Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 181 of 290
Found at i:58339381 original size:4 final size:4
Alignment explanation
Indices: 58339372--58339405 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
58339362 AAGTTTTATT
58339372 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
58339406 AATTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:58344611 original size:12 final size:12
Alignment explanation
Indices: 58344592--58344625 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58344582 AAAAAGAAAA
58344592 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
58344604 GTGTGAAAAAGT
1 GAGTGAAAAGGT
58344616 GAGTGAAAAG
1 GAGTGAAAAG
58344626 AAACGAGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:58350976 original size:28 final size:28
Alignment explanation
Indices: 58350913--58351010 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
58350903 ATATTAAGTC
*
58350913 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
58350940 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
58350968 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
58350997 CGCACACTTAGTGC
1 CGCACACTTAGTGC
58351011 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:58355871 original size:12 final size:12
Alignment explanation
Indices: 58355852--58355885 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58355842 AAAAAGAAAA
58355852 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
58355864 GTGTGAAAAAGT
1 GAGTGAAAAGGT
58355876 GAGTGAAAAG
1 GAGTGAAAAG
58355886 AAACGAGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:58360592 original size:15 final size:15
Alignment explanation
Indices: 58360572--58360600 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58360562 GTTATAAAGT
58360572 CTAAACTTACCCTTA
1 CTAAACTTACCCTTA
58360587 CTAAACTTACCCTT
1 CTAAACTTACCCTT
58360601 CTTGAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (15 bp):
CTAAACTTACCCTTA
Found at i:58361005 original size:12 final size:12
Alignment explanation
Indices: 58360990--58361045 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
58360980 TTATACAAGT
58360990 AAAAAAAATTCG
1 AAAAAAAATTCG
58361002 AAAAAAAAATTC-
1 -AAAAAAAATTCG
*
58361014 AAAAAAAATTTTG
1 AAAAAAAA-TTCG
58361027 AAAAAAAA-TCTG
1 AAAAAAAATTC-G
58361039 AAAAAAA
1 AAAAAAA
58361046 GTGTTTAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.24
12 10 0.26
13 19 0.50
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:58361008 original size:13 final size:13
Alignment explanation
Indices: 58360990--58361034 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
58360980 TTATACAAGT
58360990 AAAAAAAATTCGA
1 AAAAAAAATTCGA
58361003 AAAAAAAATTC-A
1 AAAAAAAATTCGA
* *
58361015 AAAAAAATTTTGA
1 AAAAAAAATTCGA
58361028 AAAAAAA
1 AAAAAAA
58361035 TCTGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:58361035 original size:13 final size:12
Alignment explanation
Indices: 58360990--58361045 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
58360980 TTATACAAGT
*
58360990 AAAAAAAATTCG
1 AAAAAAAATTTG
* *
58361002 AAAAAAAAATTC
1 AAAAAAAATTTG
58361014 AAAAAAAATTTTG
1 AAAAAAAA-TTTG
*
58361027 AAAAAAAATCTG
1 AAAAAAAATTTG
58361039 AAAAAAA
1 AAAAAAA
58361046 GTGTTTAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
12 27 0.73
13 10 0.27
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:58361988 original size:15 final size:15
Alignment explanation
Indices: 58361957--58361999 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
58361947 AAGAGAAAAT
*
58361957 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AGAAGAA
*
58361973 AAAGCAAAAGAAGAA
1 AAAGAAAAAGAAGAA
58361988 AAAGAAAAAGAA
1 AAAGAAAAAGAA
58362000 ATAAATAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAGAA
Found at i:58361990 original size:21 final size:22
Alignment explanation
Indices: 58361958--58362013 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
58361948 AGAGAAAATA
58361958 AAGAAAAGAAAAGAAAAAGCAA
1 AAGAAAAGAAAAGAAAAAGCAA
*
58361980 AAGAAGA-AAAAGAAAAAG-AA
1 AAGAAAAGAAAAGAAAAAGCAA
*
58362000 ATA-AATAGAAAAGA
1 A-AGAAAAGAAAAGA
58362014 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (22 bp):
AAGAAAAGAAAAGAAAAAGCAA
Found at i:58362090 original size:12 final size:12
Alignment explanation
Indices: 58362082--58362106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58362072 TTTGAAAAGC
58362082 AAAAAGAAAATG
1 AAAAAGAAAATG
58362094 AAAAAGAAAATG
1 AAAAAGAAAATG
58362106 A
1 A
58362107 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:58362103 original size:18 final size:18
Alignment explanation
Indices: 58362076--58362131 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
58362066 AAAGCCTTTG
58362076 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
58362095 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
58362113 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
58362130 AA
1 AA
58362132 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:58362160 original size:32 final size:31
Alignment explanation
Indices: 58362082--58362165 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
58362072 TTTGAAAAGC
* *
58362082 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATTTGAGAGTG
* *
58362112 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATTTGAGAGTG
*
58362142 AAAAAAAAAGATGAAAAAGAAATT
1 AAAAAGAAA-ATGAAAAAGAAATT
58362166 GAAACAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 8 0.18
30 24 0.55
31 2 0.05
32 10 0.23
ACGTcount: A:0.65, C:0.01, G:0.20, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATTTGAGAGTG
Found at i:58365792 original size:30 final size:30
Alignment explanation
Indices: 58365758--58365854 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
58365748 TAAACTAAAA
58365758 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
58365788 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
58365818 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
58365848 TGAGCTA
1 TGAGCTA
58365855 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:58366896 original size:13 final size:13
Alignment explanation
Indices: 58366878--58366902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58366868 TGGTCATCAT
58366878 GGTGTGAACACAA
1 GGTGTGAACACAA
58366891 GGTGTGAACACA
1 GGTGTGAACACA
58366903 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:58367419 original size:30 final size:30
Alignment explanation
Indices: 58367385--58367481 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
58367375 TAAACTAAAA
* *
58367385 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
58367415 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
58367445 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
58367475 TGAGCTA
1 TGAGCTA
58367482 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:58369589 original size:30 final size:30
Alignment explanation
Indices: 58369537--58369621 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
58369527 TTCTTTTGTT
* *
58369537 TCAATTTCTTTTTC-ATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCGTTC-TCTTTTTCAATC
58369567 TCAAATTTC-TTTTCGTTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCGTTCTCTTTTTCAATC
* *
58369597 TCATTTTCTTTTTCGTTTTCTTTTT
1 TCAATTTCTTTTTCGTTCTCTTTTT
58369622 GCTTTTCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.10
30 35 0.73
31 8 0.17
ACGTcount: A:0.12, C:0.22, G:0.02, T:0.64
Consensus pattern (30 bp):
TCAATTTCTTTTTCGTTCTCTTTTTCAATC
Found at i:58369639 original size:12 final size:12
Alignment explanation
Indices: 58369624--58369654 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
58369614 TTCTTTTTGC
58369624 TTTTCAAAGGCT
1 TTTTCAAAGGCT
58369636 TTTTCAAAGGCT
1 TTTTCAAAGGCT
58369648 TTTTCAA
1 TTTTCAA
58369655 GTTCTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:58369744 original size:15 final size:15
Alignment explanation
Indices: 58369704--58369747 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
58369694 CTTGCCTCTC
*
58369704 TTTTCTTTTTATTTCA
1 TTTTCTTTTT-CTTCA
* *
58369720 TTTTCATTTTCTTCT
1 TTTTCTTTTTCTTCA
58369735 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
58369748 TTCTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTTCTTCA
Found at i:58371693 original size:18 final size:19
Alignment explanation
Indices: 58371649--58371695 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
58371639 ATTTACAAAA
*
58371649 AAAAAGAAATATGAAATTAT
1 AAAAA-AAATACGAAATTAT
*
58371669 AAAAAAAATACGAAGTTAT
1 AAAAAAAATACGAAATTAT
58371688 AAAAAAAA
1 AAAAAAAA
58371696 CAAGTGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (19 bp):
AAAAAAAATACGAAATTAT
Found at i:58374939 original size:30 final size:31
Alignment explanation
Indices: 58374905--58374964 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
58374895 AGCTCCAATC
* *
58374905 AGCTCACTTGAGCTTGTTT-CAGCTCGTTTG
1 AGCTCAATTGAGCTTCTTTCCAGCTCGTTTG
*
58374935 AGCTCAATTTAGCTTCTTTCCAGCTCGTTT
1 AGCTCAATTGAGCTTCTTTCCAGCTCGTTT
58374965 CTTTTACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (31 bp):
AGCTCAATTGAGCTTCTTTCCAGCTCGTTTG
Found at i:58379505 original size:23 final size:22
Alignment explanation
Indices: 58379454--58379505 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
58379444 CCTCGTCTTT
*
58379454 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
58379476 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
58379499 TTCTTTT
1 TTCTTTT
58379506 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:58382704 original size:27 final size:27
Alignment explanation
Indices: 58382674--58382765 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
58382664 ATTACCAAAG
* * *
58382674 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
*
58382701 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCGTTT
**
58382728 TA-CCTTTATTTTACAAAATTACCGTTT
1 TACCCTCGA-TTTACAAAATTACCGTTT
58382755 TACCCTCGATT
1 TACCCTCGATT
58382766 GTGAAGTTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.07
27 46 0.85
28 4 0.07
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCGTTT
Found at i:58382802 original size:27 final size:27
Alignment explanation
Indices: 58382772--58382895 Score: 115
Period size: 27 Copynumber: 4.6 Consensus size: 27
58382762 GATTGTGAAG
* *
58382772 TTACTAAAATACCCCTA-TAGGATAGAA
1 TTACCAAAATACCCCTAGTAGG-TAAAA
**
58382799 TTACCAAAATACCCCTAGTTTGTAAAA
1 TTACCAAAATACCCCTAGTAGGTAAAA
**
58382826 TTACCAAAATACCCCTAGTTTGTAAAA
1 TTACCAAAATACCCCTAGTAGGTAAAA
** * * * **
58382853 TTTTCGAAATACCACTGGTTTGTAAAA
1 TTACCAAAATACCCCTAGTAGGTAAAA
58382880 TTACCAAAATACCCCT
1 TTACCAAAATACCCCT
58382896 GATTTACAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 81 0.98
28 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
TTACCAAAATACCCCTAGTAGGTAAAA
Found at i:58382842 original size:54 final size:54
Alignment explanation
Indices: 58382772--58382895 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
58382762 GATTGTGAAG
* * *
58382772 TTACTAAAATACCCCTA-TAGGATAGAATTACCAAAATACCCCTAGTTTGTAAAA
1 TTACCAAAATACCCCTAGTAGG-TAAAATTACCAAAATACCACTAGTTTGTAAAA
** ** * *
58382826 TTACCAAAATACCCCTAGTTTGTAAAATTTTCGAAATACCACTGGTTTGTAAAA
1 TTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGTTTGTAAAA
58382880 TTACCAAAATACCCCT
1 TTACCAAAATACCCCT
58382896 GATTTACAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 58 0.97
55 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.30
Consensus pattern (54 bp):
TTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGTTTGTAAAA
Found at i:58382906 original size:27 final size:27
Alignment explanation
Indices: 58382797--58382920 Score: 153
Period size: 27 Copynumber: 4.6 Consensus size: 27
58382787 TATAGGATAG
58382797 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
58382824 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
** * * *
58382851 AATTTTCGAAATACCACTGGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
**
58382878 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
58382905 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
58382921 TTGACTTTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.04
27 81 0.96
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:58382907 original size:54 final size:54
Alignment explanation
Indices: 58382797--58383003 Score: 172
Period size: 54 Copynumber: 3.8 Consensus size: 54
58382787 TATAGGATAG
* * *
58382797 AATTACCA-AAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTA-AA
1 AATTA-CAGAAATACCACTGGTTTGTAAAATTACCAAAATACCCCT-GATT-TACAA
* *
58382852 ATTTTC-GAAATACCACTGGTTTGTAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACAGAAATACCACTGGTTTGTAAAATTACCAAAATACCCCTGATTTACAA
* * * ** *
58382905 AATTACAGAAATACC-CTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAA
1 AATTACAGAAATACCAC-TG-GTTTGT-AAAATTACCA-AAATACCCCTGATTTACAA
* * * * *
58382961 AATTACTGAAATACCATTGGTTTGTAGATTTACCAAAACACCC
1 AATTACAGAAATACCACTGGTTTGTAAAATTACCAAAATACCC
58383004 TTGTAGGATG
Statistics
Matches: 121, Mismatches: 22, Indels: 19
0.75 0.14 0.12
Matches are distributed among these distances:
52 2 0.02
53 10 0.08
54 57 0.47
55 13 0.11
56 39 0.32
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
AATTACAGAAATACCACTGGTTTGTAAAATTACCAAAATACCCCTGATTTACAA
Found at i:58382993 original size:27 final size:27
Alignment explanation
Indices: 58382858--58382983 Score: 103
Period size: 27 Copynumber: 4.6 Consensus size: 27
58382848 TAAAATTTTC
* ** *
58382858 GAAATACCACTGGTTTGTAAAATTACC
1 GAAATACCATTGGTTTACAAAATTACT
* ** * *
58382885 AAAATACCCCTGATTTACAAAATTACA
1 GAAATACCATTGGTTTACAAAATTACT
* *
58382912 GAAATACCCTTGACTTT-CTAAAAATTA-T
1 GAAATACCATTG-GTTTAC--AAAATTACT
58382940 AGAAATACCATTGGTTTACAAAATTACT
1 -GAAATACCATTGGTTTACAAAATTACT
58382968 GAAATACCATTGGTTT
1 GAAATACCATTGGTTT
58382984 GTAGATTTAC
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
27 55 0.68
28 7 0.09
29 19 0.23
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (27 bp):
GAAATACCATTGGTTTACAAAATTACT
Found at i:58383060 original size:27 final size:27
Alignment explanation
Indices: 58383028--58383097 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
58383018 GACTAAAATA
58383028 CCCCTAATA-GGTAAAAAGACCGTAAAG
1 CCCCT-ATAGGGTAAAAAGACCGTAAAG
**
58383055 CCCCTATAGGGTAAAGTGACCGTAATA-
1 CCCCTATAGGGTAAAAAGACCGTAA-AG
* *
58383082 CCCCTGTATGGTAAAA
1 CCCCTATAGGGTAAAA
58383098 TGATGAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 32 0.89
28 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (27 bp):
CCCCTATAGGGTAAAAAGACCGTAAAG
Found at i:58383966 original size:24 final size:25
Alignment explanation
Indices: 58383894--58383971 Score: 113
Period size: 25 Copynumber: 3.2 Consensus size: 25
58383884 GAGGAAGTGC
* **
58383894 AAAAAGGGCTATGCCCCAGTTTACC
1 AAAAAGGGCTTTGCCCCAGTTTATT
*
58383919 GAAAAGGGCTTTGCCCCAGTTTATT
1 AAAAAGGGCTTTGCCCCAGTTTATT
58383944 AAAAAGGGCTTTGCCCCAG-TTATT
1 AAAAAGGGCTTTGCCCCAGTTTATT
58383968 AAAA
1 AAAA
58383972 GAGGCTAGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 9 0.19
25 39 0.81
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAAGGGCTTTGCCCCAGTTTATT
Found at i:58389043 original size:21 final size:22
Alignment explanation
Indices: 58388998--58389051 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
58388988 GACATCTGCA
58388998 ATTAAACACATTAAAACAAACTT
1 ATTAAACACATTAAAAC-AACTT
*
58389021 ATTAAACACATTTAAAC-ACTT
1 ATTAAACACATTAAAACAACTT
58389042 ATTAAACACA
1 ATTAAACACA
58389052 AAACATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 14 0.47
23 16 0.53
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.28
Consensus pattern (22 bp):
ATTAAACACATTAAAACAACTT
Found at i:58389048 original size:11 final size:11
Alignment explanation
Indices: 58389017--58389050 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
58389007 ATTAAAACAA
58389017 ACTTATTAAAC
1 ACTTATTAAAC
*
58389028 ACAT-TTAAAC
1 ACTTATTAAAC
58389038 ACTTATTAAAC
1 ACTTATTAAAC
58389049 AC
1 AC
58389051 AAAACATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (11 bp):
ACTTATTAAAC
Found at i:58390120 original size:13 final size:13
Alignment explanation
Indices: 58390102--58390126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58390092 AATAGTTGTG
58390102 TGTTATTTAATTA
1 TGTTATTTAATTA
58390115 TGTTATTTAATT
1 TGTTATTTAATT
58390127 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:58392311 original size:19 final size:20
Alignment explanation
Indices: 58392279--58392319 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
58392269 GAATGAAATC
58392279 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
58392299 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
58392318 GA
1 GA
58392320 AAATGAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:58393573 original size:40 final size:40
Alignment explanation
Indices: 58393518--58393695 Score: 263
Period size: 40 Copynumber: 4.5 Consensus size: 40
58393508 CGGATGGTAA
* *
58393518 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
58393558 CCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
58393598 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
58393638 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
58393678 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
58393696 TACTTGGTCT
Statistics
Matches: 129, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 17 0.13
40 111 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:58400884 original size:39 final size:40
Alignment explanation
Indices: 58400708--58400884 Score: 243
Period size: 40 Copynumber: 4.5 Consensus size: 40
58400698 GGATGGTAAT
* *
58400708 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
*
58400748 TGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
58400788 CGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
***
58400828 CGGGCTAAGTCCCGAAGGCATTTGAATGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
*
58400868 C-GGCTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
58400885 TACTTGGTCT
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 17 0.14
40 107 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:58404306 original size:13 final size:13
Alignment explanation
Indices: 58404288--58404312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58404278 AATAGTTGTG
58404288 TGTTATTTAATTA
1 TGTTATTTAATTA
58404301 TGTTATTTAATT
1 TGTTATTTAATT
58404313 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:58406680 original size:29 final size:29
Alignment explanation
Indices: 58406647--58406706 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
58406637 ATAACCAAAC
*
58406647 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
58406676 CTACATAAACTTCATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
58406705 CT
1 CT
58406707 TTCAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:58415374 original size:79 final size:80
Alignment explanation
Indices: 58415291--58415438 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 80
58415281 ATAGTAACTT
* * *
58415291 GCACAATTGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTACGGG-CTTAG
1 GCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAA-GCCTACGGGACTTAG
58415353 CCCGGAATTAGCATCTC
64 CCCGGAATTAGCATCTC
** * * *
58415370 GCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAGCCTACGGGACTTAGCC
58415435 CGGA
66 CGGA
58415439 CATCATTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.05
79 36 0.62
80 19 0.33
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
GCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAGCCTACGGGACTTAGCC
CGGAATTAGCATCTC
Found at i:58415438 original size:40 final size:41
Alignment explanation
Indices: 58415254--58415438 Score: 195
Period size: 40 Copynumber: 4.6 Consensus size: 41
58415244 GCTACTCGTT
* *
58415254 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTT-GCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTCGCA
* * *
58415294 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTCGCA
* * *
58415334 CAAATGCCTACGGG-CTTAGCCCGGA-ATTAGCATC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTTCGCA
* * * *
58415373 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTCGCA
58415414 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58415439 CATCATTCAA
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 74 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTCGCA
Found at i:58418263 original size:29 final size:29
Alignment explanation
Indices: 58418230--58418289 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
58418220 ATAACCAAAC
*
58418230 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
58418259 CTACATAAACTTCATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
58418288 CT
1 CT
58418290 TTCAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:58422387 original size:20 final size:20
Alignment explanation
Indices: 58422355--58422401 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
58422345 TTTTTATTTC
*
58422355 CTTTTCTTTTTCTTCC-ATGT
1 CTTTT-TTTTTCTCCCGATGT
*
58422375 CTTTTTTTCTTCTCCCGATTT
1 CTTTTTTT-TTCTCCCGATGT
58422396 CTTTTT
1 CTTTTT
58422402 CTCGCTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 11 0.48
21 9 0.39
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (20 bp):
CTTTTTTTTTCTCCCGATGT
Found at i:58424819 original size:20 final size:19
Alignment explanation
Indices: 58424783--58424820 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
58424773 TTAAAATATG
*
58424783 AAAACTTATTAATTTAAAT
1 AAAACTTATTAAATTAAAT
58424802 AAAACTTAATTAAATTAAA
1 AAAACTT-ATTAAATTAAA
58424821 AAGTCCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAACTTATTAAATTAAAT
Found at i:58426222 original size:20 final size:20
Alignment explanation
Indices: 58426199--58426244 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
58426189 CCAGCTACTC
58426199 GAGCTCCATCCAGCTCATTT
1 GAGCTCCATCCAGCTCATTT
** **
58426219 GAGCTCGTTTTAGCTCATTT
1 GAGCTCCATCCAGCTCATTT
58426239 GAGCTC
1 GAGCTC
58426245 AACCGAGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (20 bp):
GAGCTCCATCCAGCTCATTT
Found at i:58426223 original size:10 final size:10
Alignment explanation
Indices: 58426210--58426245 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
58426200 AGCTCCATCC
58426210 AGCTCATTTG
1 AGCTCATTTG
* *
58426220 AGCTCGTTTT
1 AGCTCATTTG
58426230 AGCTCATTTG
1 AGCTCATTTG
58426240 AGCTCA
1 AGCTCA
58426246 ACCGAGCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (10 bp):
AGCTCATTTG
Found at i:58427186 original size:41 final size:41
Alignment explanation
Indices: 58427141--58427218 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
58427131 TATATGCAGA
*
58427141 TCATCTTTAGCTCAAGTTACCTCAGAGTACTCTACACTAAC
1 TCATCTTTAGCTCAAGATACCTCAGAGTACTCTACACTAAC
* *
58427182 TCATCTTTAGCTCAAGATAGCTTAGAGTACTCTACAC
1 TCATCTTTAGCTCAAGATACCTCAGAGTACTCTACAC
58427219 CAGCTCACGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (41 bp):
TCATCTTTAGCTCAAGATACCTCAGAGTACTCTACACTAAC
Found at i:58428757 original size:21 final size:21
Alignment explanation
Indices: 58428729--58428781 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
58428719 AAAGGAAAAG
*
58428729 AAAT-GAGCTGAAACAAGCTA
1 AAATCGAGCTCAAACAAGCTA
*
58428749 AAATCGAGCTCAAACAAGCTG
1 AAATCGAGCTCAAACAAGCTA
58428770 AAA-CGAGCTCAA
1 AAATCGAGCTCAA
58428782 GTGAGCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (21 bp):
AAATCGAGCTCAAACAAGCTA
Found at i:58429855 original size:22 final size:22
Alignment explanation
Indices: 58429827--58429890 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
58429817 TCACAACTTT
*
58429827 TTTTCTTTTCTCTTTCATTTTG
1 TTTTCTTTTCTTTTTCATTTTG
58429849 TTTTC-TTTCTTTTTCATTTTG
1 TTTTCTTTTCTTTTTCATTTTG
*
58429870 TTTTTTTTTCTTTTTCATTTT
1 TTTTCTTTTCTTTTTCATTTT
58429891 CACATTCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 19 0.49
22 20 0.51
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTCTTTTTCATTTTG
Found at i:58433068 original size:12 final size:13
Alignment explanation
Indices: 58433051--58433079 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
58433041 TTAAACTAAG
58433051 TAAATAAAT-AAA
1 TAAATAAATAAAA
58433063 TAAATAAATAAAA
1 TAAATAAATAAAA
58433076 TAAA
1 TAAA
58433080 AATAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:58438696 original size:52 final size:53
Alignment explanation
Indices: 58438605--58438704 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 53
58438595 ATGTAAGTCC
* * *
58438605 ATATCATATATATGGCTTTGGAGACATGAATGAGCCATGTAAGCCCATATTAG
1 ATATCATATATATGGCATTGGAGACAGGAATAAGCCATGTAAGCCCATATTAG
** *
58438658 ATAT-ATATATATGGCATTGGAGACAGGAATAATTCATGTAAGTCCAT
1 ATATCATATATATGGCATTGGAGACAGGAATAAGCCATGTAAGCCCAT
58438705 GTCGAAGACA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
52 37 0.90
53 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (53 bp):
ATATCATATATATGGCATTGGAGACAGGAATAAGCCATGTAAGCCCATATTAG
Found at i:58439462 original size:12 final size:12
Alignment explanation
Indices: 58439447--58439471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58439437 AAAGGAGTTC
58439447 GAAAAAAAAATT
1 GAAAAAAAAATT
58439459 GAAAAAAAAATT
1 GAAAAAAAAATT
58439471 G
1 G
58439472 CATACGGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:58447347 original size:10 final size:10
Alignment explanation
Indices: 58447318--58447360 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
58447308 AAATGAACTG
*
58447318 AAACGAGCTA
1 AAACGAGCTC
58447328 AAATCGAGCTC
1 AAA-CGAGCTC
*
58447339 AAACGAGCTG
1 AAACGAGCTC
58447349 AAACGAGCTC
1 AAACGAGCTC
58447359 AA
1 AA
58447361 GTGAGCTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (10 bp):
AAACGAGCTC
Found at i:58447357 original size:20 final size:21
Alignment explanation
Indices: 58447318--58447360 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
58447308 AAATGAACTG
58447318 AAACGAGCTAAAATCGAGCTC
1 AAACGAGCTAAAATCGAGCTC
*
58447339 AAACGAGCTGAAA-CGAGCTC
1 AAACGAGCTAAAATCGAGCTC
58447359 AA
1 AA
58447361 GTGAGCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (21 bp):
AAACGAGCTAAAATCGAGCTC
Found at i:58447366 original size:20 final size:21
Alignment explanation
Indices: 58447318--58447369 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
58447308 AAATGAACTG
*
58447318 AAACGAGCTAAAATCGAGCTC
1 AAACGAGCTGAAATCGAGCTC
58447339 AAACGAGCTGAAA-CGAGCTC
1 AAACGAGCTGAAATCGAGCTC
**
58447359 AAGTGAGCTGA
1 AAACGAGCTGA
58447370 TTGGAGCTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (21 bp):
AAACGAGCTGAAATCGAGCTC
Found at i:58448450 original size:16 final size:16
Alignment explanation
Indices: 58448424--58448467 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
58448414 TACAATACCA
58448424 AAAAAACAAACAAAAGT
1 AAAAAA-AAACAAAAGT
*
58448441 AAAAAAAAAC-CAAGT
1 AAAAAAAAACAAAAGT
*
58448456 TAAAAAAAACAA
1 AAAAAAAAACAA
58448468 CAAAACACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.57
16 4 0.17
17 6 0.26
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAAAAAAACAAAAGT
Found at i:58449133 original size:14 final size:14
Alignment explanation
Indices: 58449114--58449144 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58449104 GGGATAGTTG
58449114 AAGAAAGGCTAAGA
1 AAGAAAGGCTAAGA
*
58449128 AAGAAAGGTTAAGA
1 AAGAAAGGCTAAGA
58449142 AAG
1 AAG
58449145 GTTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGAAAGGCTAAGA
Found at i:58456066 original size:8 final size:7
Alignment explanation
Indices: 58456035--58456065 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
58456025 GCCTATCATA
58456035 TCTCCCT
1 TCTCCCT
58456042 TCTCCCT
1 TCTCCCT
58456049 TCTCCCT
1 TCTCCCT
58456056 TCCTCCCT
1 T-CTCCCT
58456064 TC
1 TC
58456066 CATTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (7 bp):
TCTCCCT
Found at i:58456418 original size:25 final size:25
Alignment explanation
Indices: 58456374--58456421 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
58456364 CTTTTTCCCT
*
58456374 TTATTTATTATTCTTATTTCTATTA
1 TTATTTATTATTATTATTTCTATTA
58456399 TTATTTATTATTA-TATTTTCTAT
1 TTATTTATTATTATTA-TTTCTAT
58456422 CATTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTTATTATTATTATTTCTATTA
Found at i:58458461 original size:37 final size:37
Alignment explanation
Indices: 58458411--58458489 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
58458401 TTATTACGAA
* *
58458411 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
58458448 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
58458485 GTCTT
1 GTCTT
58458490 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:58458686 original size:47 final size:47
Alignment explanation
Indices: 58458608--58459190 Score: 1013
Period size: 47 Copynumber: 12.4 Consensus size: 47
58458598 CCCTTCGGGA
* * * * * * *
58458608 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
58458655 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58458702 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
58458749 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58458796 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58458843 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58458890 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58458937 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58458984 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58459031 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58459078 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
58459125 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
58459172 CTTATCACATATATACACT
1 CTTATCACATATATACACT
58459191 GTCTTGGCTG
Statistics
Matches: 515, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 515 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:58462708 original size:78 final size:80
Alignment explanation
Indices: 58462555--58462710 Score: 192
Period size: 78 Copynumber: 2.0 Consensus size: 80
58462545 CGAATACACG
* * * * *
58462555 TCACCAGCATGATTGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCACCGATATATAACTAGCACCAATGCTCTTCGGAA
58462620 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
* * *
58462635 TCACTAGCATGAATGCTCTT-GGGACTTAGC-CCGATTTAGTAACTCGCACCAATGC-CTTCGGA
1 TCACCAGCATGAATGCTCTTCGGGACTTAGCACCGATATA-TAACTAGCACCAATGCTCTTCGGA
* *
58462697 TCTTAGTCCGGATA
65 ACTTAGCCCGGATA
58462711 TGGTCACTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 25 0.38
79 22 0.34
80 18 0.28
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (80 bp):
TCACCAGCATGAATGCTCTTCGGGACTTAGCACCGATATATAACTAGCACCAATGCTCTTCGGAA
CTTAGCCCGGATACA
Found at i:58462748 original size:40 final size:40
Alignment explanation
Indices: 58462568--58462748 Score: 167
Period size: 40 Copynumber: 4.6 Consensus size: 40
58462558 CCAGCATGAT
* * *
58462568 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
* * **
58462608 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
* * *
58462648 TGCTCTT-GGGACTTAGCCC-GATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACCAA
* *
58462687 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACCAA
*
58462727 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
58462749 CATCATTCGA
Statistics
Matches: 115, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
38 10 0.09
39 30 0.26
40 68 0.59
41 7 0.06
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
Found at i:58463130 original size:29 final size:27
Alignment explanation
Indices: 58463058--58463130 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 27
58463048 ATAATCAACC
*
58463058 ACGCACACTTAGTGCCATGTACTTTAA
1 ACGCACACTTAGTGCCATGCACTTTAA
*
58463085 ACTCACACTTAGTGCCATGCA-TTTCAA
1 ACGCACACTTAGTGCCATGCACTTT-AA
*
58463112 GCCCGCACACTTAGTGCCA
1 --ACGCACACTTAGTGCCA
58463131 ATCTCACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 21 0.54
29 15 0.38
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (27 bp):
ACGCACACTTAGTGCCATGCACTTTAA
Found at i:58465085 original size:37 final size:37
Alignment explanation
Indices: 58465035--58465113 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
58465025 TTATTACGAA
* *
58465035 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
58465072 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
58465109 GTCTT
1 GTCTT
58465114 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:58465310 original size:47 final size:47
Alignment explanation
Indices: 58465232--58465767 Score: 928
Period size: 47 Copynumber: 11.4 Consensus size: 47
58465222 CCCTTCGGGA
* * * * * * * *
58465232 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
58465279 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
58465326 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
58465373 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
58465420 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
58465467 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
58465514 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
58465561 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
58465608 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
58465655 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
58465702 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
58465749 CTTATCACATATATACACT
1 CTTATCACATATATACACT
58465768 GTCTTGGCTG
Statistics
Matches: 470, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 470 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:58470259 original size:99 final size:94
Alignment explanation
Indices: 58470130--58470304 Score: 217
Period size: 99 Copynumber: 1.8 Consensus size: 94
58470120 TAAAATGCTG
*
58470130 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCG-AGGCCGACGCCATGTCCCAGA
1 ATGCAATGTCCCAGACATGGTCTTACACTGAC-A-C-AAATCGTA-GCCGACG-CATGTCCCAGA
58470194 CATGGTCTTACACTAGCTCTCACATATCCGTGCCA
61 CAT-GTCTTACACTAGCTCTCACATATCCGTGCCA
* * * ** * *
58470229 ATGCAATGTCCTATACATGGTCTTATACTGACACATCTCGTAGTCGATGCATGTCCCAGACATGT
1 ATGCAATGTCCCAGACATGGTCTTACACTGACACAAATCGTAGCCGACGCATGTCCCAGACATGT
58470294 CTTACACTAGC
66 CTTACACTAGC
58470305 ACACACTATC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
94 13 0.19
95 14 0.21
96 9 0.13
97 2 0.03
98 1 0.01
99 28 0.42
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (94 bp):
ATGCAATGTCCCAGACATGGTCTTACACTGACACAAATCGTAGCCGACGCATGTCCCAGACATGT
CTTACACTAGCTCTCACATATCCGTGCCA
Found at i:58473046 original size:40 final size:40
Alignment explanation
Indices: 58473002--58473086 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
58472992 TACAATTCCG
58473002 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
1 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
**
58473042 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGGGCA
1 GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
58473082 GTTTT
1 GTTTT
58473087 AGTTTTCTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (40 bp):
GTTTTCACCATTCTGGCAATTTCATCCATAATTCAGACCA
Found at i:58473081 original size:22 final size:22
Alignment explanation
Indices: 58473016--58473081 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
58473006 TCACCATTCT
58473016 GGCAATTTCATCCATAATTCAG
1 GGCAATTTCATCCATAATTCAG
** * *
58473038 ACCAGTTTTCA-CC---ATTC-T
1 GGCA-ATTTCATCCATAATTCAG
58473056 GGCAATTTCATCCATAATTCAG
1 GGCAATTTCATCCATAATTCAG
58473078 GGCA
1 GGCA
58473082 GTTTTAGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 5 0.17
18 4 0.13
19 4 0.13
21 4 0.13
22 8 0.27
23 5 0.17
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (22 bp):
GGCAATTTCATCCATAATTCAG
Found at i:58474825 original size:26 final size:27
Alignment explanation
Indices: 58474787--58474858 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
58474777 TATAGGGTAG
58474787 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTACAA
*
58474814 AATTACTG-AATACCGTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTACAA
**
58474840 AATTACCAAAATACCCTTG
1 AATTACTGAAATACCCTTG
58474859 ATTAGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 23 0.57
27 17 0.43
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGGTTTACAA
Found at i:58474868 original size:27 final size:27
Alignment explanation
Indices: 58474838--58475074 Score: 244
Period size: 27 Copynumber: 8.8 Consensus size: 27
58474828 GTTGGTTTAC
*
58474838 AAAATTACCAAAATACCCTTGATTAGT
1 AAAATTACCAAAATACCCTTGATTTGT
58474865 AAAATTACCAAAATACCCTCT-ATTTGT
1 AAAATTACCAAAATACCCT-TGATTTGT
58474892 AAAATTACCAAAATACACC-TGATTTGT
1 AAAATTACCAAAATAC-CCTTGATTTGT
* ** * **
58474919 GAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * **
58474946 AAAATTATCGAAATACCCTTGACCTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* *
58474973 AAAATTACCAAAATACCCCTGATTTGG
1 AAAATTACCAAAATACCCTTGATTTGT
** * *
58475000 AAAATTATTAAAATACCCTTGGTTTGG
1 AAAATTACCAAAATACCCTTGATTTGT
*
58475027 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * * *
58475054 AGATTTACAAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
58475075 TAGGGTGAAA
Statistics
Matches: 178, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.02
27 172 0.97
28 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGT
Found at i:58475408 original size:40 final size:40
Alignment explanation
Indices: 58475317--58475433 Score: 173
Period size: 40 Copynumber: 2.9 Consensus size: 40
58475307 AAGAAATTGG
*
58475317 GGATCACATGGTTGTTTGACGACTGTGGATCCACCGATTAA
1 GGATCACATGGTTGCTTGACGAC-GTGGATCCACCGATTAA
*
58475358 GAATCACATGGTTGCTTGACGATCGT-GATCCACCGATTAA
1 GGATCACATGGTTGCTTGACGA-CGTGGATCCACCGATTAA
*
58475398 GGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
1 GGATCACATGGTTGCTTGACGA-CGTGGATCCACCG
58475434 GTGGCTTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
40 37 0.54
41 31 0.45
42 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGATCACATGGTTGCTTGACGACGTGGATCCACCGATTAA
Found at i:58475627 original size:22 final size:22
Alignment explanation
Indices: 58475576--58475639 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
58475566 CCAATTATTT
*
58475576 TGATTATGGCTTTGTGCCAACC
1 TGATTATGGCTATGTGCCAACC
* *
58475598 T-ACATATGGCTCTGTGCCAACC
1 TGA-TTATGGCTATGTGCCAACC
*
58475620 TGATTATGGTTATGTGCCAA
1 TGATTATGGCTATGTGCCAA
58475640 ACGTATTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
TGATTATGGCTATGTGCCAACC
Found at i:58476539 original size:110 final size:111
Alignment explanation
Indices: 58476323--58476543 Score: 419
Period size: 110 Copynumber: 2.0 Consensus size: 111
58476313 TTGGGAAATT
58476323 TATTTAGTATGCTTAATATCTATTAGAAGTAGGACGCGATTTTCTAAAACAACAAATGGTTTTCA
1 TATTTAGTATGCTTAATATCTATTAGAAGTAGGACGCGATTTTCTAAAACAACAAATGGTTTTCA
58476388 AAATATCACGTTTCCGCAACTGTTTAAAATTAAGCTTCCGCAACAA
66 AAATATCACGTTTCCGCAACTGTTTAAAATTAAGCTTCCGCAACAA
58476434 TATTTAGTATGCTTAATATCTATTAGAAGTAGGACGCGATTTTCTAAAAACAAC-AAT-GTTTTC
1 TATTTAGTATGCTTAATATCTATTAGAAGTAGGACGCGATTTTCT-AAAACAACAAATGGTTTTC
58476497 AAAATATCACGTTTCCGCAACTGTTTAAAATTAAGCTTCCGCAACAA
65 AAAATATCACGTTTCCGCAACTGTTTAAAATTAAGCTTCCGCAACAA
58476544 GTAAGGNNNN
Statistics
Matches: 109, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
110 53 0.49
111 48 0.44
112 8 0.07
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (111 bp):
TATTTAGTATGCTTAATATCTATTAGAAGTAGGACGCGATTTTCTAAAACAACAAATGGTTTTCA
AAATATCACGTTTCCGCAACTGTTTAAAATTAAGCTTCCGCAACAA
Found at i:58476687 original size:30 final size:31
Alignment explanation
Indices: 58476653--58476711 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
58476643 NNNNNNNTCA
58476653 AGTAA-GCCTTAAGGGAATTAACGTTTCAAC
1 AGTAAGGCCTTAAGGGAATTAACGTTTCAAC
*
58476683 AGTAAGGCTTTAAGGGAATTAACGTTTCA
1 AGTAAGGCCTTAAGGGAATTAACGTTTCA
58476712 CAGGTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (31 bp):
AGTAAGGCCTTAAGGGAATTAACGTTTCAAC
Found at i:58481356 original size:100 final size:100
Alignment explanation
Indices: 58481175--58481456 Score: 363
Period size: 100 Copynumber: 2.8 Consensus size: 100
58481165 ATTGTGAGAA
* * ** * *
58481175 CACATATGTAGTACTATGTGCAGGCTACTATGTGT-TTAAGATGGTTTTAGGTC-AAGTGTGTAG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAA-AT--TGTTAGGTCGCA-TGTGTAG
58481238 TACTAAGTGCAGGCTACTACATGTACCAAAT-TGTTAGGT
62 TACTAAGTGCAGGCTACTACATGTACCAAATGT-TTAGGT
*
58481277 CCCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACT
* *
58481342 AAGTGCAGGCTACTACGTGTATCAAATGTTTAGGT
66 AAGTGCAGGCTACTACATGTACCAAATGTTTAGGT
** ** * *
58481377 CATGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGACTGTTAGGTCGCATGTGTAGTACT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACT
58481442 AAGTGCAGGCTACTA
66 AAGTGCAGGCTACTA
58481457 TGCGTACCAG
Statistics
Matches: 161, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
100 123 0.76
101 2 0.01
102 34 0.21
103 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (100 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTACATGTACCAAATGTTTAGGT
Found at i:58481403 original size:150 final size:152
Alignment explanation
Indices: 58481181--58481465 Score: 468
Period size: 150 Copynumber: 1.9 Consensus size: 152
58481171 AGAACACATA
* * *
58481181 TGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGTCAAGTGTGTAGTACTAAGT
1 TGTAGTACTAAGTGCAGGCTACTACGTGTTCAAGATGGTTTTAGGTCAAGTGTGTAGTACTAAGT
* *
58481246 GCAGGCTACTACATGTACCAAATTGTTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGTG
66 GCAGGCTACTACATGTACCAAACTGTTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGCG
58481311 TACCAAATTGTTAGGTCGCATG
131 TACCAAATTGTTAGGTCGCATG
*
58481333 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAA-AT-G-TTTAGGTCATGTGTGTAGTACTAAG
1 TGTAGTACTAAGTGCAGGCTACTACGTGT-TCAAGATGGTTTTAGGTCAAGTGTGTAGTACTAAG
* *
58481395 TGCAGGCTACTACATGTACCAGACTGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGC
65 TGCAGGCTACTACATGTACCAAACTGTTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGC
58481460 GTACCA
130 GTACCA
58481466 GAGAGCTTCG
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
150 91 0.73
151 1 0.01
152 29 0.23
153 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (152 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTTCAAGATGGTTTTAGGTCAAGTGTGTAGTACTAAGT
GCAGGCTACTACATGTACCAAACTGTTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTATGCG
TACCAAATTGTTAGGTCGCATG
Found at i:58481467 original size:50 final size:50
Alignment explanation
Indices: 58481231--58481465 Score: 346
Period size: 50 Copynumber: 4.7 Consensus size: 50
58481221 TTAGGTCAAG
* *
58481231 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTGTTAGGTCCCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
*
58481281 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATTGTTAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
* ***
58481331 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAA-TGTTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTG-TTAGGTCGCA
* * *
58481381 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGACTGTTAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
* *
58481431 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
58481466 GAGAGCTTCG
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
49 2 0.01
50 162 0.98
51 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCA
Found at i:58482317 original size:14 final size:14
Alignment explanation
Indices: 58482298--58482326 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58482288 AATAAATAGA
58482298 AAGAATTTGAAAAT
1 AAGAATTTGAAAAT
58482312 AAGAATTTGAAAAT
1 AAGAATTTGAAAAT
58482326 A
1 A
58482327 GCATGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (14 bp):
AAGAATTTGAAAAT
Found at i:58491497 original size:18 final size:20
Alignment explanation
Indices: 58491456--58491499 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
58491446 TGGGCTAAGG
58491456 ACACGGGCGTGTCCAGAGCC
1 ACACGGGCGTGTCCAGAGCC
*
58491476 ACACGGGCGTGT-GAGA-CC
1 ACACGGGCGTGTCCAGAGCC
58491494 ACACGG
1 ACACGG
58491500 CCTACCCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 3 0.13
20 12 0.52
ACGTcount: A:0.23, C:0.32, G:0.36, T:0.09
Consensus pattern (20 bp):
ACACGGGCGTGTCCAGAGCC
Found at i:58500144 original size:24 final size:24
Alignment explanation
Indices: 58500077--58500151 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
58500067 GCTATCTGGT
58500077 GCTCCCTGA-TAATAACTCTT-TGGA
1 GCTCCCTGATTAA-AACTCTTAT-GA
* * *
58500101 GTTACCTG-TT-AAGCTC-TATGA
1 GCTCCCTGATTAAAACTCTTATGA
58500122 GCTCCCTGATTAAAACTCTTATGA
1 GCTCCCTGATTAAAACTCTTATGA
58500146 GTCTCC
1 G-CTCC
58500152 TGTTTAGCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
21 9 0.23
22 7 0.18
23 6 0.15
24 13 0.33
25 4 0.10
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (24 bp):
GCTCCCTGATTAAAACTCTTATGA
Found at i:58502142 original size:9 final size:9
Alignment explanation
Indices: 58502123--58502156 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
58502113 ATTCTCGAAA
58502123 AAAATAAGTC
1 AAAA-AAGTC
58502133 AAAAAAGTC
1 AAAAAAGTC
*
58502142 AAAAAAATC
1 AAAAAAGTC
58502151 AAAAAA
1 AAAAAA
58502157 TACGAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAAAAGTC
Found at i:58508267 original size:30 final size:30
Alignment explanation
Indices: 58508233--58508328 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
58508223 TAAACTAAAA
58508233 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
58508263 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
58508293 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
58508323 TGAGCT
1 TGAGCT
58508329 CGGTTTAGCT
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:58509950 original size:25 final size:25
Alignment explanation
Indices: 58509922--58509969 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
58509912 CTATAACGTG
* * *
58509922 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATAACCATTATACCCCTAGGTA
58509947 AAAATAACCATTATACCCCTAGG
1 AAAATAACCATTATACCCCTAGG
58509970 GATATGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (25 bp):
AAAATAACCATTATACCCCTAGGTA
Found at i:58510022 original size:10 final size:10
Alignment explanation
Indices: 58510009--58510047 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
58509999 CTGTTTTATA
58510009 CATGATATGC
1 CATGATATGC
58510019 CATGATATGC
1 CATGATATGC
58510029 ACATGATATGC
1 -CATGATATGC
*
58510040 CATTATAT
1 CATGATAT
58510048 ATTCATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (10 bp):
CATGATATGC
Found at i:58510034 original size:21 final size:21
Alignment explanation
Indices: 58510008--58510047 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58509998 ACTGTTTTAT
58510008 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
*
58510029 ACATGATATGCCATTATAT
1 ACATGATATGCCATGATAT
58510048 ATTCATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:58510127 original size:25 final size:25
Alignment explanation
Indices: 58510093--58510162 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
58510083 GAGGAAGTGC
*
58510093 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
58510118 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
58510143 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
58510163 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:58510175 original size:24 final size:24
Alignment explanation
Indices: 58510092--58510175 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 24
58510082 GGAGGAAGTG
*
58510092 CAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAGGGCTTTGCCCCAGTTTAT
58510116 CGAAAAGGGCTTTGCCCCAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
58510141 CAAAAAGGGCTTTGCCCCAG-TTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
*
58510165 TAAAAGAGGCT
1 CAAAAG-GGCT
58510176 AGGCCTCCAG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.09
24 9 0.16
25 41 0.75
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:58510186 original size:50 final size:50
Alignment explanation
Indices: 58510093--58510187 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
58510083 GAGGAAGTGC
**
58510093 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
**
58510143 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
58510188 ATATGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 24 0.62
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:58518822 original size:16 final size:15
Alignment explanation
Indices: 58518798--58518828 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
58518788 AACTGTTTTA
58518798 TTACAAATTTCACTT
1 TTACAAATTTCACTT
58518813 TTACATAATTTCACTT
1 TTACA-AATTTCACTT
58518829 ACTCCATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (15 bp):
TTACAAATTTCACTT
Found at i:58538749 original size:14 final size:15
Alignment explanation
Indices: 58538689--58538749 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
58538679 CTTGGGTTTA
58538689 TTTATTCTGGATTTC
1 TTTATTCTGGATTTC
*
58538704 TTTATTCTGGGTTT-
1 TTTATTCTGGATTTC
58538718 TTCTA-TCTTGGATTTC
1 TT-TATTC-TGGATTTC
*
58538734 TTTATTC-GGTTTTC
1 TTTATTCTGGATTTC
58538748 TT
1 TT
58538750 GTTATCTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.31
15 23 0.59
16 4 0.10
ACGTcount: A:0.10, C:0.13, G:0.15, T:0.62
Consensus pattern (15 bp):
TTTATTCTGGATTTC
Found at i:58542729 original size:50 final size:50
Alignment explanation
Indices: 58542564--58542839 Score: 183
Period size: 51 Copynumber: 5.5 Consensus size: 50
58542554 CTGGTATGCA
* * * * * *
58542564 TAGTAACCTGCACTTAGTACTAGACATGCGAC-CAACAATC-GGTGCACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAG
* * * * *
58542612 TAGTAGCCTACACTTAGTACTACACACGTGA-TTGAAGT-TCTCGGGTATGC-A-
1 TAGTAGCCTGCACTTAGTACTACACATGCGACAT-AACTATCT--GGTA--CAAG
*
58542663 TAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAG
* * * * * * *
58542713 TAGTAGTCTGCACTTAGTACTACACACGTGA-TTGAAGT-TGTTGGGTACGCA-
1 TAGTAGCCTGCACTTAGTACTACACATGCGACAT-AACTAT-CT-GGTAC-AAG
* * * * *
58542764 TAGTAGCCTGTACTTGGTACTACATATTCGACCTAACTATCTGGTACAAG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAG
*
58542814 TAGTAGCTTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
58542840 CGTGACCTAA
Statistics
Matches: 171, Mismatches: 39, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
48 29 0.17
49 5 0.03
50 63 0.37
51 67 0.39
52 6 0.04
53 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAG
Found at i:58542759 original size:101 final size:99
Alignment explanation
Indices: 58542556--58542844 Score: 391
Period size: 101 Copynumber: 2.9 Consensus size: 99
58542546 GACGCTATCT
* * * * * *
58542556 GGTATGCATAGTAACCTGCACTTAGTACTAGACATGCGACCAACAATC-GGTGCACGTAGTAGCC
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAACTATCTGGTACAAGTAGTAG-C
*
58542620 TACACTTAGTACTACACACGTGATTGAAGTTCTCG
65 TGCACTTAGTACTACACACGTGATTGAAGTTCTCG
*
58542655 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACATGTAGTAGT
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGAC-TAACTATCTGGTACAAGTAGTAG-
* *
58542720 CTGCACTTAGTACTACACACGTGATTGAAGTTGTTG
64 CTGCACTTAGTACTACACACGTGATTGAAGTTCTCG
* * * * *
58542756 GGTACGCATAGTAGCCTGTACTTGGTACTACATATTCGACCTAACTATCTGGTACAAGTAGTAGC
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CTAACTATCTGGTACAAGTAGTAGC
58542821 TTGCACTTAGTACTACACACGTGA
65 -TGCACTTAGTACTACACACGTGA
58542845 CCTAAAACCA
Statistics
Matches: 170, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
99 38 0.22
100 7 0.04
101 124 0.73
102 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (99 bp):
GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAACTATCTGGTACAAGTAGTAGCT
GCACTTAGTACTACACACGTGATTGAAGTTCTCG
Found at i:58542847 original size:50 final size:50
Alignment explanation
Indices: 58542564--58542849 Score: 196
Period size: 50 Copynumber: 5.7 Consensus size: 50
58542554 CTGGTATGCA
* * * * * * *
58542564 TAGTAACCTGCACTTAGTACTAGACATGCGACC-AACAATC-GGTGCACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGGTACAAG
* * *
58542612 TAGTAGCCTACACTTAGTACTACACACGTGA-TTGAAGT-TCTCGGGTATGC-A-
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AACTATCT--GGTA--CAAG
* * * *
58542663 TAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGGTACAAG
* * * * *
58542713 TAGTAGTCTGCACTTAGTACTACACACGTGA-TTGAAGT-TGTTGGGTACGCA-
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AACTAT-CT-GGTAC-AAG
* * * *
58542764 TAGTAGCCTGTACTTGGTACTACATA-TTCGACCTAACTATCTGGTACAAG
1 TAGTAGCCTGCACTTAGTACTACACACGT-GACCTAACTATCTGGTACAAG
*
58542814 TAGTAGCTTGCACTTAGTACTACACACGTGACCTAA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
58542850 AACCATTTAA
Statistics
Matches: 180, Mismatches: 38, Indels: 38
0.70 0.15 0.15
Matches are distributed among these distances:
48 29 0.16
49 5 0.03
50 71 0.39
51 68 0.38
52 6 0.03
53 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGGTACAAG
Found at i:58542867 original size:101 final size:101
Alignment explanation
Indices: 58542562--58542892 Score: 294
Period size: 101 Copynumber: 3.3 Consensus size: 101
58542552 ATCTGGTATG
* * * * * * * *
58542562 CATAGTAACCTGCACTTAGTACTAGACATGCGAC-CAACAATC-GGTGCACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAGTAGTAGTCTGCAC
* *** * ** **
58542625 TTAGTACTACACACGTGATTGAAGTTC-TCGGGTATG
66 TTAGTACTACACACGTGACT-AAAACCATTGGAAACA
*
58542661 CATAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACATGTAGTAGTCTGCAC
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAGTAGTAGTCTGCAC
* * **** ** *
58542726 TTAGTACTACACACGTGATTGAAGTTGTTGGGTACG
66 TTAGTACTACACACGTGACTAAAACCATTGGAAACA
* * * * *
58542762 CATAGTAGCCTGTACTTGGTACTACATATTCGACCTAACTATCTGGTACAAGTAGTAG-CTTGCA
1 CATAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAGTAGTAGTC-TGCA
*
58542826 CTTAGTACTACACACGTGACCTAAAACCATT-TAAACA
65 CTTAGTACTACACACGTGA-CTAAAACCATTGGAAACA
*
58542863 CATAGTAGCCTGCACATAGTACTACACATG
1 CATAGTAGCCTGCACTTAGTACTACACATG
58542893 TGTTCTCACA
Statistics
Matches: 192, Mismatches: 35, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
99 32 0.17
100 9 0.05
101 146 0.76
102 5 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (101 bp):
CATAGTAGCCTGCACTTAGTACTACACATGCGACATAACTATCTGGTACAAGTAGTAGTCTGCAC
TTAGTACTACACACGTGACTAAAACCATTGGAAACA
Found at i:58548351 original size:34 final size:33
Alignment explanation
Indices: 58548308--58548374 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
58548298 CGTATCAGTA
* *
58548308 ACAGTTCAGTTTCTGT-TAAGGCCTTAGCCCATT
1 ACAGTTCAGTATCAGTGT-AGGCCTTAGCCCATT
*
58548341 ACAGTATCAGTATCAGTGTGGGCCTTAGCCCATT
1 ACAGT-TCAGTATCAGTGTAGGCCTTAGCCCATT
58548375 TCAATAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 5 0.17
34 23 0.79
35 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (33 bp):
ACAGTTCAGTATCAGTGTAGGCCTTAGCCCATT
Found at i:58550096 original size:46 final size:46
Alignment explanation
Indices: 58550043--58550218 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
58550033 TATTTGGGCA
* *
58550043 TCCGAACTCATTAAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
58550089 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* *
58550134 CATCCGAGCTCATTGACTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
58550182 -CCTGAGCTCATTGAGTTGAGTCCGAGTTCTCTTATGG
1 TCC-GAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
58550219 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 5 0.05
46 58 0.55
47 26 0.25
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:58550198 original size:93 final size:93
Alignment explanation
Indices: 58550039--58550210 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
58550029 CGGATATTTG
* * *
58550039 GGCATCCGAACTCATTAAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTAACTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
58550104 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
58550132 GGCATCCGAGCTCATTGACTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCATTGA
1 GGCATCCGAACTCATTAACTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCATTGA
58550196 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
58550211 TCTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTAACTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:58553182 original size:30 final size:30
Alignment explanation
Indices: 58553087--58553183 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
58553077 AGCTCACTCC
*
58553087 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
58553117 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
58553147 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
58553177 TAGCTCA
1 TAGCTCA
58553184 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:58556292 original size:27 final size:27
Alignment explanation
Indices: 58556262--58556436 Score: 199
Period size: 27 Copynumber: 6.4 Consensus size: 27
58556252 ATTGTACAGA
*
58556262 ACTAAGTGTGCGATTTGACTATGTTGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
** *
58556289 ACTAAGTGTGCGAAATGAATATG-ATGC
1 ACTAAGTGTGCGATTTGACTATGTA-GC
* * **
58556316 ACTAAGTGTGCGAATTGACCATGCGGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
58556343 ACTAAGTGTGCGAGTTTGACTATGTAGC
1 ACTAAGTGTGCGA-TTTGACTATGTAGC
* *
58556371 ACTAAGTGTGCGATTTGATTACGTAGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
* * *
58556398 ACTAAGTGTGCGAGTTGATTATATAGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
*
58556425 ACTGAGTGTGCG
1 ACTAAGTGTGCG
58556437 GACTCAATAT
Statistics
Matches: 127, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
ACTAAGTGTGCGATTTGACTATGTAGC
Found at i:58556373 original size:82 final size:81
Alignment explanation
Indices: 58556262--58556415 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 81
58556252 ATTGTACAGA
* *
58556262 ACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTG
1 ACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGTG
58556326 CGAATTGACCATGCGGC
65 CGAATTGACCATGCGGC
** *
58556343 ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTG
1 ACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
*
58556408 CGAGTTGA
65 CGAATTGA
58556416 TTATATAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 13 0.20
82 51 0.78
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
ACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGC
GAATTGACCATGCGGC
Found at i:58556427 original size:82 final size:81
Alignment explanation
Indices: 58556256--58556436 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
58556246 GATTAAATTG
* * *
58556256 TACAGAACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
58556321 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
58556337 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
58556401 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
58556419 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
58556437 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 17 0.20
82 66 0.80
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:58564566 original size:49 final size:49
Alignment explanation
Indices: 58564494--58564718 Score: 288
Period size: 49 Copynumber: 4.5 Consensus size: 49
58564484 TGAGGGCACG
* *
58564494 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACA
* * ** * *
58564543 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCACA
* * ** *
58564594 TGTGTAGTAATAAGTGCAGGCTACTACGTGTATCAGATGGTTTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AATTGGTCACA
* *
58564644 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACA
58564693 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
58564719 TGCGTACTAG
Statistics
Matches: 149, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
49 68 0.46
50 43 0.29
51 38 0.26
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACA
Found at i:58564683 original size:101 final size:98
Alignment explanation
Indices: 58564490--58564718 Score: 305
Period size: 101 Copynumber: 2.3 Consensus size: 98
58564480 ATTGTGAGGG
*
58564490 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGTGTAGTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCACATGTGTAGTACTA
* **
58564555 AGTGCAGGCTACTATGCGTACTTGATAACTTCGAT
66 AGTGCAGGCTACTACGCGTACCGGATAA-TT-GAT
* * * ** *
58564590 CACGTGTGTAGTAATAAGTGCAGGCTACTACGTGTATCAGATGGTTTGGTCACGTGTGTAGTACT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAT-AATTGGTCACATGTGTAGTACT
* *
58564655 AAGTGCAGGCTACTACGTGTACCGGATAATTGGT
65 AAGTGCAGGCTACTACGCGTACCGGATAATTGAT
* *
58564689 CGCATGTGTAGTACTAAGTGCAGGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
58564719 TGCGTACTAG
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
99 29 0.26
100 41 0.36
101 43 0.38
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (98 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCACATGTGTAGTACTA
AGTGCAGGCTACTACGCGTACCGGATAATTGAT
Found at i:58567490 original size:15 final size:16
Alignment explanation
Indices: 58567472--58567505 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
58567462 TCTCGTACCA
58567472 TGGATTTCTTTA-TCT
1 TGGATTTCTTTATTCT
58567487 TGGATTTCTTTATTCT
1 TGGATTTCTTTATTCT
58567503 TGG
1 TGG
58567506 CTTCTCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (16 bp):
TGGATTTCTTTATTCT
Found at i:58569587 original size:30 final size:30
Alignment explanation
Indices: 58569547--58569607 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
58569537 TTCCCGAGCC
*
58569547 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGCCAAAATG-GTAATTATGCAAAAGTT
* *
58569577 TAGGGCCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGCCAAAATGGTAATTATGCAAAAGTT
58569607 T
1 T
58569608 GTATTAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGCCAAAATGGTAATTATGCAAAAGTT
Found at i:58570333 original size:49 final size:50
Alignment explanation
Indices: 58570261--58570485 Score: 283
Period size: 49 Copynumber: 4.5 Consensus size: 50
58570251 TGAGGGCACG
**
58570261 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
* * * * * * *
58570310 TGTGTAGGACTAAGTGCAAGCTACTATGCGTACCTGATAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TTAGGTCACA
* * ** *
58570361 TGTGTAGTACTAAGTGCAGGCCACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
* *
58570411 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
58570460 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
58570486 TGCGTACTAG
Statistics
Matches: 147, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
49 66 0.45
50 46 0.31
51 35 0.24
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
Found at i:58579448 original size:24 final size:25
Alignment explanation
Indices: 58579420--58579483 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
58579410 TCAACCAAAT
* * *
58579420 TCGCACACATAGTGCTA-ATTAAGC
1 TCGCACACATAGTGCCATACTAAAC
58579444 TCGCACACATAGTGCCATACTAAAC
1 TCGCACACATAGTGCCATACTAAAC
58579469 -CGCACACATAGTGCC
1 TCGCACACATAGTGCC
58579484 TGAAATTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (25 bp):
TCGCACACATAGTGCCATACTAAAC
Found at i:58579666 original size:94 final size:94
Alignment explanation
Indices: 58579518--58579957 Score: 790
Period size: 94 Copynumber: 4.7 Consensus size: 94
58579508 ATTCAAATCT
* *
58579518 GCACAGATAGTGCCAATGTTAACTCATTATAATAAGGTAATTTACTTAATTCAAATAGCATATAA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATAA
58579583 AATCTGCACACAAAGTGACATTTAATTCC
66 AATCTGCACACAAAGTGACATTTAATTCC
*
58579612 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGTAATTTACTTAATTCAAATAGCATATAA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATAA
58579677 AATCTGCACACAAAGTGACATTTAATTCC
66 AATCTGCACACAAAGTGACATTTAATTCC
58579706 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATAA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATAA
*
58579771 AATCTGCACACAAAGTGACATTTAATTTC
66 AATCTGCACACAAAGTGACATTTAATTCC
*
58579800 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGAAATTTACTTAATTCAAATAGCATATAA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATAA
*
58579865 AATCTACACACAAAGTGACATTTAATTCC
66 AATCTGCACACAAAGTGACATTTAATTCC
* * * *
58579894 GTACACATAGTGCCAATGTTAACTCATTATAATATGGCAACTTACTTAATTTAAATAGCATATA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATA
58579958 CGGTCACCTT
Statistics
Matches: 335, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 335 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (94 bp):
GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTAATTCAAATAGCATATAA
AATCTGCACACAAAGTGACATTTAATTCC
Found at i:58584260 original size:39 final size:39
Alignment explanation
Indices: 58584217--58584330 Score: 183
Period size: 39 Copynumber: 2.9 Consensus size: 39
58584207 GGACATATTG
* *
58584217 CCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAATT
1 CCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAATT
*
58584256 CCAGCACATAGCCTGCGGACCTTAAGTTCGGATATAATT
1 CCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAATT
**
58584295 CCAGCACATAGCCTATGGACCTTAAGTCCGGATATA
1 CCAGCACATAGCCTGCGGACCTTAAGTCCGGATATA
58584331 CTTCATCACT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAATT
Found at i:58584260 original size:78 final size:77
Alignment explanation
Indices: 58584167--58584330 Score: 174
Period size: 78 Copynumber: 2.1 Consensus size: 77
58584157 GAATTTAAAC
* * *
58584167 CCGGTATAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGC-CTGGACAT-ATTGCCAGCACGTAG
1 CCGGTATAATACCAGCAC-ATAGCCTGC-GGACCTTAAGCTC-GGACATAATT-CCAGCACATAG
*
58584228 CCTGCGGACCTTAAGT
62 CCTACGGACCTTAAGT
* * *
58584244 CCGGTTATAATTCCAGCACATAGCCTGCGGACCTTAAGTTCGGATATAATTCCAGCACATAGCCT
1 CCGG-TATAATACCAGCACATAGCCTGCGGACCTTAAGCTCGGACATAATTCCAGCACATAGCCT
*
58584309 ATGGACCTTAAGT
65 ACGGACCTTAAGT
58584322 CCGGATATA
1 CCGG-TATA
58584331 CTTCATCACT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
77 8 0.11
78 61 0.84
79 4 0.05
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (77 bp):
CCGGTATAATACCAGCACATAGCCTGCGGACCTTAAGCTCGGACATAATTCCAGCACATAGCCTA
CGGACCTTAAGT
Found at i:58590525 original size:20 final size:20
Alignment explanation
Indices: 58590502--58590555 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
58590492 AGTTTTTCCC
*
58590502 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
58590522 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
58590542 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
58590556 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:58590537 original size:30 final size:30
Alignment explanation
Indices: 58590502--58590575 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
58590492 AGTTTTTCCC
58590502 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
58590532 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
58590562 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
58590576 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:58590565 original size:20 final size:20
Alignment explanation
Indices: 58590502--58590566 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
58590492 AGTTTTTCCC
* * * *
58590502 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
58590522 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
58590541 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
58590562 AGCTC
1 AGCTC
58590567 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:58591969 original size:12 final size:12
Alignment explanation
Indices: 58591952--58591977 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58591942 AAAAAAATCG
58591952 AAATTCAAAAAA
1 AAATTCAAAAAA
58591964 AAATTCAAAAAA
1 AAATTCAAAAAA
58591976 AA
1 AA
58591978 GTGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:58593085 original size:6 final size:6
Alignment explanation
Indices: 58593062--58593187 Score: 69
Period size: 6 Copynumber: 20.7 Consensus size: 6
58593052 AAAGAAATTG
* * * *
58593062 AAAG-A AAACAA AAAGAA AATGAA AAAGAA AATGCA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
58593109 ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTG-A AAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA
* *
58593158 AATGAA AAAAAA AAATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAA--GAA AAAGAA AAAG
58593188 CGAAAAAAGA
Statistics
Matches: 88, Mismatches: 26, Indels: 13
0.69 0.20 0.10
Matches are distributed among these distances:
5 8 0.09
6 68 0.77
7 3 0.03
8 9 0.10
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.08
Consensus pattern (6 bp):
AAAGAA
Found at i:58593145 original size:14 final size:12
Alignment explanation
Indices: 58593048--58593185 Score: 79
Period size: 12 Copynumber: 11.0 Consensus size: 12
58593038 AGAAAGAGAT
*
58593048 TGAAAAAGAAAT
1 TGAAAAAGAAAA
58593060 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
58593070 -CAAAAAGAAAA
1 TGAAAAAGAAAA
58593081 TGAAAAAGAAAA
1 TGAAAAAGAAAA
*
58593093 TGCAAAAGAAAA
1 TGAAAAAGAAAA
* **
58593105 AGAAATCGAAAAA
1 TGAAAAAG-AAAA
58593118 GTGAGAGAAAAAGAAAA
1 -T----GAAAAAGAAAA
58593135 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
58593149 TTG-AAAAG-AAA
1 -TGAAAAAGAAAA
*
58593160 TGAAAAAAAAAAA
1 TG-AAAAAGAAAA
58593173 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
58593186 AGCGAAAAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
10 9 0.09
11 11 0.11
12 37 0.38
13 17 0.18
14 11 0.11
15 2 0.02
16 1 0.01
17 4 0.04
18 5 0.05
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:58593153 original size:15 final size:14
Alignment explanation
Indices: 58593126--58593185 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
58593116 AAGTGAGAGA
58593126 AAAAGAAAATGAAG
1 AAAAGAAAATGAAG
*
58593140 AAAAGAAAAT--TG
1 AAAAGAAAATGAAG
58593152 AAAAG-AAATGAA-
1 AAAAGAAAATGAAG
*
58593164 AAAAAAAAATTG-A-
1 AAAAGAAAA-TGAAG
58593177 AAAAGAAAA
1 AAAAGAAAA
58593186 AGCGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 4 0.11
12 10 0.26
13 12 0.32
14 12 0.32
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAAGAAAATGAAG
Found at i:58593186 original size:14 final size:14
Alignment explanation
Indices: 58593124--58593205 Score: 54
Period size: 14 Copynumber: 6.3 Consensus size: 14
58593114 AAAAGTGAGA
58593124 GAAAAAG-AAAA-T
1 GAAAAAGAAAAATT
58593136 GAAGAAA-AGAAAATT
1 GAA-AAAGA-AAAATT
58593151 G-AAAAG--AAA-T
1 GAAAAAGAAAAATT
*
58593161 GAAAAAAAAAAATT
1 GAAAAAGAAAAATT
**
58593175 GAAAAAGAAAAAGC
1 GAAAAAGAAAAATT
*
58593189 GAAAAA-AGAAATT
1 GAAAAAGAAAAATT
58593202 GAAA
1 GAAA
58593206 GAGAGCTTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
10 2 0.04
11 7 0.13
12 3 0.06
13 17 0.31
14 23 0.43
15 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.17, T:0.10
Consensus pattern (14 bp):
GAAAAAGAAAAATT
Found at i:58593239 original size:33 final size:33
Alignment explanation
Indices: 58593202--58593264 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
58593192 AAAAGAAATT
58593202 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
58593235 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
58593265 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:58595057 original size:20 final size:20
Alignment explanation
Indices: 58595034--58595087 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
58595024 AGTTTTTCCC
*
58595034 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
58595054 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
58595074 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
58595088 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Done.