAACGATGCCATTTT
CTGAGCATTCGGGGATTTAGTGGCGTTTTCGGTGAAGCGCCGCTAATGC
Found at i:2988168 original size:147 final size:146
Alignment explanation
Indices: 2988014--2988339 Score: 327
Period size: 147 Copynumber: 2.2 Consensus size: 146
2988004 GAAATGTAGT
* * *
2988014 CGTTTTGTCTATGGTATTAGTGGCGTTTTTCAGGAAACGCCACAAGCTTGA-GTAAACTGCTGGG
1 CGTTTTGTATAT-GTATTAGTGGCGTTTTTCAGAAAACGCCACAAGCTTGAGGT-AACTGCTGAG
* * **
2988078 GAAATGACTTC-GTTTGAACTTATATTTAGTGGCGCTTTACTTAAAACGCCGCAAAGTTGTTCTA
64 GAAATGACTGCAGTTTG-ACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTA
**
2988142 ACATTTATAGAAACGATTC
128 ACATTTATAGAAACGAGGC
* * ** * * * *
2988161 CGTTTTGTAAATGTTATTCGTGGCGATTTTTC-GAAAACGCCACCGGTTTGAGGTAAGTGTTGAT
1 CGTTTTGTATATG-TATTAGTGGCG-TTTTTCAGAAAACGCCACAAGCTTGAGGTAACTGCTGAG
* * * * * *
2988225 GAAGTGACTGCATTTTGATTTATAGTTAGTGGCGCTTTCCTTAAAACGCCGCAAAAATGTTTTGA
64 GAAATGACTGCAGTTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAA
* *
2988290 CATTTATTGATACGAGGC
129 CATTTATAGAAACGAGGC
*
2988308 CGTTTTGCTGTAT-TATTAGTGGCGTTTATTCA
1 CGTTTTG-TATATGTATTAGTGGCGTTT-TTCA
2988340 AAAGCGCTGC
Statistics
Matches: 144, Mismatches: 28, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
145 3 0.02
146 14 0.10
147 112 0.78
148 15 0.10
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (146 bp):
CGTTTTGTATATGTATTAGTGGCGTTTTTCAGAAAACGCCACAAGCTTGAGGTAACTGCTGAGGA
AATGACTGCAGTTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAACA
TTTATAGAAACGAGGC
Found at i:2988523 original size:20 final size:20
Alignment explanation
Indices: 2988498--2988539 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2988488 TATAGTTTAG
2988498 GGTTTAGGGTTTACGATATA
1 GGTTTAGGGTTTACGATATA
* * *
2988518 GGTTTAGTGTTTTCGATTTA
1 GGTTTAGGGTTTACGATATA
2988538 GG
1 GG
2988540 GTTTGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.31, T:0.45
Consensus pattern (20 bp):
GGTTTAGGGTTTACGATATA
Found at i:2988627 original size:21 final size:21
Alignment explanation
Indices: 2988603--2988657 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2988593 TCGTATATAG
2988603 TTTGGGGTTTAGGGTTTAAGA
1 TTTGGGGTTTAGGGTTTAAGA
* ** *
2988624 TTTGGGGTTTAAGGTTTGGGG
1 TTTGGGGTTTAGGGTTTAAGA
2988645 TTTGGGGTTTAGG
1 TTTGGGGTTTAGG
2988658 CCGTTTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.13, C:0.00, G:0.44, T:0.44
Consensus pattern (21 bp):
TTTGGGGTTTAGGGTTTAAGA
Found at i:2988654 original size:14 final size:14
Alignment explanation
Indices: 2988608--2988647 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2988598 TATAGTTTGG
*
2988608 GGTTTAGGGTTTAA
1 GGTTTGGGGTTTAA
*
2988622 GATTTGGGGTTTAA
1 GGTTTGGGGTTTAA
2988636 GGTTTGGGGTTT
1 GGTTTGGGGTTT
2988648 GGGGTTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (14 bp):
GGTTTGGGGTTTAA
Found at i:2989323 original size:9 final size:9
Alignment explanation
Indices: 2989292--2990377 Score: 444
Period size: 9 Copynumber: 122.1 Consensus size: 9
2989282 CGCAATCAAT
2989292 ACTTACATA
1 ACTTACATA
*
2989301 TCTTACATA
1 ACTTACATA
2989310 A--TACATA
1 ACTTACATA
2989317 ACTTACATA
1 ACTTACATA
2989326 A--TACA-A
1 ACTTACATA
*
2989332 CACTTACACA
1 -ACTTACATA
*
2989342 ACTTAAATA
1 ACTTACATA
*
2989351 ACTTATATA
1 ACTTACATA
*
2989360 ACTTGCATA
1 ACTTACATA
*
2989369 ACTTATATA
1 ACTTACATA
*
2989378 A-TAACATA
1 ACTTACATA
2989386 A--TACATA
1 ACTTACATA
* *
2989393 GCCTACATA
1 ACTTACATA
2989402 ACTTACATA
1 ACTTACATA
2989411 ACTTACATA
1 ACTTACATA
* *
2989420 AATTAAATA
1 ACTTACATA
2989429 ACTTACATA
1 ACTTACATA
2989438 ACTTACATA
1 ACTTACATA
2989447 ACTTACATA
1 ACTTACATA
*
2989456 ACTTAAATA
1 ACTTACATA
2989465 ACTTACATA
1 ACTTACATA
2989474 A--TACATA
1 ACTTACATA
*
2989481 ACCTT-CCTA
1 A-CTTACATA
*
2989490 ACTTACATT
1 ACTTACATA
*
2989499 ATTTACATA
1 ACTTACATA
2989508 A-TAGTACATA
1 ACT--TACATA
2989518 ACTTACATA
1 ACTTACATA
** *
2989527 TTTTTTTCTAAATA
1 ----ACT-TACATA
2989541 ACTTACATA
1 ACTTACATA
* *
2989550 AATTAAATA
1 ACTTACATA
2989559 ACTTACATA
1 ACTTACATA
2989568 ACTTACATA
1 ACTTACATA
* *
2989577 A-ATA-ATT
1 ACTTACATA
*
2989584 A--TAAATA
1 ACTTACATA
**
2989591 AGATACATA
1 ACTTACATA
* *
2989600 ACAGT-GATA
1 AC-TTACATA
2989609 TACTTACAT-
1 -ACTTACATA
*
2989618 -CATACATA
1 ACTTACATA
*
2989626 TCTTACATA
1 ACTTACATA
** * *
2989635 ACCAAAATTTGT
1 ACTTACA--T-A
*
2989647 A-TGTACAAGA
1 ACT-TAC-ATA
2989657 ACTTACATA
1 ACTTACATA
*
2989666 ACTTA-TTAA
1 ACTTACAT-A
* *
2989675 TATTTATATAA
1 -ACTTACAT-A
2989686 ACTTACATA
1 ACTTACATA
*
2989695 ACTATCACACAA
1 ACT-T-ACA-TA
*
2989707 ACTTATATGTAA
1 ACTTACA--T-A
2989719 ACTTACATA
1 ACTTACATA
2989728 A--TACATAA
1 ACTTACAT-A
*
2989736 ATTTACATA
1 ACTTACATA
2989745 A--TACATA
1 ACTTACATA
2989752 ACTT--ATA
1 ACTTACATA
* *
2989759 A---AAAAA
1 ACTTACATA
* *
2989765 ATTTATATAA
1 ACTTACAT-A
*
2989775 ACTGACATA
1 ACTTACATA
* *
2989784 A--TATATT
1 ACTTACATA
2989791 ACTTACATATTA
1 ACTTAC--A-TA
2989803 ACTTACATA
1 ACTTACATA
* *
2989812 AGTTATCTACA
1 ACTTA-C-ATA
*
2989823 AGCTTATATGTAA
1 A-CTTACA--T-A
*
2989836 ACTTGCATA
1 ACTTACATA
* *
2989845 AGTTATGTAATA
1 ACTTA---CATA
* *
2989857 ACATA-ACA
1 ACTTACATA
2989865 ACTTACATA
1 ACTTACATA
2989874 A--TACATA
1 ACTTACATA
* *
2989881 GCATACATA
1 ACTTACATA
2989890 ACTTACATA
1 ACTTACATA
*
2989899 A--TACAAA
1 ACTTACATA
2989906 ACTTACATA
1 ACTTACATA
*
2989915 ACTTAAATA
1 ACTTACATA
* *
2989924 TCTTACACA
1 ACTTACATA
2989933 ACTTACATA
1 ACTTACATA
*
2989942 ACCTACATA
1 ACTTACATA
2989951 A--TACATTTA
1 ACTTACA--TA
2989960 ACTTACATA
1 ACTTACATA
2989969 ACTTACATA
1 ACTTACATA
*
2989978 ACTTACAAA
1 ACTTACATA
2989987 ACTTACATA
1 ACTTACATA
*
2989996 ACTTAAATA
1 ACTTACATA
* *
2990005 TCTTACACA
1 ACTTACATA
2990014 ACTTACATA
1 ACTTACATA
*
2990023 ACCTACATA
1 ACTTACATA
2990032 A--TACATTTA
1 ACTTACA--TA
2990041 ACTTACATA
1 ACTTACATA
*
2990050 ACTTATATA
1 ACTTACATA
2990059 ACTTACATAA
1 ACTTACAT-A
*
2990069 TACATA-ATA
1 -ACTTACATA
2990078 ACTTAC--A
1 ACTTACATA
2990085 AC-TACATA
1 ACTTACATA
* *
2990093 ACGTACATT
1 ACTTACATA
**
2990102 ACTTTGATA
1 ACTTACATA
2990111 ACTTACATA
1 ACTTACATA
2990120 ACTTACATA
1 ACTTACATA
*
2990129 A--TACAAA
1 ACTTACATA
2990136 ACTTACATA
1 ACTTACATA
*
2990145 ACTTAAATA
1 ACTTACATA
* *
2990154 TCTTACACA
1 ACTTACATA
2990163 ACTTACATA
1 ACTTACATA
*
2990172 ACCTACATA
1 ACTTACATA
2990181 A--TACATTTA
1 ACTTACA--TA
2990190 ACTTACATA
1 ACTTACATA
2990199 ACTTACATAA
1 ACTTACAT-A
*
2990209 TACATA-ATA
1 -ACTTACATA
2990218 ACTTAC--A
1 ACTTACATA
2990225 AC-TACATA
1 ACTTACATA
* *
2990233 ACGTACATT
1 ACTTACATA
**
2990242 ACTTTGATA
1 ACTTACATA
2990251 ACTTACATA
1 ACTTACATA
2990260 ACTTACATA
1 ACTTACATA
* *
2990269 A--TGCACA
1 ACTTACATA
**
2990276 ACTGGCATA
1 ACTTACATA
* *
2990285 GCTTACTTA
1 ACTTACATA
2990294 A--TACATA
1 ACTTACATA
2990301 ACTTACATA
1 ACTTACATA
*
2990310 A--TACACA
1 ACTTACATA
2990317 ACTTACATA
1 ACTTACATA
* *
2990326 GCTTACTTA
1 ACTTACATA
2990335 A--TACATA
1 ACTTACATA
2990342 ACTTACATA
1 ACTTACATA
2990351 A--TACATA
1 ACTTACATA
*
2990358 CACGTACATA
1 -ACTTACATA
2990368 ACTTACATA
1 ACTTACATA
2990377 A
1 A
2990378 TTTAATTAAT
Statistics
Matches: 807, Mismatches: 161, Indels: 218
0.68 0.14 0.18
Matches are distributed among these distances:
6 12 0.01
7 121 0.15
8 36 0.04
9 502 0.62
10 60 0.07
11 34 0.04
12 33 0.04
13 4 0.00
14 5 0.01
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.33
Consensus pattern (9 bp):
ACTTACATA
Found at i:2989390 original size:60 final size:61
Alignment explanation
Indices: 2989311--2989447 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 61
2989301 TCTTACATAA
* * * **
2989311 TACATAACTTACATAATACA-A-CACTTACACAACTTAAATAACTTATATAACTTGCATAACT
1 TACATAACTAACATAATACATAGC-C-TACACAACTTAAATAACTTACATAAATTAAATAACT
* * *
2989372 TATATAA-TAACATAATACATAGCCTACATAACTTACATAACTTACATAAATTAAATAACT
1 TACATAACTAACATAATACATAGCCTACACAACTTAAATAACTTACATAAATTAAATAACT
*
2989432 TACATAACTTACATAA
1 TACATAACTAACATAA
2989448 CTTACATAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
60 47 0.75
61 15 0.24
62 1 0.02
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.31
Consensus pattern (61 bp):
TACATAACTAACATAATACATAGCCTACACAACTTAAATAACTTACATAAATTAAATAACT
Found at i:2989741 original size:17 final size:17
Alignment explanation
Indices: 2989716--2989756 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2989706 AACTTATATG
2989716 TAAACTTACATAATACA
1 TAAACTTACATAATACA
*
2989733 TAAATTTACATAATACA
1 TAAACTTACATAATACA
2989750 T-AACTTA
1 TAAACTTA
2989757 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAACTTACATAATACA
Found at i:2990100 original size:52 final size:54
Alignment explanation
Indices: 2989977--2990233 Score: 193
Period size: 52 Copynumber: 4.9 Consensus size: 54
2989967 TAACTTACAT
* * * *
2989977 AACTTACAAAACTTACATAACTTA-AATATCTTACACAACTTACATAACCTACATAA
1 AACTTACATAACTTACATAACTTATAATAACTTACATAAC-TACATAA--TACTTAA
* *
2990033 TACATT---TAACTTACATAACTTAT-ATAACTTACATAA-TACATAATAACTTAC
1 AAC-TTACATAACTTACATAACTTATAATAACTTACATAACTACATAAT-ACTTAA
* * *
2990084 AAC-TACATAACGTACATTACTT-TGATAACTTACATAACTTACATAATAC--AA
1 AACTTACATAACTTACATAACTTATAATAACTTACATAAC-TACATAATACTTAA
* * * * *
2990135 AACTTACATAACTTAAATATCTTA-CACAACTTACATAACCTACATAATACATT-T
1 AACTTACATAACTTACATAACTTATAATAACTTACATAA-CTACATAATAC-TTAA
*
2990189 AACTTACATAACTTACATAA-TACATAATAACTTAC--AACTACATAA
1 AACTTACATAACTTACATAACT-TATAATAACTTACATAACTACATAA
2990234 CGTACATTAC
Statistics
Matches: 162, Mismatches: 22, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
51 11 0.07
52 78 0.48
53 6 0.04
54 53 0.33
55 8 0.05
56 2 0.01
57 2 0.01
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.32
Consensus pattern (54 bp):
AACTTACATAACTTACATAACTTATAATAACTTACATAACTACATAATACTTAA
Found at i:2990208 original size:140 final size:144
Alignment explanation
Indices: 2989958--2990270 Score: 535
Period size: 140 Copynumber: 2.2 Consensus size: 144
2989948 ATAATACATT
2989958 TAACTTACATAACTTACATAACTTACAAAACTTACATAACTTAAATATCTTACACAACTTACATA
1 TAACTTACATAACTTACATAA--TACAAAACTTACATAACTTAAATATCTTACACAACTTACATA
2990023 ACCTACATAATACATTTAACTTACATAACTTATATAACTTACATAATACATAATAACTTACAACT
64 ACCTACATAATACATTTAACTT--ATAAC---TATAACTTACATAATACATAATAACTTACAACT
2990088 ACATAACGTACATTACTTTGA
124 ACATAACGTACATTACTTTGA
2990109 TAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAAC
1 TAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAAC
2990174 CTACATAATACATTTAAC-T-T-AC-ATAACTTACATAATACATAATAACTTACAACTACATAAC
66 CTACATAATACATTTAACTTATAACTATAACTTACATAATACATAATAACTTACAACTACATAAC
2990235 GTACATTACTTTGA
131 GTACATTACTTTGA
2990249 TAACTTACATAACTTACATAAT
1 TAACTTACATAACTTACATAAT
2990271 GCACAACTGG
Statistics
Matches: 162, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
140 75 0.46
144 2 0.01
145 1 0.01
148 1 0.01
149 62 0.38
151 21 0.13
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.33
Consensus pattern (144 bp):
TAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAAC
CTACATAATACATTTAACTTATAACTATAACTTACATAATACATAATAACTTACAACTACATAAC
GTACATTACTTTGA
Found at i:2990220 original size:19 final size:18
Alignment explanation
Indices: 2990196--2990233 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2990186 TTTAACTTAC
2990196 ATAACTTACATAATACATA
1 ATAACTTACA-AATACATA
*
2990215 ATAACTTACAACTACATA
1 ATAACTTACAAATACATA
2990233 A
1 A
2990234 CGTACATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAACTTACAAATACATA
Found at i:2990367 original size:17 final size:16
Alignment explanation
Indices: 2990333--2990368 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2990323 ATAGCTTACT
*
2990333 TAATACATAACTTACA
1 TAATACATAACGTACA
2990349 TAATACATACACGTACA
1 TAATACATA-ACGTACA
2990366 TAA
1 TAA
2990369 CTTACATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (16 bp):
TAATACATAACGTACA
Found at i:2993035 original size:21 final size:21
Alignment explanation
Indices: 2992983--2993050 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
2992973 CTACAACTTA
* * *
2992983 AAGCAGAGGCGGCAACGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
*
2993004 AAGCAGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* *
2993025 AAGCAGAGGCTACAGCGCGAG
1 AAGCAGAGGCTGCAGCGAGAG
2993046 AAGCA
1 AAGCA
2993051 ACAAGAGAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.21, G:0.40, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:2993129 original size:21 final size:21
Alignment explanation
Indices: 2993103--2993173 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
2993093 CTACAACTTA
* *
2993103 AAGCAGAGGCGGCAGTAAGGG
1 AAGCAGAGGCTGCAGCAAGGG
*
2993124 AAGCAGCGGCTGCAGCGAA-GG
1 AAGCAGAGGCTGCAGC-AAGGG
* *
2993145 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCAAGGG
2993166 AAGCAGAG
1 AAGCAGAG
2993174 TAGAACAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.93
22 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCAAGGG
Found at i:2993161 original size:120 final size:120
Alignment explanation
Indices: 2992943--2993170 Score: 377
Period size: 120 Copynumber: 1.9 Consensus size: 120
2992933 GACCACATTT
* *
2992943 GAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAACGAGGGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAACAAGGGAAGC
*
2993008 AGAGGCTGCAGCAAGAGAAGCAGAGGCTACAGCGCGAGAAGCAACAAGAGAAGCA
66 AGAGGCTGCAGCAAGAGAAGCAGAGGCTACAGCGAGAGAAGCAACAAGAGAAGCA
**
2993063 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGTAAGGGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAACAAGGGAAGC
* *
2993128 AGCGGCTGCAGCGAAG-GAAGCAGAGGCTGCAGCGAGAGAAGCA
66 AGAGGCTGCAGC-AAGAGAAGCAGAGGCTACAGCGAGAGAAGCA
2993171 GAGTAGAACA
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
120 97 0.97
121 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.32, T:0.09
Consensus pattern (120 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAACAAGGGAAGC
AGAGGCTGCAGCAAGAGAAGCAGAGGCTACAGCGAGAGAAGCAACAAGAGAAGCA
Found at i:2993658 original size:85 final size:84
Alignment explanation
Indices: 2993503--2993709 Score: 285
Period size: 85 Copynumber: 2.5 Consensus size: 84
2993493 TTGTGATGAA
* * ** * *
2993503 AGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTAGTTAAGCGTCGCTACAGAACATGATCT
1 AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTGTTAAGCACCACTAAAGAACATGATCT
2993568 TTAGCGGCGTTTTTT-TCT-
66 TTAGCGGCGTTTTTTAT-TG
*
2993586 AGACGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGCACCACTAAAGAACATGAT
1 AG-CGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTGTTAAGCACCACTAAAGAACATGAT
2993651 CTTTAGCGGCGTTTTTTATTG
64 CTTTAGCGGCGTTTTTTATTG
*
2993672 AGCGCCGCTAAAGAACATGA-CTTTTAGCGGTGTTTTTT
1 AGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTT
2993710 CTGTAAACGC
Statistics
Matches: 111, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
83 2 0.02
84 36 0.32
85 70 0.63
86 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (84 bp):
AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTGTTAAGCACCACTAAAGAACATGATCT
TTAGCGGCGTTTTTTATTG
Found at i:2993709 original size:42 final size:42
Alignment explanation
Indices: 2993440--2993709 Score: 289
Period size: 42 Copynumber: 6.4 Consensus size: 42
2993430 AATCCCAAAA
* * *
2993440 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATTA-CTT
1 TTAGCGGCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGATC-T
* * * * *
2993483 TTCGCGGCGCTTGTGATGAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGATCT
* * *
2993526 TTAACGGCG-TTTTTAGTTAAGCGTCGCTACAGAACATGATCT
1 TTAGCGGCGTTTTTTA-TTAAGCGCCGCTAAAGAACATGATCT
2993568 TTAGCGGCGTTTTTT-TCT-AGACGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTAT-TAAG-CGCCGCTAAAGAACATGATCT
* * *
2993610 TTAGCGGCGTCTTTTTTTTAAGCACCACTAAAGAACATGATCT
1 TTAGCGGCGT-TTTTTATTAAGCGCCGCTAAAGAACATGATCT
*
2993653 TTAGCGGCGTTTTTTATTGAGCGCCGCTAAAGAACATGA-CTT
1 TTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGATC-T
*
2993695 TTAGCGGTGTTTTTT
1 TTAGCGGCGTTTTTT
2993710 CTGTAAACGC
Statistics
Matches: 194, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.02
42 104 0.54
43 82 0.42
44 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGATCT
Found at i:3003115 original size:17 final size:17
Alignment explanation
Indices: 3003089--3003124 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3003079 GTGTGTTTTG
*
3003089 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
3003106 TTTTGACTGCATGACAT
1 TTTTGACTGCATGACAT
3003123 TT
1 TT
3003125 CATCATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:3005521 original size:20 final size:20
Alignment explanation
Indices: 3005496--3005536 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
3005486 AATGTTCTTT
3005496 CATTCTTTAT-GATTTTTTTC
1 CATTCTTT-TGGATTTTTTTC
3005516 CATTCTTTTGGATTTTTTTC
1 CATTCTTTTGGATTTTTTTC
3005536 C
1 C
3005537 TGCCAGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.63
Consensus pattern (20 bp):
CATTCTTTTGGATTTTTTTC
Found at i:3007945 original size:89 final size:88
Alignment explanation
Indices: 3007773--3008406 Score: 711
Period size: 89 Copynumber: 7.1 Consensus size: 88
3007763 GAGTAGCAGT
*
3007773 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA-AAAACAGATCTTGTCTTCATATACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
* *
3007837 GGTGTGAAGTAGATCAAAGATAAC
66 GG-GTGAAGTAGATCGAAGAAAAC
*
3007861 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
* * *
3007926 GGCGTGAAGTAGATCAAAGATAGC
66 GG-GTGAAGTAGATCGAAGAAAAC
* * *
3007950 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
3008015 AGGGTGAAGTAGATCGAAGAAAAC
66 -GGGTGAAGTAGATCGAAGAAAAC
*** * * * * ***
3008039 AGATCTTGTCTTCATGTACCGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
* *
3008103 GGTGGCGAAGTAGATCGAAGAAAGC
66 -G-GGTGAAGTAGATCGAAGAAAAC
* *** *
3008128 AGATCTTATCTTCATGTATTAGG-GG-GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTAC
1 AGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTAC
* * *
3008191 TGGCGTGAAGTAGATCAAAGATAGC
65 TGG-GTGAAGTAGATCGAAGAAAAC
* * *
3008216 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
*
3008281 AGGGGGAAGTAGATCGAAGAAAAC
66 -GGGTGAAGTAGATCGAAGAAAAC
*** * * * * * ***
3008305 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
* *
3008369 GGTGGCGAAGCAGATCGAAGAAAAC
66 -G-GGTGAAGTAGATCGAAGAAAAC
*
3008394 AGATATTGTCTTC
1 AGATCTTGTCTTC
3008407 GTGTATTGGC
Statistics
Matches: 471, Mismatches: 66, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
87 3 0.01
88 141 0.30
89 320 0.68
90 7 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (88 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
GGGTGAAGTAGATCGAAGAAAAC
Found at i:3008466 original size:44 final size:44
Alignment explanation
Indices: 3008418--3008628 Score: 144
Period size: 44 Copynumber: 4.8 Consensus size: 44
3008408 TGTATTGGCA
3008418 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
* ** **** * * *
3008462 TGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAG--GTTACAG
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG-T--AG
* * * ** *
3008507 TGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAATAG
1 TGGAGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGTAG
*
3008550 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
* * * * *
3008594 TGGAGCAGATCGAAGATGACAGATTTTACCTCCCT
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCT
3008629 GAGGTTACAG
Statistics
Matches: 121, Mismatches: 36, Indels: 20
0.68 0.20 0.11
Matches are distributed among these distances:
41 3 0.02
42 2 0.02
43 18 0.15
44 82 0.68
45 15 0.12
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
Found at i:3008478 original size:133 final size:133
Alignment explanation
Indices: 3007799--3008413 Score: 970
Period size: 133 Copynumber: 4.6 Consensus size: 133
3007789 TACTGGTGGC
** * *
3007799 GAAGTAGATCGAAA-A-AACAGATCTTGTCTTCATATACTGGT-GTGAAGTAGATCAAAGATAA-
1 GAAGTAGATC-AAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AAG
* *** * *
3007860 CAGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
64 CAGATCTTATCTTCATGTATTAGG-GG-GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTA
3007924 CTGGCGT
127 CTGGCGT
*
3007931 GAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
* *
3007996 GATCTTATCTTCATGTATTAGGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACCGG
66 GATCTTATCTTCATGTATTAGGGGGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
3008061 CGT
131 CGT
*
3008064 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
3008129 GATCTTATCTTCATGTATTAGGGGGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
66 GATCTTATCTTCATGTATTAGGGGGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
3008194 CGT
131 CGT
*
3008197 GAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
3008262 GATCTTATCTTCATGTATTAGGGGGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
66 GATCTTATCTTCATGTATTAGGGGGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
3008327 CGT
131 CGT
* * *
3008330 GAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
1 GAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
* * *
3008395 GATATTGTCTTCGTGTATT
66 GATCTTATCTTCATGTATT
3008414 GGCATGGAGT
Statistics
Matches: 452, Mismatches: 26, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
131 3 0.01
132 11 0.02
133 404 0.89
134 32 0.07
135 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (133 bp):
GAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
GATCTTATCTTCATGTATTAGGGGGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
CGT
Found at i:3008667 original size:132 final size:132
Alignment explanation
Indices: 3008418--3008670 Score: 445
Period size: 132 Copynumber: 1.9 Consensus size: 132
3008408 TGTATTGGCA
* ***
3008418 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTG
1 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACA
3008483 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAT
66 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAT
3008548 AG
131 AG
*
3008550 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACA
1 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACA
3008615 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTCC
66 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTCC
3008671 TTGAAGTTAC
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
131 3 0.03
132 112 0.97
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACA
GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAT
AG
Found at i:3008704 original size:132 final size:132
Alignment explanation
Indices: 3008417--3008713 Score: 382
Period size: 132 Copynumber: 2.2 Consensus size: 132
3008407 GTGTATTGGC
* * ** **
3008417 ATGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
1 ATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGAC
* *
3008482 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
66 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAA
*
3008547 TA
131 CA
* * ** *
3008549 GTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGAC
1 ATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGAC
* *
3008614 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTCCTTGAAGT
66 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTCCCTG-AGC
*
3008678 TACA
129 AACA
* * *
3008682 ATGGAGTGGATT-AAAACCACAGATCTCATCTC
1 ATGGAATAGATTGAAAACCACAGATCTTATCTC
3008714 TCTGAAGTTG
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
131 3 0.02
132 130 0.90
133 12 0.08
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
ATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGAC
AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAA
CA
Found at i:3010522 original size:22 final size:22
Alignment explanation
Indices: 3010482--3010523 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3010472 TTTTTTATTT
* * *
3010482 TCTATTTTTTATTTTTATATAC
1 TCTATATTTTATATATATATAC
3010504 TCTATATTTTATATATATAT
1 TCTATATTTTATATATATAT
3010524 GCTAATACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (22 bp):
TCTATATTTTATATATATATAC
Found at i:3011705 original size:7 final size:7
Alignment explanation
Indices: 3011693--3011717 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3011683 AATAAAATGA
3011693 AAATAGG
1 AAATAGG
3011700 AAATAGG
1 AAATAGG
3011707 AAATAGG
1 AAATAGG
3011714 AAAT
1 AAAT
3011718 GCATAATAAT
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
AAATAGG
Found at i:3014714 original size:18 final size:18
Alignment explanation
Indices: 3014691--3014742 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
3014681 GAAACTCTAT
3014691 ATCCTTCTGGGATTTTAA
1 ATCCTTCTGGGATTTTAA
3014709 ATCCTTCTGGGATTTTAA
1 ATCCTTCTGGGATTTTAA
*
3014727 ATCCTTCAGGGATTTT
1 ATCCTTCTGGGATTTT
3014743 CATATAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (18 bp):
ATCCTTCTGGGATTTTAA
Found at i:3016217 original size:16 final size:16
Alignment explanation
Indices: 3016196--3016239 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
3016186 TAGATGCATC
3016196 TACCAAAATCATATAA
1 TACCAAAATCATATAA
3016212 TACCAAAATCATATAA
1 TACCAAAATCATATAA
*
3016228 TATCAAAATCAT
1 TACCAAAATCAT
3016240 CCACATGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (16 bp):
TACCAAAATCATATAA
Found at i:3019717 original size:23 final size:23
Alignment explanation
Indices: 3019691--3019766 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
3019681 ATAAGTGCCA
3019691 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3019714 CACTGATATGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3019737 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3019760 CACTGAT
1 CACTGAT
3019767 CAATAACACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3020803 original size:11 final size:9
Alignment explanation
Indices: 3020774--3020873 Score: 69
Period size: 9 Copynumber: 10.4 Consensus size: 9
3020764 AAAAATATTT
3020774 TTTTTCATAA
1 TTTTT-ATAA
3020784 TTTTTATAA
1 TTTTTATAA
3020793 TTTTGTAATAA
1 TTTT-T-ATAA
* *
3020804 TTTTAATGA
1 TTTTTATAA
3020813 -TTTT-TAA
1 TTTTTATAA
3020820 TTTTTAAATATA
1 TTTTT--ATA-A
3020832 GTTTTTATAAA
1 -TTTTTAT-AA
*
3020843 TTTTTAAAA
1 TTTTTATAA
*
3020852 TTTTTAAAA
1 TTTTTATAA
*
3020861 TTTTTAAAA
1 TTTTTATAA
3020870 TTTT
1 TTTT
3020874 GAAAAATTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
7 2 0.03
8 7 0.09
9 35 0.46
10 12 0.16
11 13 0.17
12 2 0.03
13 5 0.07
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3020881 original size:10 final size:9
Alignment explanation
Indices: 3020833--3020878 Score: 74
Period size: 9 Copynumber: 5.0 Consensus size: 9
3020823 TTAAATATAG
3020833 TTTTTATAAA
1 TTTTTA-AAA
3020843 TTTTTAAAA
1 TTTTTAAAA
3020852 TTTTTAAAA
1 TTTTTAAAA
3020861 TTTTTAAAA
1 TTTTTAAAA
*
3020870 TTTTGAAAA
1 TTTTTAAAA
3020879 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
9 29 0.83
10 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:3021891 original size:10 final size:10
Alignment explanation
Indices: 3021876--3021913 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
3021866 ATATTTTATT
3021876 ATAATTTTTA
1 ATAATTTTTA
*
3021886 ATAATTTATA
1 ATAATTTTTA
*
3021896 TTAATTTTTA
1 ATAATTTTTA
3021906 ATAATTTT
1 ATAATTTT
3021914 CAAATGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:3030164 original size:30 final size:29
Alignment explanation
Indices: 3030116--3030204 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 29
3030106 TCAGTTAATT
3030116 AATAAAGTATGGTCAAATATGTCTAGATA
1 AATAAAGTATGGTCAAATATGTCTAGATA
* *
3030145 AATAAAATATGGATCAAATATGTTTAGATA
1 AATAAAGTATGG-TCAAATATGTCTAGATA
3030175 AATAAAGTATTGGTCAAATATGTCTAGATA
1 AATAAAGTA-TGGTCAAATATGTCTAGATA
3030205 CTCTCATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
29 11 0.20
30 40 0.74
31 3 0.06
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.33
Consensus pattern (29 bp):
AATAAAGTATGGTCAAATATGTCTAGATA
Found at i:3036262 original size:13 final size:13
Alignment explanation
Indices: 3036244--3036290 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
3036234 CAAAACAGGC
3036244 TTTTAGCGGCGCT
1 TTTTAGCGGCGCT
3036257 TTTTA--GGC-C-
1 TTTTAGCGGCGCT
3036266 -TTTAGCGGCGCT
1 TTTTAGCGGCGCT
*
3036278 TTTTAGCGCCGCT
1 TTTTAGCGGCGCT
3036291 AAAAGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
8 4 0.14
10 4 0.14
11 4 0.14
13 16 0.57
ACGTcount: A:0.09, C:0.26, G:0.28, T:0.38
Consensus pattern (13 bp):
TTTTAGCGGCGCT
Found at i:3036269 original size:21 final size:21
Alignment explanation
Indices: 3036240--3036283 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3036230 ACACCAAAAC
*
3036240 AGGCTTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
3036261 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
3036282 AG
1 AG
3036284 CGCCGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.30, T:0.39
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGCTTTTT
Found at i:3036438 original size:43 final size:43
Alignment explanation
Indices: 3036375--3036473 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
3036365 TTTTAGAAAT
** * *
3036375 AAACGCCGCTAAAGGTCATGACCTTTAGCGTCG-TTTTTCCCAG
1 AAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTT-CCAC
* * *
3036418 AAACGCCGCTATAGACCATGATCTTTAGCGACGCTTTTTTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTTCCAC
3036461 AAACGCCGCTAAA
1 AAACGCCGCTAAA
3036474 AACATAATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 42 0.89
44 5 0.11
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTTCCAC
Found at i:3040055 original size:19 final size:19
Alignment explanation
Indices: 3040029--3040075 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3040019 CTGAAACCAA
3040029 AATTTATAATAGGCATTCT
1 AATTTATAATAGGCATTCT
*
3040048 AGTTTATAATAGGCATTCT
1 AATTTATAATAGGCATTCT
3040067 AATTTATAA
1 AATTTATAA
3040076 CAGATTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (19 bp):
AATTTATAATAGGCATTCT
Found at i:3041676 original size:14 final size:14
Alignment explanation
Indices: 3041632--3041693 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
3041622 CCGAATCTCT
*
3041632 AAACCCTAAATCACC
1 AAACCCTAAA-CCCC
* *
3041647 -AACTCTTAACCCC
1 AAACCCTAAACCCC
*
3041660 AAACCCTAAATCCC
1 AAACCCTAAACCCC
*
3041674 AAACCCCAAACCCC
1 AAACCCTAAACCCC
3041688 TAAACC
1 -AAACC
3041694 TTATTAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 3 0.08
14 29 0.78
15 5 0.14
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.13
Consensus pattern (14 bp):
AAACCCTAAACCCC
Found at i:3041681 original size:7 final size:7
Alignment explanation
Indices: 3041654--3041693 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
3041644 ACCAACTCTT
3041654 AACCCCA
1 AACCCCA
*
3041661 AACCCTA
1 AACCCCA
*
3041668 AATCCCA
1 AACCCCA
3041675 AACCCCA
1 AACCCCA
3041682 AACCCCTA
1 AACCCC-A
3041690 AACC
1 AACC
3041694 TTATTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.42, C:0.50, G:0.00, T:0.07
Consensus pattern (7 bp):
AACCCCA
Found at i:3041685 original size:28 final size:29
Alignment explanation
Indices: 3041630--3041693 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
3041620 TCCCGAATCT
* **
3041630 CTAAACCCTAAATCACCAACTCTTAACCC
1 CTAAACCCTAAATCACCAACCCCAAACCC
3041659 C-AAACCCTAAATC-CCAAACCCCAAACCC
1 CTAAACCCTAAATCACC-AACCCCAAACCC
3041687 CTAAACC
1 CTAAACC
3041694 TTATTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 22 0.73
29 6 0.20
ACGTcount: A:0.41, C:0.45, G:0.00, T:0.14
Consensus pattern (29 bp):
CTAAACCCTAAATCACCAACCCCAAACCC
Found at i:3041768 original size:14 final size:14
Alignment explanation
Indices: 3041749--3041787 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3041739 ACTCTAACCC
*
3041749 AACCCCAAATCCCT
1 AACCCCAAACCCCT
*
3041763 AACCCCTAACCCCT
1 AACCCCAAACCCCT
3041777 AACCCCCAAAC
1 AA-CCCCAAAC
3041788 ATTATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.36, C:0.54, G:0.00, T:0.10
Consensus pattern (14 bp):
AACCCCAAACCCCT
Found at i:3041771 original size:7 final size:7
Alignment explanation
Indices: 3041749--3041782 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3041739 ACTCTAACCC
*
3041749 AACCCCA
1 AACCCCT
*
3041756 AATCCCT
1 AACCCCT
3041763 AACCCCT
1 AACCCCT
3041770 AACCCCT
1 AACCCCT
3041777 AACCCC
1 AACCCC
3041783 CAAACATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.56, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCCT
Found at i:3041812 original size:96 final size:95
Alignment explanation
Indices: 3041654--3041867 Score: 315
Period size: 96 Copynumber: 2.2 Consensus size: 95
3041644 ACCAACTCTT
* * * *
3041654 AACCCCAAA-CCCTAAATCCCAAACCCCAAACCCCTAAACCTTATTAATATATAAATTTAAAAAC
1 AACCCCAAATCCCT-AACCCCTAACCCCAAACCCCCAAACATTATTAATATATAAATTTAAAAAC
*
3041718 ACTAATTAATCTAAAT-CTCAAACTCTAACCC
65 ACTAATTAATCTAAATCCT-AAACCCTAACCC
*
3041749 AACCCCAAATCCCTAACCCCTAACCCCTAACCCCCAAACATTATTTAATATATAAATTTAAAAAC
1 AACCCCAAATCCCTAACCCCTAACCCCAAACCCCCAAACATTA-TTAATATATAAATTTAAAAAC
*
3041814 TCTAATTAATCTAAATCCTAAACCCTAACCC
65 ACTAATTAATCTAAATCCTAAACCCTAACCC
*
3041845 GACCCCAAATCCCTAACCCCTAA
1 AACCCCAAATCCCTAACCCCTAA
3041868 ACATTATTTA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
95 33 0.31
96 73 0.68
97 2 0.02
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (95 bp):
AACCCCAAATCCCTAACCCCTAACCCCAAACCCCCAAACATTATTAATATATAAATTTAAAAACA
CTAATTAATCTAAATCCTAAACCCTAACCC
Found at i:3041859 original size:82 final size:82
Alignment explanation
Indices: 3041764--3041917 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 82
3041754 CAAATCCCTA
* * *
3041764 ACCCCTAACCCCTAACCCCCAAACATTATTTAATATATAAATTTAAAA-ACTCTAATTAATCTAA
1 ACCCCAAACCCCTAACCCCCAAACATTATTTAATAAATAAA-TTAAAACACACTAATTAATCTAA
*
3041828 ATCCTAAACCCTAACCCG
65 ACCCTAAACCCTAACCCG
* * *
3041846 ACCCCAAATCCCTAACCCCTAAACATTATTTAATAAATAAATTAAAACACACTAATTAATTTAAA
1 ACCCCAAACCCCTAACCCCCAAACATTATTTAATAAATAAATTAAAACACACTAATTAATCTAAA
3041911 CCCTAAA
66 CCCTAAA
3041918 TCCTTAACTC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 6 0.09
82 58 0.91
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (82 bp):
ACCCCAAACCCCTAACCCCCAAACATTATTTAATAAATAAATTAAAACACACTAATTAATCTAAA
CCCTAAACCCTAACCCG
Found at i:3041933 original size:21 final size:21
Alignment explanation
Indices: 3041909--3041966 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3041899 AATTAATTTA
* *
3041909 AACCCTAAATCCTTAACTCTT
1 AACCCTAAATCCTTAACCCCT
*
3041930 AACCTCTAACTCC-TAACCCCT
1 AACC-CTAAATCCTTAACCCCT
3041951 AACCCATAAA-CCTTAA
1 AACCC-TAAATCCTTAA
3041967 ATCACAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.10
21 20 0.67
22 7 0.23
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCTAAATCCTTAACCCCT
Found at i:3042486 original size:41 final size:41
Alignment explanation
Indices: 3042381--3042493 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
3042371 AAAATGTTTT
3042381 GCGGCGCTTTTCAAAAAACGCCGCTAAAGCCTCGAGCATTA
1 GCGGCGCTTTTCAAAAAACGCCGCTAAAGCCTCGAGCATTA
*** * *
3042422 GCGGCG-TTTCTTGGAAAATGCCGCTAAAG-ATCTGAGCATTA
1 GCGGCGCTTT-TCAAAAAACGCCGCTAAAGCCTC-GAGCATTA
*
3042463 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
1 GCGGCGCTTTTCAAAAAACGCCGCTAAAGCC
3042494 CCGAAAGGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
40 5 0.09
41 50 0.86
42 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTCAAAAAACGCCGCTAAAGCCTCGAGCATTA
Found at i:3042615 original size:39 final size:40
Alignment explanation
Indices: 3042548--3042672 Score: 130
Period size: 40 Copynumber: 3.1 Consensus size: 40
3042538 CGTTTTTGCA
* *
3042548 GCTAATGATT-ATTTTTAGCGGCGCTTTTA-G-GAAAGCGTC
1 GCTAATGCTTGATTTTTAGCGGCG-TTTTATGTG-AAGCGCC
* *
3042587 GCTAATGCTTGATCTTTAGCGGCGTTTTATGTGATGCGCC
1 GCTAATGCTTGATTTTTAGCGGCGTTTTATGTGAAGCGCC
* * * *
3042627 GCTAATGCTCGATTTTTAGCGGCGTTTTTTGTCCAAACGCC
1 GCTAATGCTTGATTTTTAGCGGCGTTTTATGT-GAAGCGCC
3042668 GCTAA
1 GCTAA
3042673 AAGCGCTGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.19
40 47 0.65
41 11 0.15
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (40 bp):
GCTAATGCTTGATTTTTAGCGGCGTTTTATGTGAAGCGCC
Found at i:3043022 original size:17 final size:18
Alignment explanation
Indices: 3043000--3043033 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3042990 GTACGTGTAT
3043000 AAATGTATATAT-TATAG
1 AAATGTATATATATATAG
3043017 AAATGTATATATATATA
1 AAATGTATATATATATA
3043034 ACAAAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
AAATGTATATATATATAG
Found at i:3043076 original size:3 final size:3
Alignment explanation
Indices: 3043068--3043098 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3043058 AAAATGAGTA
3043068 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3043099 TCAAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3043170 original size:17 final size:17
Alignment explanation
Indices: 3043150--3043182 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3043140 ATAAAATAGA
3043150 AATACAATAAC-AATAAT
1 AATACAA-AACTAATAAT
3043167 AATACAAAACTAATAA
1 AATACAAAACTAATAA
3043183 CAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AATACAAAACTAATAAT
Found at i:3045000 original size:1 final size:1
Alignment explanation
Indices: 3044994--3045022 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3044984 CGCTATTTGC
3044994 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3045023 GGTTCCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3047263 original size:2 final size:2
Alignment explanation
Indices: 3047256--3047280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3047246 GGCCAACAAG
3047256 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 A
3047281 AAGAGGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3050333 original size:13 final size:11
Alignment explanation
Indices: 3050297--3050327 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3050287 CCGCCCGTAT
3050297 TAATTTTTATA
1 TAATTTTTATA
*
3050308 TTATTTTTATA
1 TAATTTTTATA
3050319 TAATTTTTA
1 TAATTTTTA
3050328 AATATATATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:3050498 original size:30 final size:30
Alignment explanation
Indices: 3050449--3050511 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3050439 TCTTAACAAG
* *
3050449 CAAATGCCTCTAAATTAATAACAAAATTAA
1 CAAACGCCTCTAAAATAATAACAAAATTAA
* *
3050479 CAAACGCCTTTAAAATAATAACAAGATTAA
1 CAAACGCCTCTAAAATAATAACAAAATTAA
3050509 CAA
1 CAA
3050512 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAACGCCTCTAAAATAATAACAAAATTAA
Found at i:3051084 original size:4 final size:4
Alignment explanation
Indices: 3051077--3051104 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3051067 GATAACCTCT
3051077 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
3051105 AACTCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:3058963 original size:38 final size:38
Alignment explanation
Indices: 3058912--3058987 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3058902 GTGAGATGAG
3058912 ACTTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
1 ACTTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
3058950 ACTTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
1 ACTTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
3058988 TCCCATCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (38 bp):
ACTTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
Found at i:3062052 original size:11 final size:11
Alignment explanation
Indices: 3062036--3062080 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
3062026 CAAAAACATC
3062036 AAATAAAAATA
1 AAATAAAAATA
3062047 AAATAAAAAT-
1 AAATAAAAATA
3062057 AAATAAATAA-A
1 AAATAAA-AATA
*
3062068 AAA-AATAATA
1 AAATAAAAATA
3062078 AAA
1 AAA
3062081 AATATCTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 2 0.07
10 13 0.43
11 15 0.50
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:3062064 original size:19 final size:19
Alignment explanation
Indices: 3062040--3062084 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3062030 AACATCAAAT
*
3062040 AAAAATAAAATAAA-AATA
1 AAAAATAAAAAAAATAATA
3062058 AATAAATAAAAAAAATAATA
1 AA-AAATAAAAAAAATAATA
3062078 AAAAATA
1 AAAAATA
3062085 TCTCTTTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 2 0.08
19 16 0.67
20 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAATAAAAAAAATAATA
Found at i:3062876 original size:41 final size:41
Alignment explanation
Indices: 3062819--3063062 Score: 148
Period size: 41 Copynumber: 5.7 Consensus size: 41
3062809 TTCTTTTGTA
*
3062819 TGCTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATC
* * * * ***
3062860 TGCTCTACTGCAACTTCAGAGAGATAATAATATCTGGGTTTTAATC
1 TGCTCCACTGCAACTTCAG-G-GA-GATAAGA-CT-GGATGCGATC
* * * * *
3062906 TGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTG-TC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGG---ATGC-GATC
* * *
3062950 TGCTCCACTGCAACTTCAGGCAGATAAGACTAGATGCGATT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATC
* * * * * *
3062991 TGCTCTACTGTAACTTCAGAGAGATAAGACTTGCTATCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAC-TG-GA--TGCGATC
* *
3063036 CGCTCCACTGCAACTTCGGGGAGATAA
1 TGCTCCACTGCAACTTCAGGGAGATAA
3063063 AATTTGCTAT
Statistics
Matches: 150, Mismatches: 39, Indels: 24
0.70 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 48 0.32
42 3 0.02
43 7 0.05
44 39 0.26
45 29 0.19
46 23 0.15
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATC
Found at i:3063060 original size:45 final size:45
Alignment explanation
Indices: 3062771--3063167 Score: 248
Period size: 45 Copynumber: 9.1 Consensus size: 45
3062761 CTATGATTTT
* * * * *
3062771 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
** * * * *
3062815 TGTATGCTCCACTACAACTTCAGGGAGATAAGAC-TG-GA--TGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
* * * * * * *
3062856 GATCTGCTCTACTGCAACTTCAGAGAGATAATAATAT-CTGGGT-TTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCT--ATCTTC
* * * *
3062902 AATCTGCTCCACTGTAACTTCAGGGAGATAGGA-TTGGTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
** * * *
3062946 TGTCTGCTCCACTGCAACTTCAGGCAGATAAGACTAG--A--TGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
* * * * *
3062987 GATTTGCTCTACTGTAACTTCAGAGAGATAAGACTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
* * * *
3063032 AATCCGCTCCACTGCAACTTCGGGGAGATAAAATTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
* ** ** * *
3063077 AGTCTGCTCTGCTGCAACTTCAGGGAGATAAGGTTTGCCATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
* *
3063122 AGTCTG-TCCCACTGCAACTTCA-GG-GATAAGACTTGCTTTCTTC
1 AATCTGCT-CCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
3063165 AAT
1 AAT
3063168 TTTAACGCCA
Statistics
Matches: 264, Mismatches: 74, Indels: 31
0.72 0.20 0.08
Matches are distributed among these distances:
41 58 0.22
43 19 0.07
44 63 0.24
45 96 0.36
46 28 0.11
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTC
Found at i:3063061 original size:86 final size:85
Alignment explanation
Indices: 3062906--3063062 Score: 215
Period size: 86 Copynumber: 1.8 Consensus size: 85
3062896 GGTTTTAATC
* * * * ** *
3062906 TGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGC
1 TGCTCCACTGTAACTTCAGAGAGATAAGATTGCTATCTTCAATCCGCTCCACTGCAACTTCAGGC
3062971 AGATAAGACTAGATGCGATT
66 AGATAAGACTAGATGCGATT
* *
3062991 TGCTCTACTGTAACTTCAGAGAGATAAGACTTGCTATCTTCAATCCGCTCCACTGCAACTTCGGG
1 TGCTCCACTGTAACTTCAGAGAGATAAGA-TTGCTATCTTCAATCCGCTCCACTGCAACTTCAGG
*
3063056 GAGATAA
65 CAGATAA
3063063 AATTTGCTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 26 0.43
86 35 0.57
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (85 bp):
TGCTCCACTGTAACTTCAGAGAGATAAGATTGCTATCTTCAATCCGCTCCACTGCAACTTCAGGC
AGATAAGACTAGATGCGATT
Found at i:3063076 original size:131 final size:130
Alignment explanation
Indices: 3062723--3063108 Score: 447
Period size: 131 Copynumber: 3.0 Consensus size: 130
3062713 ACTGAGGTTT
* * * * * * *
3062723 GATGCGATCTGCTATACTGCAA-TTCATAGTGATGAG-ATCTATGATTTTAATCCGCTCCACTGC
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAATATCTGATTTCAATCCGCTCCACTGC
* * * *
3062786 AACTTCAGGGAGATAGGATTGATTTCTTTTGTATGCTCCACTACAACTTCAGGGAGATAAGACTG
66 AACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * * *
3062851 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAATAATATCTGGGTTTTAATCTGCTCCACTG
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAATATCT-GATTTCAATCCGCTCCACTG
* * *
3062916 TAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGCAGATAAGACT
65 CAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
3062981 A
130 A
* * *
3062982 GATGCGATTTGCTCTACTGTAACTTCAGAGAGATAAGACT-TGCT-ATCTTCAATCCGCTCCACT
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAATAT-CTGAT-TTCAATCCGCTCCACT
* ** * * * **
3063045 GCAACTTCGGGGAGATAAAATTTGCTATCTTCAGTCTGCTCTGCTGCAACTTCAGGGAGATAAG
64 GCAACTTCAGGGAGATAGGA-TTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAG
3063109 GTTTGCCATC
Statistics
Matches: 219, Mismatches: 33, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
128 21 0.10
129 11 0.05
130 35 0.16
131 152 0.69
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (130 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAATATCTGATTTCAATCCGCTCCACTGC
AACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
Found at i:3063615 original size:259 final size:259
Alignment explanation
Indices: 3063118--3064453 Score: 1754
Period size: 259 Copynumber: 5.2 Consensus size: 259
3063108 GGTTTGCCAT
* * ** * * * * *
3063118 CTTTAGTCTGTCCCACTGCAACTTCAGGG-A-TAAGACTTGCTTTC-TTCAATTTTAACGCCAGG
1 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGAC-TGGTTACTTTCAGTCTTAACGACAGG
* * * *** * *
3063180 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTGCTACAGTGCTAGGGAAATCAGATTTGC
65 GAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCGC
* * * * *
3063245 TACCTTTAGCCTTAATCCGTTCCACTATAATGCCAAAGAGATTGGATTCGCTGCCCT-TAGCTTT
130 TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTG-CCTACAGCTTT
* * * * *
3063309 AATACACTCCACTTCAGCTATTCCATTCCACTGCAATGTCAGGGAAACAACATTTGCTACCTTTA
194 AATCCGCTCCACTTCAGCTATTTCATTCCACTGCAATGTCAGGGAAACAAGATTCGCTACCTTTA
3063374 G
259 G
3063375 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGACAGGG
1 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGACAGGG
* * * *
3063440 AGGTAAGATTTGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACACCAGGGAAACCAGATTCGCT
66 AGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCGCT
* * *
3063505 ACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAACTGTAA
131 ACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGCTTTAA
* * ** *
3063570 TCCGCTCCACTTCAGCTATTTCATTCCACTACAACGTTTGGGAAACAAGATTCGCTACCTCTAG
196 TCCGCTCCACTTCAGCTATTTCATTCCACTGCAATGTCAGGGAAACAAGATTCGCTACCTTTAG
* * * * *
3063634 CTTTAATCTGTTCC-CTTGCGACATCAGAGAAGTAAGACTGGTTACTCTCAATCTTAAC-ACCAG
1 CTTTAATCTGTTCCAC-TGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGA-CAG
*
3063697 GGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGAGAAATCAGATTCG
64 GGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCG
* * *
3063762 CTACATTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTT
129 CTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGCTTT
* *
3063827 AATCCGCTCCACTTCAGCT-TTAATCTATTCCACTGCAATGCCAGGGAAATAAGATTCGCTACCT
194 AATCCGCTCCACTTCAGCTATT--TC-ATTCCACTGCAATGTCAGGGAAACAAGATTCGCTACCT
3063891 TTAG
256 TTAG
3063895 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGACAGGG
1 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGACAGGG
* * * * * * *
3063960 GGGTAAGATTCGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACACCACGAAAACCAGATTCACT
66 AGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCGCT
* *
3064025 ACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGCTGTAA
131 ACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGCTTTAA
* * * ** *
3064090 TCCGCTGCACCTCAGCTATTTCATTCCACTACAACATCTGGGAAACAAGATTCGCTACCTTTAG
196 TCCGCTCCACTTCAGCTATTTCATTCCACTGCAATGTCAGGGAAACAAGATTCGCTACCTTTAG
* * * ** * * *
3064154 CTTTAATTTGTTCCCCTGCGACGTCAGAGAAGTAAGACTGGTTACTCTCAGTCTTAAC-ACCAAG
1 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGA-CAGG
* *
3064218 GAGATAAGATTCGCTACCCTCAACTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCGC
65 GAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCGC
* * * *
3064283 TTCCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGTTGCCCACAGCTTTA
130 TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGCTTTA
*
3064348 ATCCGCTCCACTTCAGCT-TTAATCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTT
195 ATCCGCTCCACTTCAGCTATT--TC-ATTCCACTGCAATGTCAGGGAAACAAGATTCGCTACCTT
*
3064412 TAA
257 TAG
* * *
3064415 CTTTAATCTGTTCCACTACAACGCTAGGGAAGTAAGACT
1 CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACT
3064454 AGTGTCTTCA
Statistics
Matches: 937, Mismatches: 126, Indels: 28
0.86 0.12 0.03
Matches are distributed among these distances:
257 25 0.03
258 16 0.02
259 595 0.64
260 6 0.01
261 291 0.31
262 4 0.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (259 bp):
CTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGACAGGG
AGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATTCGCT
ACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGCTTTAA
TCCGCTCCACTTCAGCTATTTCATTCCACTGCAATGTCAGGGAAACAAGATTCGCTACCTTTAG
Found at i:3063838 original size:51 final size:50
Alignment explanation
Indices: 3063689--3063839 Score: 131
Period size: 51 Copynumber: 3.0 Consensus size: 50
3063679 TCTCAATCTT
** *
3063689 AACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGC
1 AACACCAAAGAGAT-AGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTGC
* * * ** * ** *
3063740 AACACCAGAGAAATCAGATTCGCTACATTTAGCTTTAATCTATTCCACTGT
1 AACACCAAAGAGAT-AGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTGC
** * *
3063791 AATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTCCACT
1 AACACCAAAGAGATA-GATTCGCTGCCCTCAGCTTTAATCTGCTCCACT
3063840 TCAGCTTTAA
Statistics
Matches: 76, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
50 1 0.01
51 75 0.99
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (50 bp):
AACACCAAAGAGATAGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTGC
Found at i:3063858 original size:21 final size:21
Alignment explanation
Indices: 3063820--3063860 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3063810 TCGCTGCCCA
*
3063820 CAGCTTTAATCCGCTCCACTT
1 CAGCTTTAATCCACTCCACTT
* *
3063841 CAGCTTTAATCTATTCCACT
1 CAGCTTTAATCCACTCCACT
3063861 GCAATGCCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (21 bp):
CAGCTTTAATCCACTCCACTT
Found at i:3063977 original size:520 final size:520
Alignment explanation
Indices: 3063163--3064453 Score: 2109
Period size: 520 Copynumber: 2.5 Consensus size: 520
3063153 CTTGCTTTCT
* * * * * *** *
3063163 TCAATTTTAACGCCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTGCTACAGTGCT
1 TCAATCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACC
* * ** * *
3063228 AGGGAAATCAGATTTGCTACCTTTAGCCTTAATCCGTTCCACTATAATGCCAAAGAGATTGGATT
66 AGGGAAATCAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
** * * * * *
3063293 CGCTGCCCTTAGCTTTAATACACTCCACTTCAGC--TATTCCATTCCACTGCAATGTCAGGGAAA
131 CGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAA
* *
3063356 CAACATTTGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACT
196 CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACT
*
3063421 TTCAGTCTTAACGACAGGGAGGTAAGATTTGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACAC
261 TTCAGTCTTAACGACAGGGAGGTAAGATTCGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACAC
* * *
3063486 CAGGGAAACCAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGAT
326 CACGAAAACCAGATTCACTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGAT
* * *
3063551 TCGCTGCCTACAACTGTAATCCGCTCCACTTCAGCTATTTCATTCCACTACAACGTTTGGGAAAC
391 TCGCTGCCTACAACTGTAATCCGCTCCACCTCAGCTATTTCATTCCACTACAACATCTGGGAAAC
*
3063616 AAGATTCGCTACCTCTAGCTTTAATCTGTTCCCTTGCGACATCAGAGAAGTAAGACTGGTTACTC
456 AAGATTCGCTACCTCTAGCTTTAATCTGTTCCCCTGCGACATCAGAGAAGTAAGACTGGTTACTC
3063681 TCAATCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACC
1 TCAATCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACC
* *
3063746 AGAGAAATCAGATTCGCTACATTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
66 AGGGAAATCAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
3063811 CGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAA
131 CGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAA
*
3063876 TAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACT
196 CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACT
*
3063941 TTCAGTCTTAACGACAGGGGGGTAAGATTCGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACAC
261 TTCAGTCTTAACGACAGGGAGGTAAGATTCGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACAC
3064006 CACGAAAACCAGATTCACTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGAT
326 CACGAAAACCAGATTCACTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGAT
* *
3064071 TCGCTGCCTACAGCTGTAATCCGCTGCACCTCAGCTATTTCATTCCACTACAACATCTGGGAAAC
391 TCGCTGCCTACAACTGTAATCCGCTCCACCTCAGCTATTTCATTCCACTACAACATCTGGGAAAC
* * *
3064136 AAGATTCGCTACCTTTAGCTTTAATTTGTTCCCCTGCGACGTCAGAGAAGTAAGACTGGTTACTC
456 AAGATTCGCTACCTCTAGCTTTAATCTGTTCCCCTGCGACATCAGAGAAGTAAGACTGGTTACTC
* * * *
3064201 TCAGTCTTAACACCAAGGAGATAAGATTCGCTACCCTCAACTTTAATCTGCTCCGCTGCAACACC
1 TCAATCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACC
*
3064266 AGGGAAATCAGATTCGCTTCCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
66 AGGGAAATCAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
*
3064331 CGTTGCCCACAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAA
131 CGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAA
* * * *
3064396 CAAGATTCGCTACCTTTAACTTTAATCTGTTCCACTACAACGCTAGGGAAGTAAGACT
196 CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACT
3064454 AGTGTCTTCA
Statistics
Matches: 717, Mismatches: 54, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
518 143 0.20
520 574 0.80
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (520 bp):
TCAATCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACC
AGGGAAATCAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
CGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAATGCCAGGGAAA
CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACT
TTCAGTCTTAACGACAGGGAGGTAAGATTCGCTGCCCTCAGCTTTAATTTGCTCCGCTGCAACAC
CACGAAAACCAGATTCACTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGAT
TCGCTGCCTACAACTGTAATCCGCTCCACCTCAGCTATTTCATTCCACTACAACATCTGGGAAAC
AAGATTCGCTACCTCTAGCTTTAATCTGTTCCCCTGCGACATCAGAGAAGTAAGACTGGTTACTC
Found at i:3064378 original size:21 final size:21
Alignment explanation
Indices: 3064340--3064380 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3064330 TCGTTGCCCA
*
3064340 CAGCTTTAATCCGCTCCACTT
1 CAGCTTTAATCCACTCCACTT
* *
3064361 CAGCTTTAATCTATTCCACT
1 CAGCTTTAATCCACTCCACT
3064381 GCAATGCCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (21 bp):
CAGCTTTAATCCACTCCACTT
Found at i:3074293 original size:19 final size:19
Alignment explanation
Indices: 3074255--3074294 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3074245 ATTATGAAAT
* *
3074255 AAAATAAAATAACTAGGAA
1 AAAATAAAATAACGAAGAA
*
3074274 AAAATAAATTAACGAAGAA
1 AAAATAAAATAACGAAGAA
3074293 AA
1 AA
3074295 TCTCAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAATAAAATAACGAAGAA
Found at i:3079243 original size:17 final size:20
Alignment explanation
Indices: 3079221--3079258 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
3079211 ACCCTACATC
3079221 AATAATT-AAT-TAGG-TAA
1 AATAATTGAATCTAGGCTAA
3079238 AATAATTGAATCTAGGCTAA
1 AATAATTGAATCTAGGCTAA
3079258 A
1 A
3079259 GGAACTCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 4 0.22
20 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (20 bp):
AATAATTGAATCTAGGCTAA
Found at i:3093320 original size:43 final size:43
Alignment explanation
Indices: 3093136--3093320 Score: 126
Period size: 43 Copynumber: 4.3 Consensus size: 43
3093126 TTTTCCGCAT
** * * * *
3093136 AAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTA-ACCC
1 AAACGCCGCTAAAGGTCATGTTATTTAGCAGTGCTTTTATA-GC
* * *** * *
3093179 AAACGCCGTTAAAGATCATGACCTTTAGCGGTGCCTTTATAAG-
1 AAACGCCGCTAAAGGTCATGTTATTTAGCAGTGCTTTTAT-AGC
* * *
3093222 ATACACCGCTAAAGGTCATGTTATTTAGCAGTGCTTTTATAGG
1 AAACGCCGCTAAAGGTCATGTTATTTAGCAGTGCTTTTATAGC
* * * *
3093265 AAACGTCACTAAATGTCATGTTTTTTAGC-G-GCGTTTCTATAGC
1 AAACGCCGCTAAAGGTCATGTTATTTAGCAGTGC-TTT-TATAGC
3093308 AAACGCCGCTAAA
1 AAACGCCGCTAAA
3093321 AAACATGACA
Statistics
Matches: 112, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
41 2 0.02
42 6 0.05
43 103 0.92
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTATTTAGCAGTGCTTTTATAGC
Found at i:3093335 original size:43 final size:43
Alignment explanation
Indices: 3093288--3093371 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
3093278 TGTCATGTTT
*
3093288 TTTAGCGGCGTTT-CTATAGCAAA-CGCCGCTAAAAAACATGACA
1 TTTAGCGACGTTTCCTATA--AAAGCGCCGCTAAAAAACATGACA
* * *
3093331 TTTAGTGACGTTTCCTATAAAAGCGCTGCTAAAGAACATGA
1 TTTAGCGACGTTTCCTATAAAAGCGCCGCTAAAAAACATGA
3093372 TGTTCATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 3 0.09
43 27 0.77
44 5 0.14
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (43 bp):
TTTAGCGACGTTTCCTATAAAAGCGCCGCTAAAAAACATGACA
Done.